Molecular modeling, docking and dynamic simulations of growth hormone receptor (GHR) of Labeo rohita.

Growth hormones (GH) have diverse functions like growth promotion, metabolism, appetite, reproduction and social behavior in vertebrates, which is mediated through the growth hormone receptor (GHR). This work was aimed to analyze structural features, homology modeling and molecular docking of Labeo rohita GHR protein. A physicochemical characteristic, like molecular weight was 67.2 kDa and hydropathicity was 0.336. Protein modeling and structure confirmation of L. rohita GHR protein showed 92.7% residues are in the favored region. Selection of ligands and molecular docking shown Melengestrol and Riboflavin ligand showed uppermost binding energy values -7.8 and -7.3 kcal/mol. Molecular interactions describe conventional hydrogen bonding of Melengestrol was observed with VAL94, GLU97, GLU95, TRP57, PHE33, THR34, PRO35, ASP36, PRO37, ARG49, GLY292, LYS291, ILE290, ALA287, LYS289 residues. Riboflavin hydrogen bonds interaction was at PRO37, ASP36, PRO35, THR34, ARG49, SER144, VAL443, GLN442, PRO284, ASP294, ILE285, PRO286, SER408, ALA287, GLY292, LYS291, ILE290, PRO288, LYS287. Molecular dynamics simulation outcomes revealed that complex 2 (Riboflavin and GHR protein) is better than complex1 (Melengestrol and GHR protein). Overall, the results of the present work lead identification of novel molecules that may be agonistic of growth hormone receptor protein and can be used to surge growth in fish. Communicated by Ramaswamy H. Sarma.

Structural analysis, molecular docking and molecular dynamics simulations of G-protein-coupled receptor (kisspeptin) in fish.

Kisspeptins are neuropeptide that has emerged as an essential gatekeeper for reproduction and onset of puberty in higher vertebrates including fish. In present study, structural analysis, molecular docking and molecular dynamics simulations of kisspeptin receptor (kiss2r) were carried out, which is a G-protein-coupled receptor. An open reading frame of kiss2r is 1101 bp encoding a putative protein of 366 amino acids. Secondary structure protein consists of alpha helix 69.70%, beta-turn 2%, disordered 18% and 43% transmembrane helix. Sub-cellular localization and gene ontology revealed kiss2r protein is maximum localized in the plasma membrane (99.1%) with score of 4.958 and gene ontology analysis showed molecular function of 89.8%, biological process 30.6% and cellular component 41.2%. Homology modeling and structure validation of kiss2r confirm 97.5% residues are in the favored region and 2.5% residues are in the allowed region. Virtual screening of ligands and molecular docking revealed 2-(4-(2-Carboxyethyl) phenethylamino) 5'-N-ethylcarboxamidoadenosine and N-ethyl-5'-carboxamido adenosine ligand exhibited highest binding energy values 9.437 and 7.476 kcal/mol. Molecular interactions depict conventional hydrogen bonding with GLU197 THR198 GLN288 HIS297 LYS303 and TYR313 residues. Molecular dynamic simulation results revealed that complex 2 (N-ethyl-5'-carboxamido adenosine and kiss2r protein) is better than complex 1 (2-(4-(2-Carboxyethyl) phenethylamino)-5'-N-ethylcarboxamidoadenosine and kiss2r protein) and its connotation in drug designing. The outcome of this work sheds light on the protein modeling, molecular docking and virtual screening of agonist ligands against kiss2 and thus may significantly contribute in designing and optimizing therapeutic strategies to cure various reproductive dysfunctions in fish. Abbreviations3-Dthree-dimensionala.aAmino acidBLASTBasic local alignment search toolAMBERAssisted Model Building with Energy RefinementCDScoding sequenceCIDCompound identification numberDOPEDiscrete optimized protein energyGnRHGonadotropin-releasing hormoneGPR54G protein-coupled receptor 54GROMACSGroningen Machine for Chemicals SimulationsGUIGraphical user interfaceHPGHypothalamic-pituitary-gonadalKiss1rkisspeptin1 receptorkiss2rkisspeptin2 receptorMEGAMolecular Evolutionary Genetics Analysis.MDMolecular dynamicsNCBINational Center for Biotechnology InformationORFOpen reading framePDBProtein Data BankRMSDRoot-mean-square deviationSBDDStructure-based drug designingTMDsTransmembrane domainsYASARAYet Another Scientific Artificial Reality ApplicationCommunicated by Ramaswamy H. Sarma.

Genome-Wide identification of doublesex and Mab-3-Related transcription factor (DMRT) genes in nile tilapia (oreochromis niloticus).

Doublesex and Mab-3-related transcription factor (DMRT) gene family is extensively known for its contribution in sex determination and differentiation across phyla. Here we report the identification of five DM (doublesex and mab-3) domain genes in the Nile tilapia which includes DMRT1, DMRTa2, DMRT2a, DMRT2b and DMRT3a. The full-length sequence of DMRT genes ranges from 3526 (DMRTA2) to 1471bp (DMRT1) which encode putative proteins series from 469 to 372 amino acids. All the DMRT proteins contained at least one conserved DNA-binding DM domain. Sub-cellular localization and gene ontology revealed DMRT1 protein is maximum localized in nuclear region and gene ontology analysis showed the molecular function of 48.2%, biological process 43.6% and cellular component 25%. Chromosomal location and synteny analysis displayed that DMRT genes mostly cluster linkage group 12. Altogether, our findings provide vital genomic information for future studies of biochemical, physiological, and phylogenetic studies on DMRT genes in teleost.