Elaboration of Simplest Folding Structures in 2-Dimensional Lattice with Delta-Hemolysin and Its Variants in HP Model
Elaboration of Simplest Folding Structures in 2-Dimensional Lattice with Delta-Hemolysin and Its Variants in HP Model作者机构：State Key Laboratory of Non-food Biomass Enzyme Technology National Engineering Research Center for Non-Food Biorefinery Guangxi Key Laboratory of Biorefinery Guangxi Academy of Sciences Nanning China
出 版 物：《Journal of Biomedical Science and Engineering》 (生物医学工程（英文）)
年 卷 期：2019年第12卷第5期
页 面：293-309页
学科分类：1002[医学-临床医学] 100214[医学-肿瘤学] 10[医学]
主 题：Folding Structure Delta-Hemolysin HP Model Hydrophobicity Index Lattice Minimal Energy Native State
摘 要：Although the advanced 3-dimensional structure measurements provide more and more detailed structures in Protein Data Bank, the simplest 2-dimensional lattice model still looks meaningful because 2-dimensional structures play a complementary role with respect to 3-dimensional structures. In this study, the folding structures of delta-hemolysin and its six variants were studied at 2-dimensional lattice, and their amino acid contacts in folding structures were considered according to HP model with the aid of normalized amino acid hydrophobicity index. The results showed that: 1) either delta-hemolysin or each of its variants could find any of its folding structure in one eighth of 1,129,718,145,924 folding structures because of symmetry, which reduces the time required for folding, 2) the impact of pH on folding structures is varying and associated directly with the amino acid sequence itself, 3) the changes in folding structures of variants appeared different case by case, and 4) the assigning of hydrophobicity index to each amino acid was a way to distinguish folding structures at the same native state. This study can help to understand the structure of delta-hemolysin, and such an analysis can shed lights on NP-problem listed in millennium prize because the HP folding in lattice belongs to a sub-problem of NP-problem.
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