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At least 127 records · Page 7Linked to original sources
PubMed1994

Influence of slight sequence changes on the free energy of a single stranded ribonucleic acid molecule.

Single-stranded ribonucleic acid molecules take a variety of secondary structures. The free energy (g) of a given secondary structure of a molecule is calculated from the Boltzmann weighted summation over the states of this molecule taking this secondary structure. Likewise, the free energy (G) of a molecule is calculated from the summation over the states of this molecule, which takes various secondary structures. The g-value can be evaluated by Salser's method (1977, Cold Spring Harbor Symp. Quantum Biol. 42, 985-1002). By use of these values, the G-value can also be obtained. Computer studies utilizing this method reveal that there is a particular class of molecules whose G-values tend to increase when the sequences are slightly changed. As far as we examined, such molecules take few secondary structures that fulfill the following two conditions simultaneously: (i) The g-value is close to that of the optimal secondary structure. (ii) The structure is very different from the optimal secondary structure. Here, the optimal secondary structure means the one with the lowest g-value among all the secondary structures taken by the molecule.

Base Sequence↗
PubMed1990

Theoretical calculations on calcium channel drugs: is electron transfer involved mechanistically?

Theoretical studies were done on calcium channel drugs in order to gain insight into the mode of action. Empirical force field calculations with nifedipine, a calcium channel antagonist, indicate that the E-conformation at the ring juncture is lower in energy than the Z-conformation. This energy difference is only 0.2 kcal/mol when the esters in the 3- and 5-positions of the dihydropyridine (DHP) ring are both synperiplanar (sp, sp). Molecular orbital calculations on the ground and excited states in the Z-conformation with the esters in the (ap, sp) conformation show a low lying excited state with substantial intramolecular electron transfer (ET) character. This excited state is only 1.8 eV higher in energy than the ground state and corresponds to a transfer of approximately 0.3 electron from the DHP ring to the nitrobenzene moiety. We suggest that ET may play an important role in the mechanism of action, either intramolecular or, as previously proposed, intermolecular, along with lipophilicity and steric effects.

Calcium Channel Blockers↗
PubMedDate not supplied

Information and artifact in computed tomography image statistics.

In conventional computed tomography images only the average CT number, which is a first-order statistical parameter, is used to characterize the tissues by giving an estimate of tissue density. Second order statistical parameters such as the signal variance and cross-correlation function have also been used to obtain additional information to discriminate between certain tissues and lesions. However, the contribution of quantum noise to the signal variance and cross-correlation function creates, for the conventional CT patient dose, a background signal often larger than the signal containing the information about tissue structure. The misleading information, called "artifacts", in second-order image statistics caused by quantum noise, is studied.

Information Theory↗
PubMed1990

Solution behavior of methyl beta-xylobioside: conformational flexibility revealed by n.m.r. measurements and theoretical calculations.

The conformations of methyl beta-xylobioside in solution have been determined by n.m.r. spectroscopy. Interglycosidic 3JC,H values and the chemical shifts of the 13C resonances were measured at various temperatures in the range 238-378 K for solutions in 1,4-dioxane, methanol, methyl sulfoxide, and water. The temperature and solvent dependencies of the data obtained suggest conformational flexibility. Quantum-chemical PCILO calculations, with evaluation of the solvent effects, and molecular mechanics calculations revealed the existence of 7 low-energy regions for which the geometries and energies were determined. The computed abundances of conformers and averaged J values accord with the experimental data.

Carbohydrate Conformation↗
PubMed1986

Molecular determinants for the agonist activity of 2-methylhistamine and 4-methylhistamine at H2-receptors.

A model for drug action at the histamine H2-receptor has been evaluated computationally for the agonists 2- and 4-methylhistamine. Based on molecular properties calculated for molecular structures optimized with ab initio quantum mechanical methods, the activities of these compounds and their potencies relative to histamine are found to be explained by the previously proposed model. Recognized in the N3-H tautomeric form of their monocations, both compounds exhibit a change in ring tautomeric preference when the cationic side chain is neutralized. This change makes possible their participation in a proposed proton relay event that was postulated to initiate the receptor response of H2-agonists. The relative concentrations of the mono- and dication forms of the molecules in equimolar concentrations of histamine and the two derivatives are calculated from the values of the molecular electrostatic potentials at the ring protonation sites. Because the monocation is the species recognized at the H2-receptor, the reduced potency of 2-methylhistamine relative to histamine and to the 4-methyl derivative is explained by the finding that 2-methylhistamine will have the lowest concentration of the recognized species. The rank order of potencies obtained from the ratio of monocationic species of the molecules is in agreement with experimental results.

Methylhistamines↗
PubMed1988

Role of primary and secondary protein structure in neurotransmitter receptor activation mechanisms.

A proton transfer triggered by a ligand interacting with the receptor had been suggested as the initial step in the activation of a receptor for the neurotransmitter serotonin (5-hydroxy-tryptamine; 5-HT). To evaluate the role of the receptor macromolecule in modulating the primary molecular event in ligand-mediated activation, the process of proton transfer was analysed in the environment of a protein model for the 5-HT receptor. In the absence of a detailed receptor structure, the enzyme actinidin was chosen as the model for the receptor based on criteria obtained from structure-activity considerations on the ligands. The first simulation of a mechanism for receptor activation was performed on this model using methods of theoretical chemistry to study the effect of specific structural elements. The premise is that the role of the elements of secondary structure of soluble proteins (e.g. actinidin) in determining structure-function relations in these macromolecules is maintained when these elements are part of membrane-bound receptor proteins. Results from the calculations of the effects of the six alpha helices of actinidin on the proton transfer process from the imidazolium side chain of His 162 to the thiol side chain of Cys 25 in the protein show that the helices contribute in different ways to modulate the energy of proton transfer. The largest helix, A1, opposes the proton transfer through the effect of the helix dipole. The charged residues (primary structure) in helix A3 favor the proton transfer, and mask the effect of its helix dipole (secondary structure) which opposes the transfer. The direction of the proton transfer simulated for the activation mechanism is opposite to that assumed in the catalytic process of the thiol protease, and the entire protein environment opposes the transfer. This supports the specific role of the ligand in triggering the proton transfer as a response to its binding.

Computer Graphics↗
PubMed1989

Three-dimensional imaging of neurons by confocal fluorescence microscopy.

The study of neuronal architecture by means of confocal laser microscopy is described. Optical serial sectioning has been performed on whole-mount specimens, and the resulting stacks of digitally recorded images have been processed with the help of a computer. Specimen preparation is described, as well as the instrument and its performance. It is shown that the limits in photometric quality are set by photon quantum noise. As both light absorption and scattering was low in the studied specimens, the maximum scanning depth was limited mainly by the working distance of the objectives. Compared with traditional methods, confocal microscopy in combination with digital image processing has the following advantages: (1) a truly three-dimensional (3-D) reconstruction is obtained, (2) the specimen remains intact, (3) a higher resolution can be obtained, (4) the process is automated and less time-consuming and (5) various kinds of data processing are possible.

Animals↗
PubMed1990

Two-dimensional COSY and two-dimensional NOE spectroscopy of d(AC)4.d(GT)4: extraction of structural constraints.

Pure absorption phase, proton two-dimensional nuclear Overhauser effect (2D NOE) and double-quantum-filtered COSY (DQF-COSY) spectra were recorded for d(AC)4.d(GT)4. A full proton resonance assignment was made, except for the 5' and 5" protons. A new semiautomatic method for improved quantitation of 2D NOE peak intensities was developed, and its limitations and usefulness were examined. With this new method, 2D NOE intensity sets at several mixing times were obtained. Simulations of the 1'2', 1'2", and 2'3' DQF-COSY cross-peaks were compared with experimental data, establishing an alternating sugar pucker for the alternating purine-pyrimidine sequence. Scalar coupling constants for the sugar ring protons, derived from the fitting of the simulated spectra, are reported. Complete relaxation matrix analysis of the 2D NOE spectrum verified this alternating structure for all NOE interactions between nonexchangeable protons. Both the DQF-COSY and the 2D NOE results qualitatively indicate that the structure of d(AC)4.d(GT)4 resembles wrinkled D-DNA in aqueous solution.

Computer Simulation↗
PubMed1991

Changes in the electron density of the cofactor NADPH on binding to E. coli dihydrofolate reductase.

Quantum-mechanical electron density calculations reveal that a significant polarization is induced in the cofactor NADPH (reduced nicotinamide adenine dinucleotide phosphate) on binding to the enzyme dihydrofolate reductase. The calculations indicate that electron density corresponding to approximately 0.7 electron charges is shifted within the molecule, extending over more than 20 A. Further calculations on proposed enzyme mutants show that the polarization of NADPH on binding to DHFR is, in large part, induced by a motif of three positively charged residues. This motif was also identified to be directly responsible for the positive electrostatic potential surrounding the cofactor binding site in the enzyme. The possibility of this long-range polarization of NADPH was originally proposed based on a previous study of ligand binding to DHFR where a conserved structural motif of three positively charged residues was found to play a major role in polarizing the substrate folate over its entire length of 18 A.

Arginine↗
PubMed1985

Computer simulations of complex chemical systems.

In this paper, after a brief description on our approach to simulations of chemical systems, some of the results obtained are discussed. Four examples are reported: 1) liquid water simulation which takes in account a four-body potential; 2) hydration networks in a crystal; 3) water and ion structures in DNA; 4) proton tunneling in DNA base pairs. We include also a short description of a parallel system we have assembled.

Base Composition↗
PubMed1991

Efficient method for the generation and display of electrostatic potential surfaces from ab-initio wavefunctions.

A cost effective color graphics representation of molecular electrostatic potential surfaces employing the cumulative atomic or bond multipole moments has been described. A general description of the method used to obtain cumulative multipole moments directly from ab-initio wavefunctions is given, along with an outline of the algorithm for generating electrostatic potential surfaces in the molecular graphics programs MOL17 (FORTRAN 77, Silicon Graphics 3130 and 4D series workstations) and PCMCAMM (Turbo Pascal, IBM PC and PS/2 computers). Examples are given that illustrate the convergence of the multiple expansion, the degree of basis-set dependence compensated by the use of higher atomic moments, and the effect of placing additional expansion centers along the bonds.

Amino Acids↗