Analyses of the folding sites of irregular β-trefoil fold proteins through sequence-based techniques and Go-model simulations.

ABSTRACT:

Background

The details of the folding mechanisms have not yet been fully understood for many proteins, and it is believed that the information on the folding mechanism of a protein is encoded in its amino acid sequence. β-trefoil proteins are known to have the same 3D scaffold, namely, a three-fold symmetric scaffold, despite the proteins' low sequence identity among superfamilies. In this study, we extract an initial folding unit from the amino acid sequences of irregular β-trefoil proteins by constructing an average distance map (ADM) and utilizing inter-residue average distance statistics to determine the relative contact frequencies for residue pairs in terms of F values. We compare our sequence-based prediction results with the packing between hydrophobic residues in native 3D

SUBMITTER: Kimura R 

PROVIDER: S-EPMC7477875 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature