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  • Inhibitor
  • In this study, we report four new crystal structures of human GGT1 (hGGT1) that show conformational changes within the active site as the enzyme progresses from the free enzyme to inhibitor-bound tetrahedral transition states and finally to the glutamate-bound structure prior to the release of this final product of the reaction. (osti.gov)
  • The serine-borate-bound hGGT1 crystal structure demonstrates that serine-borate occupies the active site of the enzyme, resulting in an enzyme-inhibitor complex that replicates the enzyme's tetrahedral intermediate/transition state. (osti.gov)
  • Our analysis finds a consensus among enzyme-bound conformations of the inhibitor, and suggests that favoring this conformation could be used to develop inhibitors with greater potency or isoform selectivity. (rsc.org)
  • Here, we have been able to quantitatively reconstruct the complete binding process of the enzyme-inhibitor complex trypsin-benzamidine by performing 495 molecular dynamics simulations of free ligand binding of 100 ns each, 187 of which produced binding events with an rmsd less than 2 Å compared to the crystal structure. (pnas.org)
  • The binding paths obtained are able to capture the kinetic pathway of the inhibitor diffusing from solvent (S0) to the bound (S4) state passing through two metastable intermediate states S2 and S3. (pnas.org)
  • Rather than directly entering the binding pocket the inhibitor appears to roll on the surface of the protein in its transition between S3 and the final binding pocket, whereas the transition between S2 and the bound pose requires rediffusion to S3. (pnas.org)
  • The ability to reconstruct by simple diffusion the binding pathway of an enzyme-inhibitor binding process demonstrates the predictive power of unconventional high-throughput molecular simulations. (pnas.org)
  • On the Mechanism of Action of Urocanase Observation of the Enzyme-Bound NAD+ -Inhibitor Adduct by 13C NMR Spectroscopy. (docme.ru)
  • my enzyme shows suicide inhibition, how do i identify the inhibitor? (protocol-online.org)
  • Kinetics
  • enzyme kinetics , rate of reaction and 2 more. (protocol-online.org)
  • In biochemistry, the Lineweaver-Burk plot (or double reciprocal plot) is a graphical representation of the Lineweaver-Burk equation of enzyme kinetics, described by Hans Lineweaver and Dean Burk in 1934. (wikipedia.org)
  • The Lineweaver-Burk plot was widely used to determine important terms in enzyme kinetics, such as Km and Vmax, before the wide availability of powerful computers and non-linear regression software. (wikipedia.org)
  • ligand
  • The understanding of protein-ligand binding is of critical importance for biomedical research, yet the process itself has been very difficult to study because of its intrinsically dynamic character. (pnas.org)
  • bZIP domain Comparison of nucleic acid simulation software DNA-binding domain Helix-loop-helix Helix-turn-helix HMG-box Leucine zipper Lexitropsin (a semi-synthetic DNA-binding ligand) Single-strand binding protein Zinc finger Created from PDB 1LMB Created from PDB 1RVA Travers, A. A. (1993). (wikipedia.org)
  • ions
  • Transglutaminase (TGase) enzymes catalyze the formation of covalent cross-links between protein-bound glutamines and lysines in a calcium-dependent manner, but the role of Ca(2+) ions remains unclear. (rcsb.org)
  • Upon proteolysis, the enzyme exothermally acquires two more Ca(2+) ions that activate the enzyme, are exchangeable and are functionally replaceable by other lanthanide trivalent cations. (rcsb.org)
  • Two-metal ion mechanism is one of the possible catalytic mechanisms of BamHI since the BamHI crystal structure has the ability to bind two metal ions at the active site, which is suitable for the classical two-metal ion mechanism to proceed. (wikipedia.org)
  • Two-metal ion mechanism is the use of two metal ions to catalyze the cleavage reaction of restriction enzyme. (wikipedia.org)
  • Many enzymes require calcium ions as a cofactor. (wikipedia.org)
  • homology
  • Docking experiments on HD1-A and HD1-B homology models revealed that the different compounds selectivity profiles could be addressed to different binding modes as observed for the reference compound SAHA. (nih.gov)
  • Amino acid sequencing of the 150-kDa band revealed sequence identity to carbamyl phosphate synthetase I (CPS I) and a high degree of homology to the related trifunctional enzyme known as CAD (for carbamyl phosphate synthetase, aspartate transcarbamylase, and dihydroorotase). (unl.edu)
  • The N-terminal half shares moderate homology with regions of calmodulin and M-calpain, suggesting that it may also bind calcium. (wikipedia.org)
  • distorts
  • The double reciprocal plot distorts the error structure of the data, and it is therefore unreliable for the determination of enzyme kinetic parameters. (wikipedia.org)
  • molecule
  • These structures are the first structures for any eukaryotic GGT that include a molecule in the active site covalently bound to the catalytic Thr-381. (osti.gov)
  • In biochemistry, allosteric regulation (or allosteric control) is the regulation of an enzyme by binding an effector molecule at a site other than the enzyme's active site. (wikipedia.org)
  • membranes
  • I. Chemical composition and enzyme content of plasma membranes isolated from rat liver. (springer.com)
  • Modulates the receptor complexes of the brain membranes, i.e. benzodiazepine, GABA, acetylcholine receptors by increasing their binding ability. (wikipedia.org)
  • reaction
  • in the model plant species Arabidopsis thaliana C-5 sterol desaturase catalyzes the reaction twice as fast with NADH while in S. cerevisiae the enzyme has little preference. (wikipedia.org)
  • peptide
  • The studies cited above lead to the eventual cloning of the human Formyl peptide receptor 1, a G protein coupled receptor that binds FMLP and other formylated oligopeptides to mediate their stimulatory actions on human and rabbit neutrophils. (wikipedia.org)
  • antioxidant
  • In general, increasing our knowledge about the antioxidant and antiatherogenic enzyme will assist in determining efficient preventive and therapeutic strategies in the management of human disorders, particularly vascular diseases and those which are associated with negative regulation of PON1. (eurekaselect.com)
  • replication
  • We present evidence that pTP binds to a multifunctional pyrimidine biosynthesis enzyme found at replication domains on the NM. (unl.edu)
  • kinetic
  • An estimation of the standard free energy of binding gives Δ G ° = -5.2 ± 0.4 kcal/mol (cf. the experimental value -6.2 kcal/mol), and a two-states kinetic model k on = (1.5 ± 0.2) × 10 8 M -1 s -1 and k off = (9.5 ± 3.3) × 10 4 s -1 for unbound to bound transitions. (pnas.org)
  • Computational
  • Computational methods to identify the DNA binding sequence specificity have been proposed to make a good use of the abundant sequence data in the post-genomic era. (wikipedia.org)