Molecular characterization and computational structure prediction of activin receptor type IIB in aseel and broiler chicken
The present study was formulated to characterize and comprehend the molecular structural characteristics of ACTRIIB receptor in Aseel and control broiler (CB) populations. The full length coding sequence (1539 bp) of the receptor was amplified, cloned, sequenced and analyzed using bioinformatic tool...
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| Veröffentlicht in: | Research in veterinary science 2019-10, Vol.126, p.139-149 |
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| creator | Vishnu, P Guru Bhattacharya, T K Bhushan, Bharat Kumar, Pushpendra Chatterjee, R N Paswan, Chandan Prasad, A Rajendra Divya, D Dushyanth, K |
| description | The present study was formulated to characterize and comprehend the molecular structural characteristics of ACTRIIB receptor in Aseel and control broiler (CB) populations. The full length coding sequence (1539 bp) of the receptor was amplified, cloned, sequenced and analyzed using bioinformatic tools. The physico chemical properties of protein and structural features like secondary structure, solvent accessibility and disorder regions were computed. The 3D structure was predicted by I-TASSER and evaluated by Ramachandran Plot and tools under Structural Analysis and Verification Server. The nucleotides differences between CB and Aseel were c. [156G > A; 210 T > C; 493C > T; c.520G > C; 665A > C; 686G > A; 937C > G; 1011A > C; 1130A > G; 1208 T > A; 1326 T > C; 1433 T > C]. The amino acid substitutions between CB and Aseel were p. [(Pro165Ser; Glu174Gln; Gln222Pro; Ser229Asn; His313Asp; Gln377Arg; Val403Asp; and Ile478Thr)]. While, the silent changes includes p. [(Lys53=; Glu71=; Leu337=; Asp442=)]. The molecular weight of mature protein was predicted to be 55.51 kDa and 57.80 kDa in Aseel and CB, respectively. The higher rank 3D model had a C-score of -1.60 in Aseel and - 1.41 in CB, while the estimated TM-score (0.54 ± 0.14) and RMSD (5.8 ± 1.2 Å) were found to be similar in Aseel and CB. Among the 512 residues, >90% were in favored region, 4.7% in allowed region and |
| doi_str_mv | 10.1016/j.rvsc.2019.08.025 |
| format | Article |
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The full length coding sequence (1539 bp) of the receptor was amplified, cloned, sequenced and analyzed using bioinformatic tools. The physico chemical properties of protein and structural features like secondary structure, solvent accessibility and disorder regions were computed. The 3D structure was predicted by I-TASSER and evaluated by Ramachandran Plot and tools under Structural Analysis and Verification Server. The nucleotides differences between CB and Aseel were c. [156G > A; 210 T > C; 493C > T; c.520G > C; 665A > C; 686G > A; 937C > G; 1011A > C; 1130A > G; 1208 T > A; 1326 T > C; 1433 T > C]. The amino acid substitutions between CB and Aseel were p. [(Pro165Ser; Glu174Gln; Gln222Pro; Ser229Asn; His313Asp; Gln377Arg; Val403Asp; and Ile478Thr)]. While, the silent changes includes p. [(Lys53=; Glu71=; Leu337=; Asp442=)]. The molecular weight of mature protein was predicted to be 55.51 kDa and 57.80 kDa in Aseel and CB, respectively. The higher rank 3D model had a C-score of -1.60 in Aseel and - 1.41 in CB, while the estimated TM-score (0.54 ± 0.14) and RMSD (5.8 ± 1.2 Å) were found to be similar in Aseel and CB. Among the 512 residues, >90% were in favored region, 4.7% in allowed region and <1.5% in disallowed region in both Aseel and CB. The pattern of contact map was comparable in Aseel and CB. The Hydrogen bond plots of the Aseel and CB shared similar secondary structure pattern. The ACTRIIB protein was predicted to interact with ACVR1B, ACVR1C, INHBA, SMAD 1,2,5,7 & 9 and BMPR1A&B. Clustal and phylogenetic analysis implied that both the lines were closely related and formed a sub cluster with in avian cluster. The current research provides insights about structural and functional aspects of the receptor and also aids in understanding the evolutionary history of ACTRIIB.</description><identifier>ISSN: 0034-5288</identifier><identifier>EISSN: 1532-2661</identifier><identifier>DOI: 10.1016/j.rvsc.2019.08.025</identifier><identifier>PMID: 31491670</identifier><language>eng</language><publisher>England: Elsevier Limited</publisher><subject>Activin ; Activin Receptors, Type II - genetics ; Activin Receptors, Type II - metabolism ; ActRIIb protein ; Amino Acid Sequence ; Amino acids ; Animals ; Base Sequence ; Birds ; Chemical properties ; Chickens - genetics ; Cloning ; Clusters ; Computer applications ; Experiments ; Gene Expression Regulation ; Genetic Variation ; Hydrogen bonds ; Kinases ; Ligands ; Molecular structure ; Molecular weight ; Nucleotides ; Organic chemistry ; Phylogenetics ; Phylogeny ; Poultry ; Predictions ; Protein Conformation ; Protein structure ; Proteins ; Secondary structure ; Smad protein ; Structural analysis ; Structure-function relationships ; Thermal cycling ; Three dimensional models ; Veterinary medicine</subject><ispartof>Research in veterinary science, 2019-10, Vol.126, p.139-149</ispartof><rights>Copyright © 2019 Elsevier Ltd. All rights reserved.</rights><rights>2019. Elsevier Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c282t-89c3b000780106ffc8029775aa95e94b3e030c0685fa5c2674cec0922b41360f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31491670$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Vishnu, P Guru</creatorcontrib><creatorcontrib>Bhattacharya, T K</creatorcontrib><creatorcontrib>Bhushan, Bharat</creatorcontrib><creatorcontrib>Kumar, Pushpendra</creatorcontrib><creatorcontrib>Chatterjee, R N</creatorcontrib><creatorcontrib>Paswan, Chandan</creatorcontrib><creatorcontrib>Prasad, A Rajendra</creatorcontrib><creatorcontrib>Divya, D</creatorcontrib><creatorcontrib>Dushyanth, K</creatorcontrib><title>Molecular characterization and computational structure prediction of activin receptor type IIB in aseel and broiler chicken</title><title>Research in veterinary science</title><addtitle>Res Vet Sci</addtitle><description>The present study was formulated to characterize and comprehend the molecular structural characteristics of ACTRIIB receptor in Aseel and control broiler (CB) populations. The full length coding sequence (1539 bp) of the receptor was amplified, cloned, sequenced and analyzed using bioinformatic tools. The physico chemical properties of protein and structural features like secondary structure, solvent accessibility and disorder regions were computed. The 3D structure was predicted by I-TASSER and evaluated by Ramachandran Plot and tools under Structural Analysis and Verification Server. The nucleotides differences between CB and Aseel were c. [156G > A; 210 T > C; 493C > T; c.520G > C; 665A > C; 686G > A; 937C > G; 1011A > C; 1130A > G; 1208 T > A; 1326 T > C; 1433 T > C]. The amino acid substitutions between CB and Aseel were p. [(Pro165Ser; Glu174Gln; Gln222Pro; Ser229Asn; His313Asp; Gln377Arg; Val403Asp; and Ile478Thr)]. While, the silent changes includes p. [(Lys53=; Glu71=; Leu337=; Asp442=)]. The molecular weight of mature protein was predicted to be 55.51 kDa and 57.80 kDa in Aseel and CB, respectively. The higher rank 3D model had a C-score of -1.60 in Aseel and - 1.41 in CB, while the estimated TM-score (0.54 ± 0.14) and RMSD (5.8 ± 1.2 Å) were found to be similar in Aseel and CB. Among the 512 residues, >90% were in favored region, 4.7% in allowed region and <1.5% in disallowed region in both Aseel and CB. The pattern of contact map was comparable in Aseel and CB. The Hydrogen bond plots of the Aseel and CB shared similar secondary structure pattern. The ACTRIIB protein was predicted to interact with ACVR1B, ACVR1C, INHBA, SMAD 1,2,5,7 & 9 and BMPR1A&B. Clustal and phylogenetic analysis implied that both the lines were closely related and formed a sub cluster with in avian cluster. The current research provides insights about structural and functional aspects of the receptor and also aids in understanding the evolutionary history of ACTRIIB.</description><subject>Activin</subject><subject>Activin Receptors, Type II - genetics</subject><subject>Activin Receptors, Type II - metabolism</subject><subject>ActRIIb protein</subject><subject>Amino Acid Sequence</subject><subject>Amino acids</subject><subject>Animals</subject><subject>Base Sequence</subject><subject>Birds</subject><subject>Chemical properties</subject><subject>Chickens - genetics</subject><subject>Cloning</subject><subject>Clusters</subject><subject>Computer applications</subject><subject>Experiments</subject><subject>Gene Expression Regulation</subject><subject>Genetic Variation</subject><subject>Hydrogen bonds</subject><subject>Kinases</subject><subject>Ligands</subject><subject>Molecular structure</subject><subject>Molecular weight</subject><subject>Nucleotides</subject><subject>Organic chemistry</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Poultry</subject><subject>Predictions</subject><subject>Protein Conformation</subject><subject>Protein structure</subject><subject>Proteins</subject><subject>Secondary structure</subject><subject>Smad protein</subject><subject>Structural analysis</subject><subject>Structure-function relationships</subject><subject>Thermal cycling</subject><subject>Three dimensional models</subject><subject>Veterinary medicine</subject><issn>0034-5288</issn><issn>1532-2661</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpdkU9vFCEYh4mxsWv1C3gwJF68zPgCM_w5alN1kzZe9EwY9p3IOjuMwDRp_fJlt9WDJwJ5fj9eeAh5w6BlwOSHfZtus285MNOCboH3z8iG9YI3XEr2nGwARNf0XOtz8jLnPQB0jKkX5FywzjCpYEP-3MQJ_Tq5RP1Pl5wvmMK9KyHO1M076uNhWctp7yaaS1p9WRPSJeEu-BMWR1pj4TbMNKHHpcREy92CdLv9ROuhy4jTqWxIMUx4vCn4Xzi_ImejmzK-flovyI_PV98vvzbX375sLz9eN55rXhptvBjq7EoDAzmOXgM3SvXOmR5NNwgEAR6k7kfXey5V59GD4XzomJAwigvy_rF3SfH3irnYQ8gep8nNGNdsOdfSdB3jpqLv_kP3cU316ZUSoKRS9eMqxR8pn2LOCUe7pHBw6c4ysEc1dm-PauxRjQVtq5oaevtUvQ4H3P2L_HUhHgBK0owB</recordid><startdate>201910</startdate><enddate>201910</enddate><creator>Vishnu, P Guru</creator><creator>Bhattacharya, T K</creator><creator>Bhushan, Bharat</creator><creator>Kumar, Pushpendra</creator><creator>Chatterjee, R N</creator><creator>Paswan, Chandan</creator><creator>Prasad, A Rajendra</creator><creator>Divya, D</creator><creator>Dushyanth, K</creator><general>Elsevier Limited</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QG</scope><scope>7QP</scope><scope>7QR</scope><scope>7T5</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U7</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>201910</creationdate><title>Molecular characterization and computational structure prediction of activin receptor type IIB in aseel and broiler chicken</title><author>Vishnu, P Guru ; 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The full length coding sequence (1539 bp) of the receptor was amplified, cloned, sequenced and analyzed using bioinformatic tools. The physico chemical properties of protein and structural features like secondary structure, solvent accessibility and disorder regions were computed. The 3D structure was predicted by I-TASSER and evaluated by Ramachandran Plot and tools under Structural Analysis and Verification Server. The nucleotides differences between CB and Aseel were c. [156G > A; 210 T > C; 493C > T; c.520G > C; 665A > C; 686G > A; 937C > G; 1011A > C; 1130A > G; 1208 T > A; 1326 T > C; 1433 T > C]. The amino acid substitutions between CB and Aseel were p. [(Pro165Ser; Glu174Gln; Gln222Pro; Ser229Asn; His313Asp; Gln377Arg; Val403Asp; and Ile478Thr)]. While, the silent changes includes p. [(Lys53=; Glu71=; Leu337=; Asp442=)]. The molecular weight of mature protein was predicted to be 55.51 kDa and 57.80 kDa in Aseel and CB, respectively. The higher rank 3D model had a C-score of -1.60 in Aseel and - 1.41 in CB, while the estimated TM-score (0.54 ± 0.14) and RMSD (5.8 ± 1.2 Å) were found to be similar in Aseel and CB. Among the 512 residues, >90% were in favored region, 4.7% in allowed region and <1.5% in disallowed region in both Aseel and CB. The pattern of contact map was comparable in Aseel and CB. The Hydrogen bond plots of the Aseel and CB shared similar secondary structure pattern. The ACTRIIB protein was predicted to interact with ACVR1B, ACVR1C, INHBA, SMAD 1,2,5,7 & 9 and BMPR1A&B. Clustal and phylogenetic analysis implied that both the lines were closely related and formed a sub cluster with in avian cluster. The current research provides insights about structural and functional aspects of the receptor and also aids in understanding the evolutionary history of ACTRIIB.</abstract><cop>England</cop><pub>Elsevier Limited</pub><pmid>31491670</pmid><doi>10.1016/j.rvsc.2019.08.025</doi><tpages>11</tpages></addata></record> |
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| ispartof | Research in veterinary science, 2019-10, Vol.126, p.139-149 |
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| subjects | Activin Activin Receptors, Type II - genetics Activin Receptors, Type II - metabolism ActRIIb protein Amino Acid Sequence Amino acids Animals Base Sequence Birds Chemical properties Chickens - genetics Cloning Clusters Computer applications Experiments Gene Expression Regulation Genetic Variation Hydrogen bonds Kinases Ligands Molecular structure Molecular weight Nucleotides Organic chemistry Phylogenetics Phylogeny Poultry Predictions Protein Conformation Protein structure Proteins Secondary structure Smad protein Structural analysis Structure-function relationships Thermal cycling Three dimensional models Veterinary medicine |
| title | Molecular characterization and computational structure prediction of activin receptor type IIB in aseel and broiler chicken |
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