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Cutoff variation induces different topological properties: A new discovery of amino acid network within protein
- Source :
- Journal of Theoretical Biology. 256:408-413
- Publication Year :
- 2009
- Publisher :
- Elsevier BV, 2009.
-
Abstract
- An increasing attention has been dedicated to the characterization of complex networks within the protein world. Before now most investigations about protein structures were only considered where the interactive cutoff distance R c =5 or 7 A. It is noteworthy that the length of peptide bond is about 1.5 A, the length of hydrogen bond is about 3 A, the range of London-van der Waals force is about 5 A and the range of hydrophobic effect can reach to 12 A in protein molecule. Present work reports a study on the topological properties of the amino acid network constructed by different interactions above. The results indicate that the small-world property of amino acid network constructed by the peptide and hydrogen bond, London-van der Waals force and the hydrophobic effect is strong, very strong and relatively weak, respectively. Besides, there exists a precise exponential relation C ∝ k −0.5 at R c =12 A. It means that the amino acid network constructed by the hydrophobic effect tend to be hierarchical. Functional modules could be the cause for hierarchical modularity architecture in protein structures. This study on amino acid interactive network for different interactions facilitates the identification of binding sites which is strongly linked with protein function, and furthermore provides reasonable understanding of the underlying laws of evolution in genomics and proteomics.
- Subjects :
- Models, Molecular
Statistics and Probability
Protein Conformation
Peptide
Topology
General Biochemistry, Genetics and Molecular Biology
Hydrophobic effect
Structure-Activity Relationship
Protein structure
Animals
Molecule
Peptide bond
Amino Acids
Binding site
chemistry.chemical_classification
Binding Sites
General Immunology and Microbiology
Hydrogen bond
Applied Mathematics
Proteins
Hydrogen Bonding
General Medicine
Amino acid
chemistry
Modeling and Simulation
General Agricultural and Biological Sciences
Hydrophobic and Hydrophilic Interactions
Subjects
Details
- ISSN :
- 00225193
- Volume :
- 256
- Database :
- OpenAIRE
- Journal :
- Journal of Theoretical Biology
- Accession number :
- edsair.doi.dedup.....7b3a1513c088535c4bb486f241dfa12d