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Molecular Dynamics of Folded and Disordered Polypeptides in Comparison with Nuclear Magnetic Resonance Measurement

Yu, Lei
http://orcid.org/0000-0003-0159-1968
http://rave.ohiolink.edu/etdc/view?acc_num=osu1521650422218055

Abstract Details

2018, Master of Science, Ohio State University, Chemistry.
With continuous increase in computer speed, molecular dynamics (MD) simulations have become a crucial biophysical method for the understanding of biochemical processes at atomic detail. However, current molecular mechanics force fields optimized for globular proteins often result in overly collapsed structures for intrinsically disordered proteins (IDPs). In order to study the relevant biological functions of IDPs, it is of great importance to utilize the appropriate force fields. Chemical shifts and J-coupling measurements from solution nuclear magnetic resonance (NMR) experiments serve as a common ground for force field assessment. Various combinations of protein force fields and water models were assessed by the direct comparison between back-calculated NMR parameters and experimental data. TIP4P-D water model was proven to improve the accuracy of back-calculation by producing more realistic dihedral angle ψ distributions. Amber99SBnmr1-ILDN and RSFF2+ force fields were shown to be optimal choices for tripeptide and IDP fragment simulations. The stability of the simulated two-helix bundle (THB) domain in the eukaryotic Na+/Ca2+ exchanger (NCX) suggested the transferable performance of Amber99SBnmr1-ILDN force field in company with TIP4P-D water model in folded proteins. Based on the assessment results, a research plan for future improvement of force fields by rebalancing dihedral angle distributions was proposed.
Rafael Brüschweiler (Advisor)
Sherwin Singer (Committee Member)
52 p.
Biophysics; Chemistry; Physical Chemistry
Molecular Dynamics; Nuclear Magnetic Resonance; Intrinsically Disordered Protein

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Citations

  • Yu, L. (2018). Molecular Dynamics of Folded and Disordered Polypeptides in Comparison with Nuclear Magnetic Resonance Measurement [Master's thesis, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1521650422218055

    APA Style (7th edition)

  • Yu, Lei. Molecular Dynamics of Folded and Disordered Polypeptides in Comparison with Nuclear Magnetic Resonance Measurement. 2018. Ohio State University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1521650422218055.

    MLA Style (8th edition)

  • Yu, Lei. "Molecular Dynamics of Folded and Disordered Polypeptides in Comparison with Nuclear Magnetic Resonance Measurement." Master's thesis, Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1521650422218055

    Chicago Manual of Style (17th edition)

osu1521650422218055
519
© 2018, all rights reserved.
This open access ETD is published by The Ohio State University and OhioLINK.