Detection Methods Of Repeat Protein And Folding Mechanism Of β-hairpin

The primary sequence of a protein encodes the information that is required for its structure formation. Therefore, it is very meaningful for studying the relationship between amino acid sequence, protein structure and biological function. Understanding these can provide important insights into the formation of protein structure, and establish the foundation of protein structure design and prediction. Furthermore, by studying the characters of protein folding, we are able to identify critical biologically-active regions, and can use this information to design new drugs for the therapy of various diseases relevant to protein misfolding, such as Alzheimer's Disease, Parkinson's disease, and scrapie.In this paper, we have an interest in works of three aspects, including digital-reversal algorithm, detection of repeat protein structural characters and folding mechanism ofβ-hairpin.Firstly, we present two kinds of digital-reversal algorithm. One is not-inplace digital-reversal algorithm based on progressive index mapping, having a new feature which data are accessed sequentially on a computer. Another is inplace digital-reversal algorithm based on cross-sum addressing, can be implemented with data-swap operation of butterfly type or wing type, the latter have higher efficiency. By minimizing the number of index mapping operations, unrolling the innermost loop, and vectorizing data operations, the proposed algorithms can obtain higher efficiency than known fastest approaches.Then, several new approaches are proposed to discovery the fold characters of repeat proteins from their sequence, structure, and interaction. Hamming distance, dRMSD score, contact energy are separately used to measure the similarity of protein sequence, structure and interaction. Puzzle transform is used to process these similarity data set. Furthermore, these data are calculated and drawn into Dotplot, Recurrence Plot, and/or Correlation Plot. By these methods, we aim to determine the most reasonable evolutionary origin of repeat protein structural characters.Finally, by all-atom molecular dynamics simulation ofβ-hairpin, we find that zip-out model and hydrophobic cluster model can elucidate the fold mechanism ofβ-hairpin. Because of huge atom number of general protein in solution, it is a great challenge for molecular dynamics simulation of large protein at atom resolution. Therefore, some common protein build blocks, such as alpha helix bundle,βhairpin,βsheet, and miniprotein, are used as normal structure. It is more difficult to compute for more latter structure. So, we selectβhairpin to study fold mechanism of protein, and obtain 7 successful folding trajectories from 60 calculations. The results show that P hairpin can fold into the native state through multiple pathways, depending on the ways of the formation of the hydrophobic core.