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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Citations
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
Cited by
The power of coarse graining in biomolecular simulations
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
Self-citationStructure-phenotype correlations of human CYP21A2 mutations in congenital adrenal hyperplasia
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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