Cutoff variation induces different topological properties: a new discovery of amino acid network within protein.

Department of Physics, Wuhan University, Wuhan 430072, China.
Journal of Theoretical Biology (Impact Factor: 2.35). 12/2008; 256(3):408-13. DOI: 10.1016/j.jtbi.2008.09.042
Source: PubMed

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 7A. It is noteworthy that the length of peptide bond is about 1.5A, the length of hydrogen bond is about 3A, the range of London-van der Waals force is about 5A and the range of hydrophobic effect can reach to 12A 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 is proportional to k(-0.5) at R(c)=12A. 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.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Amino acid networks (AANs) are undirected networks consisting of amino acid residues and their interactions in three-dimensional protein structures. The analysis of AANs provides novel insight into protein science, and several common amino acid network properties have revealed diverse classes of proteins. In this review, we first summarize methods for the construction and characterization of AANs. We then compare software tools for the construction and analysis of AANs. Finally, we review the application of AANs for understanding protein structure and function, including the identification of functional residues, the prediction of protein folding, analyzing protein stability and protein-protein interactions, and for understanding communication within and between proteins.
    Amino Acids 03/2014; · 3.91 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Topology is an essential aspect of protein structure. The network paradigm is increasingly used to describe the topology and dynamics of proteins. In this paper, the effect of topology on residue interaction network was investigated for two different proteins: Dronpa and a DNA clamp, which have cylindrical and toroidal topologies, respectively. Network metrics including characteristic path lengths, clustering coefficients, and diameters were calculated to investigate their global topology parameters such as small-world properties and packing density. Measures of centrality including betweenness, closeness, and residue centrality were computed to predict residues critical to function. Additionally, the detailed topology of the hydrophobic pocket in Dronpa, and communication pathways across the interface in the DNA clamp, were investigated using the network. The results are presented and discussed with regard to existing residue interaction network properties of globular proteins and Elastic network models on Dronpa and the DNA clamp. The topological principle underlying residue interaction networks provided insight into the architectural organization of proteins.
    Journal of Theoretical Biology 01/2014; · 2.35 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: One proposed HIV vaccine strategy is to induce Gag-specific CD8(+) T-cell responses that can corner the virus, through fitness cost of viral escape and unavailability of compensatory mutations. We show here that the most variable capsid residues principally comprise escape mutants driven by protective alleles HLA-B*57, -5801, and -8101 and covarying HLA-independent polymorphisms that arise in conjunction with these escape mutations. These covarying polymorphisms are potentially compensatory and are concentrated around three tropism-determining loops of p24, suggesting structural interdependencies. Our results demonstrate complex patterns of adaptation of HIV under immune selection pressure, the understanding of which should aid vaccine design.
    Journal of Virology 02/2011; 85(3):1384-90. · 5.08 Impact Factor