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1.
S. Rendine.
MODELLING INTERMOLECULAR FORCES IN BIOMOLECULES: FROM PROTEIN-PROTEIN INTERACTIONS TO HALOGEN BONDS.
Degree: 2012, Università degli Studi di Milano
URL: http://hdl.handle.net/2434/167913 
► The accurate description and evaluation of the intermolecular interactions has a great importance in the molecular modelling of biological systems. Protein-protein interactions, in particular, being…
(more)
▼ The accurate description and evaluation of the intermolecular interactions has a great importance in the molecular modelling of biological systems.
Protein-protein interactions, in particular, being involved in virtually every cellular process, are nowadays the object of thorough studies aimed at the understanding and modulation of the underlying mechanism. In the Part I of the present work, it will be shown how, through a computational approach, it is possible to get an in-depth analysis of the network of interactions occurring at the interface between tubulin subunits and how vinblastine, a commonly used anticancer agents, is able to interfere with the correct protein association, so having a therapeutic effect. In the Part II, the self-association of the bacterial protein FtsZ will be studied, showing that the detailed description of the protein-protein interactions can provide key information for the de-novo design of inhibiting molecules.
Finally, in the Part II, the attention will be focused on the computational study of halogen bonding, which is found to have a great relevance in the recognition process between biological macromolecules and halogenated agents. In particular, it will be shown that a specific approach is mandatory for its correct description in the framework of the classical force-fields.
Advisors/Committee Members: tutor: M. Sironi, tutor%3A%20S.%20Pieraccini%22%29&pagesize-30">co-
tutor: S. Pieraccini,
SIRONI, MAURIZIO.
Subjects/Keywords: Settore CHIM/02 - Chimica Fisica
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APA (6th Edition):
Rendine, S. (2012). MODELLING INTERMOLECULAR FORCES IN BIOMOLECULES: FROM PROTEIN-PROTEIN INTERACTIONS TO HALOGEN BONDS. (Thesis). Università degli Studi di Milano. Retrieved from http://hdl.handle.net/2434/167913
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):
Rendine, S.. “MODELLING INTERMOLECULAR FORCES IN BIOMOLECULES: FROM PROTEIN-PROTEIN INTERACTIONS TO HALOGEN BONDS.” 2012. Thesis, Università degli Studi di Milano. Accessed January 19, 2021.
http://hdl.handle.net/2434/167913.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Rendine, S.. “MODELLING INTERMOLECULAR FORCES IN BIOMOLECULES: FROM PROTEIN-PROTEIN INTERACTIONS TO HALOGEN BONDS.” 2012. Web. 19 Jan 2021.
Vancouver:
Rendine S. MODELLING INTERMOLECULAR FORCES IN BIOMOLECULES: FROM PROTEIN-PROTEIN INTERACTIONS TO HALOGEN BONDS. [Internet] [Thesis]. Università degli Studi di Milano; 2012. [cited 2021 Jan 19].
Available from: http://hdl.handle.net/2434/167913.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Rendine S. MODELLING INTERMOLECULAR FORCES IN BIOMOLECULES: FROM PROTEIN-PROTEIN INTERACTIONS TO HALOGEN BONDS. [Thesis]. Università degli Studi di Milano; 2012. Available from: http://hdl.handle.net/2434/167913
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
2.
F. Dapiaggi.
MOLECULAR MODELING OF EBOLA VIRUS INHIBITORS.
Degree: 2018, Università degli Studi di Milano
URL: http://hdl.handle.net/2434/545872
► In this PhD thesis computational methods have been employed in order to study different biologically relevant systems. In the first part of the thesis two…
(more)
▼ In this PhD thesis computational methods have been employed in order to study different biologically relevant systems. In the first part of the thesis two Ebola virus proteins were studied, namely Viral Protein 24 (VP24) and Viral Protein 35 (VP35), responsible for the inhibition of the immune response .
After a brief theoretical introduction to the main computational methods employed in the thesis, a study of VP35 in complex with small organic molecules is presented. These
compounds are able to inhibit the interaction between VP35 and viral nucleoprotein. This study confirms the experimental findings highlighting new important key interactions
between the protein the inhibitors. Moreover, an Essential Dynamics analysis points out an interesting collective motion of the apo-form that is hindered by the presence of the
ligands.
Afterwards, the protein-protein interaction VP24-Karyopherin (KPNA) is studied. An atomistic analysis of the interactions at the interface leads to the design of a
nonapeptide with VP24 binding capability. The peptide is derived from a KPNA subsequence and could potentially inhibit the VP24-KPNA interaction.
Subsequently an analysis on the pockets present on VP24 surface in different solvents is performed. Once the most promising pocket has been located, a virtual screening on a
subset of ZINC database is carried out, leading to the identification of few classes of molecules potentially able to bind VP24.
Finally the effect of the osmolytes on VP24 protein structure is studied, pointing out how osmoprotectants and urea have opposite effects on the protein, the former stabilizing
the folded state and the latter shifting the equilibrium to the denatured state.
In the second part of the manuscript the study of the interaction of an antimicrobial peptide with a lipid membrane is presented. This work was carried out in the
University of Groningen under the supervision of Prof. Siewert Jan Marrink in order to deepen the Coarse Grain method.
Advisors/Committee Members: tutor: M. Sironi, tutor%3A%20S.%20Pieraccini%22%29&pagesize-30">co-
tutor: S. Pieraccini,
coordinatore: E. Licandro,
LICANDRO, EMANUELA.
Subjects/Keywords: Ebola; Virus; Computational; Chemistry; Molecular dynamics; Free energy; MMPBSA; Docking; Coarse Grain; VP24; VP35; Virtual Screening; Osmolytes; Protein; Osmoprotectants; Denaturants; Inhibitors; Peptide; Settore CHIM/02 - Chimica Fisica
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APA (6th Edition):
Dapiaggi, F. (2018). MOLECULAR MODELING OF EBOLA VIRUS INHIBITORS. (Thesis). Università degli Studi di Milano. Retrieved from http://hdl.handle.net/2434/545872
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):
Dapiaggi, F.. “MOLECULAR MODELING OF EBOLA VIRUS INHIBITORS.” 2018. Thesis, Università degli Studi di Milano. Accessed January 19, 2021.
http://hdl.handle.net/2434/545872.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Dapiaggi, F.. “MOLECULAR MODELING OF EBOLA VIRUS INHIBITORS.” 2018. Web. 19 Jan 2021.
Vancouver:
Dapiaggi F. MOLECULAR MODELING OF EBOLA VIRUS INHIBITORS. [Internet] [Thesis]. Università degli Studi di Milano; 2018. [cited 2021 Jan 19].
Available from: http://hdl.handle.net/2434/545872.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Dapiaggi F. MOLECULAR MODELING OF EBOLA VIRUS INHIBITORS. [Thesis]. Università degli Studi di Milano; 2018. Available from: http://hdl.handle.net/2434/545872
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
3.
C. Pontremoli.
EVOLUTIONARY ANALYSES PROVIDE INSIGHT INTO HOST-PATHOGEN INTERACTIONS AND DIET-RELATED ADAPTATIONS.
Degree: 2017, Università degli Studi di Milano
URL: http://hdl.handle.net/2434/470653
► ABSTRACT INTRODUCTION Genetic diversity plays an important role in the survival and adaptability of all species. When a population environment (meaning, for instance, climatic conditions,…
(more)
▼ ABSTRACT
INTRODUCTION
Genetic diversity plays an important role in the survival and adaptability of all species. When a population environment (meaning, for instance, climatic conditions, pathogens, and food availability) changes, the population is subject to a selective pressure. Variation in the population gene pool provides variable traits which can be selected for, via natural selection, leading to an adaptive change to survive. Genetic diversity is generated by a combination of different evolutionary processes such as mutation, genetic drift, migration and natural selection.
Natural selection leaves a distinctive molecular signature in genomes. Such molecular signatures can be detected with evolutionary tests that can be divided into those that search for selection at the inter-species level (e.g., human versus primates and mammals) and those that focus on within-species data (e.g., among human populations). In my work, I used evolutionary studies to analyze genes under different selective pressures.
In a first study, I investigate the evolutionary history of genes possibly involved in diet adaptation. Changes in food availability and diet likely created strong selective pressures on multiple biological processes. In humans, the agricultural revolution favored carbohydrate consumption. I exploit the availability of genome sequences from different organisms, together with resequencing data of ancient DNA samples to perform a comprehensive evolutionary analysis of genes involved in sugar absorption/digestion at the brush-border and to test when adaptive alleles arose.
In a second set of studies, I use evolutionary analyses to investigate the interaction between host proteins and viral/protozoan/bacterial protein products. Molecules that participate in immune response are expected to be engaged in a constant arms-race with pathogens and to harbour the molecular signatures of such a conflict. I thus investigate the evolutionary history of genes involved in immune defense, such as antiviral sensing proteins, genes with IFN-inducible properties and antiviral effectors. I also investigate the evolutionary history of the complement system, an innate immunity effector, and of bacterial-encoded complement- interacting proteins.
Nevertheless, not only genes with specific defense function, but also molecules involved in central homeostatic processes may be engaged in genetic conflicts with pathogens. This is exemplified by (i) the sterol transporter NPC1, used as receptor for filoviruses entry and (ii) basigin, a multifunctional protein with a role in trophoblast function and in spermatogenesis which is used for erythrocyte invasion by Plasmodium falciparum. I therefore study the evolutionary history of these genes and of their viral/microbial interactors.
AIM OF THE WORK
The purpose of my project is to use evolutionary analyses to investigate and describe adaptive events at candidate genes subject to different selective pressures, in species ranging from mammals to viruses/protozoa/bacteria. In particular, I…
Advisors/Committee Members: tutor: M. Biasin, tutor%3A%20M.%20Sironi%22%29&pagesize-30">co-
tutor:
M.
Sironi,
direttore del dottorato: M. Clerici,
BIASIN, MARA,
CLERICI, MARIO SALVATORE.
Subjects/Keywords: Settore BIO/18 - Genetica
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APA (6th Edition):
Pontremoli, C. (2017). EVOLUTIONARY ANALYSES PROVIDE INSIGHT INTO HOST-PATHOGEN INTERACTIONS AND DIET-RELATED ADAPTATIONS. (Thesis). Università degli Studi di Milano. Retrieved from http://hdl.handle.net/2434/470653
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):
Pontremoli, C.. “EVOLUTIONARY ANALYSES PROVIDE INSIGHT INTO HOST-PATHOGEN INTERACTIONS AND DIET-RELATED ADAPTATIONS.” 2017. Thesis, Università degli Studi di Milano. Accessed January 19, 2021.
http://hdl.handle.net/2434/470653.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Pontremoli, C.. “EVOLUTIONARY ANALYSES PROVIDE INSIGHT INTO HOST-PATHOGEN INTERACTIONS AND DIET-RELATED ADAPTATIONS.” 2017. Web. 19 Jan 2021.
Vancouver:
Pontremoli C. EVOLUTIONARY ANALYSES PROVIDE INSIGHT INTO HOST-PATHOGEN INTERACTIONS AND DIET-RELATED ADAPTATIONS. [Internet] [Thesis]. Università degli Studi di Milano; 2017. [cited 2021 Jan 19].
Available from: http://hdl.handle.net/2434/470653.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Pontremoli C. EVOLUTIONARY ANALYSES PROVIDE INSIGHT INTO HOST-PATHOGEN INTERACTIONS AND DIET-RELATED ADAPTATIONS. [Thesis]. Università degli Studi di Milano; 2017. Available from: http://hdl.handle.net/2434/470653
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
4.
S. Chaurasia.
IN SILICO STUDY OF PROTEIN PROTEIN INTERACTION STABILIZATION AND MECHANICAL FORCE APPLICATION ON BIOMOLECULES.
Degree: 2014, Università degli Studi di Milano
URL: http://hdl.handle.net/2434/229253
► Targeting protein-protein interactions is a challenging task in drug discovery process. Despite the challenges, several studies have provided evidences for the development of small molecules…
(more)
▼ Targeting protein-protein interactions is a challenging task in drug discovery process. Despite the challenges, several studies have provided evidences for the development of small molecules modulating protein-protein interactions. In Part I, it is demonstrated that how a small molecule can induce the formation of an otherwise unstable protein-protein complex. A study of the stabilization of a FKBP12-FRB complex by a small molecule rapamycin is presented. The stability of the complex is analyzed and its interactions are characterized at the atomic level by performing free energy calculations and computational alanine scanning. It is shown that rapamycin stabilizes the complex by acting as a bridge between the two proteins; and the complex is stable only in the presence of rapamycin. The reported results and the good performance of standard molecular modeling techniques in describing the model system can be interesting not only in the design and development of improved molecules acting as FKBP12–FRB protein interaction stabilizers, but also in the somehow neglected study of protein-protein interactions stabilizers in general.
In Part II, studies regarding computational modeling of the application of mechanical force to biomolecules is presented. This part is further divided into two chapters since the investigations have been performed on two biological systems. In the first chapter of Part II (chapter 6), it is described that how the osmolyte molecules affect the mechanical unfolding of a peptide. The mechanical unfolding of peptide has been performed by using Steered Molecular Dynamics. In this study, the effect of four different osmolytes on the free energy difference between the folded and the denatured state have been calculated. The observed trend mirrors the expected behavior of the studied osmolytes and unfolding pathways analysis allows an insight into the mechanism of action of osmolytes.
After the successful application of Steered molecular dynamics technique on the β-hairpin peptide, the same is applied on tubulin heterodimers for the in-depth study of the lateral and longitudinal interactions which are responsible for the stability and dynamics of the microtubules. In the other chapter of Part II (chapter 7), these interactions are studied with the help of mechanical dissociation of the tubulin heterodimers. These studies have allowed the identification of the critical interactions responsible for the binding of tubulin heterodimers laterally as well as longitudinally. The observations obtained could be important for the design of compounds that target these interactions and acts as microtubule inhibitors or stabilizers.
Advisors/Committee Members: tutor: S. Pieraccini, tutor%3A%20M.%20Sironi%22%29&pagesize-30">co-
tutor:
M.
Sironi,
coordinator: E. Licandro,
PIERACCINI, STEFANO,
LICANDRO, EMANUELA.
Subjects/Keywords: protein-protein interactions; FKBP12-rapamycin-FRB; computational alanine scanning; steered molecular dynamics; free energy calculations; microtubules; osmolytes; Settore CHIM/02 - Chimica Fisica
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Chaurasia, S. (2014). IN SILICO STUDY OF PROTEIN PROTEIN INTERACTION STABILIZATION AND MECHANICAL FORCE APPLICATION ON BIOMOLECULES. (Thesis). Università degli Studi di Milano. Retrieved from http://hdl.handle.net/2434/229253
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):
Chaurasia, S.. “IN SILICO STUDY OF PROTEIN PROTEIN INTERACTION STABILIZATION AND MECHANICAL FORCE APPLICATION ON BIOMOLECULES.” 2014. Thesis, Università degli Studi di Milano. Accessed January 19, 2021.
http://hdl.handle.net/2434/229253.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Chaurasia, S.. “IN SILICO STUDY OF PROTEIN PROTEIN INTERACTION STABILIZATION AND MECHANICAL FORCE APPLICATION ON BIOMOLECULES.” 2014. Web. 19 Jan 2021.
Vancouver:
Chaurasia S. IN SILICO STUDY OF PROTEIN PROTEIN INTERACTION STABILIZATION AND MECHANICAL FORCE APPLICATION ON BIOMOLECULES. [Internet] [Thesis]. Università degli Studi di Milano; 2014. [cited 2021 Jan 19].
Available from: http://hdl.handle.net/2434/229253.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Chaurasia S. IN SILICO STUDY OF PROTEIN PROTEIN INTERACTION STABILIZATION AND MECHANICAL FORCE APPLICATION ON BIOMOLECULES. [Thesis]. Università degli Studi di Milano; 2014. Available from: http://hdl.handle.net/2434/229253
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
. 
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