Search results for "Models"
showing 10 items of 8211 documents
Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step.
2015
Highlights • The possible role of enzymatic reaction dynamical effects is examined. • Solution reactions usefully inform the issue of dynamical effects in enzymes. • Division into regions containing and away from the transition state is important. • Motions in passage to/from the transition state need not lead to dynamical effects. • Transition State Theory is usually a reasonable description of enzyme kinetics.
Hydrolysis of Phosphotriesters: A Theoretical Analysis of the Enzymatic and Solution Mechanisms
2012
A theoretical study on the alkaline hydrolysis of paraoxon, one of the most popular organophosphorus pesticides, in aqueous solution and in the active site of Pseudomonas diminuta phosphotriesterase (PTE) is presented. Simulations by means of hybrid quantum mechanics/molecular mechanics (QM/MM) potentials show that the hydrolysis of paraoxon takes place through an A(N)D(N) or associative mechanism both in solution and in the active site of PTE. The results correctly reproduce the magnitude of the activation free energies and can be used to rationalize the observed kinetic isotope effects (KIEs) for the hydrolysis of paraoxon in both media. Enzymatic hydrolysis of O,O-diethyl p-chlorophenyl …
The mechanism of hydrolysis of beta-glycerophosphate by kidney alkaline phosphatase.
1975
1. To identify the functional groups that are involved in the conversion of β-glycerophosphate by alkaline phosphatase (EC 3.1.3.1) from pig kidney, the kinetics of alkaline phosphatase were investigated in the pH range 6.6-10.3 at substrate concentrations of 3 μM-30 mM. From the plots of log ṼH+ against pH and log ṼH+/KH+m against pH one functional group with pK = 7.0 and two functional groups with pK = 9.1 were identified. These groups are involved in substrate binding. Another group with pK = 8.8 was found, which in its unprotonated form catalyses substrate conversion. 2. GSH inhibits the alkaline phosphatase reversibly and non-competitively by attacking the bound Zn(II). 3. The influenc…
Chemical model systems for cellular nitros(yl)ation reactions.
2009
S-nitros(yl)ation belongs to the redox-based posttranslational modifications of proteins but the underlying chemistry is controversial. In contrast to current concepts involving the autoxidation of nitric oxide ( • NO, nitrogen monoxide), we and others have proposed the formation of peroxynitrite (oxoperoxonitrate (1-)) as an essential intermediate. This requires low cellular fluxes of 'NO and superoxide ( • O 2 - ), for which model systems have been introduced. We here propose two new systems for nitros(yl)ation that avoid the shortcomings of previous models. Based on the thermal decomposition of 3-morpholinosydnonimine, equal fluxes of • NO and • O 2 - were generated and modulated by the …
A core cochlear phenotype in USH1 mouse mutants implicates fibrous links of the hair bundle in its cohesion, orientation and differential growth
2008
The planar polarity and staircase-like pattern of the hair bundle are essential to the mechanoelectrical transduction function of inner ear sensory cells. Mutations in genes encoding myosin VIIa, harmonin, cadherin 23,protocadherin 15 or sans cause Usher syndrome type I (USH1, characterized by congenital deafness, vestibular dysfunction and retinitis pigmentosa leading to blindness) in humans and hair bundle disorganization in mice. Whether the USH1 proteins are involved in common hair bundle morphogenetic processes is unknown. Here, we show that mouse models for the five USH1 genetic forms share hair bundle morphological defects. Hair bundle fragmentation and misorientation (25-52° mean ki…
Valence Topological Charge-Transfer Indices for Reflecting Polarity: Correction for Heteromolecules
2005
Valence topological charge-transfer (CT) indices are applied to the calculation of dipole moments mu. The mu calculated by algebraic and vector semisums of the CT indices are defined. The model is generalized for molecules with heteroatoms and corrected for sp(3)-heteromolecules. The ability of the indices for the description of the molecular charge distribution is established by comparing them with mu of the valence-isoelectronic series of cyclopentadiene, benzene and styrene. Two CT indices, mu(vec) (vector semisum of vertex-pair mu) and mu(vec)V (valence mu(vec)) are proposed. The mu(vec) behaviour is intermediate between mu(vec) and mu(experiment). The correction is produced in the corr…
Electrostatic Contribution to the Surface Pressure of Charged Monolayers Containing Polyphosphoinositides
2008
Structural and functional studies of lateral heterogeneity in biological membranes have underlined the importance of membrane organization in biological function. Most inquiries have focused on steric determinants of membrane organization, such as headgroup size and acyl-chain saturation. This manuscript reports a combination of theory and experiment that shows significant electrostatic contributions to surface pressures in monolayers of phospholipids where the charge spacing is smaller than the Bjerrum length. For molecules with steric cross sections typical of phospholipids in the cell membrane (approximately 50 A(2)), only polyphosphoinositides achieve this threshold. The most abundant s…
The role of fluorine in the stereoselective tandem Aza-Michael addition to acrylamide acceptors: An experimental and theoretical mechanistic study
2007
Aza-Michael additions of alpha-amino esters to fluorinated acceptors take place in a highly stereoselective manner, to give partially modified Psi-[NHCH2]retropeptides incorporating a hydrolytically stable trifluoroalanine mimic. The reaction mechanism has been investigated experimentally and theoretically, in order to explain the effect of the trifluoromethyl group on the reactivity and the origins of the experimentally observed stereocontrol. The reaction is a two-step process, involving a tandem aza-Michael addition followed by a stereoselective hydrogen transfer. Both steps are base-catalyzed. The high level of stereocontrol is the result of a combination of electrostatic interactions a…
Weak Interactions Modulating the Dimensionality in Supramolecular Architectures in Three New Nickel(II)-Hydrazone Complexes, Magnetostructural Correl…
2011
Three different ONO donor acetyl hydrazone Schiff bases have been synthesized from the condensation of acetic hydrazide with three different carbonyl compounds: salicylaldehyde (HL(1)), 2-hydroxyacetophenone (HL(2)), and 2, 3-dihydroxybenzaldehyde (HL(3)). These tridentate ligands are reacted with Ni(OOCCF(3))(2)·xH(2)O to yield three new Ni(II) complexes having distorted octahedral geometry at each Ni center: [Ni(L(1))(OOCCF(3))(CH(3)OH)](2) (1), [Ni(L(2))(OOCCF(3))(H(2)O)](2) (2), and [Ni(L(3))(L(3)H)](OOCCF(3))(H(2)O)(1.65)(CH(3)OH)(0.35) (3). The ligands and the complexes have been characterized by elemental analysis and IR and UV-vis spectroscopy, and the structures of the complexes ha…
Two dimensional self-assembly of bis-acylureas having various functional end groups.
2011
We present the synthesis and morphology study of thirteen bis-acylurea molecules with various functional end groups. The bis-acylureas have two acylurea groups, -NH-CO-NH-CO-, divided by a pentamethylene spacer, -(CH(2))(5)-, and two symmetric functional end groups, such as, aliphatic, benzyl, mono- and bi-thiophenyl, sulfur-containing, and propargyl (HC[triple bond]CCH(2)-) moieties. The bis-acylureas were synthesized by the coupling reactions of ureas with pimeloyl chloride or pimelic acid. Upon cooling from hot isotropic solutions, the bis-acylureas spontaneously form supermolecules. In the cases of aliphatic, benzyl, mono- and bi-thiophenyl functional groups, two dimensional supramolecu…