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. 2015;16 Suppl 13(Suppl 13):S2.
doi: 10.1186/1471-2164-16-S13-S2. Epub 2015 Dec 16.

Computer analysis of protein functional sites projection on exon structure of genes in Metazoa

Irina V Medvedeva, Pavel S Demenkov, Vladimir A Ivanisenko

Computer analysis of protein functional sites projection on exon structure of genes in Metazoa

Irina V Medvedeva et al. BMC Genomics. 2015.

Abstract

Background: Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of exon-intron structure of the coding gene is still an actual problem.

Results: One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the exon boundaries to the gene structure. In this paper, we examined the discontinuity of the functional sites in the exon-intron structure of genes and the distribution of lengths and phases of the functional site encoding exons in vertebrate genes. We have shown that the DNA fragments coding the functional sites were in the same exons, or in close exons. The observed tendency to cluster the exons that code functional sites which could be considered as the unit of protein evolution. We studied the characteristics of the structure of the exon boundaries that code, and do not code, functional sites in 11 Metazoa species. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the exon shuffling.

Conclusions: These results characterize the features of the coding exon-intron structure that affect the functionality of the encoded protein and allow a better understanding of the emergence of biological diversity.

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Figures

Figure 1
Figure 1
Exon length distribution in ECFS and ENFS.
Figure 2
Figure 2
Functional site area projected on exon structure of encoding gene.
Figure 3
Figure 3
The distribution among ECFS encoding functional site amino acid residue on 5' border and ENFS by exon phase on 5' exon border.
Figure 4
Figure 4
Functional site type distribution in symmetric exons and all.
See this image and copyright information in PMC

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References

    1. Liu M, Walch H, Wu Sh, Grigoriev A. Significant expansion of exon-bordering protein domains during animal proteome evolution. Nucl Acids Res. 2005;33(1):95–105. - PMC - PubMed
    1. Kawashima T, Kawashima S, Tanaka C. et al.Domain shuffling and the evolution of vertebrates. Genome Research. 2009;19(8):1393–1403. - PMC - PubMed
    1. Cancherini DV, França GS, de Souza SJ. The role of exon shuffling in shaping protein-protein interaction networks. BMC Genomics. 2010;11(Suppl 5):S11. - PMC - PubMed
    1. Ponting CP, Russell RR. The natural history of protein domains. Annu Rev Biophys Biomol Struct. 2002;31:45–71. - PubMed
    1. Takahashi K, Noguti T, Hojo H, Yamauchi K, Kinoshita M, Aimoto S, Ohkubo T, Go M. A mini-protein designed by removing a module from barnase: molecular modeling and NMR measurements of the conformation. Protein Eng. 1999;12(8):673–680. - PubMed

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