Influence of protonation on substrate and inhibitor interactions at the active site of human monoamine oxidase-A

Although substrate conversion mediated by human monoaminooxidase (hMAO) has been associated with the deprotonated state of their amine moiety, data regarding the influence of protonation on substrate binding at the active site are scarce. Thus, in order to assess protonation influence, steered molecular dynamics (SMD) runs were carried out. These simulations revealed that the protonated form of the substrate serotonin (5-HT) exhibited stronger interactions at the protein surface compared to the neutral form. The latter displayed stronger interactions in the active site cavity. These observations support the possible role of the deprotonated form in substrate conversion. Multigrid docking studies carried out to rationalize the role of 5-HT protonation in other sites besides the active site indicated two energetically favored docking sites for the protonated form of 5-HT on the enzyme surface. These sites seem to be interconnected with the substrate/inhibitor cavity, as revealed by the tunnels observed by means of CAVER program. pK(a) calculations in the surface loci pointed to Glu32?, Asp32?, His???, and Asp132 as candidates for a possible in situ deprotonation step. Docking analysis of a group of inhibitors (structurally related to substrates) showed further interactions with the same two docking access sites. Interestingly, the protonated/deprotonated amine moiety of almost all compounds attained different docking poses in the active site, none of them oriented to the flavin moiety, thus producing a more variable and less productive orientations to act as substrates. Our results highlight the role of deprotonation in facilitating substrate conversion and also might reflect the necessity of inhibitor molecules to adopt specific orientations to achieve enzyme inhibition.     

Nuclear shadowing in Glauber–Gribov theory with Q 2-evolution

We consider deep inelastic scattering off nuclei in the Regge limit within the Glauber–Gribov model. Using unitarized parton distribution functions for the proton, we find sizeable shadowing effects on the nuclear total and longitudinal structure functions, $F_{2}^{A}$ and $F_{L}^{A}$ , in the low-x limit. Extending a fan-diagram analysis for the large-mass region of coherent diffraction off nuclei to high Q ², we also find significant shadowing effects in this kinematical regime. Finally, we discuss the shortcomings of our approach and possible extensions of the model to other kinematical regimes.     

Separation of brombuterol enantiomers in capillary electrophoresis with cyclodextrin‐type chiral selectors and investigation of structure of selector‐selectand complexes using nuclear magnetic resonance spectroscopy

The major goal of this study was to determine the affinity pattern of brombuterol (BB) enantiomers toward various cyclodextrins (CD) and to evaluate the potential of NMR spectroscopy for understanding fine mechanisms of interactions between CDs and BB enantiomers. Separation of BB enantiomers was performed in a fused‐silica capillary using a phosphate buffer, pH 2.5, at the room temperature in the normal polarity mode. It was shown once again that CE in combination with NMR spectroscopy represents a very sensitive tool for studies of affinity patterns and structure of CD complexes with chiral guests. Although opposite affinity patterns of BB enantiomers were observed toward native β‐ and γ‐CDs, no significant differences between the structures of the complexes of these two CDs with BB were detected by NMR spectroscopy. In contrary to this, the opposite affinity pattern of BB enantiomers toward β‐CD and its two sulfated derivatives, heptakis (2,3‐O‐diacetyl‐6‐sulfo)‐β‐CD (HDAS‐β‐CD) and heptakis (2‐O‐methyl‐3,6‐di‐O‐sulfo)‐β‐CD (HMDS‐β‐CD) was associated with major differences in the structure of the complexes. In addition, it was shown again that HMDS‐β‐CD provides separation of enantiomers without formation of inclusion‐type complex with the chiral analyte.     

A novel Barton decarboxylation produces a 1,4-phenyl radical rearrangement domino reaction

A novel 1,4-Phenyl radical rearrangement (1,4-PhRR) is described in a typical Barton decarboxylation procedure. While carrying out this reaction in presence of a N,N-disubstituted β-amino acid derivative, the decarboxyphenyl rearranged derivative is obtained, as well as in presence of β-N,N-acylamide. On the other hand, secondary amines give the β-lactam derivative without rearrangement, as well as N-Fmoc derivatives give the normal decarboxylation reaction. In regards of amines which are far away from the carboxylic group, such as δ-amino acid derivatives, the reaction occur through a typical Barton decarboxylation without rearrangement. The diversity of the reaction proves synthetic usefulness paving the way to interesting biologically active compounds.     

Microbiological assay for ceftazidime injection

A simple, sensitive, and specific biodiffusion assay for the antibacterial ceftazidime was developed using a strain of Staphylococcus epidermidis (ATCC 12228) as the test organism. Ceftazidime was measured in powder for injection at concentrations ranging from 100 to 400 microg/mL. The calibration graph for ceftazidime was linear (r2 = 1), and the method validation showed that it was precise (relative standard deviation = 0.415) and accurate. The results obtained by biodiffusion assay were statistically calculated by linear parallel model and by means of regression analysis and were verified using analysis of variance. It was concluded that the microbiological assay is satisfactory for in vitro quantification of the antibacterial activity of ceftazidime in pharmaceuticals.     

The scale dependent nuclear effects in parton distributions for practical applications

The scale dependence of the ratios of parton distributions in a proton of a nucleus A and in the free proton, , is studied within the framework of the lowest order leading-twist DGLAP evolution. By evolving the initial nuclear distributions obtained with the GRV-LO and CTEQ4L sets at a scale , we show that the ratios are only moderately sensitive to the choice of a specific modern set of free parton distributions. We propose that to a good first approximation, this parton distribution set-dependence of the nuclear ratios can be neglected in practical applications. With this result, we offer a numerical parametrization of for all parton flavours i in any , and at any and any for computing cross sections of hard processes in nuclear collisions. Received: 10 August 1998 / Published online: 27 April 1999     

Implementation of a medium-modified parton shower algorithm

We present a Monte Carlo implementation of medium-induced gluon radiation in the final-state branching process. Medium effects are introduced through an additive term in the splitting functions. We have implemented such modification within PYTHIA. We show the medium effects on the hump-backed plateau, and the transverse-momentum and angular distributions with respect to the parent parton. As expected, with increasing medium densities there is an increase (decrease) of partons with small (large) momentum fraction, and angular broadening is observed. The effects on the transverse-momentum distributions are more involved, with an enhancement of low- and intermediate-p _T partons and a decrease at large p _T, which is related to energy conservation, and to the lack of momentum exchange with the medium in our approach.     

Even-dimensional topological gravity from Chern–Simons gravity

It is shown that the topological action for gravity in 2n  -dimensions can be obtained from the (2n+1)$(2n+1)$-dimensional Chern–Simons gravity genuinely invariant under the Poincaré group. The 2n  -dimensional topological gravity is described by the dynamics of the boundary of a (2n+1)$(2n+1)$-dimensional Chern–Simons gravity theory with suitable boundary conditions.     

Retinal Conformation and Dynamics in Activation of Rhodopsin Illuminated by Solid‐state 2H NMR Spectroscopy†

Solid‐state NMR spectroscopy gives a powerful avenue for investigating G protein‐coupled receptors and other integral membrane proteins in a native‐like environment. This article reviews the use of solid‐state ²H NMR to study the retinal cofactor of rhodopsin in the dark state as well as the meta I and meta II photointermediates. Site‐specific ²H NMR labels have been introduced into three regions (methyl groups) of retinal that are crucially important for the photochemical function of rhodopsin. Despite its phenomenal stability ²H NMR spectroscopy indicates retinal undergoes rapid fluctuations within the protein binding cavity. The spectral lineshapes reveal the methyl groups spin rapidly about their three‐fold (C₃) axes with an order parameter for the off‐axial motion of For the dark state, the ²H NMR structure of 11‐cis‐retinal manifests torsional twisting of both the polyene chain and the β‐ionone ring due to steric interactions of the ligand and the protein. Retinal is accommodated within the rhodopsin binding pocket with a negative pretwist about the C11=C12 double bond. Conformational distortion explains its rapid photochemistry and reveals the trajectory of the 11‐cis to trans isomerization. In addition, ²H NMR has been applied to study the retinylidene dynamics in the dark and light‐activated states. Upon isomerization there are drastic changes in the mobility of all three methyl groups. The relaxation data support an activation mechanism whereby the β‐ionone ring of retinal stays in nearly the same environment, without a large displacement of the ligand. Interactions of the β‐ionone ring and the retinylidene Schiff base with the protein transmit the force of the retinal isomerization. Solid‐state ²H NMR thus provides information about the flow of energy that triggers changes in hydrogen‐bonding networks and helix movements in the activation mechanism of the photoreceptor.