scholarly journals Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding

2008 ◽  
Vol 130 (9) ◽  
pp. 2817-2831 ◽  
Author(s):  
Robert Abel ◽  
Tom Young ◽  
Ramy Farid ◽  
Bruce J. Berne ◽  
Richard A. Friesner
Keyword(s):  
Ligand Binding ◽  
Active Site ◽  
Factor Xa

scholarly journals Human YKL-39 is a pseudo-chitinase with retained chitooligosaccharide-binding properties

2012 ◽  
Vol 446 (1) ◽  
pp. 149-157 ◽  
Author(s):  
Marianne Schimpl ◽  
Christina L. Rush ◽  
Marie Betou ◽  
Ian M. Eggleston ◽  
Anneliese D. Recklies ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Active Site ◽  
Elevated Serum ◽  
Serum Levels ◽  
Chitinase Activity ◽  
Active Site Residues ◽  
Binding Properties ◽  
Binding Partners ◽  
Tryptophan Residues

The chitinase-like proteins YKL-39 (chitinase 3-like-2) and YKL-40 (chitinase 3-like-1) are highly expressed in a number of human cells independent of their origin (mesenchymal, epithelial or haemapoietic). Elevated serum levels of YKL-40 have been associated with a negative outcome in a number of diseases ranging from cancer to inflammation and asthma. YKL-39 expression has been associated with osteoarthritis. However, despite the reported association with disease, the physiological or pathological role of these proteins is still very poorly understood. Although YKL-39 is homologous to the two family 18 chitinases in the human genome, it has been reported to lack any chitinase activity. In the present study, we show that human YKL-39 possesses a chitinase-like fold, but lacks key active-site residues required for catalysis. A glycan screen identified oligomers of N-acetylglucosamine as preferred binding partners. YKL-39 binds chitooligosaccharides and a newly synthesized derivative of the bisdionin chitinase-inhibitor class with micromolar affinity, through a number of conserved tryptophan residues. Strikingly, the chitinase activity of YKL-39 was recovered by reverting two non-conservative substitutions in the active site to those found in the active enzymes, suggesting that YKL-39 is a pseudo-chitinase with retention of chitinase-like ligand-binding properties.

scholarly journals The role of endothelium in factor Xa regulation: the effect of plasma proteinase inhibitors and hirudin

Blood ◽  
1988 ◽  
Vol 71 (5) ◽  
pp. 1321-1328 ◽  
Author(s):  
RC Friedberg ◽  
PO Hagen ◽  
SV Pizzo
Keyword(s):  
Active Site ◽  
Proteinase Inhibitor ◽  
Human Factor ◽  
Antithrombin Iii ◽  
Proteinase Inhibitors ◽  
Factor Xa ◽  
Proteolytic Degradation ◽  
Chromogenic Substrates ◽  
And Function

Abstract The role of endothelium in the inhibition of human factor Xa was studied in a plasma environment. Human factor Xa can bind to and function on bovine aortic endothelium in a manner similar to that of bovine factor Xa. Approximately 70% of the bound factor Xa is subject to inhibition by plasma proteinase inhibitors, and the remaining 30% is irreversibly bound as part of a 125 Kd membrane-associated complex not subject to proteolytic degradation. The proportion reversibly bound and its rate of release do not alter with changes in calcium, citrate, heparin, or active proteinase inhibitor concentrations. The principal plasma proteinase inhibitor of human factor Xa was antithrombin III, which accounted for 60% to 65% of factor Xa released from endothelium, with alpha 1-proteinase inhibitor inactivating 20% to 25% and alpha 2- macroglobulin approximately 15%. All of the reversibly bound factor Xa was identified in complex with one of these three proteinase inhibitors. The thrombin active-site inhibitor hirudin was found to markedly accelerate the displacement of reversibly bound factor Xa from the endothelium and to associate specifically with factor Xa without a loss of activity toward chromogenic substrates, perhaps accounting for a novel mechanism of anticoagulation.

scholarly journals The effect of haem ligands on the redox states of the hexa-haem nitrite reductase from Wolinella succinogenes

1990 ◽  
Vol 271 (1) ◽  
pp. 253-257 ◽  
Author(s):  
R S Blackmore ◽  
P M A Gadsby ◽  
C Greenwood ◽  
A J Thomson
Keyword(s):  
Ligand Binding ◽  
Nitrite Reductase ◽  
Active Site ◽  
Redox State ◽  
Stopped Flow ◽  
Ligand Binding Site ◽  
Wolinella Succinogenes ◽  
Redox States ◽  
Cyanide Binding

The nitrite reductase of Wolinella succinogenes containing six covalently bound haem groups has one haem group that will not reduce fully in the presence of excess Na2S2O4. The effect of the extrinsic ligands CO and cyanide on the redox state of this haem was studied by e.p.r. and magnetic c.d. spectroscopy. It was found that both ligands increased the extent of reduction of this haem group, and that in the case of CO binding the level of reduction was correlated with the extent of CO saturation of the enzyme. Stopped-flow studies of the effect of cyanide binding on the rate of dithionite reduction showed that the rate of reduction of the ligand-binding site was increased in the presence of cyanide. This suggests that reduction of the haem groups at the active site is thermodynamically unfavourable in the absence of an extrinsic ligand. The role of the ‘non-reducing’ haem group and the effect of ligands on this centre and on the rate of reduction are discussed in relation to the reduction of nitrite by this enzyme.

Abstract 30: Tissue Factor Pathway Inhibitor α Inhibits Prothrombinase via a Three-Step Mechanism

2017 ◽  
Vol 37 (suppl_1) ◽  
Author(s):  
Jeremy P Wood ◽  
Alan E Mast
Keyword(s):  
Active Site ◽  
Inhibitory Activity ◽  
Thrombin Generation ◽  
Platelet Rich Plasma ◽  
Factor Xa ◽  
Prothrombinase Complex ◽  
Factor Va ◽  
Direct Binding ◽  
Affinity Interaction

TFPIα inhibits early forms of the prothrombinase complex (factor Xa (FXa), factor Va (FVa)), though the inhibitory mechanism is not entirely understood. One step of inhibition is a high affinity interaction between a TFPIα C-terminal basic region (BR) (252-LIKTKRKRKK-261) and an acidic region (AR) present in FXa-activated and platelet-released forms of FVa. We investigated two additional potential mechanistic steps: (1) binding of the second Kunitz-type inhibitory domain (K2) of TFPIα to the FXa active site; and (2) the function of uncharged residues L252, I253, and T255 within the BR, which are evolutionarily conserved, suggesting they have activity. Direct inhibition of FXa was investigated using TFPIα with an altered K2 (TFPI-R107A) incapable of binding FXa. TFPI-R107A inhibited purified prothrombinase 17-fold weaker than TFPIα (IC50 = 30.6nM vs. 1.8nM) and did not inhibit FXa-initiated thrombin generation in platelet-rich plasma (PRP). Therefore, direct binding of FXa and K2 is required for efficient inhibition of prothrombinase under physiological conditions. Similarly, the role of L252, I253, and T255 was investigated by substituting them with alanine (TFPI-AAKA). The IC50 for prothrombinase inhibition by TFPI-AAKA was 10.4nM, and it had reduced inhibitory activity in PRP, revealing that these residues are also required for efficient prothrombinase inhibition. The role of L252, I253, and T255 was further probed using the peptide LIKTKRKRKK, which inhibited purified prothrombinase (IC50 = 1.0μM) and thrombin generation in PRP at 1μM. AAKAKRKRKK had very little activity in either assay (~20% prothrombinase inhibition with 225μM peptide), but bound the FVa AR equivalently to LIKTKRKRKK (K d = 5.9nM and 6.0nM, respectively). Thus, the basic residues are responsible for AR binding, while a second step, mediated by L252-T255, is necessary for inhibitory activity. These residues may be necessary for displacement of FXa from FVa, as proposed by Bunce et al. We propose that prothrombinase inhibition by TFPIα involves three steps: (1) the TFPIα BR basic residues bind the FVa AR; (2) residues L252-T255 block prothrombinase assembly; and (3) K2 binds the FXa active site. All three steps are required for physiologic inhibition of prothrombinase by TFPIα.

scholarly journals The role of endothelium in factor Xa regulation: the effect of plasma proteinase inhibitors and hirudin

Blood ◽  
1988 ◽  
Vol 71 (5) ◽  
pp. 1321-1328
Author(s):  
RC Friedberg ◽  
PO Hagen ◽  
SV Pizzo
Keyword(s):  
Active Site ◽  
Proteinase Inhibitor ◽  
Human Factor ◽  
Antithrombin Iii ◽  
Proteinase Inhibitors ◽  
Factor Xa ◽  
Proteolytic Degradation ◽  
Chromogenic Substrates ◽  
And Function

The role of endothelium in the inhibition of human factor Xa was studied in a plasma environment. Human factor Xa can bind to and function on bovine aortic endothelium in a manner similar to that of bovine factor Xa. Approximately 70% of the bound factor Xa is subject to inhibition by plasma proteinase inhibitors, and the remaining 30% is irreversibly bound as part of a 125 Kd membrane-associated complex not subject to proteolytic degradation. The proportion reversibly bound and its rate of release do not alter with changes in calcium, citrate, heparin, or active proteinase inhibitor concentrations. The principal plasma proteinase inhibitor of human factor Xa was antithrombin III, which accounted for 60% to 65% of factor Xa released from endothelium, with alpha 1-proteinase inhibitor inactivating 20% to 25% and alpha 2- macroglobulin approximately 15%. All of the reversibly bound factor Xa was identified in complex with one of these three proteinase inhibitors. The thrombin active-site inhibitor hirudin was found to markedly accelerate the displacement of reversibly bound factor Xa from the endothelium and to associate specifically with factor Xa without a loss of activity toward chromogenic substrates, perhaps accounting for a novel mechanism of anticoagulation.

scholarly journals Role of conformational change and K-path ligands in controlling cytochrome c oxidase activity

2017 ◽  
Vol 45 (5) ◽  
pp. 1087-1095 ◽  
Author(s):  
Jian Liu ◽  
Carrie Hiser ◽  
Shelagh Ferguson-Miller
Keyword(s):  
Cytochrome C ◽  
Ligand Binding ◽  
Cytochrome C Oxidase ◽  
Conformational Change ◽  
Conformational Changes ◽  
Active Site ◽  
Mutant Form ◽  
Gating Mechanism ◽  
Proton Uptake

Given the central role of cytochrome c oxidase (CcO) in health and disease, it is an increasingly important question as to how the activity and efficiency of this key enzyme are regulated to respond to a variety of metabolic states. The present paper summarizes evidence for two modes of regulation of activity: first, by redox-induced conformational changes involving the K-proton uptake path; and secondly, by ligand binding to a conserved site immediately adjacent to the entrance of the K-path that leads to the active site. Both these phenomena highlight the importance of the K-path in control of CcO. The redox-induced structural changes are seen in both the two-subunit and a new four-subunit crystal structure of bacterial CcO and suggest a gating mechanism to control access of protons to the active site. A conserved ligand-binding site, first discovered as a bile salt/steroid site in bacterial and mammalian oxidases, is observed to bind an array of ligands, including nucleotides, detergents, and other amphipathic molecules. Highly variable effects on activity, seen for these ligands and mutations at the K-path entrance, can be explained by differing abilities to inhibit or stimulate K-path proton uptake by preventing or allowing water organization. A new mutant form in which the K-path is blocked by substituting the conserved carboxyl with a tryptophan clarifies the singularity of the K-path entrance site. Further study in eukaryotic systems will determine the physiological significance and pharmacological potential of ligand binding and conformational change in CcO.

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