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.

Sudha Ramaiah

Department of Bio-Sciences

School of Bio Sciences and Technology

Vellore Campus

Vaideeswaran S

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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Bioorganic Chemistry

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Arginine and Lysine interactions with p residues in metalloproteins

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

Journal of Microbial & Biochemical Technology

Role of Cation-π Interactions in the Structural Stability of Bacterial Exotoxins

We have investigated the roles played by C-H⋯π interactions in RNA binding proteins. There was an average of 55 C-H⋯π interactions per protein and also there was an average of one significant C-H⋯π interaction for every nine residues in the 59 RNA binding proteins studied. Main-chain to side-chain C-H⋯π interactions is the predominant type of interactions in RNA binding proteins. The donor atom contribution to C-H⋯π interactions was mainly from Phe, Tyr, Trp, Pro, Gly, Lys, His and Ala residues. The acceptor atom contribution to main-chain to side-chain C-H⋯π and side-chain to side-chain C-H⋯π interactions was mainly from Phe and Tyr residues. On the contrary, the acceptor atoms of Trp residues contributed to all the four types of C-H⋯π interactions. Also, Trp contributed both donor and acceptor atoms in main-chain to side-chain, main-chain to side-chain five-member aromatic ring and side-chain to side-chain C-H⋯π interactions. The secondary structure preference analysis of C-H⋯π interacting residues showed that, Arg, Gln, Glu, His, Ile, Leu, Lys, Met, Phe and Tyr preferred to be in helix, while Ala, Asp, Cys, Gly, Trp and Val preferred to be in strand conformation. Long-range C-H⋯π interactions are the predominant type of interactions in RNA binding proteins. More than 50% of C-H⋯π interacting residues had a higher conservation score. Significant percentage of C-H⋯π interacting residues had one or more stabilization centers. Seven percent of the theoretically predicted stabilizing residues were also involved in C-H⋯π interactions and hence these residues may also contribute additional stability to RNA binding proteins. © 2007 Elsevier B.V. All rights reserved.

International Journal of Biological Macromolecules

Investigations on C–H⋯π interactions in 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.

Journal	Data powered by TypesetBioorganic Chemistry
Publisher	Data powered by TypesetElsevier BV
ISSN	0045-2068
Open Access	0