J Chem Inf Model - Parallel and antiparallel ?-strands differ in amino acid composition and availability of short constituent sequences.

Tópicos

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Resumo

One of the important secondary structures in proteins is the ?-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 ?-strand structures based on strand length and amino acid composition, focusing on differences between parallel and antiparallel ?-strands. Antiparallel strands were more frequent and slightly longer than parallel strands. Overall, the majority of ?-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 ?-sheets, especially in parallel strands, was highly correlated with amino acid hydrophobicity. This correlation was not observed in a-helices and 3(10)-helices. In addition, we examined the frequency of 400 amino acid doublets and 8000 amino acid triplets in ?-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 ?-strand structures and the differences between parallel and antiparallel ?-strands, which can potentially be applied to the secondary structure prediction and the functional design of protein sequences in the future.

Resumo Limpo

one import secondari structur protein strand howev due complex less character helic structur use repres threedimension protein structur data protein data bank character strand structur base strand length amino acid composit focus differ parallel antiparallel strand antiparallel strand frequent slight longer parallel strand overal major sheet antiparallel sheet howev mix sheet reason abund parallel sheet relat rare notabl nonpolar aliphat hydrocarbon amino acid valin isoleucin leucin observ high frequenc strand abund parallel antiparallel strand relat amino acid occurr sheet especi parallel strand high correl amino acid hydrophob correl observ ahelic helic addit examin frequenc amino acid doublet amino acid triplet strand base avail measur relat count doublet triplet identifi triplet specif found either parallel antiparallel strand identifi zerocount triplet occur either parallel antiparallel strand despit fact probabilist suppos occur sever time taken togeth present studi reveal essenti featur strand structur differ parallel antiparallel strand can potenti appli secondari structur predict function design protein sequenc futur

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