title: Optimal number of coarse-grained sites in different components of large biomolecular complexes.
abstract: The computational study of large biomolecular complexes (molecular machines, cytoskeletal filaments, etc.) is a formidable challenge facing computational biophysics and biology. To achieve biologically relevant length and time scales, coarse-grained (CG) models of such complexes usually must be built and employed. One of the important early stages in this approach is to determine an optimal number of CG sites in different constituents of a complex. This work presents a systematic approach to this problem. First, a universal scaling law is derived and numerically corroborated for the intensity of the intrasite (intradomain) thermal fluctuations as a function of the number of CG sites. Second, this result is used for derivation of the criterion for the optimal number of CG sites in different parts of a large multibiomolecule complex. In the zeroth-order approximation, this approach validates the empirical rule of taking one CG site per fixed number of atoms or residues in each biomolecule, previously widely used for smaller systems (e.g., individual biomolecules). The first-order corrections to this rule are derived and numerically checked by the case studies of the  Escherichia coli  ribosome and Arp2/3 actin filament junction. In different ribosomal proteins, the optimal number of amino acids per CG site is shown to differ by a factor of 3.5, and an even wider spread may exist in other large biomolecular complexes. Therefore, the method proposed in this paper is valuable for the optimal construction of CG models of such complexes.
authors.affiliation: Department of Chemistry, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States.
authors.forename: Anton V
authors.initials: AV
authors.lastname: Sinitskiy
authors.forename: Marissa G
authors.initials: MG
authors.lastname: Saunders
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Voth
mesh_terms: D000199:Actins / Q000737:chemistry; D000818:Animals; D002645:Chickens; D004926:Escherichia coli / Q000737:chemistry; D006801:Humans; D007894:Leishmania mexicana / Q000201:enzymology; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D011770:Pyruvate Kinase / Q000737:chemistry; D011817:Rabbits; D054681:Ribosome Subunits, Large, Bacterial / Q000737:chemistry; D054680:Ribosome Subunits, Small, Bacterial / Q000737:chemistry; D012270:Ribosomes / Q000737:chemistry*; D025801:Ubiquitin / Q000737:chemistry
chemical_list: D000199:Actins; D011506:Proteins; D025801:Ubiquitin; D011770:Pyruvate Kinase; C421864:hen egg lysozyme; D009113:Muramidase