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SMS 2.0: An Updated Database to Study the Structural Plasticity of Short Peptide Fragments in Non-redundant Proteins

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Genomics, Proteomics & Bioinformatics 2012年第1期10卷 44-50页

作者： Dheeraj Ravella Muthukumarasamy Uthaya Kumar Durairaj Sherlin Mani Shankar marthandan kirti vaishnavi Kanagaraj Sekar Bioinformatics Centre (Centre of Excellence in Structural Biology and Bio-computing) Supercomputer Education and Research Centre Indian Institute of Science Bangalore 560012 India

The function of a protein molecule is greatly influenced by its three-dimensional （3D） structure and therefore structure prediction will help identify its biological function. We have updated Sequence, Motif and Structure （SMS）, the database of structurally rigid peptide fragments, by combining amino acid sequences and the corre- sponding 3D atomic coordinates of non-redundant （25%） and redundant （90%） protein chains available in the Protein Data Bank （PDB）. SMS 2.0 provides information pertaining to the peptide fragments of length 5-14 resi- dues. The entire dataset is divided into three categories, namely, same sequence motifs having similar, intermedi- ate or dissimilar 3D structures. Further, options are provided to facilitate structural superposition using the pro- gram structural alignment of multiple proteins （STAMP） and the popular JAVA plug-in （Jmol） is deployed for visualization. In addition, functionalities are provided to search for the occurrences of the sequence motifs in other structural and sequence databases like PDB, Genome Database （GDB）, Protein Information Resource （PIR） and Swiss-Prot. The updated database along with the search engine is available over the World Wide Web through the following URL http：//***/sms/.

关键词： non-redundant protein chains sequence motifs 3D structure structural superposition

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Homepeptide Repeats:Implications for Protein Structure,Function and Evolution

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Genomics, Proteomics & Bioinformatics 2012年第4期10卷 217-225页

作者： Muthukumarasamy Uthayakumar Bowdadu Benazir Sanjeev Patra marthandan kirti vaishnavi Manickam Gurusaran Kanagarajan Sureka Jeyaraman Jeyakanthan Kanagaraj Sekar Supercomputer Education and Research Centre Indian Institute of ScienceBangalore 560012India Department of Bioinformatics Alagappa UniversityKaraikudi 630003India

Analysis of protein sequences from Mycobacterium tuberculosis H37Rv （Mtb H37Rv） was performed to identify homopeptide repeat- containing proteins （HRCPs）. Functional annotation of the HRCPs showed that they are preferentially involved in cellular metabolism. Furthermore, these homopeptide repeats might play some specific roles in protein-protein interaction. Repeat length differences among Bacteria, Archaea and Eukaryotes were calculated in order to identify the conservation of the repeats in these divergent kingdoms. From the results, it was evident that these repeats have a higher degree of conservation in Bacteria and Archaea than in Eukaryotes. In addi- tion, there seems to be a direct correlation between the repeat length difference and the degree of divergence between the species. Our study supports the hypothesis that the presence of homopeptide repeats influences the rate of evolution of the protein sequences in which they are embedded. Thus, homopeptide repeat may have structural, functional and evolutionary implications on proteins.

关键词： Homopeptide repeats Disordered regions Replication slippage Protein domains Rate of evolution

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维普期刊数据库

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