Immune peptides modelling of Culex pipiens sp by in silico methods.

Background: In the past 60 years, antibiotics have been critical in the fight against infectious diseases caused by bacteria and other microbes. Development of resistance to the antibiotics is emerging as a major public health issue which has resulted in the search for new antibiotics in order to maintain a pool of effective drugs at all times. Currently, there is a great interest in cationic peptides as antibiotics. These are reported to destroy the host cell membrane rather interacting with the other cell components, which may not face emergence of resistance. In mosquitoes, peptides like cecropin, defensin and gambicin reported to have inhibitory effect on bacteria, fungi and parasites. These peptides are well-characterized at both the biochemical and molecular level from Anopheles and Culex species, yet their 3D structures were not reported. Methods: Defensin, cecropin and gambicin immune peptides of Culex pipiens was characterised to have antiparasitic, antibacterial and antifungal activities. Since the crystal structure of defensin, cecropin and gambicin are not yet available their 3D structures were determined using homology modeling and Rosetta fragment insertion methods and were validated. Results: Stereo chemical evaluation indicated that defensin and gambicin showed that 100% residues of constructed model lie in the most favoured and allowed regions. Cecropin iso-forms A and B showed 100% while C showed 97.6% residues that lie in most favoured and allowed regions, which indicated quality models. Conclusion: Predicted model provide insight into their structure and aid in the development of novel antibiotic peptides.

Assessing the relationship among physicochemical properties of proteins with respect to hydrophobicity: A case study on AGC kinase superfamily.

Understanding the protein structures is crucial, as it is involved in every cellular activity. Several experimental techniques, such as X-Ray crystallography, nuclear magnetic resonance and electron microscopy are available to gain insight about the structure and function of a protein molecule. Gigantic data on protein structural and sequential information is deposited in various repositories regularly which provide us the scope for more theoretical studies. Hydrophobicity always plays a vital role in tertiary structure formation and behavior of a protein molecule. This study focuses on elucidating influence of several physicochemical properties on hydrophobicity of AGC kinase proteins. AGC kinase superfamily is selected due to its tremendous structural and functional variability and sequence data availability. A combined data mining and stochastic approach confirmed that out of 47 parameters, transmembrane tendency influences the target variable most, followed by percent buried residues, GRAVY (Grand Average Hydropathicity) and aliphatic index. Calculating the influence of different physicochemical parameters and their interrelation will aid tremendously in the future of protein science.