title: Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome.
abstract: Biopolymers are of dynamic nature and undergo functional motions spanning a large spectrum of timescales. To study the internal dynamics of nano-sized molecular complexes that exceed hundred thousands of atoms with atomic detail is computationally inefficient. Therefore, to achieve both the spatial and temporal scales of biological interest coarse-grained models of macromolecules are often used. By uniting groups of atoms into single interacting centers one decreases the resolution of the system and gets rid of the irrelevant degrees of freedom. This simplification, even though it requires parameterization, makes the studies of biomolecular dynamics computationally tractable and allows us to reach beyond the microsecond time frame. Here, I review the coarse-grained models of macromolecules composed of proteins and nucleic acids. I give examples of one-bead models that were developed to investigate the internal dynamics and focus on their applications to the ribosome--the nanoscale protein synthesis machine.
authors.affiliation: Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, Warsaw 02-106, Poland. joanna@icm.edu.pl
authors.forename: Joanna
authors.initials: J
authors.lastname: Trylska
mesh_terms: D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D012270:Ribosomes / Q000737:chemistry* / Q000648:ultrastructure*
chemical_list: D001704:Biopolymers