The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations
Abstract
Coarse-grained molecular dynamics provides a means for simulating the assembly and the interactions of membrane protein/lipid complexes at a reduced level of representation, allowing longer and larger simulations. We describe a fragment-based protocol for converting membrane simulation systems, comprising a membrane protein embedded in a phospholipid bilayer, from coarse-grained to atomistic resolution, for further refinement and analysis via atomistic simulations. Overall, this provides a method for generating an accurate and well equilibrated membrane protein/lipid complex. We exemplify the protocol using the acid-sensing/amiloride-sensitive ion channel protein (ASIC) channel protein, a trimeric integral membrane protein. The method is further evaluated using a test set of 10 different membrane proteins of differing size and complexity. Simulations are assessed in terms of protein conformational drift, lipid/protein interactions, and lipid dynamics.
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Cites
PROCHECK: a program to check the stereochemical quality of protein structures
Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993) · Journal of Applied Crystallography · doi:10.1107/s0021889892009944 · Cited by 24,581
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Ingólfsson, H. I., Lopez, C. A., Uusitalo, J. J., de Jong, D. H., Gopal, S. M., Periole, X., & Marrink, S. J. (2014) · WIREs Computational Molecular Science · doi:10.1002/wcms.1169 · Cited by 572
Two decades of Martini: Better beads, broader scope
Marrink, S. J., Monticelli, L., Melo, M. N., Alessandri, R., Tieleman, D. P., & Souza, P. C. T. (2023) · WIREs Computational Molecular Science · doi:10.1002/wcms.1620 · Cited by 255
Classical Electrostatics for Biomolecular Simulations
Cisneros, G. A., Karttunen, M., Ren, P., & Sagui, C. (2014) · Chemical Reviews · doi:10.1021/cr300461d · Cited by 259
CG2AT2: An enhanced fragment-based approach for serial multi-scale molecular dynamics simulations
Vickery, O. N., & Stansfeld, P. J. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00295 · Cited by 150
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Haider, S., Islam, B., D’Atri, V., Sgobba, M., Poojari, C., Sun, L., Yuen, T., Zaidi, M., & New, M. I. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1221133110 · Cited by 127
Metadata
- Authors
- Stansfeld, P. J., & Sansom, M. S. P.
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2011-03-16
- Volume
- 7
- Issue
- 4
- Pages
- 1157-1166
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- OpenAlex
- W2052299042
- Cited by
- 231
- References
- 1
- FWCI
- 6.82
- Type
- journal article
- Language
- en
- Open access
- closed
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- Stansfeld, P. J., & Sansom, M. S. P. (2011). From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations. Journal of Chemical Theory and Computation. https://doi.org/10.1021/ct100569y
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