Structure of Human Des(1-45) Factor Xa at 2·2 Å Resolution

Padmanabhan, K.; Tulinsky, A.; Park, Chang H.; Bode, Wolfram; Huber, Robert; Blankenship, Dale T.; Cardin, Alan D.; Kisiel, W

doi:10.1006/jmbi.1993.1441

Cited by 416 publications

(411 citation statements)

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“…Molecular models of the inhibitors were constructed using SYBYL (Tripos Associate) and model building performed using O [26]. Coordinates of the inhibitors were transferred to those of factor Xa [14] (PDB code lhcg.pdb) and human c~-thrombin [27] (PDB code lfph.pdb) through superposition of conserved residues around the active sites of trypsin, factor Xa and thrombin using the programme O [26]. Data collection and refinement statistics are given in Table 1.…”

Section: Methodsmentioning

confidence: 99%

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Crystal structures of factor Xa specific inhibitors in complex with trypsin: structural grounds for inhibition of factor Xa and selectivity against thrombin

1995

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Crystal structures of DX9065a and a related bisamidino-aryl inhibitor specific for the blood-clotting factor Xa have been solved in complex with bovine ~-trypsin to a resolution of 1.9 A. Each inhibitor exhibits an extended conformation along the active site, in contrast to the compact folded structures observed for thrombin specific inhibiturs. Few direct contacts (predominantly in the S1 pocke0 are made between trypsin and the inhibitors. Transfer of the inhibitors to the active site of factor Xa suggests a three-site interaction: salt bridge formation at the base of the primary specificity pocket, extensive hydrophobie surface burial and a weak electrostatic interaction between the distal basic component of the inhibitor and an electronegative cavity of factor Xa formed by three backbone carbonyl oxygens. Additivity of these three interactions is the basis for the observed strong inhibition of factor Xa and provides a framework for the design of novel factor Xa inhibitors. A propionic acid group of the inhibitor would clash with the thrombin specific '60-insertion loop', thus conferring selectivity against thrombin.

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Section: Methodsmentioning

confidence: 99%

“…The recent crystallographic structure determination of factor Xa [14] provides an opportunity to apply a structure-based approach to the search for specific inhibitors. However, the active site of factor Xa is blocked in the crystal form examined and no crystals of inhibited factor Xa have been reported as yet.…”

Section: Introductionmentioning

confidence: 99%

Crystal structures of factor Xa specific inhibitors in complex with trypsin: structural grounds for inhibition of factor Xa and selectivity against thrombin

1995

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“…FVIIa contains four domains. The serine protease (SP) and epidermal growth factor (EGF-2) domains in the crystal structure of human factor Xa [5] are highly homologous in primary structure to those found in FVIIa. The NMR structures of the EGF-1 domain of human factors IX and X [6,7] provide a close model for the EGF-I domain in FVIIa.…”

Section: Introductionmentioning

confidence: 99%

Factor VIIa and the extracellular domains of human tissue factor form a compact complex: A study by X‐ray and neutron solution scattering

et al. 1995

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The four-domain structure of human factor Vlla and the two-domain structure of tissue factor form a tight complex to initiate blood coagulation. By solution scattering, the mean X-ray and neutron radii of gyration Re (which determine macromolecular elongation) were found to be 3.25 nm, 2.13 nm and 3.14 nm (+ 0.13 rim) for factor VIIa, the extracellular region of tissue factor and their complex in that order. The mean cross-sectional radii of gyration Rxs were 1.33 rim, 0.56 nm and 1.42 nm ( + 0.13 nm) in that order. The mean lengths were 10.3 nm, 7.7 nm and 10.2 nm in that order. The data show that, in solution, the free proteins have extended domain structures, and the complex is formed by a compact side-by-side alignment of the two proteins along their long axes. The high binding affinity of tissue factor for factor Vlla may thus be accounted for by the occurrence of many intermolecular contacts in the complex.

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“…Medium-resolution NMR solution structures have been described for human EGF (Cooke et al, 1987;Hommel et al, 1992) and murine EGF (Montelione et al, 1986(Montelione et al, , 1987(Montelione et al, , 1992Kohda & Inagaki, 1992a, 1992b, and for several homologous proteins including hTGFa (Kline et al, 1990;Harvey et al, 1991;Moy et al, 1993) and the EGF-like domains from bovine coagulation factor X (Selander-Sunnerhagen et al, 1992; Energy refinement of mECF and hTGFa NMR structures Ullner et al, 1992), human factor 1X (Huang et al, 1991;Baron et al, 1992), human tissue-type plasminogen activator (Smith et al, 1994), and human urokinase-type plasminogen activator (Hansen et al, 1994). X-ray crystal structures of the EGF-like domains of human E-selectin (Graves et al, 1994;Weis, 1994) and human factor Xa (Padmanabhan et al, 1993) have also been determined recently.…”

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confidence: 99%

Simulated annealing with restrained molecular dynamics using CONGEN: Energy refinement of the NMR solution structures of epidermal and type‐α transforming growth factors

et al. 1996

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The new functionality of the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168;Bassolino-Klimas D et al., 1996, Protein Sci5:593-603) has been applied for energy refinement of two previously determined solution NMR structures, murine epidermal growth factor (mEGF) and human type-a transforming growth factor (hTGFa). A summary of considerations used in converting experimental NMR data into distance constraints for CONGEN is presented. A general protocol for simulated annealing with restrained molecular dynamics is applied to generate NMR solution structures using CONGEN together with real experimental NMR data. A total of 730 NMR-derived constraints for mEGF and 424 NMR-derived constraints for hTGFa were used in these energy-refinement calculations. Different weighting schemes and starting conformations were studied to check and/or improve the sampling of the low-energy conformational space that is consistent with all constraints. The results demonstrate that loosened (i.e., "relaxed") sets of the EGF and hTGFa internuclear distance constraints allow molecules to overcome local minima in the search for a global minimum with respect to both distance restraints and conformational energy. The resulting energy-refined structures of mEGF and hTGFa are compared with structures determined previously and with structures of homologous proteins determined by NMR and X-ray crystallography.

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Structure of Human Des(1-45) Factor Xa at 2·2 Å Resolution

Cited by 416 publications

References 0 publications

Crystal structures of factor Xa specific inhibitors in complex with trypsin: structural grounds for inhibition of factor Xa and selectivity against thrombin

Crystal structures of factor Xa specific inhibitors in complex with trypsin: structural grounds for inhibition of factor Xa and selectivity against thrombin

Factor VIIa and the extracellular domains of human tissue factor form a compact complex: A study by X‐ray and neutron solution scattering

Simulated annealing with restrained molecular dynamics using CONGEN: Energy refinement of the NMR solution structures of epidermal and type‐α transforming growth factors

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