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Integration of NMR and SAXS with Atomistic Simulations for Characterizing the Structure and Dynamics of Multi-Domain Proteins

Debiec, Karl (2017) Integration of NMR and SAXS with Atomistic Simulations for Characterizing the Structure and Dynamics of Multi-Domain Proteins. Doctoral Dissertation, University of Pittsburgh. (Unpublished)

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In the seven decades since the first atomic-level structures of biomolecules were determined, the development and application of novel research methods has led to an advanced understanding of biological functions at the molecular level. In addition to experimental methods, key advances have been spurred by computer simulations, which provide an in silico representation of accumulated prior knowledge of biomolecular structure and dynamics. These models can be used both (i) as a complement to experimental results, filling in the gaps where experimental information is not accessible, and (ii) as complete representations, directing future research. Critically, the validity of either application depends on the accuracy of the models used. In this work, I aspired to combine computational and experimental methods to characterize the structure and dynamics of the flexibly linked two-domain protein MoCVNH3. In Chapter 1 I describe my motivation, and the suspected simulation artifacts observed in our preliminary simulations, which led me to investigate how accurately simulation models represent salt bridge interactions. Chapter 2 details my comparison of current models (“force fields”), for which significant variation but consistent overstabilization of salt bridges was discovered. This work motivated the development of a new force field, AMBER ff15ipq, which corrects, to some degree, the overstabilization and introduces extensive improvements, described in Chapter 3. Finally, in Chapter 4, I applied this new force field in simulations of MoCVNH3, for which I collected extensive experimental data leading to the determination of a structural ensemble. I validated the simulations against the experimental data set, and identified further directions for improvement. Overall, the work presented here demonstrates the power of integrating experimental and computational methods.


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Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Debiec, Karlkarl.t.debiec@gmail.comktd3!
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee ChairGronenborn, Angelaamg100@pitt.eduamg100
Committee MemberChong, Lillianltchong@pitt.edultchong
Committee MemberHorne, Sethhorne@pitt.eduhorne
Committee MemberCase,
Date: 23 September 2017
Date Type: Publication
Defense Date: 21 July 2017
Approval Date: 23 September 2017
Submission Date: 27 July 2017
Access Restriction: No restriction; Release the ETD for access worldwide immediately.
Number of Pages: 239
Institution: University of Pittsburgh
Schools and Programs: Dietrich School of Arts and Sciences > Molecular Biophysics and Structural Biology
Degree: PhD - Doctor of Philosophy
Thesis Type: Doctoral Dissertation
Refereed: Yes
Uncontrolled Keywords: integrated structural biology, multi-domain proteins, NMR, paramagnetic relaxation enhancement, small-angle X-ray scattering, molecular dynamics
Date Deposited: 24 Sep 2017 00:09
Last Modified: 24 Sep 2017 00:09


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