| Autor: |
Walker CC; Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States., Meek GA; Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States., Fobe TL; Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States., Shirts MR; Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States. |
| Jazyk: |
angličtina |
| Zdroj: |
Journal of chemical theory and computation [J Chem Theory Comput] 2021 Oct 12; Vol. 17 (10), pp. 6018-6035. Date of Electronic Publication: 2021 Sep 08. |
| DOI: |
10.1021/acs.jctc.1c00528 |
| Abstrakt: |
Coarse-grained modeling can be used to explore general theories that are independent of specific chemical detail. In this paper, we present cg_openmm, a Python-based simulation framework for modeling coarse-grained hetero-oligomers and screening them for structural and thermodynamic characteristics of cooperative secondary structures. cg_openmm facilitates the building of coarse-grained topology and random starting configurations, setup of GPU-accelerated replica exchange molecular dynamics simulations with the OpenMM software package, and features a suite of postprocessing thermodynamic and structural analysis tools. In particular, native contact analysis, heat capacity calculations, and free energy of folding calculations are used to identify and characterize cooperative folding transitions and stable secondary structures. In this work, we demonstrate the capabilities of cg_openmm on a simple 1-1 Lennard-Jones coarse-grained model, in which each residue contains 1 backbone and 1 side-chain bead. By scanning both nonbonded and bonded force-field parameter spaces at the coarse-grained level, we identify and characterize sets of parameters which result in the formation of stable helices through cooperative folding transitions. Moreover, we show that the geometries and stabilities of these helices can be tuned by manipulating the force-field parameters. |
| Databáze: |
MEDLINE |
| Externí odkaz: |
|
