Sphere-based residue environment property explorations on protein 3D structure
Date Issued
2008
Date
2008
Author(s)
Chang, Chia-Chen
Abstract
The structure of a protein is crucial to its function. In particular, the residue-residue contact on local structure was directly related to the protein function. Residue-residue contact was correlated with folding and stability of proteins. Mining the residue-residue contact can help scientist understand residue environmental information; for example, exploring the side-chain distribution can support the study of protein structure, protein function and disordered regions. In this work, our major contribution is to propose a multi-dimensional framework of sphere-based model to explore the residue environment, including to diverse residue-residue contacts. This framework also helps to analyze the relationship between local structure and residue-residue contacts. We also develop the prototype web service for demonstrating this framework.n experiment, the sphere-base framework was applied in the exploration of the information of the interaction between atoms, including complexed consisted of protein chain, DNA, RNA or heterogen atoms. In sidechain-sidechain interaction, we found the top five contacted residue pairs. In protein-protein interaction, the distribution of contacted structure was focus on the α-helix and α-helix pairs. We also comprehend the unusual overlapping on protein chains such as 1cwq, 1e0p, 1gu8, 1gtv and 1cm4. The overlapping proteins chain were record the combination of structure in different states of biological characteristics in PDB. In protein-het group interaction, we explored that 97% interaction contacted with H2O atoms, and top ranked het groups are chemical compounds used to stabilize structures for crystallization. In protein-DNA interaction, the arginine(R) and lysine(K) were preferred to contact with DNA nucleotides. We also explored that there were 29 protein chains contact with DNA and RNA nucleotides. According to observations we explored, we can comprehend the characteristics of diverse residue-residue contact and their relationship. These characteristics can give us a whole picture on residue environment of protein structures in Protein Data Bank.
Subjects
residue-residue contact
protein structure
protein function
data mining
Type
thesis
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