EurekaMag.com logo
+ Site Statistics
References:
53,869,633
Abstracts:
29,686,251
+ Search Articles
+ Subscribe to Site Feeds
EurekaMag Most Shared ContentMost Shared
EurekaMag PDF Full Text ContentPDF Full Text
+ PDF Full Text
Request PDF Full TextRequest PDF Full Text
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter
Follow on LinkedInFollow on LinkedIn

+ Translate

Parallel and antiparallel β-strands differ in amino acid composition and availability of short constituent sequences



Parallel and antiparallel β-strands differ in amino acid composition and availability of short constituent sequences



Journal of Chemical Information and Modeling 51(6): 1457-1464



One of the important secondary structures in proteins is the β-strand. However, due to its complexity, it is less characterized than helical structures. Using the 1641 representative three-dimensional protein structure data from the Protein Data Bank, we characterized β-strand structures based on strand length and amino acid composition, focusing on differences between parallel and antiparallel β-strands. Antiparallel strands were more frequent and slightly longer than parallel strands. Overall, the majority of β-sheets were antiparallel sheets; however, mixed sheets were reasonably abundant, and parallel sheets were relatively rare. Notably, the nonpolar, aliphatic hydrocarbon amino acids, valine, isoleucine, and leucine were observed at a high frequency in both strands but were more abundant in parallel than in antiparallel strands. The relative amino acid occurrence in β-sheets, especially in parallel strands, was highly correlated with amino acid hydrophobicity. This correlation was not observed in α-helices and 3(10)-helices. In addition, we examined the frequency of 400 amino acid doublets and 8000 amino acid triplets in β-strands based on availability, a measurement of the relative counts of the doublets and triplets. We identified some triplets that were specifically found in either parallel or antiparallel strands. We further identified "zero-count triplets" which did not occur in either parallel or antiparallel strands, despite the fact that they were probabilistically supposed to occur several times. Taken together, the present study revealed essential features of β-strand structures and the differences between parallel and antiparallel β-strands, which can potentially be applied to the secondary structure prediction and the functional design of protein sequences in the future.

(PDF emailed within 0-6 h: $19.90)

Accession: 054860187

Download citation: RISBibTeXText

PMID: 21520893

DOI: 10.1021/ci200027d



Related references

Antiparallel and parallel beta-strands differ in amino acid residue preferences. Nature 282(5734): 109-111, 1979

The interstrand amino acid pairs play a significant role in determining the parallel or antiparallel orientation of beta-strands. Biochemical and Biophysical Research Communications 386(3): 537-543, 2009

Prediction of the parallel/antiparallel orientation of beta-strands using amino acid pairing preferences and support vector machines. Journal of Theoretical Biology 263(3): 360-368, 2010

Structure of repeating dgt n sequences with parallel and antiparallel strands. Molekulyarnaya Biologiya (Moscow) 26(2): 452-463, 1992

Effect of amino acid composition on the twist and the relative stability of parallel and antiparallel b-sheets. Biochemistry (American Chemical Society) 22: 13-21, 1983

Parallel and antiparallel triple helices with G,A-containing third strands. Electrophoresis 20(3): 511-513, March, 1999

Availability of short amino acid sequences in proteins. Protein Science 14(3): 617-625, 2005

2-aminopurine as a probe for parallel or antiparallel orientation of strands in DNA duplex. Journal of Biomolecular Structure & Dynamics 18(6): 941-942, June, 2001

Parallel and antiparallel G*G.C base triplets in pur*pur.pyr triple helices formed with (GA) third strands. Journal of Biomolecular Structure & Dynamics 19(3): 527-534, 2002

DNA strands complementary in parallel orientation, form an antiparallel duplex at neutral pH with A-C, G-T and T-C mismatched base pairs. Progress in Biophysics & Molecular Biology 65(SUPPL 1): 74, 1996

Potential implications of availability of short amino acid sequences in proteins: an old and new approach to protein decoding and design. Biotechnology Annual Review 14: 109-141, 2008

Contributions of residue pairing to b-sheet formation: conservation and covariation of amino acid residue pairs on antiparallel b-strands. Journal of Molecular Biology 305(5): 45-59, 2001

Parallel and antiparallel Holliday junctions differ in structure and stability. Journal of Molecular Biology 221(4): 1419-1432, 1991

An intramolecular G-quadruplex structure with mixed parallel/antiparallel G-strands formed in the human BCL-2 promoter region in solution. Journal of the American Chemical Society 128(4): 1096-1098, 2006