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  • 1
    Electronic Resource
    Electronic Resource
    Premelting thermal fluctuational base pair opening probability of poly(dA) · poly(dT) as predicted by the modified self-consistent phonon theory (1991)
    New York : Wiley-Blackwell
    Biopolymers 31 (1991), S. 139-148 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We employ a mean field, modified, self-consistent phonon theory to evaluate the single base-pair opening rate and the probability of a base pair in the amino proton exchangeable state for the homopolymer poly(dA) · poly(dT) at temperatures below the helix-coil transition region. Our calculated premelting single base-pair opening probabilities are in general agreement with several available experimental estimates from imino proton exchange and formaldehyde-induced DNA melting measurements. These calculated opening probabilities, however, are in disagreement with the prediction of the helix-coil transition theory. Possible reasons for the differences are discussed, especially the possible different definition of a meaningful open state in the premelting region. The premelting open state of the modified self-consistent phonon approximation theory seems to be appropriate to describe a solvent-accessible open configuration that is sufficient to facilitate important chemical reactions such as imino proton exchange and formaldehyde reaction with the bases. This can be compared with the completely unstacked open state of the helix-coil transition theory originally defined in the helix-coil transition region. We propose that the amino proton exchangeable state is different from the open state associated with melting and only involves the breaking of the amino interbase H bond. The agreement between the calculated and experimentally estimated probability of a base pair in the amino proton exchangeable state seems to support this hypothesis.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360310202
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  • 2
    Electronic Resource
    Electronic Resource
    Hybrid Monte Carlo simulations theory and initial comparison with molecular dynamics (1993)
    New York : Wiley-Blackwell
    Biopolymers 33 (1993), S. 1307-1315 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A formal partially dynamical approach to ergodic sampling, hybrid Monte Carlo, has been adapted for the first time from its proven application in quantum chromodynamics to realistic molecular systems. A series of simulations of pancreatic trypsin inhibitor were run using temperature-rescaled molecular dynamics and hybrid Monte Carlo. It was found that simulations run using hybrid Monte Carlo equilibrated an order of magnitude faster than those run using temperature-rescaled molecular dynamics. Certain aspects of improved performance obtained using hybrid Monte Carlo are probably due to the increased efficiency with which this algorithm explores phase space. To discuss this we introduce the notion of “trajectory stiffness”. © 1993 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360330815
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  • 3
    Electronic Resource
    Electronic Resource
    Premelting thermal fluctuational interbase hydrogen-bond disrupted states of a B-DNA guanine-cytosine base pair: Significance for amino and imino proton exchange (1991)
    New York : Wiley-Blackwell
    Biopolymers 31 (1991), S. 1273-1281 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Modified self-consistent phonon theory when applied to the DNA double helix indicates the existence of fairly long-lived states in which single interbase H bonds are disrupted. One can then postulate a number of situations in which particular disrupted H bonds can enhance particular proton exchange. In this paper we postulate a number of such partially open states for a B-conformation GC base pair and calculate the probability of each of these states for a B-conformation poly(dG) · poly(dC). We compare these probabilities to those probabilities needed to explain various observed proton exchange rates. We propose that, for a GC base pair in B conformation, there are two amino proton exchangeable states - a cytosine amino proton exchangeable state and a guanine amino proton exchangeable state; both require the disruption of only the corresponding inter base H bond. The imino proton exchange, however, requires the disruption of all three inter base H bonds and this defines a third open state. Our calculated probabilities for a GC base pair in these three states are in fair agreement with available experimental estimates from measurements of amino and imino proton exchange.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360311105
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  • 4
    Electronic Resource
    Electronic Resource
    A histological study of the “stomach” and caecum in the genus Pheretima (Oligochaeta) (1941)
    New York, NY : Wiley-Blackwell
    Journal of Morphology 68 (1941), S. 507-517 
    Details
    ISSN: 0362-2525
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jmor.1050680305
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  • 5
    Electronic Resource
    Electronic Resource
    Diffusion of oxygen, nitrogen and their mixtures in carbon molecular sieve (1994)
    Hoboken, NJ : Wiley-Blackwell
    AIChE Journal 40 (1994), S. 577-585 
    Details
    ISSN: 0001-1541
    Keywords: Chemistry ; Chemical Engineering
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Diffusivities of oxygen, nitrogen and their mixtures in carbon molecular sieve are measured under conditions used for kinetic separation of air by adsorption (elevated pressures). In binary diffusion, codiffusion enhances fluxes for both components, whereas counterdiffusion has the opposite effects; for both cases, the effects are significantly more pronounced for the fast diffusing component. The multicomponent diffusion theory developed earlier in this laboratory for surface diffusion is reformulated for diffusion in molecular sieves. Multicomponent diffusivities can be predicted from the following pure-component information: concentration-dependent diffusivities and diffusional activation energies. Predicted binary diffusion results agree fairly with the experimental data for oxygen and nitrogen in carbon molecular sieve.
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/aic.690400402
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  • 6
    Electronic Resource
    Electronic Resource
    Surface diffusion of multilayer adsorbed species (1993)
    Hoboken, NJ : Wiley-Blackwell
    AIChE Journal 39 (1993), S. 599-606 
    Details
    ISSN: 0001-1541
    Keywords: Chemistry ; Chemical Engineering
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A model based on kinetic theory is derived for surface diffusion of multilayer adsorbed species on a homogeneous surface. A simple solution is obtained for expressing the concentration dependence of surface diffusivity. For monolayer adsorbate, the solution is reduced to the classical HIO model. This solution, in principle, requires no fitting parameters and is capable of predicting the unique concentration dependent behavior exhibited by multilayer surface diffusion, where the diffusivity first increases with surface concentration to a maximum followed by a decrease. Seventeen sets of experimental data from the literature are used to test the model, with fair results. It is also shown that heats of adsorption can be calculated from multilayer surface diffusivity data by using this model.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/aic.690390408
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  • 7
    Electronic Resource
    Electronic Resource
    Concentration dependence of surface diffusion and zeolitic diffusion (1991)
    Hoboken, NJ : Wiley-Blackwell
    AIChE Journal 37 (1991), S. 1579-1582 
    Details
    ISSN: 0001-1541
    Keywords: Chemistry ; Chemical Engineering
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/aic.690371015
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  • 8
    Electronic Resource
    Electronic Resource
    Siderophore-Mediated microbial iron(III) uptake: An exercise in chiral recognition (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Chirality 5 (1993), S. 359-365 
    Details
    ISSN: 0899-0042
    Keywords: synthetic siderophore analogs ; hydroxamates ; ferrichrome ; ferrioxamine ; coprogen ; Pseudomonas putida ; membrane receptors ; transport proteins ; growth promotion ; growth inhibition ; Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular recognition by microbial receptors for siderophores [natural iron(III) carriers] is examined with synthetic iron(III) carriers as structural probes. The iron(III) carriers have been designed to reproduce the two essential features of the natural siderophores: the capability to form octahedral iron(III) binding cavities and to fit specific membrane receptors. Specifically, analogs of tripodal ferrichrome and linear ferrioxamines have been prepared and examined. The ferrichrome analogs rely on C3-symmetric binders that are assembled from triscarboxylates as anchors, amino acids as bridges, and terminal hydroxamate groups as binding sites. The ferrioxamine analogs are based on linear assemblies of three identical monomers, each derived from a chiral amino acid. The deliberate use of animo acid residues as variable building blocks enables us to systematically modify the molecules' envelopes and the preferred absolute configuration of the iron(III) complexes until optimal performance is reached. Examination of the synthetic analogs in Pseudomonas putida demonstrates that the domains around the iron(III) center and their chiral sense dictate the extent of recognition by the membrane receptors. It is also shown that the synthetic siderophore analogs may be designed to either exert a broader, or a more narrow range of microbial activity than the natural siderophores. The implications of these findings are discussed in relation to the possible design of species-specific antimicrobial agents. © 1993 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/chir.530050516
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  • 9
    Electronic Resource
    Electronic Resource
    Differences in melting behavior between homopolymers and copolymers of DNA: Role of nonbonded forces for GC and the role of the hydration spine and premelting transition for AT (1993)
    New York : Wiley-Blackwell
    Biopolymers 33 (1993), S. 797-812 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Melting measurements of the mono-base-pair DNA polymers showed that the melting temperature Tm of the B-DNA homopolymer poly (dA ) · poly (dT) is higher than that of the copolymer poly [d(A-T)]. On the other hand, the Tmof the B-DNA homopolymer poly (dG) · poly (dC) is lower than that of the copolymer poly [d (G-C)]. From a structural point of view, the cross-strand base-stacking interaction in a DNA homopolymer is weaker than that in a DNA copolymer with the same base pair. One would then expect that all the DNA homopolymers are less stable than the copolymer with the same base pair. We find that the inversion of the melting order seen in the AT mono-base-pair DNA polymers is caused by the enhanced thermal stability of poly (dA) · poly (dT) from a well-defined spine of hydration attached to its minor groove. In this paper we employ the modified self-consistent phonon theory to calculate base-pair opening probabilities of four B-DNA polymers: poly(dA)-poly(dT), poly(dG) · poly(dC), poly[d(A-T)], and poly[d(G-C)] at temperatures from room temperature through the melting regions. Our calculations show that the spine of hydration can give the inverted melting order of the AT polymers as compared to the GC polymers in fair agreement with experimental measurements. Our calculated hydration spine disruption behavior in poly(dA) · poly(dT) at premelting temperatures is also in agreement with experimentally observed premelting transitions in poly (dA) · poly (dT). The work is in a sense a test of the validity of our models of nonbonded interactions and spine of hydration interactions. We find we have to develop the concept of a strained bond to fit observations in poly (dA) · poly(dT). The strained-bond concept also explains the otherwise anomalous stability of the hydration chain. © 1993 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360330508
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  • 10
    Electronic Resource
    Electronic Resource
    A cooperative self-consistent microscopic theory of thermally induced melting of a repeat sequence DNA polymer (1993)
    New York : Wiley-Blackwell
    Biopolymers 33 (1993), S. 351-362 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We attempt to extend the modified self-consistent phonon theory to describe thermal fluctuational base-pair opening of repeat sequence DNA polymers in the helix-coil transition region as well as in the premelting region. A microscopic base-pair open state is introduced and the effect of this open state is taken into account self-consistently in a mean field system that models the DNA polymer. Our analysis indicates the structure of this open state changes with temperature in such a manner that on average a base pair opens and unstacks with its neighbors more completely as temperature increases. We apply this theory to a homopolymer - poly(dG) · poly(dC) to evaluate the base-pair opening probability in a temperature range from 273 to 366.5 K. At 366.5 K the system undergoes cooperative melting. Our calculated base-pair opening probabilities are in general agreement with several experimental estimates at room temperature. The calculated probabilities show typical melting curve behavior at temperatures close to the observed melting temperature. The cooperative modified self-consistent phonon approximation approach becomes a viable microscopic theory of melting. © 1993 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360330304
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