Chirality and Protein Folding

Abstract

There are several simple criteria of folding to a native state in model proteins. One of them involves crossing of a threshold value of the RMSD distance away from the native state. Another checks whether all native contacts are established, i.e. whether the interacting amino acids come closer than some characteristic distance. We use Go-like models of proteins and show that such simple criteria may prompt one to declare folding even though fragments of the resulting conformations have a wrong sense of chirality. We propose that a better condition of folding should augment the simple criteria with the requirement that most of the local values of the chirality should be nearly native. The kinetic discrepancy between the simple and compound criteria can be substantially reduced in the Go-like models by providing the Hamiltonian with a term which favors native values of the local chirality. We study the effects of this term as a function of its amplitude and compare it to other models such as with the side groups and with the angle-dependent potentials.

To be published in a special issue of J. Phys.: Cond. Mat. (Bedlewo Workshop)

References in corpus (4)

• Universality classes in folding times of proteins
• The range of the contact interactions and the kinetics of the Go models of proteins
• Cooperativity and Contact Order in Protein Folding
• Folding of Proteins in Go Models with Angular Interactions

Cited by in corpus (9)

• Proteins in a shear flow
• Stretching and twisting of the DNA duplexes in coarse grained dynamical models
• Testing simplified protein models of the hPin1 WW domain
• Effects of confinement and crowding on folding of model proteins
• Unbinding and unfolding of adhesion protein complexes through stretching: Interplay between shear and tensile mechanical clamps
• Criteria for folding in structure-based models of proteins
• Protein simulations combining an all-atom force field with a Go term
• Stiffness of the C-terminal disordered linker affects the geometry of the active site in endoglucanase Cel8A
• Folding and Stabilization of Native-Sequence-Reversed Proteins