• Moreover, this process is reversible so that, if the pmf drops below the threshold needed to power ATP synthesis, the motor has the ability to reverse and, in some bacterial species, operates primarily as a proton pump driven by ATP hydrolysis. (elifesciences.org)
  • The Sec machinery (general secretory pathway) translocates polypeptides in an unfolded, linear configuration energetically driven by ATP hydrolysis and the proton motive force (pmf). (tamu.edu)
  • The G12A mutation reduces intrinsic K-Ras GTP hydrolysis by an unexplained mechanism. (rcsb.org)
  • 10. Structure-function analyses reveal the mechanism of the ARH3-dependent hydrolysis of ADP-ribosylation. (nih.gov)
  • The value of D2O(V) of 1.16 ( 0.14 for hydrolysis of cellotriose suggests that the large direct effect expected for proton transfer from the nucleophilic water through a water chain (Grotthus mechanism) is offset by an inverse effect arising from reversibly breaking the short, tight hydrogen bond between D221 and D175 before catalysis. (hud.ac.uk)
  • The structures of the Michaelis complexes with natural and synthetic substrates, and of the transient covalent arabinofuranosyl-enzyme intermediate represent two stable states in the double displacement mechanism, and allow thorough examination of the catalytic mechanism. (huji.ac.il)
  • The mechanism of GTP hydrolysis by Gα and rate acceleration by GAPs are also considered. (elsevierpure.com)
  • The AZ 3146 kinase activity assay mechanistic research also will abide by the stepwise response mechanism recommended for natural formylthiocholine hydrolysis [20,21] and Formula (6) provides kinetic hurdle, = 99.3 kJ?mol?1. (buyresearchchemicalss.net)
  • Analogous towards the mechanism from the AChE-catalyzed procedure, the oxime-mediated AcSCh+ hydrolysis includes two successive stagesfirst, the oximolysis, that's, the acetylation stage seen as a the stepwise system (Body 4a) and second, the deacetylation stage, seen as a the concerted HO? (buyresearchchemicalss.net)
  • Structural transitions within human Rad51 nucleoprotein filaments. (nih.gov)
  • Taken together, our results indicate that nucleotide hydrolysis by human Rad51 triggers a reversible structural transition leading to filaments with reduced helical pitch. (nih.gov)
  • Molecular dynamics simulations further indicate that G304 and G305 undergo pronounced structural changes as residue 306 undergoes a transition between 'in' and 'out' conformations. (anl.gov)
  • In 2015, Dr. Samara transitioned to a Staff Scientist Position at NIDCR/NIH, where she is now an Earl Stadtman Investigator and Chief of the Structural Biochemistry Unit. (nih.gov)
  • Although it is rarely possible to acquire experimentally-determined structures of each step along an enzyme reaction coordinate, 7A1 Fab' antigen binding fragment was able to be co-crystallized with substrate, a transition state analog (TSA), both products and heptaethylene glycol. (stanford.edu)
  • [ 28 ] Clever chemistry was used to create haptens known as transition state analogs in order to mimic the intermediate, usually unstable, chemical structures that lead to the hydrolysis reaction. (medscape.com)
  • The transition-state of dynamin's GTP hydrolysis reaction is required for fission. (nih.gov)
  • Hydrolysis may cause additional conformational changes in the super-constricted polymer, and polymer disassembly to further promote the fission reaction. (nih.gov)
  • We have also investigated different configurations of the ground state that are important in the proton transfer reaction. (iisc.ac.in)
  • Conserved residues in the motor domain have been positioned within the framework provided by the recent crystal structures, thus helping to define those residues involved in actin and ATP binding, in hydrolysis and in conformational change. (embl.de)
  • In the present study, the process of proton transfer between hydroxyl and imidazole groups, a model of the crucial step in the hydrolysis of RNA by the enzymes of the RNase A family, is investigated at the quantum mechanical level of density functional theory and perturbation theory at the MP2 level. (iisc.ac.in)
  • The results, in general, indicate the formation of a short-strong hydrogen bond and the formation of a low barrier transition state for the proton transfer model of the enzyme. (iisc.ac.in)
  • Here we report that the assembly of hexameric Rpt ring of the 19 S regulatory particle (RP) requires nucleotide binding but not ATP hydrolysis. (elsevierpure.com)
  • In the G12A K-Ras-GTP complex, the switch I region undergoes a significant reorganization such that the Tyr32 side chain points towards the GTP-binding pocket and forms a hydrogen bond to the GTP γ-phosphate, effectively stabilizing GTP in its precatalytic state, increasing the activation energy required to reach the transition state and contributing to the reduced intrinsic GTPase activity of G12A K-Ras mutants. (rcsb.org)
  • Docking crystal structures of dynamin domains into our 'super-constricted' density map shows that only the GTPase domain ground state conformation fits. (nih.gov)
  • RGS proteins are multi-functional, GTPase-accelerating proteins that promote GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signaling pathways. (medchemexpress.com)
  • Mutations that affect substrate carboxyl binding (R71N) and transition state stabilization (R63N) also yielded wild-type aspartoacylase protein levels and undetectable aspartoacylase activity. (nih.gov)
  • the side chains of TyrH50, ArgH52, ArgH58 and IleH56 adopt conformations between those found in the transition state and those in the substrate-bound state, and the side chain of TyrL94 has partial stabilization and a different rotamer (Figure 2d). (stanford.edu)
  • D175 is shown to affect protonation of D221 and to contribute to the electrostatic stabilization of the partial positive charge in the transition state. (hud.ac.uk)
  • The two catalytic residues are 4.7 Å apart, and together with other conserved residues contribute to the stabilization of the oxocarbenium ion-like transition state via charge delocalization and specific protein-substrate interactions. (huji.ac.il)
  • Acetyl-l-lysine also requires activation by metal coordination and a hydrogen bond with catalytic tyrosine Y306, which also functions in transition state stabilization. (anl.gov)
  • Thus, the G304A and G305A substitutions likely compromise the position and conformational changes of Y306 required for substrate activation and transition state stabilization. (anl.gov)
  • Hydrolysis of acetylcholine catalyzed by acetylcholinesterase (AChE), one of the most efficient enzymes in nature, occurs at the base of a deep and narrow active center gorge. (proteopedia.org)
  • Enzymes that are highly specific for hydrolysis of the D-ribose 1 phosphate bond of ADP-D-ribose 1''-phosphate to produce ADP-D-ribose and phosphate ion. (nih.gov)
  • The original paper reference is cited below: * * Development of models of active ion transport for whole-cell * modelling: cardiac sodium-potassium pump as a case study, N. * P. Smith and E. J. Crampin, 2004, Progress in Biophysics and * Molecular Biology PubMed ID: 15142754 * * 15-state State Diagram * * [[Image file: smith_2004.png]] * * The 15 states of the original model. (nih.gov)
  • How the positively charged nitrogen in the acetylcholine molecule is attracted to the ionic site on acetylcholinesterase, and hydrolysis is catalyzed at the esteric site to form choline and acetic acid. (cdc.gov)
  • Proteins incapable of transitioning to the compressed state were also highly resistant to dissociation from the DNA. (nih.gov)
  • RGS proteins markedly reduce the lifespan of GTP-bound alpha subunits by stabilising the G protein transition state. (medchemexpress.com)
  • Three flexible switch elements (switches I-III) in Gα subunits adopt different conformations in the Gα-GDP vs. Gα-GTP states and provide surfaces for conformation-dependent interaction of Gα with Gβγ complexes, RGS proteins, and effector molecules. (viquepedia.com)
  • The maps generated show that, after exposure to MgATP, E. coli ATP synthase adopts a different conformation with a catalytic subunit changing conformation substantially and the ε C-terminal domain transitioning via an intermediate 'half-up' state to a condensed 'down' state. (elifesciences.org)
  • These structures, supported by binding and inhibition data obtained on the same complexes, reveal the successive positions and orientations of the substrates bound to the peripheral site and proceeding within the gorge toward the active site, the conformations of the presumed transition state for acylation and the acyl-enzyme intermediate, and the positions and orientations of the dissociating and egressing products. (proteopedia.org)
  • The main element geometric variables for the reactant complicated (RC), transition condition (TS), intermediate (IM) and item complex (Computer) from the acetylation and deacetylation levels of AcSCh+ hydrolysis are detailed in Desk S1. (buyresearchchemicalss.net)
  • The hydrolysis of N -acyl-β-sultams generally occurs with ring opening and S-N fission in contrast to the C-N fission observed in analogous acyclic N -acyl sulfonamides. (rsc.org)
  • However, the α-substituted 4-isopropylidene β-sultam is relatively unreactive and undergoes alkaline hydrolysis with C-N fission leaving the strained 4-membered β-sultam ring intact. (rsc.org)
  • These results suggest that kinesin binding and ATP hydrolysis may cause a long-range state transition in the MT, increasing its affinity for kinesin toward its plus end. (rupress.org)
  • Kinesin is a molecular motor that transports organelles along a microtubule (MT) using the energy of ATP hydrolysis. (rupress.org)
  • Possible sources of the hidden dissipation were explored by analyzing the Langevin dynamics of the probe, which incorporates the two-state Markov stepper as a kinesin model. (elsevierpure.com)
  • Then you saw step-by-step how chymotrypsin catalyzes peptide hydrolysis. (hstalks.com)
  • It catalyzes the hydrolysis of the terminal both alpha-1,3-linked and alpha-1,6-linked mannoses from the high-mannose oligosaccharide GlcNAc(Man)5(GlcNAc)2 to yield GlcNAc(Man)3(GlcNAc)2(GlcNAc, N-acetylglucosmine), which is the committed step of complex N-glycan synthesis. (unl.edu)
  • Significant conformational changes were observed along the 7A1-catalyzed cocaine hydrolysis pathway, but are generally limited to some active site key residues and ligands themselves. (stanford.edu)
  • In the substrate cocaine-bound state, TyrH97 is fully ordered, TyrL94 displays some partial occupancy to accommodate the two side-chain rotamers of TrpH47, while the active site retains a modified "open" form (Figure 2b). (stanford.edu)
  • [ 30 ] Around the same time, Janda reported that the position of the linker in the cocaine transition state hapten was important, such that a linker attached in the methyl ester position rather than the tropane nitrogen gave better results, and having an amide group in the carbon chain of the linker was even more effective. (medscape.com)
  • K-Ras, a molecular switch that regulates cell growth, apoptosis and metabolism, is activated when it undergoes a conformation change upon binding GTP and is deactivated following the hydrolysis of GTP to GDP. (rcsb.org)
  • We report X‐ray crystallographic and 19F NMR studies of the G‐protein RhoA complexed with MgF3−, GDP, and RhoGAP, which has the mutation Arg85′Ala. When combined with DFT calculations, these data permit the identification of changes in transition state (TS) properties. (whiterose.ac.uk)
  • The mutation in the Walker B motif which impairs ATP hydrolysis does not affect Rpt ring formation. (elsevierpure.com)
  • The structure of myosin is known, but the actin-binding site is not well defined, and the mechanisms by which actin activates ATP hydrolysis by myosin, and myosin moves relative to the actin filament, developing force, are not fully understood. (embl.de)
  • The reactivity of MXenes toward water we've demonstrated not only changes the common perception about resistance of titanium carbide to hydrolysis in ambient conditions, but also points out the striking differences in chemical properties between bulk and 2-D forms of the same material," says Mochalin. (newswise.com)
  • Mochalin and lead author Huang, who works in Mochalin's research group at Missouri S&T, discuss their findings in a paper titled " Hydrolysis of 2D Transition Metal Carbides (MXenes) in Colloidal Solutions ," which was published today (January 16, 2019) in the American Chemical Society journal Inorganic Chemistry . (newswise.com)
  • To arrive at their "water-only" conclusion, Huang and Mochalin systematically tested the hydrolysis and chemical stability of MXenes Ti 3 C 2 T x and Ti 2 CT x in water and non-aqueous colloidal solutions exposed to oxygen and/or inert gas environments in different combinations, as the example shown in the image. (newswise.com)
  • This arginine residue is thought to facilitate GTP hydrolysis by stabilizing a transition-state pentavalent phosphate and is the same arginine in G s α covalently modified by cholera toxin resulting in constitutive signal activation. (viquepedia.com)
  • Antibody CDR loop movements (up to 2.3 ) and large side-chain movements (up to 9 ) alter the antibody active site from "open" to "closed" to "open" (with the approximate size changes from 320 to 500 3) for the substrate, transition state and product states, respectively. (stanford.edu)
  • The contributions of solvation and vibrational energies corresponding to the reactant, the transition state and the product configurations are also evaluated. (iisc.ac.in)
  • The computational evaluation of HOC-assisted AcSCh+ hydrolysis recommended the concerted system using the kinetic hurdle (= 0.1 M. Oximolysis Response Ester Nucleophile = 0.1 M and 25 C (Body S5). (buyresearchchemicalss.net)
  • However, there exists very little molecular detail of the specific interactions or the kinetic transitions between sub-states required for transport. (tamu.edu)
  • We have solved the structure of a transition-state-defective mutant, K44A, assembled on a lipid template, at 12.5 Å resolution using cryo-electron microscopy. (nih.gov)
  • A Rad51 mutant deficient in ATP hydrolysis is locked into an extended conformation that is incapable of transitioning to a compressed filament. (nih.gov)
  • Incorporation of a Walker B mutant Rpt subunit abrogates the ATPase activity of the 19 S RP, suggesting that failure of the mutant Rpt to undergo the conformational transition from an ATP-bound to an ADP-bound state impairs conformational changes in the other five wild-type Rpts in the Rpt ring. (elsevierpure.com)
  • They are a few atom-thick sheets with the structures of transition-metal carbides and nitrides. (newswise.com)
  • It is unclear whether Rad51 can transition directly between these different oligomeric structures without disassembling first into monomers. (nih.gov)
  • To probe the catalytic importance of the glycine-rich loop in HDAC8, we rigidified this loop by preparing the G302A, G303A, G304A, and G305A mutants and measured their steady state kinetics and determined their X-ray crystal structures. (anl.gov)
  • This suggests that the ground state conformation in deed is sufficient to achieve super-constriction and that super-constricted dynamin is trapped in a pre-hydrolysis, GTP-bound state. (nih.gov)
  • Hydrolysis of GTP in water is accelerated by coordination to K-Ras, where GTP adopts a high-energy conformation approaching the transition state. (rcsb.org)
  • A lumping scheme is presented which exploits the differences * in timescales associated with fast and slow transitions between * model states, while maintaining the thermodynamic properties * of the model. (nih.gov)
  • Their efficient functionalization with either acrylate or methacrylate groups yield monomers that could easily be polymerized by a scalable, reversible addition-fragmentation chain-transfer process into polymeric materials with high glass-transition temperatures and robust thermal stabilities, especially relative to other potentially bio-based alternatives. (udel.edu)
  • Finally, DMA measurements support the statement that a secondary relaxation was erroneously assigned as the glass transition of PVA and composites in previous reports. (hindawi.com)
  • Additionally, physicochemical properties of a material such as dissolution, bioavailability, processing, and handling qualities can be related to the glass transition temperature of the material [ 18 ]. (hindawi.com)
  • Also the optimal application and processing temperatures for polymers base materials are dependent on their glass transition temperature. (hindawi.com)
  • The above referred to acetylation response stage (oximolysis) certainly mimics just LTBP1 the initial stage from the catalytic procedure for the serine hydrolases, such as for example AcChE, however the full enzyme catalyzed procedure contains two successive levels, deacetylation and acetylation, that's, hydrolysis of seryl-acetyl-ester shaped in energetic site from the AcChE [25]. (buyresearchchemicalss.net)
  • Let's assume that oximate promotes the hydrolysis of AcSCh+ performing as pseudo-hydrolase/thioesterase, additional investigation from the destiny of pyridinium-4-oxime-ester (acetylated oxime) was essential to offer mechanistic top features of the next, deacetylation, stage of the full total catalytic procedure. (buyresearchchemicalss.net)
  • It seems that in their 2-D state, transition-metal carbides are quite reactive," says Mochalin. (newswise.com)
  • Indeed, several transition metals can generate reactive oxygen species in biologic fluids at physiologic pH, but this does not explain why the relatively weak redox-active Ni(II) is as good a carcinogen as the oxidatively very active Cr(VI). (nih.gov)
  • The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). (nih.gov)
  • Upon graduating from the American University of Beirut with a BS in Chemistry, she returned to the United States and obtained a Ph.D. in Molecular Biophysics from The Johns Hopkins University School of Medicine. (nih.gov)
  • The sharply angled conformation is similar to a myosin II atomic structure proposed to mimic the prepower stroke state. (silverchair.com)
  • It will be noted in Fig. 1 that the steady state rates achieved with 1 1M Gpp(NH)p are approximately 2-fold higher than observed with 10 mM fluoride ion. (nih.gov)
  • In the 10th lecture, you learn to think of enzyme efficiency as the lowering of the free energy of the transition state. (hstalks.com)
  • DFT calculations identify electron‐density redistribution and pinpoint why the TS for guanosine 5′‐triphosphate (GTP) hydrolysis is higher in energy when RhoA is complexed with RhoGAPArg85′Ala relative to wild‐type (WT) RhoGAP. (whiterose.ac.uk)
  • J. 13 (1986) 309, for which the principles * of free energy transduction are used to link the free energy * released from ATP hydrolysis (deltaGATP) to the transition rates * between states of the model. (nih.gov)
  • Our results show that human Rad51 can form elongated nucleoprotein filaments on DNA, but ATP hydrolysis causes a decrease in their length without concomitant dissociation of protein. (nih.gov)
  • Acyl-acyl carrier protein thioesterases (acyl-ACP TEs) catalyze the hydrolysis of the thioester bond that links the acyl chain to the sulfhydryl group of the phosphopantetheine prosthetic group of ACP. (iastate.edu)
  • The response is terminated upon GTP hydrolysis by the alpha subunit, which can then bind the beta-gamma dimer and the receptor. (medchemexpress.com)
  • Taken together, these results suggest that the ATP-bound conformational state of an Rpt subunit with the exposed C-terminal tail is competent for cellular proteasome assembly. (elsevierpure.com)
  • 17. Transition-state analysis of 2-O-acetyl-ADP-ribose hydrolysis by human macrodomain 1. (nih.gov)
  • [ 19 ] There are also esterases in tissue that will accomplish this hydrolysis [ 20 ] and the phenyl ester can be hydrolyzed by human butyryl cholinesterase (HBC) to give ecgonine methyl ester and benzoic acid. (medscape.com)
  • NIEHS research uses state-of-the-art science and technology to investigate the interplay between environmental exposures, human biology, genetics, and common diseases to help prevent disease and improve human health. (nih.gov)
  • PNP = p-nitrophenoxy) noted (RY), mimicking the transition state occurring during the carboxyester hydrolysis were synthesized and investigated as potential inhibitors of human gastric lipase (HGL) and human pancreatic lipase (HPL). (inra.fr)
  • GDL is pH-neutral, but hydrolyses in water to gluconic acid which is acidic, adding a tangy taste to foods, though it has roughly a third of the sourness of citric acid. (wikipedia.org)
  • From this it is inferred that the migrating group carries a partial positive charge in the transition state leading to the carbocation. (chemeurope.com)
  • 2-PAM is currently the only FDA approved oxime in the United States, and will be the only one discussed specifically in this case study. (cdc.gov)
  • TyrL94 and TyrH50 now hydrogen bond with the pro- R phosphonate oxygen of the TSA, and possibly constitute an oxyanion hole to stabilize the transition state. (stanford.edu)
  • Current work is focused on determining the oligomerization state of the active translocon and testing various predictions of our proposed Hairpin-Hinge translocation model. (tamu.edu)
  • Copper is a natural element and transition metal with more than one oxidation state. (europa.eu)
  • For your purpose, = 0.1 M within the pH range between 6 to 12 where in fact the price of hydrolysis is dominated by natural (H2O) and HO? (buyresearchchemicalss.net)
  • particular elements, explicitly: (kJ?mol?1) for the natural hydrolysis was calculated according to changeover condition theory [26] the following: are Boltzmanns and Plancks constants, respectively, may be the gas regular. (buyresearchchemicalss.net)