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You searched for +publisher:"Purdue University" +contributor:("Alan M. Friedman"). Showing records 1 – 2 of 2 total matches.

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Purdue University

1. Yuwen, Tairan. New experimental and theoretical tools for studying protein systems with elements of structural disorder.

Degree: PhD, Chemistry, 2014, Purdue University

Disordered proteins are one class of proteins which do not possess well-folded three-dimensional structures as their native conformations. Many eukaryotic proteins have been found to be fully disordered or contain certain disordered regions. Disordered proteins usually display several characteristic properties, such as increased motional freedom and the conformational heterogeneity caused by that. The elements of structural disorder are commonly involved in many important biological functions and are implicated in many diseases. Therefore, the study of disordered proteins has become one of the most important research topics in recent years. This thesis presents results from three different research projects; the common feature is that all systems being studied contain varying amount of structural disorder. Most results have been obtained based on experimental nuclear magnetic resonance (NMR) studies and molecular dynamics (MD) simulations. Both are among the most popular biophysical techniques for studying molecular dynamics. The first project investigates the relationship between domain cooperativity and residual dipolar coupling (RDC) parameters based on a series of two-domain chimera proteins with disordered linkers. Many eukaryotic proteins contain multiple domains and their biological functions are closely related to the property of domain cooperativity, which is often regulated by the linker region. Therefore it is necessary to develop suitable tools to characterize linker region properties in order to better understand biological functions of multidomain proteins. The second project is about the development of NMR pulse sequences for studying disordered proteins. Two new NMR pulse sequences, PD-CPMG and CP-HISQC, have been developed. Both experiments are well suited for studying intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) under physiological conditions. These two experiments produce higher precision for 15N R2 rates measurement or higher sensitivity in 1H– 15N HSQC spectra respectively. Besides, they also show many advantages over most other existing experiments for studying IDPs. The last project is about protein-peptide encounter complex study based on Crk-Sos model system. The ten-residue Sos peptide serves as a minimal model for disordered proteins. Encounter complex is an important type of intermediate state formed during many protein interactions. Such complexes are usually characterized by a large amount of motional freedom and conformational heterogeneity. Therefore their properties are considerably different from tight-binding complexes which are more commonly studied. Although it is usually quite difficult to study encounter complexes using standard biophysical techniques, in this project we have successfully characterized structural and dynamic properties of Crk-Sos electrostatic encounter complex with a combination of MD simulations and experimental NMR approaches. It can be directly seen from the structural… Advisors/Committee Members: Nikolai R. Skrynnikov, Nikolai R. Skrynnikov, Carol B. Post, Alan M. Friedman, Timothy S. Zwier, John S. Harwood.

Subjects/Keywords: Biochemistry; Biophysics; Chemistry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Yuwen, T. (2014). New experimental and theoretical tools for studying protein systems with elements of structural disorder. (Doctoral Dissertation). Purdue University. Retrieved from https://docs.lib.purdue.edu/open_access_dissertations/400

Chicago Manual of Style (16th Edition):

Yuwen, Tairan. “New experimental and theoretical tools for studying protein systems with elements of structural disorder.” 2014. Doctoral Dissertation, Purdue University. Accessed January 20, 2020. https://docs.lib.purdue.edu/open_access_dissertations/400.

MLA Handbook (7th Edition):

Yuwen, Tairan. “New experimental and theoretical tools for studying protein systems with elements of structural disorder.” 2014. Web. 20 Jan 2020.

Vancouver:

Yuwen T. New experimental and theoretical tools for studying protein systems with elements of structural disorder. [Internet] [Doctoral dissertation]. Purdue University; 2014. [cited 2020 Jan 20]. Available from: https://docs.lib.purdue.edu/open_access_dissertations/400.

Council of Science Editors:

Yuwen T. New experimental and theoretical tools for studying protein systems with elements of structural disorder. [Doctoral Dissertation]. Purdue University; 2014. Available from: https://docs.lib.purdue.edu/open_access_dissertations/400

2. Fico, Nicholas. Generation And Statistical Modeling Of Active Protein Chimeras: A Sequence Based Approach.

Degree: PhD, Biological Science, 2013, Purdue University

Generation of active protein chimeras is a valuable tool to probe the functional space of proteins. Statistical modeling is the next logical step, allowing us to build a model of gene fragment replaceability between species. In this thesis I begin to develop the statistical tools that are needed to systematically describe combinatorial protein libraries. I present three sets of diverse chimeric protein libraries developed using sequence information. The statistical model of the human N-Ras and human K-Ras-4B genes reveal a set previously unidetifed surface residues on the N-Ras G-Domain that may be involved in cellular localization. Statistical modeling of a library of chimeric proteins between A. thaliana cinnamate 4-hydroxylase (AtC4H) and S. moellendorffii cinnamate 4-hydroxylase (SmC4H) reveal a possible stabilizing effect of the N-terminal amino acids from SmC4H and, irreplaceable catalytic domains between AtC4H and SmC4H. I also show gene fragment replaceability on a small scale between functionally divergent AtC4H and A. thaliana ferulate 5-hyrdoxylase proteins. Finally, I show that commonly occurring residue pairs in the sequence record are effective covariates when modeling activity in the AtC4H-SmC4H chimeric library. Advisors/Committee Members: Alan M. Friedman, Daisuke Kihara, Alan M. Friedman, Cynthia Stauffacher, Clinton Chapple.

Subjects/Keywords: chimeric proteins; linear regression; logistic regression; phenylpropanoid; p450; ras proteins; Molecular Biology; Statistics and Probability

…ferulate 5-hydroxylase xiv ABSTRACT Fico, Nicholas J. Ph.D., Purdue University, December 2013… 

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Fico, N. (2013). Generation And Statistical Modeling Of Active Protein Chimeras: A Sequence Based Approach. (Doctoral Dissertation). Purdue University. Retrieved from https://docs.lib.purdue.edu/open_access_dissertations/144

Chicago Manual of Style (16th Edition):

Fico, Nicholas. “Generation And Statistical Modeling Of Active Protein Chimeras: A Sequence Based Approach.” 2013. Doctoral Dissertation, Purdue University. Accessed January 20, 2020. https://docs.lib.purdue.edu/open_access_dissertations/144.

MLA Handbook (7th Edition):

Fico, Nicholas. “Generation And Statistical Modeling Of Active Protein Chimeras: A Sequence Based Approach.” 2013. Web. 20 Jan 2020.

Vancouver:

Fico N. Generation And Statistical Modeling Of Active Protein Chimeras: A Sequence Based Approach. [Internet] [Doctoral dissertation]. Purdue University; 2013. [cited 2020 Jan 20]. Available from: https://docs.lib.purdue.edu/open_access_dissertations/144.

Council of Science Editors:

Fico N. Generation And Statistical Modeling Of Active Protein Chimeras: A Sequence Based Approach. [Doctoral Dissertation]. Purdue University; 2013. Available from: https://docs.lib.purdue.edu/open_access_dissertations/144

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