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Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis
Abstract
Normal mode analysis (NMA) is a leading method for studying long-time dynamics and elasticity of biomolecules. The method proceeds from complex semiempirical potentials characterizing the covalent and noncovalent interactions between atoms. It is widely accepted that such detailed potentials are essential to the success of NMA's. We show that a single-parameter potential is sufficient to reproduce the slow dynamics in good detail. Costly and inaccurate energy minimizations are eliminated, permitting direct analysis of crystal coordinates. The technique can be used for new applications, such as mapping of one crystal form to another by means of slow modes, and studying anomalous dynamics of large proteins and complexes.
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Citations
Cited by
Putnam, C. D., Hammel, M., Hura, G. L., & Tainer, J. A. (2007) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583507004635 · Cited by 1,184
Global dynamics of proteins: bridging between structure and function
Bahar, I., Lezon, T. R., Yang, L.-W., & Eyal, E. (2010) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.093008.131258 · Cited by 610
Yang, L.-W., & Bahar, I. (2005) · Structure · doi:10.1016/j.str.2005.03.015 · Cited by 273
Controlling Allosteric Networks in Proteins
Dokholyan, N. V. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00544 · Cited by 260
Protein elastic network models and the ranges of cooperativity
Yang, L., Song, G., & Jernigan, R. L. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0902159106 · Cited by 260
Metadata
- Authors
- Tirion, M. M.
- Venue
- Physical Review Letters
- Publisher
- American Physical Society (APS)
- Published
- 1996-08-26
- Volume
- 77
- Issue
- 9
- Pages
- 1905-1908
- ISSN
- 0031-9007 (ISSN-L)
- 1079-7114
- OpenAlex
- W2069777230
- Cited by
- 1,615
- References
- 0
- FWCI
- 2.85
- Type
- journal article
- Language
- en
- Open access
- closed
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- Tirion, M. M. (1996). Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. Physical Review Letters. https://doi.org/10.1103/physrevlett.77.1905
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