Characterization of the inhibition mechanism of a tissuefactor inhibiting single-chain variable fragment: a combined com
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ORIGINAL PAPER
Characterization of the inhibition mechanism of a tissue factor inhibiting single-chain variable fragment: a combined computational approach Jan-G Vermeulen 1,2
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Felicity Burt 3,4
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Esta van Heerden 1 & Leon du Preez-lategaan 1
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Muriel Meiring 2,4
Received: 13 September 2019 / Accepted: 11 March 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract The interaction of a single-chain variable fragment (scFv) directed against human tissue factor (TF) was predicted using an in silico approach with the aim to establish a most likely mechanism of inhibition. The structure of the TF inhibiting scFv (TFI-scFv) was predicted using homology modeling, and complementarity-determining regions (CDRs) were identified. The CDR was utilized to direct molecular docking between the homology model of TFIscFv and the crystal structure of the extracellular domains of human tissue factor. The rigid-body docking model was refined by means of molecular dynamic (MD) simulations, and the most prevalent cluster was identified. MD simulations predicted improved interaction between TFI-scFv and TF and propose the formation of stable complex for duration of the 600-ns simulation. Analysis of the refined docking model suggests that the interactions between TFI-scFv would interfere with the allosterical activation of coagulation factor VII (FVII) by TF. This interaction would prevent the formation of the active TF:VIIa complex and in so doing inhibit the initiation phase of blood coagulation as observers during in vitro testing. Keywords Single-chain variable fragment . Tissue factor . Coagulation . Homology modeling . Protein-protein docking . Molecular dynamics . Factor VII
Abbreviations CDR Complementarity-determining regions NPT Constant number, volume, and pressure
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00894-020-4350-7) contains supplementary material, which is available to authorized users. * Jan-G Vermeulen [email protected] 1
Department of Microbial, Biochemical and Food Biotechnology, Faculty of Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
2
Department of Haematology and Cell Biology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
3
Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
4
National Health Laboratory Service, Universitas, Bloemfontein, South Africa
NVT dsFv E. coli FVII FX Hv IgG Lv PME PBC pFv ps PSSM PDB scFv TF TF:FVIIa TFI-scFv VMD YASARA
Constant number, volume, and temperature Disulfide-stabilized variable fragments Escherichia coli Factor VII Factor X Heavy chain variable domains Immunoglobulin Light chain variable domains Particle mesh Ewald Periodic boundary conditions Permutated variable fragments Pico seconds Position-specific scoring matrix Protein data bank Single-chain variable fragment Tissue factor Tissue factor: factor VIIa complex Tissue factor inhibitor scFv Visual m
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