TY - JOUR
T1 - Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization
AU - Li, Min
AU - Zhang, John Zenghui
AU - Xia, Fei
N1 - Funding Information:
This work was supported by the National Natural Science Foundation of China (Grants 21433004 and 21473056) and the Natural Science Foundation of Shanghai (14ZR1411800). We acknowledge the support of the NYU-ECNU Center for Computational Chemistry at NYU Shanghai. We also thank the supercomputer center of ECNU for providing computer time.
Publisher Copyright:
© 2016 American Chemical Society.
PY - 2016/4/12
Y1 - 2016/4/12
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84964664279&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84964664279&partnerID=8YFLogxK
U2 - 10.1021/acs.jctc.6b00016
DO - 10.1021/acs.jctc.6b00016
M3 - Article
C2 - 26930392
AN - SCOPUS:84964664279
SN - 1549-9618
VL - 12
SP - 2091
EP - 2100
JO - Journal of chemical theory and computation
JF - Journal of chemical theory and computation
IS - 4
ER -