Prediction of Residue Status to Be Protected or Not Protected From Hydrogen Exchange Using Amino Acid Sequence Only



Nikita V Dovidchenko, Oxana V Galzitskaya*


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© Dovidchenko and Galzitskaya; Licensee Bentham Open.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.5/), which permits unrestrictive use, distribution, and reproduction in any medium, provided the original work is properly cited.

* Address correspondence to these authors at the Institute of Protein Research, Russian Academy of Sciences, Institutskaya str., 4 Pushchino, Moscow Region, 142290, Russia; E-mail: ogalzit@vega.protres.ru


Abstract

We have outlined here some structural aspects of local flexibility. Important functional properties are related to flexible segments. We try to predict regions that have been shown to exhibit the highest probability of being folded in the equilibrium intermediate or native state and will be protected from hydrogen exchange using amino acid sequence only. Our approach FoldUnfold for the prediction of unstructured regions has been applied to seven different proteins. For 80% of the residues considered in this paper we can predict correctly their status: will they be protected or not from hydrogen exchange. An additional goal of our study is to assess whether properties inferred using the bioinformatics approach are easily applicable to predict behavior of proteins in solution.