Dissimilar sequence: similar structure of proteins

Mateusz Banach; Leszek Konieczny; Irena Roterman

doi:10.1515/bams-2016-0014

Article

Dissimilar sequence: similar structure of proteins

Mateusz Banach , Leszek Konieczny and Irena Roterman

Published/Copyright: August 24, 2016

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From the journal Bio-Algorithms and Med-Systems Volume 12 Issue 3

Abstract

Sequence-to-structure relation is one of the major objects of the analysis of protein folding problem. The pair of two small proteins (domains) of similar structure (β-hairpin/α-helix/β-hairpin) generated by the chains of similar length (about 60 amino acids) with very low sequence similarity (15%) is the object of the comparable analysis of 3D structure. The criterion for similarity estimation is the status of polypeptide chain with respect to the hydrophobic core structure. The fuzzy oil drop model is applied to reveal the differentiated status of fragments of the well-defined secondary structure. This analysis allows the interpretation of the structure in other than the geometric form as it is made based on secondary structure classification. The two compared highly similar proteins appear to be different with respect to the hydrophobic core structure.

Keywords: hydrophobicity; protein structure; protein structure prediction; secondary structure

Acknowledgements

Many thanks to Anan Śmietańska for technical support.

Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.
Research funding: The work was financially supported by Collegium Medicum grant system K/ZDS/006363.
Employment or leadership: None declared.
Honorarium: None declared.
Competing interests: The funding organization(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication.

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Received: 2016-7-15

Accepted: 2016-8-2

Published Online: 2016-8-24

Published in Print: 2016-9-1

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Articles in the same Issue

https://doi.org/10.1515/bams-2016-0014

Keywords for this article

hydrophobicity; protein structure; protein structure prediction; secondary structure