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Active site dynamics in protein molecules: A stochastic boundary molecular‐dynamics approach
Abstract
The stochastic boundary molecular‐dynamics approach for studying chemical events in liquids is extended to proteins. A method for simulating the localized dynamics of a portion of a protein is developed and illustrated by an application to the bovine pancreatic trypsin inhibitor (BPTI). The dynamics of the aromatic ring atoms of Tyr 21 of BPTI are targeted as the “active site,” and the results from several different localized models are compared with those from a simulation of the entire molecule. The most consistent results are obtained with a model that consists of a buffer region composed of harmonically constrained Langevin atoms surrounding the active site region whose atoms are treated by molecular dynamics. Possible applications of the model are discussed.
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Cited by
QM/MM Methods for Biomolecular Systems
Senn, H. M., & Thiel, W. (2009) · Angewandte Chemie International Edition · doi:10.1002/anie.200802019 · Cited by 2,684
Dauber‐Osguthorpe, P., Roberts, V. A., Osguthorpe, D. J., Wolff, J., Genest, M., & Hagler, A. T. (1988) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340040106 · Cited by 2,083
QM/MM Methods for Biological Systems
Senn, H. M., & Thiel, W. (2006) · Topics in Current Chemistry · doi:10.1007/128_2006_084 · Cited by 428
Sham, Y. Y., Chu, Z. T., & Warshel, A. (1997) · The Journal of Physical Chemistry B · doi:10.1021/jp963412w · Cited by 356
Zinc binding in proteins and solution: A simple but accurate nonbonded representation
Stote, R. H., & Karplus, M. (1995) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340230104 · Cited by 354
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Metadata
- Authors
- Brooks, C. L., Brünger, A., & Karplus, M.
- Venue
- Biopolymers
- Publisher
- Wiley
- Published
- 1985-05
- Volume
- 24
- Issue
- 5
- Pages
- 843-865
- ISSN
- 0006-3525 (ISSN-L)
- 1097-0282
- OpenAlex
- W2115676532
- Cited by
- 350
- References
- 0
- FWCI
- 3.65
- Type
- journal article
- Language
- en
- Open access
- closed
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- Brooks, C. L., Brünger, A., & Karplus, M. (1985). Active site dynamics in protein molecules: A stochastic boundary molecular‐dynamics approach. Biopolymers. https://doi.org/10.1002/bip.360240509
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