title: Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization.
abstract: 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.
authors.affiliation: School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.|State Key Laboratory of Precision Spectroscopy and Department of Physics, East China Normal University , Shanghai 200062, China.
authors.forename: Min
authors.initials: M
authors.lastname: Li
authors.affiliation: State Key Laboratory of Precision Spectroscopy and Department of Physics, East China Normal University , Shanghai 200062, China.|NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China.
authors.forename: John Zenghui
authors.initials: JZ
authors.lastname: Zhang
authors.affiliation: School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.|NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Xia
mesh_terms: D000199:Actins / Q000737:chemistry; D000465:Algorithms; D000818:Animals; D018834:Chaperonin 60 / Q000737:chemistry; D004926:Escherichia coli / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000737:chemistry; D005136:Eye Proteins / Q000737:chemistry; D006801:Humans; D051379:Mice; D056004:Molecular Dynamics Simulation / Q000191:economics*; D011506:Proteins / Q000737:chemistry*; D013997:Time Factors
chemical_list: D000199:Actins; D018834:Chaperonin 60; D029968:Escherichia coli Proteins; D005136:Eye Proteins; D011506:Proteins; C529156:lengsin protein, mouse