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A Comparative Analysis of Protein Interfaces

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Proteins perform various functions through interacting with other molecules. Analyzing the characteristics of residues on the interaction interfaces provides insights into the mechanisms of these interactions. In this study, we analyze the characteristics of five different interfaces: protein-protein interfaces, protein-DNA interfaces, protein-RNA interfaces, protein-carbohydrate interfaces, and protein-ligand interfaces. The analysis reveals that these interfaces are different in residue composition. These differences in residue composition reflect the differences in the mechanisms that facility different types of interactions. Regardless of the differences in residue composition, all of the five types of interfaces are more conservative than the non-interface protein surfaces. Additionally, our results also show that it is important to consider the effect of solvent accessibility when investigating residues' propensities for different parts of the proteins.

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Keywords: (NIP); (PDB); (RIP); (rASA); DNA; HSSP; His; Interface propensity; NACCESS; Protein Cores; Protein Interfaces; PseAAc; RNA; Trp; Tyr; hydropho-bicity; interface residues; non-interface; non-interface surfaces; pro-tein-DNA; propensity; protein; protein cores; protein-RNA; residue compositions; residues; sequence; sequence entropy; van der Walls

Document Type: Research Article

Publication date: 2010-11-01

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  • Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.
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