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Research & Reviews: A Journal of Bioinformatics

Contents

1. In silico 3D Structure Modeling and Analysis of Galactoside 2-alpha-L-fucosyltransferase 1 Jasnaik Danish I., L. Hariharan, Gupta Pramodkumar P.

2. Insilico Approach to Inhibit Over Expression of CaSm Gene to Arrest Over Expressed Human LSm1 Protein in Pancreatic Carcinoma Cell Ansuman Mahato

3. Insilico Study Showing the Chemical Properties and Interaction between Auxin-Binding Protein and Auxin-Responsive GH3-8 Protein in Rice Pranati Swain, Lambodar Behera

4. Insilico 3D Structure Modeling and Docking to Find Potent Inhibitors for Thrombocytopenia Pranati Swain, Jasnaik D

5. Comparative Structural Analysis of Dep1 Protein in Oryza Sativa Pranati Swain, Lambodar Behera

Research & Reviews: A Journal of Bioinformatics ISSN: 2393-8722 (online) Volume 1, Issue 3 www.stmjournals.com

In silico 3D Structure Modeling and Analysis of Galactoside 2-alpha-L-fucosyltransferase 1 Jasnaik Danish I., L. Hariharan, Gupta Pramodkumar P.* Department of Biotechnology and Bioinformatics, D Y Patil University, CBD Belapur, Navi Mumbai, Maharashtra, India Abstract A rare group of blood known as Bombay blood group was discovered in Mumbai formerly known as Bombay more than five decades ago, which lacks A, B, AB and O type. A theoretical model of human Galactoside 2-alpha-L-fucosyltransferase 1/FUT gene is predicted. The model was generated by application of homology modeling and structure prediction approaches. As the template homology to the query sequence is too low a multiple online modeling and prediction server is used. The output has a several challenge with poor homology and predicted results, finally a scratch server and HHpred server output showed some promising results with 100% query coverage model generation and validated using ProSA and PROCHECK. Keywords: In silico, homology modeling, galactoside 2-alpha-L-fucosyltransferase, FUT 1

Research & Reviews: A Journal of Bioinformatics ISSN: 2393-8722 (online) Volume 1, Issue 3 www.stmjournals.com

Insilico Approach to Inhibit Over Expression of CaSm Gene to Arrest Over Expressed Human LSm1 Protein in Pancreatic Carcinoma Cell Ansuman Mahato* Department of Biotechnology, Garden City College, Bangalore, India Abstract Small nuclear ribonucleoproteins (snRNPs) are particles that are found in the nucleus of eukaryotic cells. They consist of one RNA (snRNA) associated with one or more proteins. snRNPs are involved in a wide variety of functions including pre-mRNA splicing (e.g., U1, U2, U4â&#x20AC;&#x201C;6, U11, U12, U4ATAC, U6ATAC snRNPs and transspliced leader RNPs), histone mRNA 39 end processing (U7 snRNP). The snRNA U6 (unlike U1, U2, U4 and U5) does not associate with the Sm proteins. In 1999 heteromer protein was identified that binds only to U6, and made up of seven proteins which are homologous to the Sm proteins. These proteins were denoted LSm (like Sm) proteins (LSm1, LSm2, LSm3, LSm4, LSm5, LSm6, and LSm7), LSm8 protein identified after that. The cancer associated Sm-like protooncogene mRNA has been found to be overexpressed in the majority of pancreatic adenocarcinomas and is necessary for the transformed phenotype in pancreatic cancer cell lines. Human Lsm1, also called CaSm (cancer-associated Sm-like) was originally identified based on elevated expression in pancreatic cancer, in several cancer-derived cell lines as well as in metastatic tumors. CaSm is also required to maintain the transformed phenotype of prostate cancer cells and it can function as a oncogene in that over-expression of this gene. In this present study some of cancer drugs like S-adenosyl-L-Homocystein, S-adenosyl-L-Homoselenocystein, Adenosyl-ornithine and S-adenosylmethionine were tested through bioinformatics tools to check whether they could suppress the overexpression of LSm1 protein.

Keywords: Protooncogene, spliceosome, CaSm, human LSm, adenocarcinomas, ribonucleoproteins

Research & Reviews: A Journal of Bioinformatics ISSN: 2393-8722 (online) Volume 1, Issue 3 www.stmjournals.com

Insilico Study Showing the Chemical Properties and Interaction between Auxin-Binding Protein and Auxin-Responsive GH3-8 Protein in Rice Pranati Swain*, Lambodar Behera Central Rice Research Institute, Cuttack, Odisha, India Abstract Auxin plays an important role in the plant growth. There are different auxin binding and auxin responsive proteins which bind and interact with auxin hormone and helps for plant development. Two different rice proteins considered for study, one protein binding to auxin and another is the auxin responsive protein. The Nuclear magnetic resonance (NMR) crystallographic structures of both the proteins are not available at Protein Data Bank (PDB). So the tertiary structures were generated by using homology modeling method. Model visualization was performed by using PyMol and discovery studio visualiser which showed the helix, sheets and turns. The model evaluation, backbone conformation and optimization were done by using PROCHECK Saves server, Atomic Non-Local Environment Assessment (ANOLEA). The Risk Management Services (RMS) values, potential energy after and before the energy minimisation was studied by using Yet Another Scientific Artificial Reality Application (YASARA) tool and SWISS-PDB viewer. The protein-protein interaction was studied by using HEX server. The protein models which were generated showed similarity with zea-mays and vititsvinifera, respectively.

Keywords: Auxin-binding protein, Auxin-responsive GH3-8 protein, homology modeling, sterio-chemical evaluation

Research & Reviews: A Journal of Bioinformatics ISSN: 2393-8722 (online) Volume 1, Issue 3 www.stmjournals.com

Insilico 3D Structure Modeling and Docking to Find Potent Inhibitors for Thrombocytopenia Pranati Swain1*, Jasnaik D2 1

Bioinformatics, Orissa University of Agriculture and Technology, Orissa, India School of Biotechnology and Bioinformatics, DY Patil University, Maharashtra, India

Abstract Lots of people are getting affected by various kinds of auto-immune disease in their day to day life and thrombocytopenia is one of them, which occurs due to lack of thrombocytes or platelets. Various kinds of vaccines, drugs are used to stop the disease, but the effect varies from person to person depending upon the immune system. In thrombocytopenia disease the integrin beta protein of human affects the personâ&#x20AC;&#x2122;s own immune system leading in the less production of thrombocytes. Here the main objective of the study is to analyse the interaction between the disease stimulating proteins and the ligands or drugs bind to the protein at its active site. The structural prediction along with the stereo-chemical evaluation of protein helped to understand the function of the protein. The active sites of protein show the ligand binding regions. 14 different drugs were considered for the study. Out of which AC1NS627 drug showed best interaction with the protein as its binding perfectly at the active site of the protein. So from the study, we can conclude that AC1NS627 is the better drug which can be used for inhibiting the activity of integrin beta protein.

Keywords: In silico homology modeling, thrombocytopenia, molecular docking

Research & Reviews: A Journal of Bioinformatics ISSN: 2393-8722 (online) Volume 1, Issue 3 www.stmjournals.com

Comparative Structural Analysis of Dep1 Protein in Oryza Sativa Pranati Swain*, Lambodar Behera Central Rice Research Institute, Cuttack, Odisha, India Abstract Dense erect panicle protein is an important protein of Oryza sativa which helps in high grain production. The objective is to find out the structure of protein and to represent the best 3D model by using insilico analysis. In Oryza sativa the dep1 is homologous to crystal structure of expb1 of zea mays, a beta-expansion and group-1 pollen allergen from maize which is responsible for plant growth and development. The following study was obtained by predicting the 3D structure of dep1 in Oryza sativau using homology modeling concept with the help of bioinformatic tools i.e., SWISS-MODEL, CPHmodels3.2 Server and PHYRE2. The 3D structures were further evaluated and steriochemical analysis was done by using RAMPAGE server for Ramachandran plot analysis. The best model was selected on the basis of Z-score and 3D-1D score.

Keywords: Oryza sativa, dense panicle1 protein, homology modeling, best structure prediction