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Interaction of factor V B-domain acidic region with its basic region and with TFPI/TFPI2: Structural insights from molecular modeling studies. 因子V b结构域酸性区域与其碱性区域以及与TFPI/TFPI2的相互作用:来自分子模拟研究的结构见解。

International biology review Pub Date : 2017-05-21 DOI: 10.18103/IBR.V1I1.1334

Kanagasabai Vadivel, Y. Kumar, M. Bunce, R. Camire, M. Bajaj, S. P. Bajaj

{"title":"Interaction of factor V B-domain acidic region with its basic region and with TFPI/TFPI2: Structural insights from molecular modeling studies.","authors":"Kanagasabai Vadivel, Y. Kumar, M. Bunce, R. Camire, M. Bajaj, S. P. Bajaj","doi":"10.18103/IBR.V1I1.1334","DOIUrl":"https://doi.org/10.18103/IBR.V1I1.1334","url":null,"abstract":"BACKGROUND\u0000Factor V (FV) B-domain contains an acidic region (FV-AR2) and a basic region (FV-BR), which interact with each other and maintain FV in a procofactor form; removal of either region via deletion/proteolysis results in an active FVa molecule. Tissue factor pathway inhibitor type-1 (TFPI) and type-2 (TFPI2) each contain a C-terminus basic segment homologous to FV-BR; this region in TFPI (and predicted in TFPI2) binds to FV-AR2 in platelet FVa (that lacks FV-BR) with high affinity and inhibits FVa function.\u0000\u0000\u0000OBJECTIVES\u0000To understand molecular interactions between FV-AR2 with FV-BR, TFPI-BR and TFPI2-BR.\u0000\u0000\u0000METHODS\u0000Circular dichroism (CD) and molecular modeling approaches.\u0000\u0000\u0000RESULTS AND CONCLUSIONS\u0000CD experiments reveal the presence of ∼20% helical content in both FV-AR2 and FV-BR but each lacks beta-sheet. Predicted structures of FV-AR2 and FV-BR, obtained using threading (I-TASSER), are consistent with the CD data and have compact folds with hydrophobic residues in the interior and charged residues on the surface. Scores from QMEAN and ModFOLD servers indicate a very high probability for each structure to be native. Predicted models of Kunitz domain-3 of TFPI and TFPI2 each with C-terminal basic tail are consistent with known homologous structures. Docking experiments using ClusPro indicate that the acidic groove of FV-AR2 has high shape complementarity to accommodate the conserved basic residues in FV-BR (1002-RKKKK-1006), TFPI-BR (256-RKRKK-260) or TFPI2-BR (191-KKKKK-195). Further, similar electrostatic interactions occur in each case. These models, in the absence of experimentally determined structures, provide a guiding point for proper mutagenesis studies in FV, TFPI and TFPI2.","PeriodicalId":91700,"journal":{"name":"International biology review","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82982128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

International biology review Pub Date : 2017-05-01

Kanagasabai Vadivel, Yogesh Kumar, Matthew W Bunce, Rodney M Camire, Madhu S Bajaj, S Paul Bajaj

{"title":"Interaction of factor V B-domain acidic region with its basic region and with TFPI/TFPI2: Structural insights from molecular modeling studies.","authors":"Kanagasabai Vadivel, Yogesh Kumar, Matthew W Bunce, Rodney M Camire, Madhu S Bajaj, S Paul Bajaj","doi":"","DOIUrl":"","url":null,"abstract":"Background: Factor V (FV) B-domain contains an acidic region (FV-AR2) and a basic region (FV-BR), which interact with each other and maintain FV in a procofactor form; removal of either region via deletion/proteolysis results in an active FVa molecule. Tissue factor pathway inhibitor type-1 (TFPI) and type-2 (TFPI2) each contain a C-terminus basic segment homologous to FV-BR; this region in TFPI (and predicted in TFPI2) binds to FV-AR2 in platelet FVa (that lacks FV-BR) with high affinity and inhibits FVa function.Objectives: To understand molecular interactions between FV-AR2 with FV-BR, TFPI-BR and TFPI2-BR.Methods: Circular dichroism (CD) and molecular modeling approaches.Results and conclusions: CD experiments reveal the presence of ∼20% helical content in both FV-AR2 and FV-BR but each lacks beta-sheet. Predicted structures of FV-AR2 and FV-BR, obtained using threading (I-TASSER), are consistent with the CD data and have compact folds with hydrophobic residues in the interior and charged residues on the surface. Scores from QMEAN and ModFOLD servers indicate a very high probability for each structure to be native. Predicted models of Kunitz domain-3 of TFPI and TFPI2 each with C-terminal basic tail are consistent with known homologous structures. Docking experiments using ClusPro indicate that the acidic groove of FV-AR2 has high shape complementarity to accommodate the conserved basic residues in FV-BR (1002-RKKKK-1006), TFPI-BR (256-RKRKK-260) or TFPI2-BR (191-KKKKK-195). Further, similar electrostatic interactions occur in each case. These models, in the absence of experimentally determined structures, provide a guiding point for proper mutagenesis studies in FV, TFPI and TFPI2.","PeriodicalId":91700,"journal":{"name":"International biology review","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568831/pdf/nihms879927.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35352226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

On fuel choice and water balance during migratory bird flights. 候鸟飞行中燃料选择与水分平衡。

International biology review Pub Date : 2015-04-16 DOI: 10.18103/IBR.V0I1.58

C. Giulivi, J. Ramsey

引用次数: 7