Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily.

ABSTRACT: PAS domains are widespread in archaea, bacteria, and eukaryota, and play important roles in various functions. In this study, we aim to explore functional evolutionary relationship among proteins in the PAS domain superfamily in view of the sequence-structure-dynamics-function relationship. We collected protein sequences and crystal structure data from RCSB Protein Data Bank of the PAS domain superfamily belonging to three biological functions (nucleotide binding, photoreceptor activity, and transferase activity). Protein sequences were aligned and then used to select sequence-conserved residues and build phylogenetic tree. Three-dimensional structure alignment was also applied to obtain structure-conserved residues. The protein dynamics were analyzed using elastic network model (ENM) and

SUBMITTER: Dong Z 

PROVIDER: S-EPMC5775171 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature