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DEFINING alpha-HELIX GEOMETRY BY C-alpha ATOM TRACE vs (phi-psi) TORSION ANGLES: A COMPARATIVE ANALYSIS

Shelar, Ashish and Kumar, Prasun and Bansal, Manju (2014) DEFINING alpha-HELIX GEOMETRY BY C-alpha ATOM TRACE vs (phi-psi) TORSION ANGLES: A COMPARATIVE ANALYSIS. In: Conference on Biomolecular Forms and Functions - A Celebration of 50 Years of the Ramachandran Map, JAN, 2013, Indian Inst Sci, Bangalore, INDIA, pp. 116-127.

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Abstract

A regular secondary structure is described by a well defined set of values for the backbone dihedral angles (phi,psi and omega) in a polypeptide chain. However in real protein structures small local variations give rise to distortions from the ideal structures, which can lead to considerable variation in higher order organization. Protein structure analysis and accurate assignment of various structural elements, especially their terminii, are important first step in protein structure prediction and design. Various algorithms are available for assigning secondary structure elements in proteins but some lacunae still exist. In this study, results of a recently developed in-house program ASSP have been compared with those from STRIDE, in identification of alpha-helical regions in both globular and membrane proteins. It is found that, while a combination of hydrogen bond patterns and backbone torsional angles (phi-psi) are generally used to define secondary structure elements, the geometry of the C-alpha atom trace by itself is sufficient to define the parameters of helical structures in proteins. It is also possible to differentiate the various helical structures by their C-alpha trace and identify the deviations occurring both at mid-positions as well as at the terminii of alpha-helices, which often lead to occurrence of 3(10) and pi-helical fragments in both globular and membrane proteins.

Item Type: Conference Proceedings
Additional Information: Copyright for this article belongs to the WORLD SCIENTIFIC PUBL CO PTE LTD, PO BOX 128 FARRER RD, SINGAPORE 9128, SINGAPORE
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Depositing User: Id for Latest eprints
Date Deposited: 17 Jul 2014 08:41
Last Modified: 17 Jul 2014 08:41
URI: http://eprints.iisc.ac.in/id/eprint/49486

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