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Queens University
1.
Hnatchuk, Daniel.
Functional characterization of a Kar3/Vik1-like Kinesin-14 heterodimer from the filamentous multinucleate fungus Ashbya gossypii
.
Degree: Biochemistry, 2012, Queens University
URL: http://hdl.handle.net/1974/7332
► Kinesins are motor proteins that convert chemical energy from ATP hydrolysis into mechanical energy used to generate force along microtubules, transporting organelles, vesicles, and proteins…
(more)
▼ Kinesins are motor proteins that convert chemical energy from ATP hydrolysis into mechanical energy used to generate force along microtubules, transporting organelles, vesicles, and proteins within the cell. Kar3 kinesins are microtubule minus-end-directed motors with pleiotropic functions in mating and mitosis of budding and fission yeast. In Saccharomyces cerevisiae, Kar3 is multifunctionalized by two non-catalytic companion proteins, Vik1 and Cik1. A Kar3-like kinesin and a single Vik1/Cik1 ortholog are also expressed by the filamentous fungus Ashbya gossypii, which exhibits different nuclear movement challenges and unique microtubule dynamics from its yeast relatives. We hypothesized that these differences in A. gossypii physiology could translate into interesting and novel differences in its versions of Kar3 and Vik1/Cik1. Presented here is a structural and functional analysis of recombinantly expressed and purified forms of these motor proteins. Compared to the previously published S. cerevisiae Kar3 motor domain structure (ScKar3MD), AgKar3MD displays differences in the conformation of the ATPase pocket. Perhaps it is not surprising then that we observed the maximal microtubule-stimulated ATPase rate (kcat) of AgKar3MD to be approximately 3-fold slower than ScKar3MD, and that the affinity of AgKar3MD for microtubules (Kd,MT) was lower than ScKar3MD. This may suggest that elements that compose the ATPase pocket and that participate in conformational changes required for efficient ATP hydrolysis or products release work differently for AgKar3 and ScKar3. There are also subtle structural differences in the disposition of the secondary structural elements in the small lobe (B1a, B1b, and B1c) at the edge of the motor domain of AgKar3 that may reflect the enhanced microtubule-depolymerization activity that we observed for this motor, or they could relate to its interactions with a different regulatory companion protein than its budding yeast counterpart. Although we were unable to gain experimentally determined high-resolution information of AgVik1, the results of Phyre2-based bioinformatics analyses may provide a structural explanation for the limited microtubule-binding activity we observed. These and other fundamental differences in AgKar3/Vik1 could explain divergent functionalities from the ScKar3/Vik1 and ScKar3/Cik1 motor assemblies.
Subjects/Keywords: Motor Proteins
;
biochemistry
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APA (6th Edition):
Hnatchuk, D. (2012). Functional characterization of a Kar3/Vik1-like Kinesin-14 heterodimer from the filamentous multinucleate fungus Ashbya gossypii
. (Thesis). Queens University. Retrieved from http://hdl.handle.net/1974/7332
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Hnatchuk, Daniel. “Functional characterization of a Kar3/Vik1-like Kinesin-14 heterodimer from the filamentous multinucleate fungus Ashbya gossypii
.” 2012. Thesis, Queens University. Accessed January 24, 2021.
http://hdl.handle.net/1974/7332.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Hnatchuk, Daniel. “Functional characterization of a Kar3/Vik1-like Kinesin-14 heterodimer from the filamentous multinucleate fungus Ashbya gossypii
.” 2012. Web. 24 Jan 2021.
Vancouver:
Hnatchuk D. Functional characterization of a Kar3/Vik1-like Kinesin-14 heterodimer from the filamentous multinucleate fungus Ashbya gossypii
. [Internet] [Thesis]. Queens University; 2012. [cited 2021 Jan 24].
Available from: http://hdl.handle.net/1974/7332.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Hnatchuk D. Functional characterization of a Kar3/Vik1-like Kinesin-14 heterodimer from the filamentous multinucleate fungus Ashbya gossypii
. [Thesis]. Queens University; 2012. Available from: http://hdl.handle.net/1974/7332
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University
2.
Trivedi, Darshan V.
Allosteric Communication and Force Generation in Myosin Motors.
Degree: 2014, Penn State University
URL: https://submit-etda.libraries.psu.edu/catalog/23282
► Muscle contraction, intracellular transport and a myriad of other mechanical functions in a cell are governed by myosin motors. Myosins utilize the chemical energy derived…
(more)
▼ Muscle contraction, intracellular transport and a myriad of other mechanical functions in a cell are governed by myosin motors. Myosins utilize the chemical energy derived from ATP hydrolysis to perform mechanical work via a cyclic interaction with actin filaments. Intricate allosteric pathways operate within the myosin molecule which leads to the coupling of different sub-domains and an efficient generation of force. The three main regions involved in this active communication are the nucleotide and actin-binding regions which are both coupled to the force-generating lever arm region. The lever arm undergoes a reversible movement defined by the recovery stroke and the powerstroke which eventually leads to the generation of force. However, the kinetic and structural details of this mechanism of force generation remain elusive. At an interface of biochemistry and biophysics, this study utilizes novel fluorophore labeling strategies combined with fluorescence spectroscopy and stopped-flow kinetics to answer these questions. Myosin V (MV) is used as a model to uncover the structural changes associated with the catalytic cycle. The rate-limiting conformational change of MV is a closed-to-open transition of the nucleotide binding region prior to the release of ADP. This study investigates the role of a specific structural element called as switch II and the magnesium (Mg) ion in the coupling between the nucleotide-and actin binding regions and their role in mediating the rate-limiting transition. Switch II was found to be critical in both these processes, while Mg played a central role in modulating the rate-limiting transition prior to ADP release. A long standing question about the precise temporal kinetics of the lever arm swing in relation to the product release steps and force generation is also unambiguously answered by this work. A novel fluorophore labeling strategy combined with stopped-flow FRET experiments unravels the kinetic mechanism of lever arm swing. The recovery stroke occurs concurrent with formation of the hydrolysis competent state. The powerstroke occurs in two phases, a fast phase precedes phosphate release and a slow phase precedes the release of ADP. These results provide direct evidence for the order of events associated with force generation in myosins.
Advisors/Committee Members: Christopher Martin Yengo, Dissertation Advisor/Co-Advisor, Christopher Martin Yengo, Committee Chair/Co-Chair, Lisa M Shantz, Committee Member, Thomas E Spratt, Special Member, Blaise Peterson, Committee Member, William O Hancock, Committee Member.
Subjects/Keywords: Myosin; Actin; FRET; Motor Proteins
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APA (6th Edition):
Trivedi, D. V. (2014). Allosteric Communication and Force Generation in Myosin Motors. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/23282
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Trivedi, Darshan V. “Allosteric Communication and Force Generation in Myosin Motors.” 2014. Thesis, Penn State University. Accessed January 24, 2021.
https://submit-etda.libraries.psu.edu/catalog/23282.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Trivedi, Darshan V. “Allosteric Communication and Force Generation in Myosin Motors.” 2014. Web. 24 Jan 2021.
Vancouver:
Trivedi DV. Allosteric Communication and Force Generation in Myosin Motors. [Internet] [Thesis]. Penn State University; 2014. [cited 2021 Jan 24].
Available from: https://submit-etda.libraries.psu.edu/catalog/23282.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Trivedi DV. Allosteric Communication and Force Generation in Myosin Motors. [Thesis]. Penn State University; 2014. Available from: https://submit-etda.libraries.psu.edu/catalog/23282
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Addis Ababa University
3.
Asmamaw, Asrat.
DYNAMICS OF MOTOR PROTEINS= A MONTE CARLO SIMULATION
.
Degree: 2012, Addis Ababa University
URL: http://etd.aau.edu.et/dspace/handle/123456789/1190
► Motor proteins are mechanochemical enzymes that convert energy released by adenosine triphosphate (ATP) hydrolysis into either linear or rotary movement. Motor proteins: kinesin, myosin and…
(more)
▼ Motor proteins are mechanochemical enzymes that convert energy released by adenosine
triphosphate (ATP) hydrolysis into either linear or rotary movement.
Motor proteins:
kinesin, myosin and dynein, that perform active movements along cytoskeletal laments
drive the long=range transport of vesicles, organelles, and other types of cargo in biological
cells. In this Monte Carlo simulation study, based on the recent experimental results and
existing theoretical models, a lattice model to study the dynamics of non=interacting
motor proteins each transporting a cargo and a new bead=spring model to study the
collective dynamics of interacting
motor proteins transporting cooperatively a common
cargo are proposed and studied.
ix
Advisors/Committee Members: Dr. Tatek Yergou (advisor).
Subjects/Keywords: MOTOR PROTEINS;
adenosine triphosphate (ATP)
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Asmamaw, A. (2012). DYNAMICS OF MOTOR PROTEINS= A MONTE CARLO SIMULATION
. (Thesis). Addis Ababa University. Retrieved from http://etd.aau.edu.et/dspace/handle/123456789/1190
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Asmamaw, Asrat. “DYNAMICS OF MOTOR PROTEINS= A MONTE CARLO SIMULATION
.” 2012. Thesis, Addis Ababa University. Accessed January 24, 2021.
http://etd.aau.edu.et/dspace/handle/123456789/1190.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Asmamaw, Asrat. “DYNAMICS OF MOTOR PROTEINS= A MONTE CARLO SIMULATION
.” 2012. Web. 24 Jan 2021.
Vancouver:
Asmamaw A. DYNAMICS OF MOTOR PROTEINS= A MONTE CARLO SIMULATION
. [Internet] [Thesis]. Addis Ababa University; 2012. [cited 2021 Jan 24].
Available from: http://etd.aau.edu.et/dspace/handle/123456789/1190.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Asmamaw A. DYNAMICS OF MOTOR PROTEINS= A MONTE CARLO SIMULATION
. [Thesis]. Addis Ababa University; 2012. Available from: http://etd.aau.edu.et/dspace/handle/123456789/1190
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Oregon
4.
Frei, Ryan.
Regulatory Elements of Drosophila Non-Muscle Myosin II.
Degree: PhD, Department of Chemistry, 2013, University of Oregon
URL: http://hdl.handle.net/1794/12954
► Non-muscle myosin II (NM-II) is present in every cell type and moves actin filaments to provide contraction within the cell. NM-II has a motor domain,…
(more)
▼ Non-muscle myosin II (NM-II) is present in every cell type and moves actin filaments to provide contraction within the cell. NM-II has a
motor domain, a neck domain that binds two light chains, a long coiled-coil tail domain, and a carboxyl-terminal tailpiece. NM-II forms bipolar filaments by associating near the carboxyl-terminus of the tail. It has long been known that both the formation of bipolar filaments and enzymatic activity of the
motor domain are regulated by phosphorylation of one of the neck-binding light chains, known as the regulatory light chain (RLC). This phosphorylation causes a large-scale conformational shift of both the
motor domains and the tail domain. However, the mechanism of this regulation and the elements that mediate the autoinhibition remain unknown.
We have taken a deletional approach to finding the elements necessary for autoinhibition and regulation of filament assembly. We have used salt- dependent pelleting assays, cell culture, and analytical ultracentrifugation to identify two small regions in the IQ motifs of the neck and the carboxyl-terminal tailpiece that are essential for autoinhibition.
Another necessary element for autoinhibition is the fold the coiled coil of the tail back on itself by means of hinge domains. We used internal deletions, pelleting assays, and thermal stability assays to identify and characterize the flexible hinge domains within the coiled-coil tail of NM-II. These hinges consist of low-stability regions of coiled coil, and can be stiffened by introducing mutations that cause the sequence to mimic a more ideal coiled coil. By defining these essential elements of autoinhibition, this work paves the way for a mechanistic understanding of the complex regulation of NM-II in the cell.
This dissertation contains unpublished co-authored material.
Advisors/Committee Members: Stevens, Tom (advisor).
Subjects/Keywords: Autoinhibition; Coiled coil; Motor proteins; Myosin
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APA ·
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MLA ·
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APA (6th Edition):
Frei, R. (2013). Regulatory Elements of Drosophila Non-Muscle Myosin II. (Doctoral Dissertation). University of Oregon. Retrieved from http://hdl.handle.net/1794/12954
Chicago Manual of Style (16th Edition):
Frei, Ryan. “Regulatory Elements of Drosophila Non-Muscle Myosin II.” 2013. Doctoral Dissertation, University of Oregon. Accessed January 24, 2021.
http://hdl.handle.net/1794/12954.
MLA Handbook (7th Edition):
Frei, Ryan. “Regulatory Elements of Drosophila Non-Muscle Myosin II.” 2013. Web. 24 Jan 2021.
Vancouver:
Frei R. Regulatory Elements of Drosophila Non-Muscle Myosin II. [Internet] [Doctoral dissertation]. University of Oregon; 2013. [cited 2021 Jan 24].
Available from: http://hdl.handle.net/1794/12954.
Council of Science Editors:
Frei R. Regulatory Elements of Drosophila Non-Muscle Myosin II. [Doctoral Dissertation]. University of Oregon; 2013. Available from: http://hdl.handle.net/1794/12954

University of California – Santa Cruz
5.
Karg, Travis.
Worst case scenario: exiting metaphase with a broken chromosome.
Degree: Molecular Cell and Developmental Biology, 2016, University of California – Santa Cruz
URL: http://www.escholarship.org/uc/item/14q191rw
► Unrepaired double strand DNA breaks can have deleterious consequences at mitosis due to the generation of acentric chromosome fragments that lack centromeres. Although acentrics are…
(more)
▼ Unrepaired double strand DNA breaks can have deleterious consequences at mitosis due to the generation of acentric chromosome fragments that lack centromeres. Although acentrics are common in cancer cells, surprisingly little is known about the mechanisms regulating kinetochore-independent chromosome segregation. Acentrics are efficiently induced in Drosophila neuroblasts by expressing an endonuclease called I-CreI. Previous reports in Drosophila have found that while acentrics lack a kinetochore, they still move to the metaphase plate and segregate to daughter cells. The delayed but ultimately successful segregation of acentrics requires a chromatin tether that connects the acentrics to the main chromosome mass. The tethers are decorated with BubR1, Aurora B and Polo kinases. Disruptions in BubR1 and Polo functions led to defects in acentric segregation and a decreased rate of survival from larvae into adulthood (synthetic lethality). This led to the conclusion that the tether provides the driving force for acentric segregation. Here, I demonstrate that acentrics are preferentially bundled with microtubules during anaphase suggesting that microtubules and motor proteins exert the force for driving acentric segregation. Interestingly, the orientation of acentrics during anaphase is random with half the acentrics segregating telomere first (telomere facing pole), while the other half segregates telomere last (telomere facing metaphase plate). This is in accord with a model in which acentrics behave as cargo capable of associating in any orientation with microtubules. By conducting a synthetic lethality screen, I found that I-CreI expressing larvae with disruptions in Klp3a, which encodes for a chromosome and microtubule-associated motor protein (chromokinesin) led to an increased rate of synthetic lethality. Through live imaging, I found defects in acentric segregation in neuroblast depleted of Klp3a. Taken together, these results suggest that the cell maintains a microtubule and Kp3a dependent mechanism to drive acentric segregation. Delayed acentric segregation during anaphase raises the question of how acentrics affect nuclear envelope reformation (NER). Here I demonstrate that acentrics enter daughter nuclei by inducing a local delay in NER, which leads to the formation of a channel in the nuclear envelope. The formation of the nuclear envelope channels is dependent on Aurora B kinase.
Subjects/Keywords: Cellular biology; Molecular biology; acentric; centromere; Chromosome; microtubule; Mitosis; motor proteins
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Karg, T. (2016). Worst case scenario: exiting metaphase with a broken chromosome. (Thesis). University of California – Santa Cruz. Retrieved from http://www.escholarship.org/uc/item/14q191rw
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Karg, Travis. “Worst case scenario: exiting metaphase with a broken chromosome.” 2016. Thesis, University of California – Santa Cruz. Accessed January 24, 2021.
http://www.escholarship.org/uc/item/14q191rw.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Karg, Travis. “Worst case scenario: exiting metaphase with a broken chromosome.” 2016. Web. 24 Jan 2021.
Vancouver:
Karg T. Worst case scenario: exiting metaphase with a broken chromosome. [Internet] [Thesis]. University of California – Santa Cruz; 2016. [cited 2021 Jan 24].
Available from: http://www.escholarship.org/uc/item/14q191rw.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Karg T. Worst case scenario: exiting metaphase with a broken chromosome. [Thesis]. University of California – Santa Cruz; 2016. Available from: http://www.escholarship.org/uc/item/14q191rw
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Rice University
6.
Teimouri, Hamid.
Stochastic Modeling of Dynamical Processes in Biological Signaling and Cellular Transport.
Degree: PhD, Natural Sciences, 2016, Rice University
URL: http://hdl.handle.net/1911/93841
► Successful cellular function and organ development rely on the effective transport of proteins and other biomolecules to specific positions. There are two basic mechanisms for…
(more)
▼ Successful cellular function and organ development rely on the effective transport of
proteins and other biomolecules to specific positions. There are two basic mechanisms for biological transport:
passive diffusion and
motor-driven active transport. This thesis presents theoretical investigations of several biophysical problems in the context of active and passive transport.
In the matter of passive diffusion, we investigate fundamental processes of biological development that are governed by multiple signaling molecules that create non-uniform concentration profiles known as morphogen gradients. It is widely believed that the establishment of morphogen gradients is a result of complex processes that involve diffusion and degradation of locally produced signaling molecules. We have developed discrete-state stochastic and continuum mean field approaches to investigate the corresponding reaction-diffusion models.
In the case of active transport, we investigate the fundamental role of local interactions between molecular motors by analyzing a new class of totally asymmetric exclusion processes where interactions are accounted for in a thermodynamically consistent fashion. This allows us to explicitly connect microscopic features of
motor proteins with their collective dynamic properties. Our theoretical analysis that combines various mean-field calculations and computer simulations suggests that the dynamic properties of molecular motors strongly depend on the interactions, and that the correlations are stronger for interacting
motor proteins.
Furthermore, we investigate all times dynamics of continuous-time random walks (CTRWs). The concept of continuous-time random walks
(CTRW) is a generalization of ordinary random walk models, and it is a powerful tool for investigating a broad spectrum of phenomena in natural, engineering, social, and economic sciences. Recently, several theoretical approaches have been developed that allowed to analyze explicitly dynamics of CTRW at all times, which is critically important for understanding mechanisms of underlying phenomena.
However, theoretical analysis has been done mostly for systems with a simple geometry. Here, we extend the original method based on generalized master equations to analyze all-time dynamics of CTRW models on complex networks.
Advisors/Committee Members: Kolomeisky, Anatoly B. (advisor), Landes, Christy (committee member), Yakobson, Boris I. (committee member).
Subjects/Keywords: Biological development; morphogen gradient; motor proteins; continuous time random walks
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
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Manager
APA (6th Edition):
Teimouri, H. (2016). Stochastic Modeling of Dynamical Processes in Biological Signaling and Cellular Transport. (Doctoral Dissertation). Rice University. Retrieved from http://hdl.handle.net/1911/93841
Chicago Manual of Style (16th Edition):
Teimouri, Hamid. “Stochastic Modeling of Dynamical Processes in Biological Signaling and Cellular Transport.” 2016. Doctoral Dissertation, Rice University. Accessed January 24, 2021.
http://hdl.handle.net/1911/93841.
MLA Handbook (7th Edition):
Teimouri, Hamid. “Stochastic Modeling of Dynamical Processes in Biological Signaling and Cellular Transport.” 2016. Web. 24 Jan 2021.
Vancouver:
Teimouri H. Stochastic Modeling of Dynamical Processes in Biological Signaling and Cellular Transport. [Internet] [Doctoral dissertation]. Rice University; 2016. [cited 2021 Jan 24].
Available from: http://hdl.handle.net/1911/93841.
Council of Science Editors:
Teimouri H. Stochastic Modeling of Dynamical Processes in Biological Signaling and Cellular Transport. [Doctoral Dissertation]. Rice University; 2016. Available from: http://hdl.handle.net/1911/93841

Rice University
7.
Kamar, Ramsey I.
Biophysical Interactions of the OHC Motor Protein Prestin: A Study at the Single Molecule Level.
Degree: PhD, Natural Sciences, 2011, Rice University
URL: http://hdl.handle.net/1911/70287
► The exquisite frequency selectivity and amplification characteristics of mammalian hearing intimately depend on the fast electromechanical motion of the outer hair cells in the cochlea.…
(more)
▼ The exquisite frequency selectivity and amplification characteristics of mammalian hearing intimately depend on the fast electromechanical motion of the outer hair cells in the cochlea. This membrane based process, termed electromotility, is driven by the protein prestin which is uniquely present in the OHC lateral wall. Voltage dependent motility, in OHCs and mammalian cells expressing prestin, is accompanied by intramembranous charge movement which is widely considered a signature of electromotility and prestin function. How prestin converts changes in membrane potential into axial length changes of OHCs is currently not understood at the molecular level. Many electromotility models predict that prestin conformational changes are the underlying mechanism connecting charge movement and motility. Currently, however, only indirect evidence for a prestin conformational change is available. Various experiments have indicated that the oligomeric states of prestin may be an important determinant of function. Numerous reports have provided varying estimates of prestin oligomeric state. However, estimates have been based on measurements performed outside the membrane making, firm biophysical conclusions difficult. Biophysical studies of prestin function have demonstrated its dependence on membrane properties. Alterations of membrane cholesterol affect voltage dependence of charge movement and motility. In addition cholesterol manipulations cause spatial redistribution of prestin and possibly change prestin oligomeric state. However, the underlying cause for prestin sensitivity to cholesterol and its relation to membrane distribution is unknown. We have applied single molecule fluorescence (SMF) imaging, single particle tracking (SPT), and Förster resonance energy transfer (FRET) to investigate prestin interactions at the molecular level. The results of our SMF experiments have suggested that prestin forms mainly tetramers and dimers in the cell membrane. Using SPT to map the trajectories of prestin in the membrane, we have found that prestin undergoes diffusion in and hops between membrane confinements of varying size. In addition, we have found that cholesterol affects the size and confinement strength of the compartments but does not affect the diffusivity within the compartments. Finally, using a combination of electrophysiology and FRET we have demonstrated that prestin undergoes voltage dependent structural changes. In total, our results refine our molecular understanding of prestin function.
Advisors/Committee Members: Raphael, Robert M. (advisor).
Subjects/Keywords: Biological sciences; Outer hair cells; Motor proteins; Prestin; Conformational change; Biophysics
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Kamar, R. I. (2011). Biophysical Interactions of the OHC Motor Protein Prestin: A Study at the Single Molecule Level. (Doctoral Dissertation). Rice University. Retrieved from http://hdl.handle.net/1911/70287
Chicago Manual of Style (16th Edition):
Kamar, Ramsey I. “Biophysical Interactions of the OHC Motor Protein Prestin: A Study at the Single Molecule Level.” 2011. Doctoral Dissertation, Rice University. Accessed January 24, 2021.
http://hdl.handle.net/1911/70287.
MLA Handbook (7th Edition):
Kamar, Ramsey I. “Biophysical Interactions of the OHC Motor Protein Prestin: A Study at the Single Molecule Level.” 2011. Web. 24 Jan 2021.
Vancouver:
Kamar RI. Biophysical Interactions of the OHC Motor Protein Prestin: A Study at the Single Molecule Level. [Internet] [Doctoral dissertation]. Rice University; 2011. [cited 2021 Jan 24].
Available from: http://hdl.handle.net/1911/70287.
Council of Science Editors:
Kamar RI. Biophysical Interactions of the OHC Motor Protein Prestin: A Study at the Single Molecule Level. [Doctoral Dissertation]. Rice University; 2011. Available from: http://hdl.handle.net/1911/70287

University of Melbourne
8.
Bullen, Hayley Elise.
Novel membrane proteins of Plasmodium falciparum.
Degree: 2011, University of Melbourne
URL: http://hdl.handle.net/11343/36895
► Apicomplexan parasites such as Plasmodium spp. cause a multitude of illnesses through infection of both human and livestock hosts. Of the Plasmodium species that infect…
(more)
▼ Apicomplexan parasites such as Plasmodium spp. cause a multitude of illnesses through infection of both human and livestock hosts. Of the Plasmodium species that infect humans, P. falciparum is associated with a large proportion of symptomatic malarial disease, resulting in approximately 800,000 deaths and a further 250 million clinical cases annually (WHO World Malaria Report, 2010). Although there are many facets that contribute to the global health catastrophe caused by malaria, including social, geographical, economic and political; the biology of the parasite itself is a major contributing factor. P. falciparum has a complex lifecycle involving stages in both its mosquito vector and human host, within which it carries out its development in distinct phases in both the liver and blood stream.
Symptomatic malaria is associated with blood-stage infection and it is investigations into this asexual life-stage that have formed the basis of my PhD research. In particular I have focused on investigating the functions of membrane proteins, particularly those residing in detergent resistant membranes. These membranes contain regions where the lipids are more ordered and enriched in proteins and are the sites of many important cellular activities such as signal transduction and membrane trafficking. Previous studies have shown that when detergent resistant membranes are recovered from the invasive merozoite stage of P. falciparum, many proteins from the parasite’s pellicle; a three-membrane layer that covers the parasite, are extracted also. Furthermore, proteins that reside in the parasitophorous vacuole, a membrane that envelops young intra-erythrocytic ring-stage parasites, also preferentially associate with the detergent resistant fraction. Within both the merozoite and ring stage parasites reside many proteins of unknown function and during my candidature I have studied several of these proteins.
Initial studies presented here have focused on the characterisation of a novel family of Apicomplexan-specific proteins termed the GAPM family which have been identified within the detergent resistant membrane fraction of P. falciparum developing merozoites. It is shown here that the GAPM family of proteins is conserved across all sequenced Apicomplexa and associate into high molecular weight structures within the inner membrane complex of both P. falciparum and the related Toxoplasma gondii. The inner membrane complex forms the innermost pair of membranes of the parasite pellicle. The data presented here demonstrates that the GAPMs bind to both the actinmyosin host-cell invasion motor on the outside of the inner membrane complex and to the parasite cytoskeletal network on the inside of the complex, possibly linking the invasion motor and cytoskeleton together. It has long been recognized in the field that for the invasion motor to work and propel the merozoite into its red blood cell host that the motor must be attached to a solid…
Subjects/Keywords: Plasmodium falciparum; membrane proteins; protein trafficking; actin-myosin motor
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Manager
APA (6th Edition):
Bullen, H. E. (2011). Novel membrane proteins of Plasmodium falciparum. (Doctoral Dissertation). University of Melbourne. Retrieved from http://hdl.handle.net/11343/36895
Chicago Manual of Style (16th Edition):
Bullen, Hayley Elise. “Novel membrane proteins of Plasmodium falciparum.” 2011. Doctoral Dissertation, University of Melbourne. Accessed January 24, 2021.
http://hdl.handle.net/11343/36895.
MLA Handbook (7th Edition):
Bullen, Hayley Elise. “Novel membrane proteins of Plasmodium falciparum.” 2011. Web. 24 Jan 2021.
Vancouver:
Bullen HE. Novel membrane proteins of Plasmodium falciparum. [Internet] [Doctoral dissertation]. University of Melbourne; 2011. [cited 2021 Jan 24].
Available from: http://hdl.handle.net/11343/36895.
Council of Science Editors:
Bullen HE. Novel membrane proteins of Plasmodium falciparum. [Doctoral Dissertation]. University of Melbourne; 2011. Available from: http://hdl.handle.net/11343/36895

University of California – Berkeley
9.
Belyy, Vladislav.
Force Generation by Cytoplasmic Dynein and Development of PhotoGate Microscopy.
Degree: Biophysics, 2016, University of California – Berkeley
URL: http://www.escholarship.org/uc/item/7pp0q58k
► Cytoskeletal motors play key roles in the organization and division of eukaryotic cells. Although detailed mechanistic understanding has been achieved for motors in the myosin…
(more)
▼ Cytoskeletal motors play key roles in the organization and division of eukaryotic cells. Although detailed mechanistic understanding has been achieved for motors in the myosin and kinesin families, the mechanochemical cycle of cytoplasmic dynein remained a subject of debate. Understanding the mechanism of dynein motility has been difficult due to its large size, unusual architecture, irregular stepping pattern, and complex regulation by a number of auxiliary proteins. In my doctoral work, I showed that the two heads of dynein utilize a load-sharing mechanism that allows them to work against hindering forces larger than the maximal force produced by a single head. Next, I demonstrated that the regulatory proteins dynactin and Bicaudal-D homolog 1 (BICD) dramatically increase the force production of human dynein and allow it to defeat a human kinesin-1 motor in a tug-of-war competition.In addition, I developed the PhotoGate method for imaging single fluorescent molecules in the crowded environment of a living cell. This method eliminates the need for fluorophore photoactivation, enabling longer single-particle tracking times and direct measurement of stoichiometry of macromolecular complexes. This technique was used to measure ligand-induced dimerization of epidermal growth factor (EGF) receptors on the cell membrane at densities of >50 molecules per μm2. It was also applied to monitor the arrivals and departures of single Adaptor Protein Phosphotyrosine Interaction PH domain and Leucine Zipper-containing-1 (APPL1) molecules at early endosomes. PhotoGate will be broadly applicable to the study of macromolecular complex formation in the densely packed conditions of the cytoplasm.
Subjects/Keywords: Biophysics; Molecular biology; Cellular biology; Dynein; Mechanochemistry; Motor proteins; Particle tracking; Photobleaching; Single-molecule
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Belyy, V. (2016). Force Generation by Cytoplasmic Dynein and Development of PhotoGate Microscopy. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/7pp0q58k
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Belyy, Vladislav. “Force Generation by Cytoplasmic Dynein and Development of PhotoGate Microscopy.” 2016. Thesis, University of California – Berkeley. Accessed January 24, 2021.
http://www.escholarship.org/uc/item/7pp0q58k.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Belyy, Vladislav. “Force Generation by Cytoplasmic Dynein and Development of PhotoGate Microscopy.” 2016. Web. 24 Jan 2021.
Vancouver:
Belyy V. Force Generation by Cytoplasmic Dynein and Development of PhotoGate Microscopy. [Internet] [Thesis]. University of California – Berkeley; 2016. [cited 2021 Jan 24].
Available from: http://www.escholarship.org/uc/item/7pp0q58k.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Belyy V. Force Generation by Cytoplasmic Dynein and Development of PhotoGate Microscopy. [Thesis]. University of California – Berkeley; 2016. Available from: http://www.escholarship.org/uc/item/7pp0q58k
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University
10.
Deffenbaugh, Nathan C.
Single-molecule microscopy step detection algorithms: kinesin motor proteins and the cellulose synthesis complex.
Degree: 2015, Penn State University
URL: https://submit-etda.libraries.psu.edu/catalog/24977
► Single-molecule microscopy is a versatile tool that can be used to investigate the stepping mechanism of motor proteins such as kinesin, and to determine the…
(more)
▼ Single-molecule microscopy is a versatile tool that can be used to investigate the stepping mechanism of
motor proteins such as kinesin, and to determine the copy number of subunits within membrane bound
proteins such as the cellulose synthesis complex. Step detection algorithms provide a means for uncovering critical information within single-molecule microscopy data collected from these systems.
Kinesin
proteins are intracellular molecular motors that utilize energy from adenosine triphosphate (ATP) in order to transmit force and transport cellular cargo along microtubule tracks. Despite the current wealth of knowledge regarding these
proteins, many unresolved mechanisms of the kinesin stepping cycle remain. Step detection algorithms that recover underlying piecewise-constant signals within noise-corrupted, single-molecule time series position data provide a strategy for resolving these mechanisms. The work presented in this thesis shows that by treating a positional time series as an observation sequence from a hidden Markov model, we can apply the model-dependent, continuous Viterbi algorithm in order to determine the most-likely hidden state sequence of the tracked
motor protein. This approach has the critical capability of keeping “phase” of plateaus within a given time series, which allows for more accurate determination of kinetic rates and
motor domain displacements associated with state transitions during stepping.
In growing plant cells, cellulose synthesis complexes (CSCs) exist in the plasma membrane as six-lobed rosettes that contain different cellulose synthase (CESA) isoforms, but the number and stoichiometry of CESAs in each CSC are unknown. To begin to address this question, we performed photobleaching of GFP-tagged AtCESA3-containing particles in living Arabidopsis thaliana cells followed by step detection analysis to estimate copy number. The step detection algorithms introduced in this work account for changes in signal variance due to changing numbers of fluorophores in order to avoid overfitting. These procedures can be applied to photobleaching data for any complex with large numbers of fluorescently tagged subunits, providing a new analytical tool with which to probe complex composition and stoichiometry.
Advisors/Committee Members: William O Hancock, Thesis Advisor/Co-Advisor.
Subjects/Keywords: single-molecule microscopy; step detection; kinesin; motor proteins; cellulose synthesis complex; hidden Markov models
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Deffenbaugh, N. C. (2015). Single-molecule microscopy step detection algorithms: kinesin motor proteins and the cellulose synthesis complex. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/24977
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Deffenbaugh, Nathan C. “Single-molecule microscopy step detection algorithms: kinesin motor proteins and the cellulose synthesis complex.” 2015. Thesis, Penn State University. Accessed January 24, 2021.
https://submit-etda.libraries.psu.edu/catalog/24977.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Deffenbaugh, Nathan C. “Single-molecule microscopy step detection algorithms: kinesin motor proteins and the cellulose synthesis complex.” 2015. Web. 24 Jan 2021.
Vancouver:
Deffenbaugh NC. Single-molecule microscopy step detection algorithms: kinesin motor proteins and the cellulose synthesis complex. [Internet] [Thesis]. Penn State University; 2015. [cited 2021 Jan 24].
Available from: https://submit-etda.libraries.psu.edu/catalog/24977.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Deffenbaugh NC. Single-molecule microscopy step detection algorithms: kinesin motor proteins and the cellulose synthesis complex. [Thesis]. Penn State University; 2015. Available from: https://submit-etda.libraries.psu.edu/catalog/24977
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Columbia University
11.
Tisdale, Sarah.
RNA-Dependent Control of Histone Gene Expression by the Spinal Muscular Atrophy Protein SMN: Mechanisms and Role in Motor Neuron Disease.
Degree: 2015, Columbia University
URL: https://doi.org/10.7916/D82B8XQQ
► Ribonucleoproteins (RNPs) are RNA-protein complexes that carry out a variety of key cellular functions and are essential for the regulation of gene expression. Small nuclear…
(more)
▼ Ribonucleoproteins (RNPs) are RNA-protein complexes that carry out a variety of key cellular functions and are essential for the regulation of gene expression. Small nuclear RNPs (snRNPs) are a class of RNPs that regulate gene expression at the level of RNA processing in the nucleus. These RNPs are subject to complex and highly regulated biogenesis pathways in order to ensure sufficient snRNP levels are present within the cell. snRNPs are required for viability of all eukaryotic cells and the importance of proper snRNP function in vivo is further highlighted by the fact that the fatal motor neuron disease spinal muscular atrophy (SMA) is caused by a genetic deficiency in the ubiquitously expressed survival motor neuron (SMN) protein, an essential component of the snRNP biogenesis machinery. The most well characterized targets of SMN for RNP assembly are the spliceosomal snRNPs, which are critical factors that carry out pre-mRNA splicing. However, SMN is not believed to be solely dedicated to spliceosomal snRNP biogenesis but rather is thought to be a general RNP assembly machine. Yet, no other RNP targets of the SMN complex had previously been characterized in a conclusive manner. Understanding the cellular targets of SMN-mediated RNP assembly is critical for elucidating basic mechanisms of RNA regulation. Furthermore, despite increased understanding of the molecular function of SMN in spliceosomal snRNP biogenesis and the cellular basis of SMA in animal models, the molecular mechanisms through which loss of SMN function leads to motor neuron disease remain poorly defined. Thus, identifying additional RNP pathways that are dependent on SMN is key to uncover the molecular mechanisms of SMA and may also help in the design of novel therapeutic approaches to this devastating childhood disorder that is currently untreatable.
In an effort to expand on the established RNP targets of SMN for assembly, in this dissertation I explore the hypothesis that SMN is required for the biogenesis and function of U7 snRNP and that disruption of this pathway induced by SMN deficiency contributes to motor neuron pathology in SMA. While structurally analogous to spliceosomal snRNPs, U7 snRNP functions not in splicing but rather in the unique 3’-end processing mechanism of replication-dependent histone mRNAs. Here, I first provide detailed molecular characterization of the in vivo functional requirement of SMN for U7 snRNP biogenesis as well as histone mRNA 3’-end processing and proper histone gene expression. I go on to demonstrate that in a mouse model of SMA U7 snRNP biogenesis and function are severely impaired by SMN deficiency and these defects occur in disease-relevant SMA motor neurons. I then describe the development of a novel molecular strategy to restore U7 snRNP activity in a setting of SMN deficiency in order to investigate the functional consequences of U7 dysfunction in SMA. Finally, I apply this U7 restoration strategy to a mouse model of SMA using AAV9-mediated gene delivery and establish that disrupted U7 activity…
Subjects/Keywords: Gene expression; Genetic regulation; Proteins – Synthesis; Biosynthesis; Motor neurons; Nucleoproteins; Molecular biology; Cytology; Neurosciences
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Tisdale, S. (2015). RNA-Dependent Control of Histone Gene Expression by the Spinal Muscular Atrophy Protein SMN: Mechanisms and Role in Motor Neuron Disease. (Doctoral Dissertation). Columbia University. Retrieved from https://doi.org/10.7916/D82B8XQQ
Chicago Manual of Style (16th Edition):
Tisdale, Sarah. “RNA-Dependent Control of Histone Gene Expression by the Spinal Muscular Atrophy Protein SMN: Mechanisms and Role in Motor Neuron Disease.” 2015. Doctoral Dissertation, Columbia University. Accessed January 24, 2021.
https://doi.org/10.7916/D82B8XQQ.
MLA Handbook (7th Edition):
Tisdale, Sarah. “RNA-Dependent Control of Histone Gene Expression by the Spinal Muscular Atrophy Protein SMN: Mechanisms and Role in Motor Neuron Disease.” 2015. Web. 24 Jan 2021.
Vancouver:
Tisdale S. RNA-Dependent Control of Histone Gene Expression by the Spinal Muscular Atrophy Protein SMN: Mechanisms and Role in Motor Neuron Disease. [Internet] [Doctoral dissertation]. Columbia University; 2015. [cited 2021 Jan 24].
Available from: https://doi.org/10.7916/D82B8XQQ.
Council of Science Editors:
Tisdale S. RNA-Dependent Control of Histone Gene Expression by the Spinal Muscular Atrophy Protein SMN: Mechanisms and Role in Motor Neuron Disease. [Doctoral Dissertation]. Columbia University; 2015. Available from: https://doi.org/10.7916/D82B8XQQ

University of Colorado
12.
Blackwell, Robert Allen.
Modeling Cytoskeletal Active Matter Systems.
Degree: PhD, Physics, 2016, University of Colorado
URL: https://scholar.colorado.edu/phys_gradetds/162
► Active networks of filamentous proteins and crosslinking motor proteins play a critical role in many important cellular processes. One of the most important microtubule-motor…
(more)
▼ Active networks of filamentous
proteins and crosslinking
motor proteins play a critical role in many important cellular processes. One of the most important microtubule-
motor protein assemblies is the mitotic spindle, a self-organized active liquid-crystalline structure that forms during cell division and that ultimately separates chromosomes into two daughter cells. Although the spindle has been intensively studied for decades, the physical principles that govern its self-organization and function remain mysterious. To evolve a better understanding of spindle formation, structure, and dynamics, I investigate course-grained models of active liquid-crystalline networks composed of microtubules, modeled as hard spherocylinders, in diffusive equilibrium with a reservoir of active crosslinks, modeled as hookean springs that can adsorb to microtubules and and translocate at finite velocity along the microtubule axis. This model is investigated using a combination of brownian dynamics and kinetic monte carlo simulation. I have further refined this model to simulate spindle formation and kinetochore capture in the fission yeast S. pombe. I then make predictions for experimentally realizable perturbations in
motor protein presence and function in S. pombe.
Advisors/Committee Members: Matthew A. Glaser, Meredith D. Betterton, Noel Clark, Leo Radzihovsky, Franck Vernerey.
Subjects/Keywords: brownian dynamics; cytoskeleton; kinetic monte carlo; motor proteins; pombe; spindle; Biophysics; Condensed Matter Physics
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Blackwell, R. A. (2016). Modeling Cytoskeletal Active Matter Systems. (Doctoral Dissertation). University of Colorado. Retrieved from https://scholar.colorado.edu/phys_gradetds/162
Chicago Manual of Style (16th Edition):
Blackwell, Robert Allen. “Modeling Cytoskeletal Active Matter Systems.” 2016. Doctoral Dissertation, University of Colorado. Accessed January 24, 2021.
https://scholar.colorado.edu/phys_gradetds/162.
MLA Handbook (7th Edition):
Blackwell, Robert Allen. “Modeling Cytoskeletal Active Matter Systems.” 2016. Web. 24 Jan 2021.
Vancouver:
Blackwell RA. Modeling Cytoskeletal Active Matter Systems. [Internet] [Doctoral dissertation]. University of Colorado; 2016. [cited 2021 Jan 24].
Available from: https://scholar.colorado.edu/phys_gradetds/162.
Council of Science Editors:
Blackwell RA. Modeling Cytoskeletal Active Matter Systems. [Doctoral Dissertation]. University of Colorado; 2016. Available from: https://scholar.colorado.edu/phys_gradetds/162

University of California – Berkeley
13.
Can, Sinan.
THE MECHANICS OF DYNEIN STEPPING AND DIRECTIONALITY.
Degree: Physics, 2018, University of California – Berkeley
URL: http://www.escholarship.org/uc/item/5qf457d7
► The ability of cytoskeletal motors to move unidirectionally along linear tracks is central to their cellular roles. While kinesin and myosin motor families have members…
(more)
▼ The ability of cytoskeletal motors to move unidirectionally along linear tracks is central to their cellular roles. While kinesin and myosin motor families have members that move in opposite directions, all dyneins studied to date exclusively move towards the microtubule minus-end. The source of dynein’s directionality remains as the central unresolved question about the mechanism of its motility. In my doctoral work, I focused on understanding the underlying mechanism of dynein’s directional motility along the microtubules in three dimensions. I used a protein engineering approach, guided by all-atom molecular dynamics simulations and high-resolution cryoEM imaging, along with the tools of single-molecule biophysics to dissect the elements of dynein motility. We successfully engineered a plus-end-directed dynein for the first time and revealed the mechanism of its directionality. This work has three major outcomes. First, by altering the length of the coiled-coil stalk that connects the dynein motor domain to the microtubule, we controlled the handedness of the helical motility of dynein around the circumference of the microtubule. This experiment showed that the stalk length of native dynein is critical for restricting sideways movement and directing dynein motility along the microtubule axis. Second, we altered the angle and length of dynein’s stalk. Remarkably, these modifications reversed the direction by which the linker swings relative to the microtubule and directed the motility towards the plus-end. Finally, similar to native dynein, the plus-end directed mutant maintains its preference to release from the microtubule when pulled towards the minus-end by an optical trap. Our results provide direct evidence for the linker swing model in which the direction the linker swings determines the direction of dynein motility. Our results also rule out the asymmetric release model that the directionality is proposed to be determined by the direction dynein favors for release from the microtubule under tension. Two critical features of dynein’s stalk, the length of its antiparallel coiled-coils and two proline residues located at its base, control the directionality by directing the linker swing towards the MT minus-end. Because both features of the stalk are fully conserved in cytoplasmic and ciliary dyneins across species, this mechanism explains the minus-end directionality of all dyneins.
Subjects/Keywords: Biophysics; biophysics; dynein; motor proteins; optical tweezers; protein engineering; single molecule imaging
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Can, S. (2018). THE MECHANICS OF DYNEIN STEPPING AND DIRECTIONALITY. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/5qf457d7
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Can, Sinan. “THE MECHANICS OF DYNEIN STEPPING AND DIRECTIONALITY.” 2018. Thesis, University of California – Berkeley. Accessed January 24, 2021.
http://www.escholarship.org/uc/item/5qf457d7.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Can, Sinan. “THE MECHANICS OF DYNEIN STEPPING AND DIRECTIONALITY.” 2018. Web. 24 Jan 2021.
Vancouver:
Can S. THE MECHANICS OF DYNEIN STEPPING AND DIRECTIONALITY. [Internet] [Thesis]. University of California – Berkeley; 2018. [cited 2021 Jan 24].
Available from: http://www.escholarship.org/uc/item/5qf457d7.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Can S. THE MECHANICS OF DYNEIN STEPPING AND DIRECTIONALITY. [Thesis]. University of California – Berkeley; 2018. Available from: http://www.escholarship.org/uc/item/5qf457d7
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Kansas
14.
LeGresley-Rush, Sarah Elizabeth.
Mathematical Methods for studying DNA and Protein Interactions.
Degree: PhD, Physics & Astronomy, 2017, University of Kansas
URL: http://hdl.handle.net/1808/26015
► Deoxyribnucleic Acid (DNA) damage can lead to health related issues such as developmental disorders, aging, and cancer. It has been estimated that damage rates may…
(more)
▼ Deoxyribnucleic Acid (DNA) damage can lead to health related issues such as developmental disorders, aging, and cancer. It has been estimated that damage rates may be as high as 100,000 per cell per day. Because of the devastating effects that DNA damage can have, DNA repair mechanisms are of great interest yet are not completely understood. To gain a better understanding of possible DNA repair mechanisms, my dissertation focused on mathematical methods for understanding the interactions between DNA and
proteins. I developed a damaged DNA model to estimate the probabilities of damaged DNA being located at specific positions. Experiments were then performed that suggested that the damaged DNA may be repositioned. These experimental results were consistent with the model's prediction that damaged DNA has preferred locations. To study how
proteins might be moving along the DNA, I studied the use of the uniform motion “n-step” model. The n-step model has been used to determine the kinetics parameters (e.g. rates at which a protein moves along the DNA, how much energy is required to move a protein along a specified amount of DNA, etc.) of
proteins moving along the DNA. Monte Carlo methods were used to simulate
proteins moving with different types of non-uniform motion (e.g. backward, jumping, etc.) along the DNA. Estimates for the kinetics parameters in the n-step model were found by fitting of the Monte Carlo simulation data. Analysis indicated that non-uniform motion of the protein may lead to over or underestimation of the kinetic parameters of this n-step model.
Advisors/Committee Members: Fischer, Christopher J. (advisor), Anthony-Twarog, Barbara J. (cmtemember), Murray, Michael J. (cmtemember), Shi, Jack J. (cmtemember), Stetler, Dean A. (cmtemember).
Subjects/Keywords: Physics; Biophysics; deoxyribonucleic acid (DNA); kinetics; motor proteins; nucleosome; nucleosome breathing; translocation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
LeGresley-Rush, S. E. (2017). Mathematical Methods for studying DNA and Protein Interactions. (Doctoral Dissertation). University of Kansas. Retrieved from http://hdl.handle.net/1808/26015
Chicago Manual of Style (16th Edition):
LeGresley-Rush, Sarah Elizabeth. “Mathematical Methods for studying DNA and Protein Interactions.” 2017. Doctoral Dissertation, University of Kansas. Accessed January 24, 2021.
http://hdl.handle.net/1808/26015.
MLA Handbook (7th Edition):
LeGresley-Rush, Sarah Elizabeth. “Mathematical Methods for studying DNA and Protein Interactions.” 2017. Web. 24 Jan 2021.
Vancouver:
LeGresley-Rush SE. Mathematical Methods for studying DNA and Protein Interactions. [Internet] [Doctoral dissertation]. University of Kansas; 2017. [cited 2021 Jan 24].
Available from: http://hdl.handle.net/1808/26015.
Council of Science Editors:
LeGresley-Rush SE. Mathematical Methods for studying DNA and Protein Interactions. [Doctoral Dissertation]. University of Kansas; 2017. Available from: http://hdl.handle.net/1808/26015

University of Pennsylvania
15.
Santiago, Celine.
Regulation Of Axon Guidance Receptor Expression And Activity During Neuronal Morphogenesis.
Degree: 2016, University of Pennsylvania
URL: https://repository.upenn.edu/edissertations/2568
► Receptors expressed on the surface of neurons during development direct cell migration, axon guidance, dendrite morphogenesis, and synapse formation by responding to cues in the…
(more)
▼ Receptors expressed on the surface of neurons during development direct cell migration, axon guidance, dendrite morphogenesis, and synapse formation by responding to cues in the neuron’s environment. The expression levels and the activity of cell surface receptors must be tightly controlled for a neuron to acquire its unique identity. Transcriptional mechanisms are essential in this process, and many studies have identified requirements for specific transcription factors during the different steps of neural circuit assembly. However, the downstream effectors by which most of these factors control morphology and connectivity remain unknown. In Chapter 1, I highlight recent work that elucidated functional relationships between transcription factors and the cellular effectors through which they regulate neural morphogenesis and synaptogenesis in multiple model systems. In Chapters 2 and 3, I present data demonstrating that the homeodomain transcription factors Hb9 and Islet control motor axon guidance in Drosophila embryos through distinct effectors: Hb9 regulates the (Roundabout) 2 receptor in a subset of motor neurons, while Islet acts in the same cells to regulate the Frazzled/DCC receptor. Genetic rescue experiments indicate that these relationships are functionally important for the guidance of motor axons to their muscle targets. In addition, Islet regulates motor neuron dendrite targeting in the central nervous system (CNS) through Frazzled, demonstrating how an individual transcription factor can control multiple aspects of neuronal connectivity through the same effector. In Chapter 4, I characterize a non-canonical function for the Robo2 receptor during midline crossing, and present data suggesting that this activity requires Robo2 to be expressed in midline cells, providing an example of how mechanisms that regulate guidance receptor gene expression are key to regulating receptor function and nervous system formation. In Chapter 5, I explore the implications of these findings, and propose future directions of research to build upon them.
Subjects/Keywords: Axon guidance; Frazzled; Homeodomain proteins; Motor neurons; Roundabout; Developmental Biology; Genetics; Neuroscience and Neurobiology
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Santiago, C. (2016). Regulation Of Axon Guidance Receptor Expression And Activity During Neuronal Morphogenesis. (Thesis). University of Pennsylvania. Retrieved from https://repository.upenn.edu/edissertations/2568
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Santiago, Celine. “Regulation Of Axon Guidance Receptor Expression And Activity During Neuronal Morphogenesis.” 2016. Thesis, University of Pennsylvania. Accessed January 24, 2021.
https://repository.upenn.edu/edissertations/2568.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Santiago, Celine. “Regulation Of Axon Guidance Receptor Expression And Activity During Neuronal Morphogenesis.” 2016. Web. 24 Jan 2021.
Vancouver:
Santiago C. Regulation Of Axon Guidance Receptor Expression And Activity During Neuronal Morphogenesis. [Internet] [Thesis]. University of Pennsylvania; 2016. [cited 2021 Jan 24].
Available from: https://repository.upenn.edu/edissertations/2568.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Santiago C. Regulation Of Axon Guidance Receptor Expression And Activity During Neuronal Morphogenesis. [Thesis]. University of Pennsylvania; 2016. Available from: https://repository.upenn.edu/edissertations/2568
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
16.
Kapitein, L.C.
Dynamics of Active and Passive Microtubule-Crosslinking Proteins.
Degree: Faculty of Earth and Life Sciences, 2007, NARCIS
URL: https://research.vu.nl/en/publications/dea70ec4-5787-434f-b5a5-9128245a1900
;
urn:nbn:nl:ui:31-1871/13147
;
dea70ec4-5787-434f-b5a5-9128245a1900
;
1871/13147
;
urn:isbn:9789086591152
;
urn:nbn:nl:ui:31-1871/13147
;
https://research.vu.nl/en/publications/dea70ec4-5787-434f-b5a5-9128245a1900
Subjects/Keywords: kinesin; microtubules; motor proteins; single molecules
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Kapitein, L. C. (2007). Dynamics of Active and Passive Microtubule-Crosslinking Proteins. (Doctoral Dissertation). NARCIS. Retrieved from https://research.vu.nl/en/publications/dea70ec4-5787-434f-b5a5-9128245a1900 ; urn:nbn:nl:ui:31-1871/13147 ; dea70ec4-5787-434f-b5a5-9128245a1900 ; 1871/13147 ; urn:isbn:9789086591152 ; urn:nbn:nl:ui:31-1871/13147 ; https://research.vu.nl/en/publications/dea70ec4-5787-434f-b5a5-9128245a1900
Chicago Manual of Style (16th Edition):
Kapitein, L C. “Dynamics of Active and Passive Microtubule-Crosslinking Proteins.” 2007. Doctoral Dissertation, NARCIS. Accessed January 24, 2021.
https://research.vu.nl/en/publications/dea70ec4-5787-434f-b5a5-9128245a1900 ; urn:nbn:nl:ui:31-1871/13147 ; dea70ec4-5787-434f-b5a5-9128245a1900 ; 1871/13147 ; urn:isbn:9789086591152 ; urn:nbn:nl:ui:31-1871/13147 ; https://research.vu.nl/en/publications/dea70ec4-5787-434f-b5a5-9128245a1900.
MLA Handbook (7th Edition):
Kapitein, L C. “Dynamics of Active and Passive Microtubule-Crosslinking Proteins.” 2007. Web. 24 Jan 2021.
Vancouver:
Kapitein LC. Dynamics of Active and Passive Microtubule-Crosslinking Proteins. [Internet] [Doctoral dissertation]. NARCIS; 2007. [cited 2021 Jan 24].
Available from: https://research.vu.nl/en/publications/dea70ec4-5787-434f-b5a5-9128245a1900 ; urn:nbn:nl:ui:31-1871/13147 ; dea70ec4-5787-434f-b5a5-9128245a1900 ; 1871/13147 ; urn:isbn:9789086591152 ; urn:nbn:nl:ui:31-1871/13147 ; https://research.vu.nl/en/publications/dea70ec4-5787-434f-b5a5-9128245a1900.
Council of Science Editors:
Kapitein LC. Dynamics of Active and Passive Microtubule-Crosslinking Proteins. [Doctoral Dissertation]. NARCIS; 2007. Available from: https://research.vu.nl/en/publications/dea70ec4-5787-434f-b5a5-9128245a1900 ; urn:nbn:nl:ui:31-1871/13147 ; dea70ec4-5787-434f-b5a5-9128245a1900 ; 1871/13147 ; urn:isbn:9789086591152 ; urn:nbn:nl:ui:31-1871/13147 ; https://research.vu.nl/en/publications/dea70ec4-5787-434f-b5a5-9128245a1900

Northeastern University
17.
Miller, Eliza Hope.
Optimization of dihydroquinazolinone for treatment of spinal muscular atrophy.
Degree: MS, Department of Chemistry and Chemical Biology, 2016, Northeastern University
URL: http://hdl.handle.net/2047/D20213404
► Spinal muscular atrophy (SMA) is an inherited neurodegenerative disease characterized by progressive muscle weakness and eventual muscle loss. It is the leading heritable cause of…
(more)
▼ Spinal muscular atrophy (SMA) is an inherited neurodegenerative disease characterized by progressive muscle weakness and eventual muscle loss. It is the leading heritable cause of infant mortality worldwide. SMA results from a dysfunction of the motor neurons in the anterior horn of the spinal cord, leading to compromised physical strength, and, eventually, patients cannot walk, eat, or breathe. Currently, there is no pharmacologic treatment for SMA. SMA is an autosomal recessive disorder caused by the deletion of the survival motor neuron gene 1 (SMN1), but a nearly identical homolog, SMN2, acts as a disease modifier: the greater the number of copies of SMN2, the less severe the disease. The amount of SMN protein expressed by SMN2 is thought to make up for the loss of SMN1. This research tested the hypothesis that a small molecule which could increase SMN protein levels could represent a novel pharmacologic treatment of SMA. Candidate dihydroquinazolinone compounds were identified with a functional, cell-based assay that screened for molecules which increase transcription of SMN2, which could, theoretically, increase SMN2 protein production. Medicinal chemical optimization of selected dihydroquinazolinones was undertaken to improve solubility and potency to enhance SMN2 transcription. In particular, an asymmetric catalysis approach was used to isolate single enantiomer dihydroquinazolinones. Overall, 65 analogs were synthesized, resulting in 17 active compounds according to the SMN2 luciferase assay. Pharmacological characterization was conducted resulting in a new lead for the series to be taken forward.
Subjects/Keywords: survival motor neuron gene; dihydroquinazolinone; Spinal muscular atrophy; Genetic aspects; Spinal muscular atrophy; Treatment; Genetic transcription; Motor neurons; Heterocyclic compounds; Proteins; Analysis
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
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APA (6th Edition):
Miller, E. H. (2016). Optimization of dihydroquinazolinone for treatment of spinal muscular atrophy. (Masters Thesis). Northeastern University. Retrieved from http://hdl.handle.net/2047/D20213404
Chicago Manual of Style (16th Edition):
Miller, Eliza Hope. “Optimization of dihydroquinazolinone for treatment of spinal muscular atrophy.” 2016. Masters Thesis, Northeastern University. Accessed January 24, 2021.
http://hdl.handle.net/2047/D20213404.
MLA Handbook (7th Edition):
Miller, Eliza Hope. “Optimization of dihydroquinazolinone for treatment of spinal muscular atrophy.” 2016. Web. 24 Jan 2021.
Vancouver:
Miller EH. Optimization of dihydroquinazolinone for treatment of spinal muscular atrophy. [Internet] [Masters thesis]. Northeastern University; 2016. [cited 2021 Jan 24].
Available from: http://hdl.handle.net/2047/D20213404.
Council of Science Editors:
Miller EH. Optimization of dihydroquinazolinone for treatment of spinal muscular atrophy. [Masters Thesis]. Northeastern University; 2016. Available from: http://hdl.handle.net/2047/D20213404
18.
Selph, Catherine.
The selective translocation of the molecular motor Kinesin-1 during the development of neuronal polarity in culture.
Degree: PhD, 2006, Oregon Health Sciences University
URL: doi:10.6083/M48P5XSK
;
http://digitalcommons.ohsu.edu/etd/2908
Subjects/Keywords: Neurons; Axons; Axonal Transport; Kinesin; Molecular Motor Proteins
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Selph, C. (2006). The selective translocation of the molecular motor Kinesin-1 during the development of neuronal polarity in culture. (Doctoral Dissertation). Oregon Health Sciences University. Retrieved from doi:10.6083/M48P5XSK ; http://digitalcommons.ohsu.edu/etd/2908
Chicago Manual of Style (16th Edition):
Selph, Catherine. “The selective translocation of the molecular motor Kinesin-1 during the development of neuronal polarity in culture.” 2006. Doctoral Dissertation, Oregon Health Sciences University. Accessed January 24, 2021.
doi:10.6083/M48P5XSK ; http://digitalcommons.ohsu.edu/etd/2908.
MLA Handbook (7th Edition):
Selph, Catherine. “The selective translocation of the molecular motor Kinesin-1 during the development of neuronal polarity in culture.” 2006. Web. 24 Jan 2021.
Vancouver:
Selph C. The selective translocation of the molecular motor Kinesin-1 during the development of neuronal polarity in culture. [Internet] [Doctoral dissertation]. Oregon Health Sciences University; 2006. [cited 2021 Jan 24].
Available from: doi:10.6083/M48P5XSK ; http://digitalcommons.ohsu.edu/etd/2908.
Council of Science Editors:
Selph C. The selective translocation of the molecular motor Kinesin-1 during the development of neuronal polarity in culture. [Doctoral Dissertation]. Oregon Health Sciences University; 2006. Available from: doi:10.6083/M48P5XSK ; http://digitalcommons.ohsu.edu/etd/2908
19.
Petrash, Hilary A.
Maintaining the Balance: Coordinating Excitation and Inhibition in a Simple Motor Circuit: A Dissertation.
Degree: Neuroscience, Department of Neurobiology; Francis Lab, 2012, U of Massachusetts : Med
URL: https://escholarship.umassmed.edu/gsbs_diss/633
► The generation of complex behaviors often requires the coordinated activity of diverse sets of neural circuits in the brain. Activation of neuronal circuits drives…
(more)
▼ The generation of complex behaviors often requires the coordinated activity of diverse sets of neural circuits in the brain. Activation of neuronal circuits drives behavior. Inappropriate signaling can contribute to cognitive disorders such as epilepsy, Parkinson’s, and addiction (Nordberg et al., 1992; Quik and McIntosh, 2006; Steinlein et al., 2012). The molecular mechanisms by which the activity of neural circuits is coordinated remain unclear. What are the molecules that regulate the timing of neural circuit activation and how is signaling between various neural circuits achieved? While much work has attempted to address these points, answers to these questions have been difficult to ascertain, in part owing to the diversity of molecules involved and the complex connectivity patterns of neural circuits in the mammalian brain.
My thesis work addresses these questions in the context of the nervous system of an invertebrate model organism, the nematode
Caenorhabditis elegans. The locomotory circuit contains two subsets of
motor neurons, excitatory and inhibitory, and the body wall muscle. Dyadic synapses from excitatory neurons coordinate the simultaneous activation of inhibitory neurons and body wall muscle. Here I identify a distinct class of ionotropic acetylcholine receptors (ACR-12R) that are expressed in GABA neurons and contain the subunit ACR-12. ACR-12R localize to synapses of GABA neurons and facilitate consistent body bend amplitude across consecutive body bends. ACR-12Rs regulate GABA neuron activity under conditions of elevated ACh release. This is in contrast to the diffuse and modulatory role of ACR-12 containing receptors expressed in cholinergic
motor neurons (ACR-2R) (Barbagallo et al., 2010; Jospin et al., 2009). Additionally, I show transgenic animals expressing ACR-12 with a mutation in the second transmembrane domain [ACR-12(V/S)] results in spontaneous contractions. Unexpectedly, I found expression of ACR-12 (V/S) results in the preferential toxicity of GABA neurons. Interestingly loss of presynaptic GABA neurons did not have any obvious effects on inhibitory NMJ receptor localization. Together, my thesis work demonstrates the diverse roles of nicotinic acetylcholine receptors (nAChRs) in the regulation of neuronal activity that underlies nematode movement. The findings presented here are broadly applicable to the mechanisms of cholinergic signaling in vertebrate models.
Advisors/Committee Members: Michael M. Francis, PhD.
Subjects/Keywords: Caenorhabditis elegans; Motor Neurons; Nicotinic Receptors; Amino Acids, Peptides, and Proteins; Animal Experimentation and Research; Nervous System; Neuroscience and Neurobiology
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Petrash, H. A. (2012). Maintaining the Balance: Coordinating Excitation and Inhibition in a Simple Motor Circuit: A Dissertation. (Doctoral Dissertation). U of Massachusetts : Med. Retrieved from https://escholarship.umassmed.edu/gsbs_diss/633
Chicago Manual of Style (16th Edition):
Petrash, Hilary A. “Maintaining the Balance: Coordinating Excitation and Inhibition in a Simple Motor Circuit: A Dissertation.” 2012. Doctoral Dissertation, U of Massachusetts : Med. Accessed January 24, 2021.
https://escholarship.umassmed.edu/gsbs_diss/633.
MLA Handbook (7th Edition):
Petrash, Hilary A. “Maintaining the Balance: Coordinating Excitation and Inhibition in a Simple Motor Circuit: A Dissertation.” 2012. Web. 24 Jan 2021.
Vancouver:
Petrash HA. Maintaining the Balance: Coordinating Excitation and Inhibition in a Simple Motor Circuit: A Dissertation. [Internet] [Doctoral dissertation]. U of Massachusetts : Med; 2012. [cited 2021 Jan 24].
Available from: https://escholarship.umassmed.edu/gsbs_diss/633.
Council of Science Editors:
Petrash HA. Maintaining the Balance: Coordinating Excitation and Inhibition in a Simple Motor Circuit: A Dissertation. [Doctoral Dissertation]. U of Massachusetts : Med; 2012. Available from: https://escholarship.umassmed.edu/gsbs_diss/633

University of Michigan
20.
Brouhard, Gary J.
Polar ejection forces in mitosis.
Degree: PhD, Cellular biology, 2004, University of Michigan
URL: http://hdl.handle.net/2027.42/124370
► During mitosis, polar ejection forces (PEFs) are hypothesized to direct prometaphase chromosomes movements by pushing chromosome arms toward the spindle equator. PEFs are postulated to…
(more)
▼ During mitosis, polar ejection forces (PEFs) are hypothesized to direct prometaphase chromosomes movements by pushing chromosome arms toward the spindle equator. PEFs are postulated to be caused by (a) plus-end directed microtubule (MT) based
motor proteins on the chromosome arms, namely chromokinesins, and (b) the polymerization of spindle MTs into the chromosome. However, the exact role of PEFs is unclear, since little is known about the magnitude or form of PEFs. This study employs optical tweezers to recreate the lateral interaction between chromosome arms and MTs in vitro to obtain the first direct measurement of the speed and force of the PEFs developed on chromosome arms. The results include forces that frequently exceed 1 pN, maximum forces of 2 – 3 pN, and velocities of 83 +/- 56 nm/s; the movements exhibit a characteristic, non-continuous motion that includes displacements of >50 nm, stalls, and backwards slippage of the MT even under low loads. This activity is attributed to chromokinesin motors based on its ATP-dependence, antibody blocking experiments, and quantitative fluorescence. At first glance, this
motor activity appears surprisingly weak and erratic, but it is ideally suited for producing PEFs that guide chromosome movements without severely deforming or damaging the local chromosome structure.
Advisors/Committee Members: Hunt, Alan J. (advisor).
Subjects/Keywords: Chromokinesin; Mitosis; Motor Proteins; Optical Tweezers; Polar Ejection Forces
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Brouhard, G. J. (2004). Polar ejection forces in mitosis. (Doctoral Dissertation). University of Michigan. Retrieved from http://hdl.handle.net/2027.42/124370
Chicago Manual of Style (16th Edition):
Brouhard, Gary J. “Polar ejection forces in mitosis.” 2004. Doctoral Dissertation, University of Michigan. Accessed January 24, 2021.
http://hdl.handle.net/2027.42/124370.
MLA Handbook (7th Edition):
Brouhard, Gary J. “Polar ejection forces in mitosis.” 2004. Web. 24 Jan 2021.
Vancouver:
Brouhard GJ. Polar ejection forces in mitosis. [Internet] [Doctoral dissertation]. University of Michigan; 2004. [cited 2021 Jan 24].
Available from: http://hdl.handle.net/2027.42/124370.
Council of Science Editors:
Brouhard GJ. Polar ejection forces in mitosis. [Doctoral Dissertation]. University of Michigan; 2004. Available from: http://hdl.handle.net/2027.42/124370

University of Colorado
21.
Kuan, Hui-Shun.
Active Pattern Formation in One and Two Dimensions.
Degree: PhD, Chemistry & Biochemistry, 2016, University of Colorado
URL: https://scholar.colorado.edu/chem_gradetds/187
► In this thesis, we studied active systems in one or two dimensions in which particles are self-propelled and repel each other. In one-dimensional models,…
(more)
▼ In this thesis, we studied active systems in one or two dimensions in which particles are self-propelled and repel each other. In one-dimensional models, we considered driven particles on single lanes or in anti-parallel overlaps with both binding/unbinding and switching between the lanes. These models are inspired by experiments on kinesin
proteins walking on microtubules or anti-parallel overlaps. In the single-lane case, we focused on length regulation controlled by end concentration or flux. In the anti-parallel overlap case, we used a phase space flow method to determine the density profiles and compared the analytic results with kinetic Monte Carlo simulations. In calculating the phase diagram, we also found a phase, the low density-high density-low density-high density phase, which was not found previously. In two dimensional systems, we studied high-aspect-ratio self-propelled rods with a repulsive potential over a wide range of packing fraction and driving to determine the nonequilibrium state diagram and dynamic behavior. Flocking and nematic-laning states occupy much of the parameter space. In the flocking state, the average internal pressure is high and structural and mechanical relaxation times are long, suggesting that rods in flocks are in a translating glassy state despite overall flock motion. In contrast, the nematic-laning state shows fluid-like behavior. The flocking state occupies regions of the state diagram at both low and high packing fraction separated by nematic-laning at low driving and a history-dependent region at higher driving; the nematic-laning state transitions to the flocking state for both compression and expansion. We propose that the laning-flocking transitions are a type of glass transition which, in contrast to other glass-forming systems, can show fluidization as density increases. The fluid internal dynamics and ballistic transport of the nematic-laning state may promote collective dynamics of rod-shaped microorganisms.
Advisors/Committee Members: Meredith D. Betterton, Matthew A. Glaser, Joel D. Eaves, Tom Perkins, Xuedong Liu.
Subjects/Keywords: Active systems; Langmuir kinetics; Microtubule; Motor proteins; Totally asymmetric simple exclusion process; Biological and Chemical Physics; Physical Chemistry
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Kuan, H. (2016). Active Pattern Formation in One and Two Dimensions. (Doctoral Dissertation). University of Colorado. Retrieved from https://scholar.colorado.edu/chem_gradetds/187
Chicago Manual of Style (16th Edition):
Kuan, Hui-Shun. “Active Pattern Formation in One and Two Dimensions.” 2016. Doctoral Dissertation, University of Colorado. Accessed January 24, 2021.
https://scholar.colorado.edu/chem_gradetds/187.
MLA Handbook (7th Edition):
Kuan, Hui-Shun. “Active Pattern Formation in One and Two Dimensions.” 2016. Web. 24 Jan 2021.
Vancouver:
Kuan H. Active Pattern Formation in One and Two Dimensions. [Internet] [Doctoral dissertation]. University of Colorado; 2016. [cited 2021 Jan 24].
Available from: https://scholar.colorado.edu/chem_gradetds/187.
Council of Science Editors:
Kuan H. Active Pattern Formation in One and Two Dimensions. [Doctoral Dissertation]. University of Colorado; 2016. Available from: https://scholar.colorado.edu/chem_gradetds/187

Rice University
22.
Jamison, Kenneth.
The biophysics of intracellular transport driven by structurally-defined systems of motor proteins.
Degree: PhD, Engineering, 2011, Rice University
URL: http://hdl.handle.net/1911/70276
► The number of motor proteins attached to cellular cargos is widely believed to influence intracellular transport processes and may play a role in transport regulation.…
(more)
▼ The number of
motor proteins attached to cellular cargos is widely believed to influence intracellular transport processes and may play a role in transport regulation. However, to date, investigating the biophysics of multiple-
motor dynamics has been challenging since the number of motors responsible for cargo motion is not easily characterized. This work examines the transport properties of structurally-defined
motor complexes containing two kinesin-1 motors, from both an experimental and theoretical perspective.
Motor complexes were synthesized using DNA as a molecular scaffold and engineered DNA-conjugated protein polymers as linkers to couple motors to scaffolds. After anchoring the
motor complexes to a bead their dynamic properties were measured using an automated optical trapping instrument that could be used to perform both static (increasing load) and force-feedback (constant load) optical trapping experiments. Data from these experiments is compared to predictions from a microscopic transition rate model of multiple kinesin dynamics. Together, these studies uncovered that multiple kinesins typically cannot cooperate since the microtubule-bound configuration of a
motor complex often prevents both kinesins from sharing cargo loads. Furthermore, multiple-
motor behaviors are influenced by the fact that
motor complexes display hysteretic force-velocity behaviors when applied loads change rapidly in time. Overall, such behaviors suggest the number of kinesins on a cargo will not be a key determinant of intracellular transport processes, and in turn, will not contribute appreciably to mechanisms that regulate cargo motion. However, this work also provides evidence that processive microtubule motors that are less efficient than kinesin (e.g., dynein) will cooperate productively, produce greater responses to
motor number, and may therefore act as a regulator of cargo transport.
Advisors/Committee Members: Diehl, Michael R. (advisor).
Subjects/Keywords: Applied sciences; Biological sciences; Intracellular transport; Motor proteins; Kinesin; Dynein; Optical traps; Molecular biology; Nanoscience; Biophysics
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Jamison, K. (2011). The biophysics of intracellular transport driven by structurally-defined systems of motor proteins. (Doctoral Dissertation). Rice University. Retrieved from http://hdl.handle.net/1911/70276
Chicago Manual of Style (16th Edition):
Jamison, Kenneth. “The biophysics of intracellular transport driven by structurally-defined systems of motor proteins.” 2011. Doctoral Dissertation, Rice University. Accessed January 24, 2021.
http://hdl.handle.net/1911/70276.
MLA Handbook (7th Edition):
Jamison, Kenneth. “The biophysics of intracellular transport driven by structurally-defined systems of motor proteins.” 2011. Web. 24 Jan 2021.
Vancouver:
Jamison K. The biophysics of intracellular transport driven by structurally-defined systems of motor proteins. [Internet] [Doctoral dissertation]. Rice University; 2011. [cited 2021 Jan 24].
Available from: http://hdl.handle.net/1911/70276.
Council of Science Editors:
Jamison K. The biophysics of intracellular transport driven by structurally-defined systems of motor proteins. [Doctoral Dissertation]. Rice University; 2011. Available from: http://hdl.handle.net/1911/70276

Duke University
23.
Chee, Mark Kuan Leng.
B-cyclin/CDK Regulation of Mitotic Spindle Assembly through Phosphorylation of Kinesin-5 Motors in the Budding Yeast, Saccharomyces cerevisiae
.
Degree: 2012, Duke University
URL: http://hdl.handle.net/10161/5419
► Although it has been known for many years that B-cyclin/CDK complexes regulate the assembly of the mitotic spindle and entry into mitosis, the full…
(more)
▼ Although it has been known for many years that B-cyclin/CDK complexes regulate the assembly of the mitotic spindle and entry into mitosis, the full complement of relevant CDK targets has not been identified. It has previously been shown in a variety of model systems that B-type cyclin/CDK complexes, kinesin-5 motors, and the SCF
Cdc4 ubiquitin ligase are required for the separation of spindle poles and assembly of a bipolar spindle. It has been suggested that in the budding yeast, Saccharomyces cerevisiae, B-type cyclin/CDK (Clb/Cdc28) complexes promote spindle pole separation by inhibiting the degradation of the kinesins-5 Kip1 and Cin8 by the anaphase-promoting complex (APC
Cdh1). I have determined, however, that the Kip1 and Cin8
proteins are actually present at wild-type levels in yeast in the absence of Clb/Cdc28 kinase activity. Here, I show that Kip1 and Cin8 are in vitro targets of Clb2/Cdc28, and that the mutation of conserved CDK phosphorylation sites on Kip1 inhibits spindle pole separation without affecting the protein's in vivo localization or abundance. Mass spectrometry analysis confirms that two CDK sites in the tail domain of Kip1 are phosphorylated in vivo. In addition, I have determined that Sic1, a Clb/Cdc28-specific inhibitor, is the SCF
Cdc4 target that inhibits spindle pole separation in cells lacking functional Cdc4. Based on these findings, I propose that Clb/Cdc28 drives spindle pole separation by direct phosphorylation of kinesin-5 motors. In addition to the positive regulation of kinesin-5 function in spindle assembly, I have also found evidence that suggests CDK phosphorylation of kinesin-5 motors at different sites negatively regulates kinesin-5 activity to prevent premature spindle pole separation. I have also begun to characterize a novel putative role for the kinesins-5 in mitochondrial genome inheritance in S. cerevisiae that may also be regulated by CDK phosphorylation. In the course of my dissertation research, I encountered problems with several established molecular biology tools used by yeast researchers that I have tried to address. I have constructed a set of 42 plasmid shuttle vectors based on the widely used pRS series for use in S. cerevisiae that can be propagated in the bacterium Escherichia coli. This set of pRSII plasmids includes new shuttle vectors that can be used with histidine and adenine auxotrophic laboratory yeast strains carrying mutations in the genes HIS2 and ADE1, respectively. My new pRSII plasmids also include updated versions of commonly used pRS plasmids from which common restriction sites that occur within their yeast-selectable biosynthetic marker genes have been removed in order to increase the availability of unique restriction sites within their polylinker regions. Hence, my pRSII plasmids are a complete set of integrating, centromere and 2 episomal plasmids with the biosynthetic…
Advisors/Committee Members: Haase, Steven B (advisor).
Subjects/Keywords: Cellular biology;
Genetics;
Biophysics;
cell division cycle;
cyclin/CDK;
homology modeling;
kinesin motor proteins;
mitotic spindle;
plasmid shuttle vectors
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Chee, M. K. L. (2012). B-cyclin/CDK Regulation of Mitotic Spindle Assembly through Phosphorylation of Kinesin-5 Motors in the Budding Yeast, Saccharomyces cerevisiae
. (Thesis). Duke University. Retrieved from http://hdl.handle.net/10161/5419
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Chee, Mark Kuan Leng. “B-cyclin/CDK Regulation of Mitotic Spindle Assembly through Phosphorylation of Kinesin-5 Motors in the Budding Yeast, Saccharomyces cerevisiae
.” 2012. Thesis, Duke University. Accessed January 24, 2021.
http://hdl.handle.net/10161/5419.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Chee, Mark Kuan Leng. “B-cyclin/CDK Regulation of Mitotic Spindle Assembly through Phosphorylation of Kinesin-5 Motors in the Budding Yeast, Saccharomyces cerevisiae
.” 2012. Web. 24 Jan 2021.
Vancouver:
Chee MKL. B-cyclin/CDK Regulation of Mitotic Spindle Assembly through Phosphorylation of Kinesin-5 Motors in the Budding Yeast, Saccharomyces cerevisiae
. [Internet] [Thesis]. Duke University; 2012. [cited 2021 Jan 24].
Available from: http://hdl.handle.net/10161/5419.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Chee MKL. B-cyclin/CDK Regulation of Mitotic Spindle Assembly through Phosphorylation of Kinesin-5 Motors in the Budding Yeast, Saccharomyces cerevisiae
. [Thesis]. Duke University; 2012. Available from: http://hdl.handle.net/10161/5419
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
24.
Goldtzvik, Yonathan Yitshak.
UNDERSTANDING THE MOTILITY OF MOLECULAR MOTORS USING THEORY AND SIMULATIONS.
Degree: Biophysics (BIPH), 2017, University of Maryland
URL: http://hdl.handle.net/1903/20356
► Molecular motors are indispensable machines that are in charge of transporting cargoes within living cells. Despite recent advances in the study of these molecules, there…
(more)
▼ Molecular motors are indispensable machines that are in charge of transporting cargoes within living cells. Despite recent advances in the study of these molecules, there is much that we still do not understand regarding the underlying mechanisms that allow them to efficiently move cargoes along polar cellular filaments. In this thesis, I report my investigation on two
motor proteins superfamilies, dyneins and kinesins. Using theoretical modeling, we provide fundamental insight into their function.
Dynein is a large
motor that transports cargo along microtubules towards their negative pole. Unlike other motors, such as conventional kinesin, the motility of dynein is highly stochastic. We developed a novel theoretical approach, which reproduces a wide variety of its properties, including the unique step size distribution observed in experiments. Furthermore, our model enables us to derive several simple expressions that can be fitted to experiment, thus providing a physical interpretation.
A less understood aspect of dynein is the complex set of allosteric transitions in response to ATP binding and hydrolysis, and microtubule binding. The resulting conformational transitions propel the
motor forward to the minus end of the microtubule. Furthermore, its activity is regulated by external strain. Using coarse grained Brownian dynamics simulations, we show that a couple of insert loops in the AAA2, a sub domain in the AAA+ ring in the
motor domain, play an important role in several of the alllosteric pathways.
Kinesins are highly processive
motor proteins that transport cargo along microtubules toward their positive poles. Experiments show that the kinesin
motor domains propel the
motor forward by passing each other in a hand-over-hand motion. However, there is a debate as to whether the
motor domains do so in a symmetrical manner or an asymmetrical motion. Using coarse grained Brownian dynamics simulations of the kinesin dimer, we show that the kinesin stepping mechanism is influenced by the size of its cargo. Furthermore, we find that stepping occurs by a combinations of both the symmetric and asymmetric mechanisms. The results I present in this thesis are a testimony that theoretical approaches are invaluable to the study of molecular motors.
Advisors/Committee Members: Thirumalai, Devarajan (advisor).
Subjects/Keywords: Biophysics; Biology; Molecular physics; Brownian Dynamics Simulations; Coarse Grained Models; Dynein; Kinesin; Molecular Motors; Motor Proteins
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APA (6th Edition):
Goldtzvik, Y. Y. (2017). UNDERSTANDING THE MOTILITY OF MOLECULAR MOTORS USING THEORY AND SIMULATIONS. (Thesis). University of Maryland. Retrieved from http://hdl.handle.net/1903/20356
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Goldtzvik, Yonathan Yitshak. “UNDERSTANDING THE MOTILITY OF MOLECULAR MOTORS USING THEORY AND SIMULATIONS.” 2017. Thesis, University of Maryland. Accessed January 24, 2021.
http://hdl.handle.net/1903/20356.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Goldtzvik, Yonathan Yitshak. “UNDERSTANDING THE MOTILITY OF MOLECULAR MOTORS USING THEORY AND SIMULATIONS.” 2017. Web. 24 Jan 2021.
Vancouver:
Goldtzvik YY. UNDERSTANDING THE MOTILITY OF MOLECULAR MOTORS USING THEORY AND SIMULATIONS. [Internet] [Thesis]. University of Maryland; 2017. [cited 2021 Jan 24].
Available from: http://hdl.handle.net/1903/20356.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Goldtzvik YY. UNDERSTANDING THE MOTILITY OF MOLECULAR MOTORS USING THEORY AND SIMULATIONS. [Thesis]. University of Maryland; 2017. Available from: http://hdl.handle.net/1903/20356
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Michigan State University
25.
Johansen, Jamie Ann.
When androgen receptors go awry : muscle specific expression triggers Spinal Bulbar Muscular Atrophy (SBMA).
Degree: PhD, Department of Neuroscience, 2008, Michigan State University
URL: http://etd.lib.msu.edu/islandora/object/etd:39373
Subjects/Keywords: Motor neurons – Diseases – Etiology; Androgens – Pathophysiology; Glutamine; Muscle proteins
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APA ·
Chicago ·
MLA ·
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CSE |
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to Zotero / EndNote / Reference
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APA (6th Edition):
Johansen, J. A. (2008). When androgen receptors go awry : muscle specific expression triggers Spinal Bulbar Muscular Atrophy (SBMA). (Doctoral Dissertation). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:39373
Chicago Manual of Style (16th Edition):
Johansen, Jamie Ann. “When androgen receptors go awry : muscle specific expression triggers Spinal Bulbar Muscular Atrophy (SBMA).” 2008. Doctoral Dissertation, Michigan State University. Accessed January 24, 2021.
http://etd.lib.msu.edu/islandora/object/etd:39373.
MLA Handbook (7th Edition):
Johansen, Jamie Ann. “When androgen receptors go awry : muscle specific expression triggers Spinal Bulbar Muscular Atrophy (SBMA).” 2008. Web. 24 Jan 2021.
Vancouver:
Johansen JA. When androgen receptors go awry : muscle specific expression triggers Spinal Bulbar Muscular Atrophy (SBMA). [Internet] [Doctoral dissertation]. Michigan State University; 2008. [cited 2021 Jan 24].
Available from: http://etd.lib.msu.edu/islandora/object/etd:39373.
Council of Science Editors:
Johansen JA. When androgen receptors go awry : muscle specific expression triggers Spinal Bulbar Muscular Atrophy (SBMA). [Doctoral Dissertation]. Michigan State University; 2008. Available from: http://etd.lib.msu.edu/islandora/object/etd:39373
26.
Pereira Frias, C.S.
Focus on the axon: from neuronal development to dynamic synapses.
Degree: 2017, University Utrecht
URL: https://dspace.library.uu.nl/handle/1874/356271
;
URN:NBN:NL:UI:10-1874-356271
;
1874/356271
;
urn:isbn:9789039368565
;
URN:NBN:NL:UI:10-1874-356271
;
https://dspace.library.uu.nl/handle/1874/356271
► Neurons acquire an optimized structure for the reception and processing of information, with long protrusions extending from the neuronal cell body. These protrusions are morphologically…
(more)
▼ Neurons acquire an optimized structure for the reception and processing of information, with long protrusions extending from the neuronal cell body. These protrusions are morphologically and functionally different from each other, and are crucial for the establishment of a dynamic and intricate neuronal network. The axon is a long protrusion responsible for the transmission of electrochemical signals to other neurons, while dendrites receive these signals. The propagation of information from the axon of one neuron to the dendrite of another happens at specialized regions called synapses. When a signal travels along the axon and reaches the presynapse, it induces the fusion of synaptic vesicles with the plasma membrane in the presynaptic terminal, releasing neurotransmitters. These neurotransmitters can bind to receptors present at the postsynaptic membrane of the receiving neuron, generating a signal that can be transmitted to the next neuron. To ensure the accurate communication between neurons, synapses must be correctly assembled during development and supplied with specific
proteins to the pre- and postsynaptic compartments. As most of the
proteins are synthesized in the cell body, they need to be transported to the proper location by
motor proteins, which use the underlying actin and microtubule cytoskeleton as rails. The axon extends considerably from the soma to reach the appropriate synaptic partners, and the molecular mechanisms underlying this process have intrigued many neuroscientists. We can study axon development in a controlled environment by culturing neurons from rodent brains. In this system, the axon is formed within the first 24 hours after plating, and the factors that support axon development and outgrowth have to be delivered by
motor proteins to the proper location. We have addressed the role of
motor proteins in the extension of the axon in hippocampal neurons. Besides their role in axonal outgrowth, we showed that
motor proteins are also required for the maintenance of synapses along the dendrites of hippocampal neurons. The presynaptic terminals are very dynamic structures, appearing, disappearing and reappearing at the same location along the axon. Inhibitory presynaptic boutons have been shown to be particularly dynamic, but the molecular mechanisms underlying these dynamics are not understood. In this thesis, we studied a new regulatory pathway of inhibitory presynaptic bouton dynamics triggered by the guidance protein Semaphorin4D.
Advisors/Committee Members: Hoogenraad, Casper, Wierenga, Corette.
Subjects/Keywords: Axon; motor proteins; synapse; presynapse; dynamics; inhibitory axons
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Pereira Frias, C. S. (2017). Focus on the axon: from neuronal development to dynamic synapses. (Doctoral Dissertation). University Utrecht. Retrieved from https://dspace.library.uu.nl/handle/1874/356271 ; URN:NBN:NL:UI:10-1874-356271 ; 1874/356271 ; urn:isbn:9789039368565 ; URN:NBN:NL:UI:10-1874-356271 ; https://dspace.library.uu.nl/handle/1874/356271
Chicago Manual of Style (16th Edition):
Pereira Frias, C S. “Focus on the axon: from neuronal development to dynamic synapses.” 2017. Doctoral Dissertation, University Utrecht. Accessed January 24, 2021.
https://dspace.library.uu.nl/handle/1874/356271 ; URN:NBN:NL:UI:10-1874-356271 ; 1874/356271 ; urn:isbn:9789039368565 ; URN:NBN:NL:UI:10-1874-356271 ; https://dspace.library.uu.nl/handle/1874/356271.
MLA Handbook (7th Edition):
Pereira Frias, C S. “Focus on the axon: from neuronal development to dynamic synapses.” 2017. Web. 24 Jan 2021.
Vancouver:
Pereira Frias CS. Focus on the axon: from neuronal development to dynamic synapses. [Internet] [Doctoral dissertation]. University Utrecht; 2017. [cited 2021 Jan 24].
Available from: https://dspace.library.uu.nl/handle/1874/356271 ; URN:NBN:NL:UI:10-1874-356271 ; 1874/356271 ; urn:isbn:9789039368565 ; URN:NBN:NL:UI:10-1874-356271 ; https://dspace.library.uu.nl/handle/1874/356271.
Council of Science Editors:
Pereira Frias CS. Focus on the axon: from neuronal development to dynamic synapses. [Doctoral Dissertation]. University Utrecht; 2017. Available from: https://dspace.library.uu.nl/handle/1874/356271 ; URN:NBN:NL:UI:10-1874-356271 ; 1874/356271 ; urn:isbn:9789039368565 ; URN:NBN:NL:UI:10-1874-356271 ; https://dspace.library.uu.nl/handle/1874/356271

Rice University
27.
Das, Rahul Kumar.
Stochastic Modeling and Simulations of Biological Transport.
Degree: PhD, Natural Sciences, 2010, Rice University
URL: http://hdl.handle.net/1911/27479
► Biological transport is an essential phenomenon for the living systems. A mechanistic investigation of biological transport processes is highly important for the characterization of physiological…
(more)
▼ Biological transport is an essential phenomenon for the living systems. A mechanistic investigation of biological transport processes is highly important for the
characterization of physiological and cellular events, the design and functioning of
several biomedical devices and the development of new therapies. To investigate the
physical-chemical details of this phenomenon, concerted efforts of both experiments
and theory are necessary.
Motor proteins constitute a major portion of the active transport in the living cell.
However, the actual mechanism of how chemical energy is converted into their directed
motion has still remained obscure. Recent experiments on
motor proteins have been
producing exciting results that have motivated theoretical studies. In order to provide
deep insight onto
motor protein's mechanochemical coupling we have used stochastic
modeling based on discrete-state chemical kinetic model. Such models enable us
to (1) resolve the contradiction between experimental observations on heterodimeric
kinesins and highly popular hand-over-hand mechanism, (2) take into account the free energy landscape modification of individual
motor domains due to interdomain
interaction, (3) recognize the effect of spatial fluctuations on biochemical properties
of molecular motors, and (4) calculate the dynamical properties such as velocities,
dispersions of complex biochemical pathways. We have also initiated the investigation
of the dynamics of coupled
motor assemblies using stochastic modeling.
Furthermore, an extensive Monte Carlo lattice simulation based study on facilitated search process of DNA-binding
proteins is presented. This simulation shows
that the accelerated search compared to pure Smoluchowski limit can be achieved
even in the case where the one-dimensional diffusion is order of magnitude slower
than the three-dimensional diffusion. We also show that facilitated search is not only
the manifestation of dimensionality reduction but correlation times play a crucial role
in the overall search times.
Finally, a more general field of stochastic processes, namely first-passage time
process is investigated. Explicit expressions of important properties, such as splitting
probailities and mean first-passage times, that are relevant to (but not limited to)
biological transport, are derived for several complex systems.
Advisors/Committee Members: Kolomeisky, Anatoly B. (advisor).
Subjects/Keywords: Motor proteins; Stochastic modeling; DNA binding proteins; Monte Carlo simulations
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Das, R. K. (2010). Stochastic Modeling and Simulations of Biological Transport. (Doctoral Dissertation). Rice University. Retrieved from http://hdl.handle.net/1911/27479
Chicago Manual of Style (16th Edition):
Das, Rahul Kumar. “Stochastic Modeling and Simulations of Biological Transport.” 2010. Doctoral Dissertation, Rice University. Accessed January 24, 2021.
http://hdl.handle.net/1911/27479.
MLA Handbook (7th Edition):
Das, Rahul Kumar. “Stochastic Modeling and Simulations of Biological Transport.” 2010. Web. 24 Jan 2021.
Vancouver:
Das RK. Stochastic Modeling and Simulations of Biological Transport. [Internet] [Doctoral dissertation]. Rice University; 2010. [cited 2021 Jan 24].
Available from: http://hdl.handle.net/1911/27479.
Council of Science Editors:
Das RK. Stochastic Modeling and Simulations of Biological Transport. [Doctoral Dissertation]. Rice University; 2010. Available from: http://hdl.handle.net/1911/27479
28.
Hou, Yuqing.
Identification and Characterization of Components of the Intraflagellar transport (IFT) Machinery: a Dissertation.
Degree: Cell Biology, Radiology, 2007, U of Massachusetts : Med
URL: https://escholarship.umassmed.edu/gsbs_diss/323
► Intraflagellar transport (IFT), the bi-directional movement of particles along the length of flagella, is required for flagellar assembly. The IFT particles are moved by…
(more)
▼ Intraflagellar transport (IFT), the bi-directional movement of particles along the length of flagella, is required for flagellar assembly. The IFT particles are moved by kinesin II from the base to the tip of the flagellum, where flagellar assembly occurs. The IFT particles are then moved in the retrograde direction by cytoplasmic dynein 1b/2 to the base of the flagellum. The IFT particles of
Chlamydomonas are composed of ~16
proteins, organized into complexes A and B. Alhough IFT is believed to transport cargoes into flagella, few cargoes have been identified and little is known about how the cargos are transported. To study the mechanism of IFT and how IFT is involved in flagellar assembly, this thesis focuses on two questions. 1) In addition to a heavy chain, DHC1b, and a light chain, LC8, what other
proteins are responsible for the retrograde movement of IFT particles? 2) What is the specific function of an individual IFT-particle protein? To address these two questions, I screened for
Chlamydomonas mutants either defective in retrograde IFT by immunofluorescence microscopy, or defective in IFT-particle
proteins and D1bLIC, a dynein light intermediate chain possibly involved in retrograde IFT, by Southern blotting. I identified several mutants defective in retrograde IFT and one of them is defective in the D1bLIC gene. I also identified several mutants defective in several IFT-particle protein genes. I then focused on the mutant defective in D1bLIC and the one defective in IFT46, which was briefly reported as an IFT complex B protein. My results show that as a subunit of the retrograde IFT
motor, D1bLIC is required for the stability of DHC1b and is involved in the attachment of IFT particles to the retrograde
motor. The P-loop in D1bLIC is not necessary for the function of D1bLIC in retrograde IFT. My results also show that as a complex B protein, IFT46 is necessary for complex B stability and is required for the transport of outer dynein arms into flagella. IFT46 is phosphorylated
in vivo and the phosphorylation is not critical for IFT46’s function in flagellar assembly.
Advisors/Committee Members: George B. Witman, Ph.D..
Subjects/Keywords: Intracellular Signaling Peptides and Proteins; Protein Transport; Dynein ATPase; Chlamydomonas; Flagella; Protozoan Proteins; Molecular Motor Proteins; Amino Acids, Peptides, and Proteins; Cells
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Hou, Y. (2007). Identification and Characterization of Components of the Intraflagellar transport (IFT) Machinery: a Dissertation. (Doctoral Dissertation). U of Massachusetts : Med. Retrieved from https://escholarship.umassmed.edu/gsbs_diss/323
Chicago Manual of Style (16th Edition):
Hou, Yuqing. “Identification and Characterization of Components of the Intraflagellar transport (IFT) Machinery: a Dissertation.” 2007. Doctoral Dissertation, U of Massachusetts : Med. Accessed January 24, 2021.
https://escholarship.umassmed.edu/gsbs_diss/323.
MLA Handbook (7th Edition):
Hou, Yuqing. “Identification and Characterization of Components of the Intraflagellar transport (IFT) Machinery: a Dissertation.” 2007. Web. 24 Jan 2021.
Vancouver:
Hou Y. Identification and Characterization of Components of the Intraflagellar transport (IFT) Machinery: a Dissertation. [Internet] [Doctoral dissertation]. U of Massachusetts : Med; 2007. [cited 2021 Jan 24].
Available from: https://escholarship.umassmed.edu/gsbs_diss/323.
Council of Science Editors:
Hou Y. Identification and Characterization of Components of the Intraflagellar transport (IFT) Machinery: a Dissertation. [Doctoral Dissertation]. U of Massachusetts : Med; 2007. Available from: https://escholarship.umassmed.edu/gsbs_diss/323
29.
Smith, Rebecca Burt.
Axonal trafficking of BMP signals in Drosophila motoneurons.
Degree: PhD, 2009, University of Alabama – Birmingham
URL: http://contentdm.mhsl.uab.edu/u?/etd,930
► The Drosophila Bone Morphogenetic Protein (BMP) Glass bottom boat (Gbb) is a ligand for the BMP type II receptor, Wishful thinking (Wit). Mutations in either…
(more)
▼ The Drosophila Bone Morphogenetic Protein (BMP) Glass bottom boat (Gbb) is
a ligand for the BMP type II receptor, Wishful thinking (Wit). Mutations in either of
these proteins impair synaptic growth at the neuromuscular junction (NMJ). Gbb is a
retrograde signal (from target to innervating neuron) that is essential for proper NMJ
development and function. Tissue-specific rescue of pathway mutants and
immunolocalization experiments indicate that the receptor-ligand interaction occurs at the
NMJ, and results in the nuclear accumulation of the phosphorylated form of the
transcription factor Mad, indicating that retrograde transport along the axon is critical for
pathway activation. We have investigated the mechanism of retrograde axonal transport
of the BMP using a signaling endosome model of signal propagation. In this model, the
receptor complex undergoes internalization at the synaptic terminal and is transported
along axon microtubules to the cell body where it then activates down-stream molecules.
Tools that we have utilized to characterize our pathway include fluorescent fusion
proteins of our BMP receptors and Mad transcription factor as well as high resolution live
imaging techniques. From our studies, we find that the receptors Wit and Tkv are being
transported in a bi-directional manner along the motoneuron axon. Mad along the axon,
however, appears diffuse and does not travel with the receptors. We see p-Mad in the
nucleus and at the synaptic terminal, however we do not see p-Mad along the axon. A
known inhibitor of the pathway, DN-Glued, dramatically decreases the amount of
moving receptor vesicles, linking receptor transport to pathway activity. Additionally,
we have found that Tkv-YFP and Wit-CFP colocalize along the axon in predominately
retrograde moving particles and lose this directionality in gbb ligand mutants, consistent
with our hypothesis of a signaling endosome. In further support of the signaling
endosome model, manipulation of the endocytic pathway results in alterations in p-Mad
levels and alterations in receptor vesicle transport. Our data suggests that, to propagate
the BMP pathway along the motoneuron axon, the receptors are traveling in a signaling
endosome that phosphorylates Mad in separate events at the synaptic terminal and
proximal cell body.
1 online resource (xiv, 154 p. : ill., digital, PDF file)
Genetics;
Joint Health Sciences;
BMP
Drosophila
motoneurons
Wit
axonal transport
synaptic plasticity
UNRESTRICTED
Advisors/Committee Members: Marques, Guillermo, Collawn, James<br>, Jiao, Kai<br>, Pozzo-Miller, Lucas<br>, Serra, Rosa<br>, Yoder, Bradley.
Subjects/Keywords: Axonal Transport<; br>;
Bone Morphogenetic Proteins – genetics<; br>;
Drosophila – genetics<; br>;
Motor Neurons<; br>;
Neuronal Plasticity<; br>;
Synapses – physiology
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Smith, R. B. (2009). Axonal trafficking of BMP signals in Drosophila motoneurons. (Doctoral Dissertation). University of Alabama – Birmingham. Retrieved from http://contentdm.mhsl.uab.edu/u?/etd,930
Chicago Manual of Style (16th Edition):
Smith, Rebecca Burt. “Axonal trafficking of BMP signals in Drosophila motoneurons.” 2009. Doctoral Dissertation, University of Alabama – Birmingham. Accessed January 24, 2021.
http://contentdm.mhsl.uab.edu/u?/etd,930.
MLA Handbook (7th Edition):
Smith, Rebecca Burt. “Axonal trafficking of BMP signals in Drosophila motoneurons.” 2009. Web. 24 Jan 2021.
Vancouver:
Smith RB. Axonal trafficking of BMP signals in Drosophila motoneurons. [Internet] [Doctoral dissertation]. University of Alabama – Birmingham; 2009. [cited 2021 Jan 24].
Available from: http://contentdm.mhsl.uab.edu/u?/etd,930.
Council of Science Editors:
Smith RB. Axonal trafficking of BMP signals in Drosophila motoneurons. [Doctoral Dissertation]. University of Alabama – Birmingham; 2009. Available from: http://contentdm.mhsl.uab.edu/u?/etd,930
30.
Hendricks, Adam G.
Collective Dynamics of Kinesin-1.
Degree: PhD, Mechanical Engineering, 2008, University of Michigan
URL: http://hdl.handle.net/2027.42/60661
► Motor proteins are the engines of biology, converting chemical energy to mechanical work in cells. Kinesin-1 is a motor protein that transports vesicles towards the…
(more)
▼ Motor proteins are the engines of biology, converting chemical energy to mechanical work in cells. Kinesin-1 is a
motor protein that transports vesicles towards the plus end of microtubules, widely believed to be responsible for anterograde transport of synaptic vesicles in neurons. Advances in single-molecule techniques have allowed the characterization of single kinesin motors in vitro at a range of loads and ATP concentrations. Single kinesin motors are capable of processive movement along the
microtubule at a maximum velocity of approximately 1 μm/s. The velocity decreases roughly linearly in response to load until reaching stall at a load of approximately
6 pN. Several theoretical models have been proposed that describe the steady-state motion of single kinesin motors. However, growing evidence suggests that kinesin functions collectively in cells, whereby several motors work in a coordinated manner to transport a vesicle. A transient description is required to describe collective dynamics, as the interactions among coupled motors induce time-varying forces on each
motor. Herein a mechanistic model of kinesin is proposed that is capable of accurately describing transient and steady-state dynamics. Each domain of the protein is modeled via a mechanical potential. The mechanical potentials are related
explicitly to the chemical kinetics of each
motor domain. The mechanistic model was used to simulate the collective behavior of coupled kinesin motors under varying loads, cargo linker stiffnesses, and numbers of motors. To analyze the simulations of coordinated transport, several metrics were developed that are specifically tailored to characterizing the synchronization of nonlinear, nonsmooth oscillators like kinesin. The model results suggest that, in the cell, coupled motors under low loads are loosely correlated. When the load is increased, such as when the cargo encounters an obstacle like another vesicle or the cytoskeleton, motors become more correlated in response to increased loads, allowing them to produce greater forces. Increasing the number of motors involved in the transport does not appreciably increase the dimensionality of the trajectory, implying large numbers of motors are able to work collectively, even without becoming fully synchronized.
Advisors/Committee Members: Epureanu, Bogdan I. (committee member), Meyhofer, Edgar (committee member), Grosh, Karl (committee member), Hunt, Alan J. (committee member).
Subjects/Keywords: Motor Proteins; Coupled Oscillators; Synchronization; Kinesin; Mechanical Engineering; Engineering
…x29; Load = 4 pN/motor. . . . . . . .
64
vii
ABSTRACT
Motor proteins are the engines of… …fully synchronized.
ix
CHAPTER I
Introduction
Motor proteins convert chemical energy into… …proteins. Another class of motor proteins, dynein, power flagella
and cillia in eukaryotes. The… …in
anaphase. The ubiquity of motor proteins in biology means the understanding of
their… …medicine, and engineering.
One class of motor proteins, kinesins, use the energy from ATP…
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Hendricks, A. G. (2008). Collective Dynamics of Kinesin-1. (Doctoral Dissertation). University of Michigan. Retrieved from http://hdl.handle.net/2027.42/60661
Chicago Manual of Style (16th Edition):
Hendricks, Adam G. “Collective Dynamics of Kinesin-1.” 2008. Doctoral Dissertation, University of Michigan. Accessed January 24, 2021.
http://hdl.handle.net/2027.42/60661.
MLA Handbook (7th Edition):
Hendricks, Adam G. “Collective Dynamics of Kinesin-1.” 2008. Web. 24 Jan 2021.
Vancouver:
Hendricks AG. Collective Dynamics of Kinesin-1. [Internet] [Doctoral dissertation]. University of Michigan; 2008. [cited 2021 Jan 24].
Available from: http://hdl.handle.net/2027.42/60661.
Council of Science Editors:
Hendricks AG. Collective Dynamics of Kinesin-1. [Doctoral Dissertation]. University of Michigan; 2008. Available from: http://hdl.handle.net/2027.42/60661
◁ [1] [2] ▶
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