Sivasakthi v

Anitha p

Kumar km

Bag s

Senthilvel p

Lavanya p

Swetha r

Anbarasu a

Ramaiah s

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Vellore Institute of Technology (VIT) is a private university located in&nbsp;Tamil Nadu, India. Founded in 1984, as Vellore Engineering College, the institution offers 20 undergraduate, 34 postgraduate, four integrated and four research programs. It has campuses in Vellore, Amravati, Bhopal and Chennai.

VIT is one of the top ranked private universities in India according to NIRF, THE and QS Rankings.&nbsp;Govt. of India has recognized&nbsp;VIT, Vellore as an&nbsp;Institution of Eminence. This has allowed VIT to take independent quality initiatives and move up in world ranking.

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Aromatic-aromatic interactions: analysis of π-π interactions in interleukins and TNF proteins.

Bioinformation

We have analyzed and compared the influence of cation-π interactions in glycoproteins (GPs), lipid-binding proteins (LBPs) and RNA-binding proteins (RBPs) in this study. We observed that all the proteins included in the study had profound cation-π interactions. There is an average of one energetically significant cation-π interaction for every 71 residues in GPs, for every 58 residues in LBPs and for every 64 residues in RBPs. Long-range contacts are predominant in all the three types of proteins studied. The pair-wise cation-π interaction energy between the positively charged and aromatic residues shows that Arg-Trp pair energy was the strongest among all six possible pairs in all the three types of proteins studied. There were considerable differences in the preference of cation-π interacting residues to different secondary structure elements and ASA and these might contribute to differences in biochemical functions of GPs, LBPs and RBPs. It was interesting to note that all the five residues involved in cation-π interactions were found to have stabilization centers in GPs, LBPs and RBPs. Majority of the cation-π interacting residues investigated in the present study had a conservation score of ≥6, the cutoff value used to identify the stabilizing residues. A small percentage of cation-π interacting residues were also present as stabilizing residues. The cation-π interaction-forming residues play an important role in the structural stability of in GPs, LBPs and RBPs. The results obtained in this study will be helpful in further understanding the stability, specificity and differences in the biochemical functions of GPs, LBPs and RBPs. © 2007 Elsevier Ltd. All rights reserved.

Journal of Theoretical Biology

Exploring the role of cation–π interactions in glycoproteins lipid-binding proteins and RNA-binding proteins

The roles played by the non-covalent interactions have been investigated for a set of six TNF proteins and nine Interleukins. The stabilizing residues have been identified by a consensus approach using the concepts of available surface area, medium and long-range interactions and conservation of amino acid residues. The cation-π interactions have been computed based on a geometric approach such as distance and energy criteria. We identified an average of 1 energetically significant cation-π interactions in every 94 residues in TNF proteins and 1 in every 62 residues in Interleukins. In TNF proteins, the cationic groups Lys preferred to be in helix while Arg preferred to be in strand regions while in Interleukins the Arg residues preferred to be in helix and Lys preferred to be in strand regions. From the available surface area calculations, we found that, almost all the cation and π residues in TNF proteins and Interleukins were either in buried or partially buried regions and none of them in the exposed regions. Medium and long-range interactions were predominant in both TNF proteins and Interleukins. It was observed that the percentage of stabilizing centers were more in TNF proteins as compared to the Interleukins, while the percentage of conserved residues were more in Interleukins than in TNF proteins. In the stabilizing residues Lys was observed to be a stabilizing residue in both TNF proteins and Interleukins. Among the aromatic group, Phe was seen to be a stabilizing residue in both TNF and Interleukins. We suggest that this study on the computation of cation-π interactions in TNF proteins and Interleukins would be very helpful in further understanding the structure, stability and functional similarity of these proteins. © 2006 Elsevier Ltd. All rights reserved.

Cytokine

Computation of non-covalent interactions in TNF proteins and interleukins

Proceedings of the National Academy of Sciences

Correction for Pushparaj et al., Retraction to Pushparaj et al. 106(24):9773

SpringerReference

Meselson-Radding Model Of Recombination (1975 Proc Natl Acad Sci USA 72:358)

Encyclopedia of Genetics, Genomics, Proteomics and Informatics

In Silico Biology

Aromatic-aromatic interactions: analysis of π-π interactions in interleukins and TNF proteins

Journal	Bioinformation
Publisher	Biomedical Informatics
ISSN	0973-8894
Open Access	Yes