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Talk- Hong Guo

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Computer Simulation and Analysis of Proteins: from Study of One Protein at a Time to Analysis of One Million Proteins All Together

  • cmb seminar
When Mar 26, 2018
from 11:00 AM to 12:30 PM
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In my talk, we will discuss our recent work on the applications of different computational approaches to study proteins. We will first show the application of molecular dynamic (MD) simulations with QM/MM potentials to understand the catalytic mechanisms of enzymes. The enzymes to be discussed include: (1) The unique Suv4-20 family of protein lysine methyltransferases (PKMTs) that generate di-methylated product (H4K20me2) based exclusively on the mono-methylated H4K20 substrate (H4K20me1) (published in JCTC, 2017); the mechanism of Ubiquitin-like NEDD8 transfer in RING E3-E2~nedd8-target Complex (published in JCIM, 2018); biosynthesis of the (4S)-α-terpinyl cation from (3S)-linalyl diphosphate (LPP) catalysed by (4S)-limonene synthase (published in Molecules: Special Issue in Free Energy Simulations, 2018). In addition, we will discuss how to apply a new approach to make identification, interpretation and extraction of biological insights from proteomes easier. By selecting representative proteomes from three domains of life, two giant DNA viruses, and collective gene sets from viruses and organelles including mitochondria, chloroplast and plasmids, we will show that systematical analyses of the interplay between protein length (L, i.e., the amino acid sequence length) and protein disorder (D, i.e., percentage of residues in a so-called intrinsically disordered state) allow us to construct a two-dimensional LD-space for describing the proteomes or gene sets (published in Int. J. Genomics, 2018). It is found that the gene distributions in this LD-space may serve as an architectural “fingerprint” shaped by the evolutionary processes.

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