Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding.

ABSTRACT: We develop coarse-grained models and effective energy functions for simulating thermodynamic and structural properties of multiprotein complexes with relatively low binding affinity (K(d) >1 microM) and apply them to binding of Vps27 to membrane-tethered ubiquitin. Folded protein domains are represented as rigid bodies. The interactions between the domains are treated at the residue level with amino-acid-dependent pair potentials and Debye-Hückel-type electrostatic interactions. Flexible linker peptides connecting rigid protein domains are represented as amino acid beads on a polymer with appropriate stretching, bending, and torsion-angle potentials. In simulations of membrane-attached protein complexes, interactions between amino acids and the membrane are described by residue-dependent s

SUBMITTER: Kim YC 

PROVIDER: S-EPMC2343030 | biostudies-literature | 2008 Feb

REPOSITORIES: biostudies-literature