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Studies on Protein Molecular Surface and Its Electrostatic Energy

Author: WangZhiGuang
Tutor: PengQunSheng
School: Zhejiang University
Course: Applied Mathematics
Keywords: protein molecular surface atoms topology graph molecular surface adsorption orientation benzene binding site electrostatic
CLC: Q51
Type: Master's thesis
Year: 2010
Downloads: 40
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Abstract

Protein plays a very crucial role in life and studying protein molecular is important. First, proteins are the main functions of cells, molecules, most of the biological functions are regulated by protein molecular. Second, protein molecular is one of most abundant elements in cell. So the study of protein molecular functions and structure is one hot problem of life science. Protein molecular functions depend on its structure, especially, the surface atoms plays a very important role in its functions. In addition, analyzing the electrostatics potential is a main tool for studying the protein molecular. We will analyze the protein molecular from the two sides above.On the basis of previous surface atoms topology SASG, we propose the data structure and algorithm of surface atoms graph SAG. Through constructing the surface atoms graph and searching SAG real surface atoms connecting subgraph, we find the real surface atoms and remove calculated as SASG brought to the excess number of atoms within molecules. On the basis of extraction of surface atoms, we construct the solvent excluded surface (SES). The result SES surface constructed using this new method is more consistent with the definition of SES surface. In addition, we apply the surface atoms into protein adsorption orientation and other issues, the results show that this new method is efficient and meaningful.We also report the discovery of a preference in the electrostatic potential between the aromatic rings in the bound ligands and nucleic acids and their cognate proteins. By analyzing a diverse set of complex structures, we have found that the electrostatic potentials of the carbon atoms of an aromatic ring are higher than those of methyl/methylene atoms in the same molecule. The discovery can greatly improve the efficiency and molecular docking accuracy.

Studies on Protein Molecular Surface and Its Electrostatic Energy

Abstract

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