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

Simple approach for ranking structure determining residues.

Author information

1
Instituto de Biotecnología, Universidad Nacional Autónoma de México , Cuernavaca , Morelos , Mexico.
2
División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica , San Luis Potosí , Mexico.
3
Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México , Cuernavaca , Morelos , Mexico.
4
Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, University of South Florida, Tampa, FL, United States; Institute for Biological Instrumentation, Russian Academy of Sciences, Puschino, Moscow Region, Russia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Russian Academy of Sciences, St. Petersburg, Russia.

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

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