期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 17, 期 10, 页码 6472-6482出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.1c00295
关键词
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资金
- Wellcome [208361/Z/17/Z]
- BBSRC [BB/P01948X/1, BB/R002517/1, BB/S003339/1]
- MRC [MR/S009213/1]
- EPSRC [EP/P020232/1, EP/L000253/1]
- University of Warwick Scientific Computing Research Technology Platform
- BBSRC [BB/S003339/1, BB/R002517/1, BB/P01948X/1] Funding Source: UKRI
- MRC [MR/S009213/1] Funding Source: UKRI
Coarse-grained molecular dynamics offers a way to simulate macromolecular complexes at a reduced level of representation, allowing for longer timescales and larger simulations. This study presents an enhanced fragment-based protocol for converting such complexes to atomistic resolution, suitable for a variety of systems including integral membrane proteins. Evaluation of the approach on 11 system configurations shows promising results in accurately describing and balancing atomic-level descriptions of macromolecular complexes.
Coarse-grained molecular dynamics provides a means for simulating the assembly and interactions of macromolecular complexes at a reduced level of representation, thereby allowing both longer timescale and larger sized simulations. Here, we describe an enhanced fragment-based protocol for converting macromolecular complexes from coarse-grained to atomistic resolution, for further refinement and analysis. While the focus is upon systems that comprise an integral membrane protein embedded in a phospholipid bilayer, the technique is also suitable for membrane-anchored and soluble protein/nucleotide complexes. Overall, this provides a method for generating an accurate and well-equilibrated atomic-level description of a macromolecular complex. The approach is evaluated using a diverse test set of 11 system configurations of varying size and complexity. Simulations are assessed in terms of protein stereochemistry, conformational drift, lipid/protein interactions, and lipid dynamics.
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