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ISSN: 0974-276X

Journal of Proteomics & Bioinformatics
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Research Article

Structural Role of Hydrophobic Core in Proteins-Selected Examples

Banach M1,2, Kalinowska B1,2, Konieczny L3 and Roterman I1*

1Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Poland

2Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Poland

3Chair of Medical Biochemistry, Jagiellonian University Medical College, Poland

Corresponding Author:
Roterman I
Department of Bioinformatics and Telemedicine, Łazarza 16, 31-530 Krakow, Poland
Tel: 48126199693
E-mail: [email protected]

Received Date: October 14, 2016; Accepted Date: November 06, 2016; Published Date: November 11, 2016

Citation: Banach M, Kalinowska B, Konieczny L, Roterman I (2016) Structural Role of Hydrophobic Core in Proteins-Selected Examples. J Proteomics Bioinform 9:276-286. doi: 10.4172/jpb.1000416

Copyright: © 2016 Banach M, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Abstract

This paper discusses the sequence/structure relation. The core question concerns the degree to which similar sequences produce similar structures and vice versa. A mechanism by which similar sequences may result in dissimilar structures is proposed, based on the Fuzzy Oil Drop (FOD) model in which structural similarity is estimated by analyzing the protein’s hydrophobic core. We show that local changes in amino acid sequences, in addition to producing local structural alterations at the substitution site, may also change the shape of the hydrophobic core, significantly affecting the overall tertiary conformation of the protein. Our analysis focuses on four sets of proteins: 1) Pair of designer proteins with specially prepared sequences; 2) Pair of natural proteins modified (mutated) to converge to a point of high-level sequence identity while retaining their respective wild-type tertiary folds; 3) Pair of natural proteins with common ancestry but with differing structures and biological profiles shaped by divergent evolution; and 4) Pair of natural proteins of high structural similarity with no sequence similarity and different biological function.

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