P anitha

V sivasakthi

P lavanya

K murugan kumar

A anbarasu

S ramaiah

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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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VIT University

Arginine and Lysine interactions with π residues in metalloproteins

Bioinformation

p-p Interactions play an important role in the stability of protein structures. In the present study, we have analyzed the influence of p-p interactions in eNOS and nNOS proteins. The contribution of these p-p interacting residues in sequential separation, secondary structure involvement, solvent accessibility and stabilization centers has been evaluated. p-p interactions stabilize the core regions within eNOS and nNOS proteins. p-p interacting residues are evolutionary conserved. There is a significant number of p-p interactions in spite of the lesser natural occurrences of p-residues in eNOS and nNOS proteins. In addition to p-p interactions, presidues also form p-p networks in both eNOS and nNOS proteins which might play an important role in the structural stability of these protein structures. © 2013 Elsevier Inc. All rights reserved.

Bioorganic Chemistry

Investigations on the role of π–π interactions and π–π networks in eNOS and nNOS proteins

β-lactam group of antibiotics is the most widely used therapeutic molecules for treating bacterial infections. The main mode of bacterial resistance to β-lactams is by β-lactamases. In the present study, we report our results on the role of cation-π interactions in β-lactamases and their environmental preferences. The number of interactions formed by arginine is higher than lysine in the cationic group, while tyrosine is comparatively higher than phenylalanine and tryptophan in the π group. Our results indicate that cation-π interactions might play an important role in the global conformational stability of β-lactamases.

Cell Biochemistry and Biophysics

Cation–π Interactions in β-Lactamases: The Role in Structural Stability

Cell adhesion molecules are important for their various roles in many cellular events and responses. In the present study, we have analyzed the roles played by cation-π interactions in the structural stability of adhesion molecules. These interactions are mainly formed by long-range contacts. The occurrence of arginine is higher than lysine to form cation-π interactions. The secondary structure preferences of interacting residues are independent of amino acid class. Cation-π interactions might stabilize the interface between the terminus and core in this class of proteins. The results obtained in the present study will be useful in understanding the contribution of cation-π interactions to the overall stability of adhesion proteins. © 2010 Springer-Verlag.

Protoplasma

Structural stability studies in adhesion molecules—role of cation–π interactions

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 energy contribution due to cation-π interactions has been computed for 37 RNA binding proteins. The contribution of these cation-π interacting residues in sequential separation, secondary structure involvement, solvent accessibility, and stabilization centers has been evaluated. Sequential separation of the cation-π involving residues show that, long range contacts predominates in all the proteins studied. Lys and Arg prefers to be in helical structures. Of the cation-π interacting residues, Arg and Lys were in the exposed regions and the aromatic residues (Phe, Tyr and Trp) were in the buried and partially buried regions in the protein structures. Stabilization centers for these proteins showed that all the five residues found in cation-π interactions are important in locating one or more of such centers. On the whole, the results presented in this work will be very useful for further investigations on the specificity and selectivity of RNA binding proteins and also for their structural studies. © 2006 Elsevier B.V. All rights reserved.

International Journal of Biological Macromolecules

Influence of cation-π interactions on 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.

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