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Prediction of protein flexibility using a conformationally restrained contact map
Author(s) -
Vera Rebecca,
SynsmirZizzamia Melissa,
Ojinnaka Sarah,
Snyder David A.
Publication year - 2018
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.25591
Subject(s) - flexibility (engineering) , protein structure , root mean square , domain (mathematical analysis) , biological system , computer science , chemistry , computational biology , mathematics , biology , physics , statistics , biochemistry , mathematical analysis , quantum mechanics
Knowledge of protein flexibility is crucial to understanding protein function. However, probing protein flexibility by either experiment or computational simulations is a difficult process. In particular, many computational approaches to understanding protein flexibility require an experimentally determined protein structure. The Conformationally Restrained Contact Map (CoRe‐CMap) approach reported here couples protein disorder predictions with protein structure predictions and only requires sequence data to predict protein flexibility. This paper reports the application of the CoRe‐CMap model to predicting Lipari‐Szabo order parameters of all proteins for which experimentally derived Lipari‐Szabo order parameters are available in the BioMagResBank: the median root mean square deviation between a protein's predicted and experimentally derived order parameters is 0.124. Additionally, application of the CoRe‐CMap model to predict Lipari‐Szabo order parameters for the 10th Type III Domain in Fibronectin and a homologous domain from Tenascin demonstrates the ability of CoRe‐CMap to predict functionally important differences in protein flexibility.