Arbitrary Resolution with Two Bead Types Coarse-Grained Strategy and Applications to Protein Recognition

J Phys Chem Lett. 2020 May 7;11(9):3263-3270. doi: 10.1021/acs.jpclett.0c00750. Epub 2020 Apr 13.

Abstract

Molecular recognition is a fundamental step in essentially any biological process. However, the kinetic processes during association and dissociation are difficult to be efficiently sampled by direct all-atom molecular dynamics simulations because of the large spatial and temporal scales. Here we propose an arbitrary resolution with two bead types (ART) coarse-grained (CG) strategy that is adept in molecular recognition. ART is a universal user-customized CG strategy that can generate a system-specific CG force field anytime and be applied to any system with an arbitrary CG resolution according to research requirements. ART CG simulations can be very efficiently performed with implicit solvation in prevalent simulation packages and provide interfaces for any enhanced sampling method. We used three applications, HLA-HIV epitope recognition, barnase-barstar association, and trimeric TRAF2 self-assembly, to validate the feasibility of the ART CG strategy, its advantages in protein recognition, and its high performance in simulations. Regular CG simulations can successfully achieve valid protein recognitions without any prior bound structure.

MeSH terms

  • Bacterial Proteins / chemistry*
  • CD8-Positive T-Lymphocytes
  • Computer Simulation
  • Epitopes, T-Lymphocyte / chemistry*
  • HIV Core Protein p24
  • HIV-1
  • HLA-B27 Antigen / chemistry*
  • Models, Molecular*
  • Ribonucleases / chemistry*
  • TNF Receptor-Associated Factor 2 / chemistry*

Substances

  • Bacterial Proteins
  • Epitopes, T-Lymphocyte
  • HIV Core Protein p24
  • HLA-B*27:05 antigen
  • HLA-B27 Antigen
  • TNF Receptor-Associated Factor 2
  • p24 protein, Human Immunodeficiency Virus Type 1
  • barstar protein, Bacillus amyloliquefaciens
  • Ribonucleases
  • Bacillus amyloliquefaciens ribonuclease