Multi-scale simulations of biological systems using the OPEP coarse-grained model

Biochem Biophys Res Commun. 2018 Mar 29;498(2):296-304. doi: 10.1016/j.bbrc.2017.08.165. Epub 2017 Sep 14.

Abstract

Biomolecules are complex machines that are optimized by evolution to properly fulfill or contribute to a variety of biochemical tasks in the cellular environment. Computer simulations based on quantum mechanics and atomistic force fields have been proven to be a powerful microscope for obtaining valuable insights into many biological, physical, and chemical processes. Many interesting phenomena involve, however, a time scale and a number of degrees of freedom, notably if crowding is considered, that cannot be explored at an atomistic resolution. To bridge the gap between reality and simulation, many different advanced computational techniques and coarse-grained (CG) models have been developed. Here, we report some applications of the CG OPEP protein model to amyloid fibril formation, the response of catch-bond proteins to two types of fluid flow, and interactive simulations to fold peptides with well-defined 3D structures or with intrinsic disorder.

Keywords: Amyloid and catch bond proteins; Coarse-grained model; Hydrodynamics; Interactive; On-lattice and off-lattice simulations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adhesins, Escherichia coli / chemistry
  • Adhesins, Escherichia coli / metabolism
  • Amyloid beta-Peptides / chemistry*
  • Amyloid beta-Peptides / metabolism
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / metabolism
  • Fimbriae Proteins / chemistry
  • Fimbriae Proteins / metabolism
  • Models, Molecular*
  • Molecular Dynamics Simulation
  • Monte Carlo Method
  • Protein Folding

Substances

  • Adhesins, Escherichia coli
  • Amyloid beta-Peptides
  • Escherichia coli Proteins
  • FimF protein, E coli
  • FimG protein, E coli
  • fimH protein, E coli
  • Fimbriae Proteins