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Search and Analysis of Identical reverse octapeptides in Unrelated Proteins

Genomics, Proteomics & Bioinformatics 2013年第2期11卷 114-121页

作者： Konda Mani Saravanan Samuel Selvaraj Department of Bioinformatics School of Life SciencesBharathidasan University

For the past few decades, intensive studies have been carried out in an attempt to under- stand how the amino acid sequences of proteins encode their three dimensional structures to perform their specific functions. In order to understand the sequence-structure relationship of proteins, sev- eral sub-sequence search studies in non-redundant sequence-structure databases have been under- taken which have given some fruitful clues. In our earlier work, we analyzed a set of 3124 non- redundant protein sequences from the Protein Data Bank （PDB） and retrieved 30 identical octapep- tides having different secondary structures. These octapeptides were characterized by using different computational procedures. This prompted us to explore the presence of octapeptides with reverse sequences and to analyze whether these octapeptides would adopt similar structures as that of their parent octapeptides. Our identical reverse octapeptide search resulted in the finding of eight octapep- tide pairs （octapeptide and reverse octapeptide） with similar secondary structure and 23 octapeptide pairs with different secondary structures. In the present work, the geometrical and biophysical char- acteristics of identical reverse octapeptides were explored and compared with unrelated octapeptide pairs by using various computational tools. We thus conclude that proteins containing identical reverse octapeptides are not very abundant and residues in the octapeptide pairs do not contribute to the stability of the protein. Furthermore, compared to unrelated octapeptides, identical reverse octapeptides do not show certain biophysical and geometrical properties.

关键词： reverse octapeptide Oetapeptide search Dipole and quadrapole Volume and surface area Protein stability

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