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Molecular Dynamics Information Improves cis-Peptide-Based Function Annotation of Proteins

Das, Sreetama and Bhadra, Pratiti and Ramakumar, Suryanarayanarao and Pal, Debnath (2017) Molecular Dynamics Information Improves cis-Peptide-Based Function Annotation of Proteins. In: JOURNAL OF PROTEOME RESEARCH, 16 (8). pp. 2936-2946.

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Official URL: http://doi.org/10.1021/acs.jproteome.7b00217

Abstract

cis-Peptide bonds, whose occurrence in proteins is rare but evolutionarily conserved, are implicated to play an important role in protein function. This has led to their previous use in a homology-independent, fragment-match-based protein function annotation method. However, proteins are not static molecules; dynamics is integral to their activity. This is nicely epitomized by the geometric isomerization of cis-peptide to trans form for molecular activity. Hence we have incorporated both static (cis-peptide) and dynamics information to improve the prediction of protein molecular function. Our results show that cis-peptide information alone cannot detect functional matches in cases where cis-trans isomerization exists but 3D coordinates have been obtained for only the trans isomer or when the cis-peptide bond is incorrectly assigned as trans. On the contrary, use of dynamics information alone includes false-positive matches for cases where fragments with similar secondary structure show similar dynamics, but the proteins do not share a common function. Combining the two methods reduces errors while detecting the true matches, thereby enhancing the utility of our method in function annotation. A combined approach, therefore, opens up new avenues of improving existing automated function annotation methodologies.

Item Type: Journal Article
Additional Information: Copy right for this article belongs to the AMER CHEMICAL SOC, 1155 16TH ST, NW, WASHINGTON, DC 20036 USA
Department/Centre: Division of Interdisciplinary Research > Supercomputer Education & Research Centre
Division of Physical & Mathematical Sciences > Physics
Depositing User: Id for Latest eprints
Date Deposited: 01 Sep 2017 09:17
Last Modified: 01 Sep 2017 09:17
URI: http://eprints.iisc.ac.in/id/eprint/57713

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