title: Reaching new levels of realism in modeling biological macromolecules in cellular environments.
abstract: An increasing number of studies are aimed at modeling cellular environments in a comprehensive and realistic fashion. A major challenge in these efforts is how to bridge spatial and temporal scales over many orders of magnitude. Furthermore, there are additional challenges in integrating different aspects ranging from questions about biomolecular stability in crowded environments to the description of reactive processes on cellular scales. In this review, recent studies with models of biomolecules in cellular environments at different levels of detail are discussed in terms of their strengths and weaknesses. In particular, atomistic models, implicit representations of cellular environments, coarse-grained and spheroidal models of biomolecules, as well as the inclusion of reactive processes via reaction-diffusion models are described. Furthermore, strategies for integrating the different models into a comprehensive description of cellular environments are discussed.
authors.affiliation: Department of Biochemistry & Molecular Biology and Department of Chemistry, Michigan State University, 603 Wilson Road, BCH 218, East Lansing, MI 48824, United States; RIKEN Quantitative Biology Center, International Medical Device Alliance (IMDA) 6F, 1-6-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: feig@msu.edu.
authors.forename: Michael
authors.initials: M
authors.lastname: Feig
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sugita
mesh_terms: D000429:Alcohol Oxidoreductases / Q000737:chemistry* / Q000378:metabolism*; D005227:Fatty Acids / Q000378:metabolism*; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D008958:Models, Molecular; D013297:Streptococcus pyogenes / Q000201:enzymology / Q000378:metabolism*
chemical_list: D005227:Fatty Acids; D000429:Alcohol Oxidoreductases; C023744:acetoacetyl-CoA reductase
keywords: Brownian dynamics; Coarse-graining; Confinement; Crowding; Implicit solvent; Reaction–diffusion
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