Evolutionary and Molecular Aspects of Indian Tomato Leaf Curl Virus Coat Protein

Sivakumar Prasanth Kumar, Saumya K. Patel, Ravi G. Kapopara,
Yogesh T. Jasrai, and Himanshu A. Pandya

Department of Bioinformatics, Applied Botany Center, University School of Sciences, Gujarat University, Ahmedabad 380 009, India
Department of Botany, University School of Sciences, Gujarat University, Ahmedabad 380 009, India

Tomato leaf curl disease (ToLCD) is manifested by yellowing of leaf lamina with upward leaf curl, leaf distortion, shrinking of the leaf surface, and stunted plant growth caused by tomato leaf curl virus (ToLCV). In the present study, we explored the evolutionary and molecular prospects of viral coat protein derived from an isolate of Vadodara district, Gujarat (ToLCGV-[Vad]), India. We found that the amino acids in coat protein required for systemic infection, viral particle formation, and insect transmission to host cells were conserved amongst Indian strains. Phylogenetic studies on Indian ToLCV coat proteins showed evolutionary compatibility with other viral taxa. Modeling of coat protein revealed a topology similar to characteristic Geminate viral particle consisting of antiparallel β-barrel motif with N-terminus α-helix. The molecular interaction of coat protein with the viral DNA required for encapsidation and nuclear shuttling was investigated through sequence- and structure-based approaches. We further emphasized the role of loops in coat protein structure as molecular recognition interface.

Download full text here:
http://www.hindawi.com/journals/ijpg/2012/417935/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529866/

http://www.academia.edu/2243782/Evolutionary_and_Molecular_Aspects_of_Indian_Tomato_Leaf_Curl_Virus_Coat_Protein

Biocomputational Analysis of Filaggrin Sequence Repeats for Rheumatoid Arthritis

Sivakumar Prasanth Kumar 1, Saumya K. Patel 1, Yogesh T. Jasrai *1, Himanshu A. Pandya 1 and Pappu Srinivasan 2

1. Department of Bioinformatics, Applied Botany Centre (ABC), University School of Sciences, Gujarat University, Ahmedabad - 380 009, India
2. Department of Bioinformatics, Science Block, Alagappa University, Karaikudi - 630 004, India.

Electronic Journal of Biology, 2012, Vol. 8(2): 29-33

You may access the complete text here: http://www.ejbio.com/pps/2012/29.pdf


Abstract

Anti-citrullinated antibodies are autoantibodies detected in the blood of rheumatoid arthritis (RA) patients in the early stage. These autoantibodies recognize an epitope of citrullinated peptides found on the surface of filaggrin protein and are crossreactive in immune response. Since the expression of filaggrin protein is associated with autoantibodies secretion, it may act as a potential serological marker for the detection of RA in early stage. In the present study, the contribution of filaggrin sequence repeats towards antigenicity was investigated using bioinformatic approaches. The electrostatic potential of citrullinated filaggrin repeats and its antigenicity was found to be the prominent factors for invoking such an immune response.

Keywords: Anti-citrullinated antibodies, epitope, filaggrin sequence repeats, rheumatoid arthritis, electrostatic potential, antigenicity.

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Exploring the polymerase activity of chikungunya viral non structural protein 4 (nsP4) using molecular modeling, epharmacophore and docking studies

S. Prasanth Kumar, Ravi G. Kapopara, Mehul I. Patni, Himanshu A. Pandya, Yogesh T. Jasrai and Saumya K. Patel. Exploring the Polymerase Activity of Chikungunya Viral non structural Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking Studies.International Journal of Pharmacy and Life Sciences 3(6): 1752-1765.


Abstract



Chikungunya viral RNA-dependent RNA polymerase (RdRp) activity is conferred by non structural protein 4
(nsp4), an important protein target towards the development of antiviral compounds. The present study deals about the development of homology model of nsP4 followed by molecular docking with known RdRp inhibitors
experimented in Hepatitis C virus (HCV), HIV-1, Paramyxovirus, etc. The predicted catalytic site and two allosteric binding sites were docked with nucleosidic and non-nucleosidic inhibitors. The best top five scoring ligands were selected based upon the interaction profiles and a common pharmacophore was developed. Further, RNA templateprimer complex was docked within the template tunnel of modeled nsP4 to study the mode of polymerase activity.


Key-Words: Chikungunya, nsP4, RdRp, Docking, Pharmacophore, Polymerase activity



Download the article


http://www.ijplsjournal.com/issues%20PDF%20files/june_2012/5.pdf

My published results now in APBS homepage in Graphical format

Dears,

I am very pleased to disclose that my published results in graphical format has been uploaded by Dr. Nathan Baker in his APBS homepage. Thank You Very Much, Sir. 

Grant of 100% Clean Award to miRNA to siRNA Program

Thanks to the Softpedia Database and its Editorial Team for considering the miRNA to siRNA Program to be available as a freeware, added to the database and granted "100% Clean Award". Special thanks for also including Protein Stability Program.

Grant ward can be viewed here:

http://www.softpedia.com/get/Science-CAD/miRNA-to-siRNA.shtml

Download this program here:

http://www.softpedia.com/get/Science-CAD/miRNA-to-siRNA.shtml

Normal Mode Analysis of Breast Cancer Resistance Protein

The following preview shows you the trajectories observed in normal mode analysis using Amber94 force field with the homology model of Breast Cancer Resistance Protein (BCRP)

Video is copyright. Please ask a concern from me before using it.

Exploring the Polymerase Activity of Chikungunya Viral non structural Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking Studies

This study will appear in International Journal of Pharmacy and Life Sciences in June Edition.


Exploring the Polymerase Activity of Chikungunya Viral non structural
Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking
Studies


S. Prasanth Kumar, Ravi G. Kapopara, Yogesh T. Jasrai and Himanshu A. Pandya
Department of Bioinformatics, ABC, Gujarat University, Ahmedabad- 380009.

Graphical Abstract

S. Prasanth Kumar, Ravi G. Kapopara, Mehul I. Patni, Himanshu A. Pandya, Yogesh T. Jasrai* and Saumya K. Patel. Exploring the Polymerase Activity of Chikungunya Viral non structural Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking Studies. International Journal of Pharmacy and Life Sciences 3(6): pp. 1752-1765.

Chikungunya viral RNA-dependent RNA polymerase (RdRp) activity is conferred by non

structural protein 4 (nsp4), an important protein target towards the development of antiviral

compounds. The present study deals about the development of homology model of nsP4

followed by molecular docking with known RdRp inhibitors experimented in Hepatitis C virus

(HCV), HIV-1, Paramyxovirus, etc. The predicted catalytic site and two allosteric binding sites

were docked with nucleosidic and non-nucleosidic inhibitors. The best top five scoring ligands

were selected based upon the interaction profiles and a common pharmacophore was developed.

Copyrighted Material. Write a concern to the corresponding author for getting the
coordinates.Contact: prasanthbioinformatics@gmail.com

Grant of 100% Clean Award to Protein Stability Program

Thanks to the Softpedia Database and its Editorial Team for considering the Protein Stability Program to be available as a freeware, added to the database and granted "100% Clean Award"

Grant ward can be viewed here:
http://www.softpedia.com/progClean/Protein-Stability-Clean-210115.html 

Full text article is available here:
http://iioablett.pitt.edu/ojs/index.php/iioablett/article/view/12 

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Energy minimization of PfCRT (Plasmodium falsciparum chloroquine resistant transporter)

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CpGP Dynamics – The Dynamics of CpG Island and Promoter to Validate Nucleosomal Gene Expression

S. Prasanth Kumar
Department of Bioinformatics, Alagappa University, Karaikudi- 630003, India.
prasanthbioinformatics@gmail.com

Abstract

Computational prediction of nucleosome positioning relies upon in vitro and in vivo experimental outcome such as sequence positioning and exclusion signatures, structural thermodynamic details, histone-DNA interaction models, etc. On the other hand, CpG island and promoter prediction programs are available which depends upon the algorithm built by the predictive power of trained experimental datasets from sequencing projects. “CpGP dynamics –The dynamics of CpG island and promoter to validate nucleosomal gene expression” is a web based program which predicts the nucleosome- positioning (NP) and exclusion (NE) signatures in the user provided nucleotide sequence and presents a graphical output. It also utilizes the sequence positions of CpG island and promoter predicted by third-party programs as input to generate graphical sequence output. These two graphical outputs can be merged to discriminate the more accurate sequence positions of CpG island and promoter from a number of likelihood predictions. The program is freely accessible at http://www.cpgpdynamics.webs.com. 

Keywords: Nucleosome Positioning and Exclusion, CpG island, Promoter, Bioinformatics.

Full text will be available at:

http://www.sersc.org/journals/IJBSBT/vol4_no2/2.pdf

(Copyright has been retained by SERSC)

Emergence of TYLCV: Bioinformatic Analysis

Soon, we will publish Bioinformatic Analysis of coat protein from TYLCV.