title: Studies on the rules of β-strand alignment in a protein β-sheet structure.
abstract: To further disclose the underlying mechanisms of protein β-sheet formation, studies were made on the rules of β-strands alignment forming β-sheet structure using statistical and machine learning approaches. Firstly, statistical analysis was performed on the sum of β-strands between each β-strand pairs in protein sequences. The results showed a propensity of near-neighbor pairing (or called "first come first pair") in the β-strand pairs. Secondly, based on the same dataset, the pairwise cross-combinations of real β-strand pairs and four pseudo-β-strand contained pairs were classified by support vector machine (SVM). A novel feature extracting approach was designed for classification using the average amino acid pairing encoding matrix (APEM). Analytical results of the classification indicated that a segment of β-strand had the ability to distinguish β-strands from segments of α-helix and coil. However, the result also showed that a β-strand was not strongly conserved to choose its real partner from all the alternative β-strand partners, which was corresponding with the ordination results of the statistical analysis each other. Thus, the rules of "first come first pair" propensity and the non-conservative ability to choose real partner, were possible important factors affecting the β-strands alignment forming β-sheet structures.
authors: College of Life Science and Key Lab. of Bioactive Materials, Ministry of Education, Nankai University, Tianjin 300071, PR China.
authors: Lei
authors: L
authors: Zhang
authors: Ning
authors: N
authors: Zhang
authors: Ji-Shou
authors: JS
authors: Ruan
authors: Tao
authors: T
authors: Zhang
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D030562:Databases, Protein; D008956:Models, Chemical; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment
chemical_list: D011506:Proteins