The interstrand amino acid pairs play a significant role in determining the parallel or antiparallel orientation of beta-strands.
It is widely considered that it is not appropriate to treat beta-pairs in isolation, since other secondary structural models (such as helices, coils), protein topology and protein tertiary structures would limit beta-strand pairing. However, to understand the underlying mechanisms of beta-sheet formation, studies ought to be performed separately on more concrete aspects. In this study, we focus on the parallel or antiparallel orientation of beta-strands. First, statistical analysis was performed on the relative frequencies of the interstrand amino acid pairs within parallel and antiparallel beta-strands. Consequently, features were extracted by singular value decomposition from the statistical results. By using the support vector machine to distinguish the features extracted from the two types of beta-strands, high accuracy was achieved (up to 99.4%). This suggests that the interstrand amino acid pairs play a significant role in determining the parallel or antiparallel orientation of beta-strands. These results may provide useful information for developing other useful algorithms to examine to the beta-strand folding pathways, and could eventually lead to protein structure predictions.
Zhang
Ning
N
Key Laboratory of Bioactive Materials, Ministry of Education and College of Life Science, Nankai University, Tianjin 300071, PR China.
Ruan
Jishou
J
Duan
Guangyou
G
Gao
Shan
S
Zhang
Tao
T
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D003627:Data Interpretation, Statistical; D008956:Models, Chemical; D017433:Protein Structure, Secondary
D000596:Amino Acids