Studies On Surface Modeling Of Protein Molecular3D Structure

Protein is the basic component of life. Almost all life is reflected by the protein structure andfunctions, and the protein molecular functions mainly depend on its structure, especially its surfacestructure has the greatest influence on protein molecular functions, it determines the protein molecularshape, the charge distribution and the spatial arrangement of the amino acid residues with theimportant functions. Therefore, the prediction and identification of the protein molecular functionsbased on its structure have an important significance for the development of the structural genomics.With the development of the molecular graphics, we can use the existing protein structure database tomake the information associated with the biological functions more intuitive and clearer with the helpof the protein molecular visualization. Today varieties of protein molecular3D visualization systemhave been developed and applied for molecular modeling and their functions are being perfected.However, most system can not realize the calculation and display of the molecular surface parameters.So it is significant to realize the calculation and visualization of the molecular surface structuralparameters based on the protein molecular surface structural features.This paper firstly has successful constructions of the VDW model, the stick-and-ball model, theribbon model and the molecular surface model for the protein molecule by making a careful analysisof the protein3D structure data file. And in the process of the molecular surface modeling, we putforward an algorithm to realize the triangular mesh generation based on the protein molecular solventexternal surface. The algorithm is robust and shows good effect in the surface mesh construction.Meanwhile, we present an algorithm to measuring the protein surface curvature. It realizes thecalculation of the surface structural parameters such as curvature and shape index. Using theseparameters, we can make a better study of the protein stability, molecular recognition and theprediction of the molecular3D structure.In this paper, we also develop a new surface structural parameter named convex-and-concave index(CCI) to describe the geometric properties of protein surface based on the protein molecular surfaceatoms. By analyzing the CCI values of the protein-protein interaction sites and ubquitination sites, wehave discovered that this parameter can give a better measure for the concavity and convexity ofprotein surface regions. Meanwhile, the parameter can be visualized and colored according to itsvalues, we can intuitively observe the protein-protein interaction sites and the shape of ligandsbinding to the protein. It provides the key clues to predicting the protein docking and new drugsresearch.At last, we create a protein molecular visualization system called ProtCC (Protein Convex-Concave Feature Analyzer) on the basis of the rational modeling from the protein molecular3D structure,coded using C++and OpenGL on the Windows platform with high visualizer functionality. It candisplay the protein structure using different modeling schemes, calculate and display the molecularsurface structural parameters directly. It also provides the visualization of the protein molecularsurface amino acids distribution according to the physical properties of amino acids, these3D graphsoffer a better way to analyzing the influence between the protein surface physical properties andprotein functions. Moreover, we have optimized the ProtCC to realize the visualization of themolecular3D structure with high quality and high efficiency.