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《第十三届全国量子化学会议报告集》2017年
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Computer Simulation and Analysis of Proteins: from Study of One Protein at a Time Based on QM/MM MD approaches to Analysis of One Million Proteins Together for Proteomes

Hong Guo  
【摘要】:Applications of different computational approaches to study proteins in biological systems will be discussed in this talk. We will first show how molecular dynamic(MD) simulations with QM/MM potentials can be applied to understand the catalytic mechanisms of individual enzymes or enzyme complexes as well as their specificity. It is demonstrated that such computational approaches can serve as powerful tools for understanding details of enzyme catalysis and predict substrate specificity. As we know, determination of complete genomes from a number of organisms have offered an unprecedented opportunity for biological research and transformed biology into a discipline that depends significantly on how to interpret large-scale data sets. By selecting representative proteomes, we will demonstrate that systematical analyses of the interplay between protein length(L, the amino acid sequence length) and protein disorder(D, the percentage of residues in a so-called intrinsically disordered state) may allow us to construct two-dimensional LD-space maps for describing the proteomes or gene sets. It is found that the gene distributions in this LDspace may serve as architectural "fingerprints" shaped by the evolutionary processes.
【分类号】:Q51

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