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PubMed1986

Hydrophobic and ionic hydration phenomena.

Computer simulation offers an increasing opportunity to examine the details of solvation structure for well-defined solution models. One can characterize idealized models that exemplify specific aspects of solution behavior or those that realistically model systems experimentally difficult to access. As an example from the first category, results are presented for the aqueous solvation structure and solvent hydrogen bonding in the presence of a small apolar solute, and these are contrasted with the quite different behavior observed for a large apolar surface. As an example from the second category, structural results are presented for hydration of an excess electron in bulk water. These latter results, obtained via recent path integral simulation methods, manifest significant solvent structural disruption compared to the case of a simple ion, due to the irregular and fluctuating shape of the quantum solute.

Chemical Phenomena↗
PubMed1991

Interaction energy studies on antibiotics nucleoside analogs 2-azaadenine.

The 2-azaadenine antibiotic is known to be a potent cytotoxic nucleoside analog. Evaluation of the interaction energy of this molecule with nucleic acid bases and base pairs has been performed using a quantum-mechanical perturbation technique. Both in-plane and stacking energies have been computed. These energy values along with their sites of association have been compared with the standard energy values and spatial positions for the nucleic acid bases during transcription. The results have been examined in the light of their biological significance.

Adenine↗
PubMed1989

Computer modelling: future directions.

Recent developments in computing and in the theory of simulation have extended greatly the successes of the modelling of ionic crystals pioneered by Mott and Littleton. This has changed the way in which computer experiments are brought to bear on an increasing range of solid-state phenomena. Yet applied science creates new demands, both in the form of new types of system and in terms of the complexity and subtlety of what is studied. The author's brief survey looks at some of the successes and gaps from interfaces and catalysts to neurotransmitters and from superconductors to slags.

Computer Simulation↗
PubMed1992

Base compositional structure of genomes.

We model the base compositional structure of the human and Escherichia coli genomes. Three particular properties are first quantified: (1) There is a significant tendency for any region of either genome to have a strand-symmetric base composition. (2) The variation in base composition from region to region, within each genome, is very much larger than expected from common homogeneous stochastic models. (3) A given local base composition tends to persist over a scale of at least kilobases (E. coli) or tens of kilobases (human). Multidomain stochastic models from the literature are reviewed and sharpened. In particular, quantitative measurements of the third property lead us to suggest a significant shift in the style of domain models, in which the variation of A+T content with position is modeled by a random walk with frequent small steps rather than with large quantum jumps. As an application, we suggest a way to reduce the amount of computation in the assembly of large sequences from sequences of randomly chosen fragments.

Escherichia coli↗
PubMed1981

Time-resolved protein fluorescence studies of intermediates in the photochemical cycle of bacteriorhodopsin.

The photolysis-induced changes in the protein fluorescence intensity (at 320 nm) during the proton-pumping cycle of bacteriorhodopsin were examined by a delayed two-pulse technique in the time range 1 microsecond-20 msec at room temperature. No detectable change in the protein fluorescence intensity was observed on the earliest time scale within the lifetime of the intermediate K590, when retinal apparently undergoes the largest structural changes. The time dependence of the relative changes in fluorescence intensity did, however, display a close correlation with the population of the L550 and M412 intermediates. From a computer numerical fit of the data, with available published kinetic parameters, the protein fluorescence quantum yields of the K590, L550, and M412 intermediates are found to be 1.0, 0.92, and 0.80 of that for native bR570, respectively. The probable mechanisms of the observed fluorescence quenching during the photochemical cycle are qualitatively discussed.

Bacteriorhodopsins↗
PubMed1992

The structure and properties of liquid water: recent theoretical advances.

Computer simulations of water, and of water in the neighborhood of biological materials, are now commonplace. However, from the molecular physicist's viewpoint existing models of water/water, water/solute, and water/substrate interactions are incorrect and potentially misleading. Almost all existing simulations of biological interest assume that the molecules are rigid, or at least that the bonds do not vibrate. In this paper we review recent advances in the theory of water interactions, emphasizing the need to construct potential energy surfaces that include vibrational degrees of freedom.

Computer Simulation↗
PubMed1986

Ab-initio quantum mechanical calculations of NMR chemical shifts in nucleic acids constituents. III. Chemical shift variations due to base stacking.

Ab inito computations of the different contributions to chemical shift variations due to intra and interstrand stacking are reported for the GC, CG, AT and TA sequences of a B DNA helix. The results obtained for the non hydrogen atoms of the GC stacks show that the chemical shift variations are mainly due to the polarization contribution, the term which decreases slowly with the intermolecular distance. Because of the weaker polarity of adenine and thymine the geometric and polarization contributions are of closer absolute magnitude for the non hydrogen atoms of the intrastrand stacks but the polarization term is the determining contribution in the corresponding interstrand stacks. For the protons which undergo smaller shifts due to the polarization (or electric field effects) the role of the geometric contribution is more important and is even the leading one for the hydrogens of cytosine and thymine in the case of intrastrand stacking. The charge transfer plus exchange term has a non negligeable value for a limited number of cases corresponding to the shortest intermolecular interatomic distances. These results are discussed in relation with the qualitative differences observed between the proton and carbon spectra of dinucleotides and B-DNA duplexes.

Base Composition↗
PubMed1975

Effect of aromatic molecules on the aggregation of C-phycocyanin. Quantum chemical calculations on phycocyanobilin and phycoerythrobilin.

The energies of the highest occupied and lowest empty molecular orbitals were calculated for the chromophore groups of the proteins phycocyanin and phycoerythrin. These tetrapyrrole groups on the algal proteins are shown to provide them with the potential of ating as efficient electron donors and acceptors. In addition, the pi electron charges and bond orders were also computed.

Chemical Phenomena↗
PubMed1985

Electron density calculations as an extension of protein structure refinement. Streptomyces griseus protease A at 1.5 A resolution.

Ab initio quantum mechanical calculations have been used to obtain details of the electron density distribution in a high-resolution refined protein structure. It is shown that with accurate atomic co-ordinates, electron density may be calculated with a quality similar to that which can be obtained directly from crystallographic studies of small organic molecules, and that this density contains information relevant to the understanding of catalysis. Atomic co-ordinates from the 1.8 A and 1.5 A resolution refinements of the crystal structure of protease A from Streptomyces griseus have been used to examine the influence of the environment on the electron density in the side-chain of the active site histidine (His57). The neighbouring aspartic acid 102 is the dominant factor in the environment, and quantum mechanical calculations have been performed on these two residues. Most interesting from the point of view of understanding the catalytic process is the effect that Asp102 has on the electron density in the region of the imidazole nitrogen (N epsilon 2) adjacent to the active site serine 195. In the positively charged imidazolium species, there is a polarization of the N epsilon 2-H bond, reducing the bonding density in a manner that may lower the height of the energy barrier for proton transfer. In the uncharged imidazole species, the proximity of Asp102 causes a movement of density from the lone pair region of the N epsilon 2 into the pi bonding region above and below the plane of the ring. Although it is shown that the primary effect of the aspartic acid is electrostatic, this movement is perpendicular to the direction of the electric field inducing it.

Amino Acid Sequence↗
PubMed1989

A new algorithm for deriving pulsatile blood flow waveforms tested using stimulated dynamic angiographic data.

In vascular pathology the assessment of disease severity and monitoring of treatment requires quantitative and reproducible measurements of arterial blood flow. We have developed a new technique for processing sequences of dynamic digital X-ray angiographic images. We have tested it using computer simulated angiographic data which includes the effect of pulsatile blood flow and X-ray quantum noise. A parametric image was formed in which the image grey-level represents dye concentration as a function of time and distance along a vessel segment. Adjacent concentration--distance profiles in the parametric image were re-registered along the vessel axis until a match occurred. A match was defined as the point where the sum of squares of the differences in the two profiles was a minimum. The distance translated per frame interval is equal to the bolus velocity. We have tested several contrast medium injection methods including constant flow and a range of discrete pulses per second. The technique proved to be robust and independent of injection technique. Average blood flow was measured for simulated pulsatile waveforms with mean flows of up to 650 ml/min (peak velocities up to 186 cm/s) in a range of diameters from 2 mm to 6 mm. The standard deviation of the error in the mean flow estimates over the whole range of velocities and vessel sizes was +/- 1.4 cm/s.

Algorithms↗