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Sequence-Structure Similarity: Do Sequentially Identical Peptide Fragments have Similar Three-Dimensional Structures?

Uthayakumar, Muthukumarasamy and Patra, Sanjeev and Nagarajan, Raju and Sekar, Kanagaraj (2012) Sequence-Structure Similarity: Do Sequentially Identical Peptide Fragments have Similar Three-Dimensional Structures? In: Current Bioinformatics, 7 (2). pp. 111-115.

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Official URL: http://www.bionity.com/en/publications/392524/sequ...

Abstract

The rapidly growing structure databases enhance the probability of finding identical sequences sharing structural similarity. Structure prediction methods are being used extensively to abridge the gap between known protein sequences and the solved structures which is essential to understand its specific biochemical and cellular functions. In this work, we plan to study the ambiguity between sequence-structure relationships and examine if sequentially identical peptide fragments adopt similar three-dimensional structures. Fragments of varying lengths (five to ten residues) were used to observe the behavior of sequence and its three-dimensional structures. The STAMP program was used to superpose the three-dimensional structures and the two parameters (Sequence Structure Similarity Score (Sc) and Root Mean Square Deviation value) were employed to classify them into three categories: similar, intermediate and dissimilar structures. Furthermore, the same approach was carried out on all the three-dimensional protein structures solved in the two organisms, Mycobacterium tuberculosis and Plasmodium falciparum to validate our results.

Item Type: Journal Article
Department/Centre: Division of Information Sciences > BioInformatics Centre
Date Deposited: 23 Jul 2012 12:23
Last Modified: 23 Jul 2012 12:23
URI: http://eprints.iisc.ernet.in/id/eprint/44647

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