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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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Immunoglobulin G1 binding with various molecular receptors: A new paradigm of IgG1 as a potential adjuvant

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Journal of Acute Disease 2019年第1期8卷 28-33页

作者： Shweta Saxena Vignesh Sounderrajan saravanan konda mani Shakila Harshavardhan Department of Molecular Microbiology School of BiotechnologyMadurai Kamaraj UniversityMadurai 625021TamilnaduIndia Centre of Advanced Study in Crystallography&Biophysics University of MadrasGuindy CampusChennai-600025TamilnaduIndia

Objective: To explore the possible IgG1 binding receptors by protein-protein docking experiments. Methods: The protein-protein cognate interactions such as IgG with Fc Receptors (FcRs) potentiate signaling cascades to ameliorate antigen uptake, processing and presentation are studied by protein-protein docking experiments. Results: However, the propensity of IgG interactions with other cognate receptors largely remains obscure. In this direction, possibilities of IgG1 binding with various five receptors were explored. In this study, we report previously unidentified associations between IgG1 and other receptors. Herein, we show that IgG1 binds to the granulocyte-macrophage receptor, β common receptor and complementaryreceptor(complementary receptor I and complementary receptor II) to form a complex structure. We show the binding ability and important protein-protein interactions of IgG1 with four receptors in comparison to Fc Receptor, and also find out the conserved amino acids and hydrophobic-hydrophobic interactions amongst them. Conclusions: Comparative interaction studies of IgG1 binding to various receptors revealed close similarities of IgG1 binding to its native receptor Fc. In conclusion, our study has shown the comparable binding efficiency of four receptors to IgG1 apart from the conventional Fc receptor.

关键词： Adjuvant Antigen presenting cells Complement receptors Effector cells Fc Receptors Immunoglobulin1 Fc

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