Structural and Sequence Characteristics of Long alpha Helices in Globular Proteins

Kumar, Sandeep and Bansal, Manju (1996) Structural and Sequence Characteristics of Long alpha Helices in Globular Proteins. In: Biophysical Journal., 71 (03). pp. 1574-1586.

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Abstract

Elucidation of the detailed structural features and sequence requirements for iv helices of various lengths could be very important in understanding secondary structure formation in proteins and, hence. in the protein folding mechanism. An algorithm to characterize the geometry of an alpha helix from its C-alpha coordinates has been developed and used to analyze the structures of long cu helices (number of residues greater than or equal to 25) found in globular proteins, the crystal structure coordinates of which are available from the Brookhaven Protein Data Bank, Ail long a helices can be unambiguously characterized as belonging to one of three classes: linear, curved, or kinked, with a majority being curved. Analysis of the sequences of these helices reveals that the long alpha helices have unique sequence characteristics that distinguish them from the short alpha helices in globular proteins, The distribution and statistical propensities of individual amino acids to occur in long alpha heices are different from those found in short alpha helices, with amino acids having longer side chains and/or having a greater number of functional groups occurring more frequently in these helices, The sequences of the long alpha helices can be correlated with their gross structural features, i.e., whether they are curved, linear, or kinked, and in case of the curved helices, with their curvature.

Item Type:	Journal Article
Publication:	Biophysical Journal.
Publisher:	Elsevier Science
Additional Information:	Copyright of this article belongs to Elsevier Science.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	07 Dec 2009 06:16
Last Modified:	19 Sep 2010 05:29
URI:	http://eprints.iisc.ac.in/id/eprint/19609

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