Simple approach for ranking structure determining residues

PeerJ. 2016 Jun 22:4:e2136. doi: 10.7717/peerj.2136. eCollection 2016.

Abstract

Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology.

Keywords: Intrinsic disorder; Molecular dynamics; Shannon dynamical entropy; Thermodynamics.

Grants and funding

ODLM and MIVV were supported by CONACYT 177224 and 185179, respectively. This work was supported by grants from DGAPA IN 217510. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.