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At least 1,099 records · Page 61Linked to original sources
PubMed1999

Modelling the catalytic reaction in human aldose reductase.

Aldose reductase (ALR2) has received considerable attention due to its possible link to long-term diabetic complications. Although crystal structures and kinetic data reveal important aspects of the reaction mechanism, details of the catalytic step are still unclear. In this paper a computer simulation study is presented that utilizes the hybrid quantum mechanical and molecular mechanical (QM-MM) potential to elucidate the nature of the hydride and proton transfer steps in the reduction of D-glyceraldehyde by ALR2. Several reaction pathways were investigated in two models with either Tyr48 or protonated His110+ acting as the potential proton donor in the active site. Calculations show that the substrate binds to ALR2 through hydrogen bonds in an orientation that facilitates the stereospecific catalytic step in both models. It is established that in the case that His110 is present in the protonated form in the native complex, it is the energetically favored proton donor compared with Tyr48 in the active pocket with neutral His110. The reaction mechanisms in the different models are discussed based on structural and energetic considerations.

Aldehyde Reductase↗
PubMedDate not supplied

Molecular similarity analysis between insect juvenile hormone and N, N-diethyl-m-toluamide (DEET) analogs may aid design of novel insect repellents.

Molecular similarity analysis of stereoelectronic properties between natural insect juvenile hormone (JH), -a synthetic insect juvenile hormone mimic (JH-mimic, undecen-2-yl carbamate), and N, N-diethyl-m-toluamide (DEET) and its analogs reveals similarities that may aid the design of more efficacious insect repellents and give a better insight into the mechanism of repellent action. The study involves quantum chemical calculations using the AM1 semi-empirical computational method enabling a conformational search for the lowest and most abundant energy conformers of JH, JH-mimic, and 15 DEET compounds, followed by complete geometry optimization of the conformers. Similarity analyses of stereoelectronic properties such as structural parameters, atomic charges, dipole moments, molecular electrostatic potentials, and highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies were performed on JH, JH-mimic and the DEET compounds. The similarity of stereoelectronic attributes of the amide/ester moiety, the negative electrostatic potential regions beyond the van der Waals surface, and the large distribution of hydrophobic regions in the compounds appear to be the three important factors leading to a similar interaction with the JH receptor. The similarity of electrostatic profiles beyond the van der Waals surface is likely to play a crucial role in molecular recognition interaction with the JH receptor from a distance. This also suggests electrostatic bioisosterism of the amide group of the DEET compounds and JH-mimic and, thus, a model for molecular recognition at the JH receptor. The insect repellent property of the DEET analogs may thus be attributed to a conflict of complementarity for the JH receptor binding sites.

Algorithms↗
PubMed2006

Computational studies of the primary phototransduction event in visual rhodopsin.

This Account addresses recent advances in the elucidation of the detailed molecular rearrangements due to the primary photochemical event in rhodopsin, a prototypical G-protein-coupled receptor (GPCR) responsible for the signal transmission cascade in the vertebrate vision process. The reviewed studies provide fundamental insight on long-standing problems regarding the assembly and function of the individual residues and bound water molecules that form the rhodopsin active site, a center that catalyzes the 11-cis/all-trans isomerization of the retinyl chromophore in the primary step of the phototransduction mechanism. Emphasis is placed on the authors' recent computational studies, based on state-of-the-art quantum mechanics/molecular mechanics (QM/MM) hybrid methods, addressing the structural refinement of the retinyl chromophore binding site in high-resolution X-ray structures of bovine visual rhodopsin, the energy storage mechanism, and the molecular origin of spectroscopic changes due to the primary photochemical event.

Isomerism↗
PubMed2002

Three-dimensional structure determination of N-(p-Tolyl)-dodecylsulfonamide from powder diffraction data and validation of structure using solid-state NMR spectroscopy.

The three-dimensional structure, conformation, and packing of molecules in the solid state are crucial components used in the optimization of many technologically useful materials properties. Single-crystal X-ray diffraction is the traditional and most effective method of determining 3-D structures in the solid state. Obtaining single crystals that are sufficiently large and free of imperfections is often laborious, time-consuming, and, occasionally, impossible. The feasibility of an integrated approach to the determination and verification of a complete three-dimensional structure for a medium-sized organic molecule without using single crystals is demonstrated for the case of an organic stabilizer compound N-(p-tolyl)-dodecylsulfonamide. The approach uses a combination of powder XRD data, several computational packages involving Monte Carlo simulations and ab initio quantum mechanical calculations, and experimental solid-state NMR chemical shifts. Structure elucidation of N-(p-tolyl)-dodecylsulfonamide revealed that the Bravais lattice is monoclinic, with cell dimensions of a = 38.773 A, b = 5.507 A, c = 9.509 A, and beta = 86.35 degrees, and a space group of P21/c.

Journal Article↗
PubMed2004

Ab initio interaction energies of hydrogen-bonded amino acid side chain[bond]nucleic acid base interactions.

Hydrogen-bonding interactions often make substantial contributions to the specificity of protein-nucleic acid complexes. Using a geometric modeling approach, we previously identified 28 possible doubly hydrogen-bonded interactions to the four unpaired RNA bases. Here we present interaction energies of these models, calculated by ab initio quantum chemical methods, and describe a correlation between the computed energies and observed frequencies of the interactions. In general, interactions with charged side chains show the most favorable energies. An Asp/Glu-G interaction may be especially favorable for recognition of unpaired guanines in RNAs. Asn and Ser/Thr/Tyr side chains are calculated to make iso-energetic interactions to the Hoogsteen face of adenine, but Asn-A interactions are much more common with DNA than RNA, and Ser/Thr/Tyr-A interactions are more common with RNA than DNA. Examination of the known interactions suggests that Ser/Thr/Tyr may be accommodated in a wider variety of protein contexts at RNA-protein interfaces. With these calculated intrinsic affinities, it should be possible to better assess the contributions of bidentate hydrogen-bonding interactions to RNA- and DNA-binding specificity.

Adenine↗
PubMed2002

Evaluation of myocardial ischemia in Kawasaki disease using an isointegral map on magnetocardiogram.

The authors have recently reported on the usefulness of the isointegral mapping technique using magnetocardiography (MCG) for the diagnosis of adult ischemic heart disease. This study evaluated myocardial ischemia in patients with Kawasaki disease (KD). The ischemia has been considered difficult to diagnose with a standard ECG. The study included 32 patients (age 3 +/- 22 years, mean 12.9 +/- 4.1 years, +/- SD) with a history of KD and 21 age-matched healthy children. Coronary arterial lesions were present in 13 patients of the KD group, MCG was carried out at rest with a multichannel superconducting quantum interference device (SQUID) system. The integral value was computed for each channel and isointegral maps were constructed during depolarization and repolarization processes. In all subjects of the control group, the integral value of repolarization was higher than that of depolarization and the isointegral map of these two processes showed similar patterns. However, the integral value of repolarization in four cases with KD (one with a history of myocardial infarction, two with a stenotic lesion in the left coronary artery, one with an aneurysmal and stenotic lesion in the right coronary artery) was lower than that of depolarization, and abnormal patterns were evident in the isointegral map. All but the case with myocardial infarction showed only mild abnormalities or almost normal on the ECG. Although sensitivity of the method for detection of myocardial ischemia was not fully assessed because of the small number of cases with significant coronary arterial stenosis, noninvasive isointegral mapping technique using the MCG could be useful for evaluation of myocardial ischemia in patients with KD.

Adolescent↗
PubMed2004

A derivation of the mixed quantum-classical Liouville equation from the influence functional formalism.

We show that the mixed quantum-classical Liouville equation is equivalent to linearizing the forward-backward action in the influence functional. Derivations are provided in terms of either the diabatic or adiabatic basis sets. An application of the mixed quantum-classical Liouville equation for calculating the memory kernel of the generalized quantum master equation is also presented. The accuracy and computational feasibility of such an approach is demonstrated in the case of a two-level system nonlinearly coupled to an anharmonic bath.

Journal Article↗
PubMed2006

Rotational spectra of 1-chloro-2-fluoroethylene. II. Equilibrium structures of the cis and trans isomer.

Equilibrium structures for the cis and trans isomer of 1-chloro-2-fluoroethylene are reported. The structures are obtained within a least-squares fit procedure using the available experimental ground-state rotational constants for various isotopic species of both forms. Vibrational effects were eliminated before the analysis using vibration-rotation interaction constants derived from computed quadratic and cubic force fields with the required quantum chemical calculations carried out using second-order Moller-Plesset perturbation as well as coupled-cluster (CC) theory. The semiexperimental or empirical equilibrium geometries obtained in this way agree well with the corresponding theoretical predictions obtained from CC calculations [at the CCSD(T) level] after extrapolation to the complete basis-set limit and inclusion of core-valence correlation corrections. The present results allow a detailed analysis of the geometrical differences between the two forms of 1-chloro-2-fluoroethylene. They are also compared to the structural data available for other halogenated ethylenes.

Journal Article↗
PubMed2004

ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures.

Analysis of protein-ligand interactions is a fundamental issue in drug design. As the detailed and accurate analysis of protein-ligand interactions involves calculation of binding free energy based on thermodynamics and even quantum mechanics, which is highly expensive in terms of computing time, conformational and structural analysis of proteins and ligands has been widely employed as a screening process in computer-aided drug design. In this paper, a web server called ProteMiner-SSM designed for efficient analysis of similar protein tertiary substructures is presented. In one experiment reported in this paper, the web server has been exploited to obtain some clues about a biochemical hypothesis. The main distinction in the software design of the web server is the filtering process incorporated to expedite the analysis. The filtering process extracts the residues located in the caves of the protein tertiary structure for analysis and operates with O(nlogn) time complexity, where n is the number of residues in the protein. In comparison, the alpha-hull algorithm, which is a widely used algorithm in computer graphics for identifying those instances that are on the contour of a three-dimensional object, features O(n2) time complexity. Experimental results show that the filtering process presented in this paper is able to speed up the analysis by a factor ranging from 3.15 to 9.37 times. The ProteMiner-SSM web server can be found at http://proteminer.csie.ntu.edu.tw/. There is a mirror site at http://p4.sbl.bc.sinica.edu.tw/proteminer/.

Binding Sites↗
PubMed2000

Topological chern indices in molecular spectra

Topological Chern indices are related to the number of rotational states in each molecular vibrational band. Modification of the indices is associated to the appearance of "band degeneracies," and exchange of rotational states between two consecutive bands. The topological dynamical origin of these indices is demonstrated through a semiclassical approach, and their values are computed in two examples. The relation with the integer quantum Hall effect is briefly discussed.

Journal Article↗
PubMed2006

Quantization of 2D hole gas in conductive hydrogenated diamond surfaces observed by electron field emission.

Discrete jumps are observed in the emitted current density (J) versus extraction electric field (E) curves in electron field emission measurements from a conductive, hydrogen-terminated air-exposed diamond surface. These jumps are well reproduced by computations based on the assumption that a 2D nanoscale quantum system with discrete energy levels exists in the diamond near-surface layer. The present results confirm the formation of well-defined quantum states of holes in the 2D surface layer present on hydrogenated air-exposed diamond surfaces.

Journal Article↗
PubMed1985

Conformational properties of molecules by ab initio quantum mechanical energy minimization.

The recent literature on the determination of minimum energy conformations by ab initio quantum mechanical techniques is reviewed. The availability of computer-coded analytical first and second derivatives of the Hartree-Fock energy makes possible calculations that will be of significant assistance in structure determination of molecules. A short review of recent progress in empirical energy minimization and molecular dynamics is provided.

Models, Chemical↗
PubMed2001

Consciousness, the brain, and spacetime geometry: an addendum. Some new developments on the Orch OR model for consciousness.

Brain action is both physically controlled and beyond computational simulation. Accordingly, there is a strong case for examining brain organization in a way that specifically seeks out structures in the brain that might plausibly support such putative non-computational action at the ill-understood borderline between quantum and classical physics. Thus, we must seek out structures in the brain where the actual physics that operates at this level could plausibly have important influence on brain action. This is the basis of the Orch-OR model that Stuart Hameroff and I have been proposing, and which he describes in the foregoing article. The case is strongly put forward that the neuronal microtubules play a key role in the required quantum/classical borderline activities which might have an essential relevance to the phenomenon of consciousness. The exploration of such deeper level of neuronal structure and function is very much a continuation of the line of work so wonderfully initiated by Cajal.

Brain↗
PubMed1992

Characterization of functional interactions of imidazoquinoxaline derivatives with benzodiazepine-gamma-aminobutyric acidA receptors.

U-78875 [imidazo[1,5-a]quinoxalin-4(5H)-one, 3-(5-cyclopropyl-1,2,4-oxadiazol-3-yl)-5-(1-methylethyl)] belongs to a series of imidazoquinoxaline derivatives, recently discovered ligands with high affinity for benzodiazepine receptors. In this study, we have examined the drug and its analogs for their modes of interaction with the receptors, with a particular emphasis on finding molecular determinants for their functional properties. Changes in the substituents on N5 and C6 of the heterocyclic ring produced no major effects on binding characteristics but yielded drugs of widely varying efficacy (antagonist to full agonist), measured as gamma-aminobutyric acid (GABA)-mediated 36Cl- uptake and t-butylbicyclophosphoro[35S]thionate binding in rat cerebrocortical membranes. The relative binding affinity and efficacy of the analogs measured in brain membranes were similar to those in cloned GABAA receptors of the alpha 1 beta 2 gamma 2 (type I) and alpha 3 beta 2 gamma 2 (type II) subtypes. The imidazoquinoxalines showed no marked subtype selectivity. Their Ki value against [3H]flunitrazepam binding for type I was only 2-3 times lower than that for type II, and their rank order for agonistic activity was the same in the two subtypes, measured as GABA-mediated Cl- currents in human kidney cells (A293) expressing the subtypes of GABAA receptors. According to computational modeling of the drugs using both molecular and quantum mechanics, the agonistic activity of the imidazoquinoxaline derivatives depends on the presence of a bulky alkyl substituent at N5 and the deformation of the substituted portion of the otherwise planar ring system induced by a bulky moiety at N5 or C6. With a fixed N5 substituent (isopropyl), the relative efficacy in the brain membranes, as well as in the cloned receptors, appeared to be dependent on the degree of the ring deformation. This out-of-plane portion of the imidazoquinoxalines can be assigned to the general region occupied by the 5-phenyl group of diazepam and other agonistic functional groups of several nonbenzodiazepine ligands. It seems that this region, apparently common to various agonistic ligands, interacts with an agonistic pocket in type I and type II subtypes of the benzodiazepine receptors in the brain. Our results also provide direct support for the view that the agonists and nonagonists share largely overlapping binding regions in the benzodiazepine receptor, which has been proposed earlier from in vivo efficacy measurements of other series of ligands.

Animals↗
PubMed1997

[Operator's systemic quanta under psychoregulating acts].

The aim of this study is to examine psychoregulatory effects for computer operator's rehabilitation. K. V. Sudakov's systemic quantum behavior conception as a methodological basis for human activity study. The comparison of quantum characteristics, such as motivation, activity result and its physiological cost up prior to and after psychoregulation for different groups of human biotypology has shown that the systemic quantum of the operator's activity is the reliable indicator of a functional condition. It has indicated that this way for rehabilitation is more effective for human beings who have predominantly parasympathicotonia and rather high initial motivation levels.

Adolescent↗
PubMed1998

Physical imaging performance of a compact computed radiography acquisition device.

A comprehensive investigation of the physical imaging performance of a Philips AC3 computed radiography system using fifth-generation image plate technology has been undertaken. Measurements include characteristic response, modulation transfer function (MTF) and Wiener spectra (WS) for standard and high resolution image plates sampled at 10 pixels/mm. These results were used to calculate noise equivalent quanta (NEQ) and detective quantum efficiency (DQE) spectral descriptions of system performance. Luminescence noise and x-ray quantum noise components were separated. From an estimate of the luminescence noise power, the average system gain was calculated and results show a substantial improvement over earlier generations of computed radiography systems for standard image plates.

Calibration↗
PubMed2006

Biological models: measuring variability with classical and quantum information.

This essay proposes methods to analyse the variability of biological data. The idea is to express the state of a biological system as a linear combination of base states in a Hilbert space. Coefficients of the linear combination can be interpreted as probabilities and informational entropy is associated to each state allowing the definition of a classical variability measure. Besides, state transition matrices can also be calculated and their norms express the dynamics of the system organization and a quantum variability measure. As the examples show, the classical measure expresses a structural variability and the quantum measure expresses a functional variability.

Computational Biology↗