Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization

Coarse-grained (CG) models are valuable tools for the study of functions of large biomolecules on large length and time scales. The definition of CG representations for huge biomolecules is always a formidable challenge. In this work, we propose a new method called fluctuation maximization coarse-gr...

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Bibliographic Details
Published in:Journal of chemical theory and computation 2016-04, Vol.12 (4), p.2091-2100
Main Authors: Li, Min, Zhang, John Zenghui, Xia, Fei
Format: Article
Language:English
Subjects:
Actins - chemistry
Algorithms
Animals
Biomolecules
Chaperonin 60 - chemistry
Coarsening
Construction
Escherichia coli - chemistry
Escherichia coli Proteins - chemistry
Eye Proteins - chemistry
Humans
Mathematical analysis
Mathematical models
Maximization
Mice
Molecular Dynamics Simulation - economics
Optimization
Proteins - chemistry
Time
Time Factors
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Summary:Coarse-grained (CG) models are valuable tools for the study of functions of large biomolecules on large length and time scales. The definition of CG representations for huge biomolecules is always a formidable challenge. In this work, we propose a new method called fluctuation maximization coarse-graining (FM-CG) to construct the CG sites of biomolecules. The defined residual in FM-CG converges to a maximal value as the number of CG sites increases, allowing an optimal CG model to be rigorously defined on the basis of the maximum. More importantly, we developed a robust algorithm called stepwise local iterative optimization (SLIO) to accelerate the process of coarse-graining large biomolecules. By means of the efficient SLIO algorithm, the computational cost of coarse-graining large biomolecules is reduced to within the time scale of seconds, which is far lower than that of conventional simulated annealing. The coarse-graining of two huge systems, chaperonin GroEL and lengsin, indicates that our new methods can coarse-grain huge biomolecular systems with up to 10 000 residues within the time scale of minutes. The further parametrization of CG sites derived from FM-CG allows us to construct the corresponding CG models for studies of the functions of huge biomolecular systems.
ISSN:1549-9618
1549-9626
DOI:10.1021/acs.jctc.6b00016