The Influence of Flanking Secondary Structures on Amino Acid Content and Typical Lengths of 3-10 HelicesReport as inadecuate

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International Journal of Proteomics - Volume 2014 2014, Article ID 360230, 13 pages -

Research Article

Department of General Chemistry, Belarusian State Medical University, Dzerzinskogo 83, 220116 Minsk, Belarus

Laboratory of Cellular Technologies, Institute of Physiology, The National Academy of Sciences of Belarus, Academicheskaya 28, 220072 Minsk, Belarus

Received 15 July 2014; Revised 19 September 2014; Accepted 27 September 2014; Published 13 October 2014

Academic Editor: Thallapuranam K. Kumar

Copyright © 2014 Vladislav Victorovich Khrustalev et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


We used 3D structures of a highly redundant set of bacterial proteins encoded by genes of high, average, and low GC-content. Four types of connecting bridges—regions situated between any of two major elements of secondary structure alpha helices and beta strands—containing a pure random coil were compared with connecting bridges containing 3-10 helices. We included discovered trends in the original “VVTAK Connecting Bridges” algorithm, which is able to predict more probable conformation for a given connecting bridge. The highest number of significant differences in amino acid usage was found between 3-10 helices containing bridges connecting two beta strands they have increased Phe, Tyr, Met, Ile, Leu, Val, and His usages but decreased usages of Asp, Asn, Gly, and Pro and those without 3-10 helices. The typical most common length of 3-10 helices situated between two beta strands and between beta strand and alpha helix is equal to 5 amino acid residues. The preferred length of 3-10 helices situated between alpha helix and beta strand is equal to 3 residues. For 3-10 helices situated between two alpha helices, both lengths 3 and 5 amino acid residues are typical.

Author: Vladislav Victorovich Khrustalev, Eugene Victorovich Barkovsky, and Tatyana Aleksandrovna Khrustaleva



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