Vijay Tripathi

Molecular modeling and docking characterization of Dectin-1 (PAMP) receptor of Bubalus bubalis

Dectin-1, is a type II transmembrane receptor protein which contains a single extracellular CTLD (C-type lectin domain), stalk, transmembrane domain and an ITAM (immunoreceptor tyrosine-based activation motifs) in its cytoplasmic tail. Dectin-1 has the ability to recognize fungal β-glucans, which are carbohydrate PAMPs found predominantly in fungal cell walls. The recognition of fungal β-glucans by Dectin-1 helps in a variety of cellular responses, like host protection, such as fungal uptake and killing, and the production of inflammatory cytokines and chemokines. In this study we predicted the 3D (three dimensional) structure of Dectin-1 receptor based on homology modeling using MODELLER 9v8 software. The TMHMM server was used for the prediction of transmembrane helices. DALI, PROFUNC, Q-Site Finder, PINTS servers and PASS software used for the prediction of functional sites in the modeled Dectin-1 receptor. The docking investigation of Dectin-1 receptor with β-glucan suggests that ASP150, ASP113, GLY106, and GLU196 amino acids are the catalytic residues which form a shallow groove in the protein surface and bind to ligand β-glucan. We hope that this work will help in in-silico screening, structure-based design, and in understanding the structural basis of ligand binding to the Dectin-1 receptor.

Discriminating lysosomal membrane protein types using dynamic neural network

This work presents a dynamic artificial neural network methodology, which classifies the proteins into their classes from their sequences alone: the lysosomal membrane protein classes and the various other membranes protein classes. In this paper, neural networks-based lysosomal-associated membrane protein type prediction system is proposed. Different protein sequence representations are fused to extract the features of a protein sequence, which includes seven feature sets; amino acid (AA) composition, sequence length, hydrophobic group, electronic group, sum of hydrophobicity, R-group, and dipeptide composition. To reduce the dimensionality of the large feature vector, we applied the principal component analysis. The probabilistic neural network, generalized regression neural network, and Elman regression neural network (RNN) are used as classifiers and compared with layer recurrent network (LRN), a dynamic network. The dynamic networks have memory, i.e. its output depends not only on the input but the previous outputs also. Thus, the accuracy of LRN classifier among all other artificial neural networks comes out to be the highest. The overall accuracy of jackknife cross-validation is 93.2% for the data-set. These predicted results suggest that the method can be effectively applied to discriminate lysosomal associated membrane proteins from other membrane proteins (Type-I, Outer membrane proteins, GPI-Anchored) and Globular proteins, and it also indicates that the protein sequence representation can better reflect the core feature of membrane proteins than the classical AA composition.

Evolutionary analysis of circumsporozoite surface protein and merozoite surface protein-1 (CSP and MSP-1) sequences of malaria parasites

Malaria, one of the worlds most common diseases, is caused by the intracellular protozoan parasite known as Plasmodium. In this study, we have determined the evolutionary relationship of two single-copy proteins, circumsporozoite protein (CSP) and merozoite surface protein-1 (MSP-1), among Plasmodium species using various bioinformatics tools and softwares. These two proteins are major blood stage antigens of Plasmodium species. This study demonstrates that the circumsporozoite protein of Plasmodium falciparum shows similarity with Plasmodium cynomolgi and Plasmodium knowlesi. The merozoite surface protein-1 of Plasmodium coatneyi forms a monophyletic group with Plasmodium knowlesi, demonstrating their close relationship and these two species also reveal similarity between the human malaria Plasmodium vivax. This Plasmodium phylogenetic arrangement is evidently crucial to identify shared derived characters as well as particular adaptation of plasmodium species from inside and between monophyletic groups.

Synergic extraction of cobalt(II) from acetate buffers by mixtures of thenoyltrifluoroacetone and iso-propylether or tetrahydrofuran

Abstract The solvent extraction of cobalt(II) from sodium acetate-acetic acid buffers into mixtures of thenoyltrifluoroacetone (HTTA) with iso-propylether (IPE) or tetrahydrofuran (THF) in benzene has been studied. The extractable species has been identified as CoX2.IPE, CoX2.THF and CoX2.2THF (where HX = HTTA). The extraction constants are reported.

Organic Acids Produced by Self-Sustaining Coacervates in Presence of p-Nitroaniline and p-Phenylene-Diamine

Oleic and malonic acids were found in control samples while p-nitroaniline addition induced production of tricarballylic acid in eight and twelve days exposed samples. Fumaric and citric acids were found in sporadic instances. Addition of p-phenylene diamine to the mixture showed a degeneration process in organic acid production. In some cases production of fumaric acid was positive.

Molecular characterization and in-silico analysis of the tissue inhibitor of metalloproteinases-3 (TIMP-3) gene of canine mammary tumor

BACKGROUND Mammary tumors are the second most common tumors (after skin tumors) in female dogs (Canis lupus familiaris). Tissue Inhibitor of Metlloproteinases-3 (TIMP-3) is a matrix associated endogenous inhibitor of Matrix Metalloproteinases (MMPs). Cancer metastasis occurs as a result of imbalance between MMPs and TIMPs. TIMP-3 is involved significantly in regulation of MMPs as well as progression of canine mammary tumor. OBJECTIVE The present study was conducted to identify the structural and functional relationship between TIMP-3 and MMP which can aid in identifying the role of these proteins in canine mammary tumor. METHODS Molecular characterization of TIMP-3 protein was done by molecular biology techniques such as gene cloning and sequencing. The homology based model of TIMP-3 protein was created and verified with a variety of available computational techniques as well as molecular dynamics simulation. RESULTS The results indicated that predicted TIMP-3 protein structure of Canis lupus familiaris was reliable and more stable. The docking of TIMP-3 protein with MMP-2 and MMP-9 represents conformational structure of these two proteins which interact with each other but if misled canresult in the progression of tumor in canine. CONCLUSIONS The three dimensional structure of TIMP-3 was generated and its interactions with MMP-2 and MMP-9, demonstrates the role of key binding residues. Until now, no structural details were available for canine TIMP-3 proteins, hence this study will broaden the horizon towards understanding the structural and functional aspects of this proteins in canine.

Molecular modeling and phylogenetic analysis of Esx homeobox-1 protein of Bubalus bubalis

ESX-1 is an X-linked gene, which encodes for a homeobox protein. The ESX-1 expressed specifically in extra-embryonic tissues during development and in the adult testis as well. In the present study, we have predicted the three-dimensional structure of ESX-1 homeobox protein of Bubalus bubalis using homology modeling. The predicted model further explored for identification of ligand binding sites, which may be useful for understanding specific role in functional site residues during catalysis. This study also demonstrated the phylogenetic analysis of ESX-1 homeobox protein of B. bubalis with different similar species. The ESX-1 homeobox protein of B. bubalis has shown similarity with Bos taurus, Ovis aries and Capra hircus species.

Molecular phylogenetics and comparative modeling of MnSOD, an enzyme involved during environmental stress conditions in Oryza sativa

Superoxide dismutases are a class of enzymes that catalyze the dismutation of superoxide into oxygen and hydrogen peroxide. As such, they are an important antioxidant defense in nearly all cells exposed to oxygen. Superoxide dismutase (SOD) acts as first line of defense against oxidative and genetic stress. Manganese superoxide dismutase (MnSOD), found in mitochondria or peroxisomes, contains Mn (III) at the active site. The three dimensional structure of MnSOD of Oryza sativa is not yet available in protein data bank so we have predicted the structure model of O. sativa MnSOD using homology modeling. The predicted model can further be explored for identification of ligand binding sites which may be useful for understanding specific role in functional site residues during catalysis. This study also demonstrated that the phylogenetic analysis of O. sativa MnSOD protein with distinct dicot and monocot plant species. The MnSOD protein of O. sativa has shown similarity with both monocot and as well as dicot plant species.

In silico analysis of different generation β lactams antibiotics with penicillin binding protein-2 of Neisseria meningitidis for curing meningococcal disease

Neisseria meningitidis is a gram negative, diplococcic pathogen responsible for the meningococcal disease and fulminant septicemia. Penicillin-binding proteins-2 (PBPs) is crucial for the cell wall biosynthesis during cell proliferation of N. meningitidis and these are the target for β-lactam antibiotics. For many years penicillin has been recognized as the antibiotic for meningococcal disease but the meningococcus has seemed to be antibiotic resistance. In the present work we have verified the molecular interaction of Penicillin binding protein-2 N. meningitidis to different generation of β-lactam antibiotics and concluded that the third generation of β-lactam antibiotics shows efficient binding with Penicillin binding protein-2 of N. meningitidis. On the basis of binding efficiency and inhibition constant, ceftazidime emerged as the most efficient antibiotic amongst the other advanced β-lactam antibiotics against Penicillin-binding protein-2 of N. meningitidis.

Detergent effect on metabolic changes in microorganisms. A review.

Detergents contain a hydrophobic hydrocarbon structure and a hydrophilic group which may be anionic, cationic, or neutral. Detergents form stable emulsions and are capable of trapping lipid-soluble materials in the interior of the hydrophobic portion of the miscelles. Application of the knowledge of detergents to the discipline of microbiology would provide interesting and accurate data for further studies.