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  • 1
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    Open "back door" in a molecular dynamics simulation of acetylcholinesterase (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-03-04
    Description: The enzyme acetylcholinesterase generates a strong electrostatic field that can attract the cationic substrate acetylcholine to the active site. However, the long and narrow active site gorge seems inconsistent with the enzyme's high catalytic rate. A molecular dynamics simulation of acetylcholinesterase in water reveals the transient opening of a short channel, large enough to pass a water molecule, through a thin wall of the active site near tryptophan-84. This simulation suggests that substrate, products, or solvent could move through this "back door," in addition to the entrance revealed by the crystallographic structure. Electrostatic calculations show a strong field at the back door, oriented to attract the substrate and the reaction product choline and to repel the other reaction product, acetate. Analysis of the open back door conformation suggests a mutation that could seal the back door and thus test the hypothesis that thermal motion of this enzyme may open multiple routes of access to its active site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gilson, M K -- Straatsma, T P -- McCammon, J A -- Ripoll, D R -- Faerman, C H -- Axelsen, P H -- Silman, I -- Sussman, J L -- New York, N.Y. -- Science. 1994 Mar 4;263(5151):1276-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Houston, TX 77204-5641.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8122110" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylcholine/metabolism ; Acetylcholinesterase/*chemistry/metabolism ; Binding Sites ; Catalysis ; Choline/metabolism ; Computer Simulation ; Crystallography, X-Ray ; Electrochemistry ; Models, Molecular ; *Protein Conformation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
    Electronic Resource
    Electronic Resource
    Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 9025-9031 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new method of simultaneously scaling and shifting the Lennard-Jones (LJ) potential in molecular dynamics (MD) and thermodynamic integration (TI) simulations is presented. The approach allows the smooth creation or annihilation of atoms or molecules in an ensemble of solvent molecules during a molecular simulation. By scaling and shifting the LJ potential in the direction of the interatomic distance between particles, the method eliminates the problem of the creation or annihilation of a large repulsive LJ potential at the initial or final state of a TI. The optimal degree of shifting and scaling the LJ potential as a function of a control variable λ was studied for the annihilation and creation of neon in aqueous solution. The method was further tested on the calculation of the free energy of aqueous solvation of a small molecule, ethanol. In contrast to linear scaling of the LJ potential during TI, the calculated free energies using the new separation-shifted scaling approach are reasonably well converged after 200–500 ps of simulation and show smaller hysteresis comparing forward and reverse TI.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.466707
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  • 3
    Electronic Resource
    Electronic Resource
    Inversion of receptor binding preferences by mutagenesis: Free energy thermodynamic integration studies on sugar binding to L-arabinose binding proteins (1993)
    s.l. : American Chemical Society
    Biochemistry 32 (1993), S. 7428-7434 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00080a013
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  • 4
    Electronic Resource
    Electronic Resource
    Free energy of hydrophobic hydration: A molecular dynamics study of noble gases in water (1986)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 85 (1986), S. 6720-6727 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The potential utility and limitations of two methods to determine free energy differences from molecular dynamics simulations (MD) are studied. The computation of the free energy of hydration of the inert gases serves as a simple but illustrative example. Good results are obtained for the inert gases from a perturbation treatment, using a reference ensemble obtained from a MD simulation of a cavity in water, if these atoms are comparable in size to the cavity and the calculated free energy differences are small. This limits the applicability of the perturbation treatment of a small number of cases. Larger free energy differences can be obtained with reasonable accuracy from MD simulations with continuously changing interaction parameters. This integration method is more generally applicable, but makes an additional simulation necessary.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.451846
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  • 5
    Electronic Resource
    Electronic Resource
    Multiconfiguration thermodynamic integration (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 95 (1991), S. 1175-1188 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A modified thermodynamic integration technique is presented to obtain free energy differences from molecular dynamics simulations. In this multiconfiguration thermodynamic integration technique, the commonly employed single configuration (slow growth) approximation is not made. It is shown, by analysis of the sources of error, how the multiconfiguration variant of thermodynamic integration allows for a soundly based assessment of the statistical error in the evaluated free energy difference. Since ensembles of configurations are generated for each integration step, a statistical error can be evaluated for each integration step. By generating ensembles of different lengths, the statistical error can be equally distributed over the integration. This eliminates the difficult problem in single configuration thermodynamic integrations of determining the best rate of change of the Hamiltonian, which is usually based on equally distributing the free energy change. At the same time, this procedure leads to a more efficient use of computer time by providing the possibility of added accuracy from separate calculations of the same Hamiltonian change. The technique is applied to a simple but illustrative model system consisting of a monatomic solute in aqueous solution. In a second example, a combination of multiconfiguration thermodynamic integration and thermodynamic perturbation is used to obtain the potentials of mean force for rotation of the sidechain dihedral angles for valine and threonine dipeptides with restrained backbones in aqueous solution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.461148
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  • 6
    Electronic Resource
    Electronic Resource
    Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations (1988)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 89 (1988), S. 5876-5886 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations is analyzed. The hydration of the ions Na+ , K+ , Ca++ , F−, Cl−, and Br− is used as the process to illustrate the potential utility of the method. A neon–water system is used as a reference system. The parameters that influence the performance and accuracy of the thermodynamic integration, in which the potential interaction parameters are gradually and continuously changed, are studied. These parameters include the total simulation time, the magnitude of the time step for the numerical integration of the equations of motion, the system size, and the cutoff radii for the intermolecular interactions. Fast convergence is found for the Gibbs free energy difference between Ne and Na+ with respect to total simulation time. The time step and system size are relatively unimportant. The use of cutoff radii, for the ion–water but especially unfortunately also the water–water intermolecular interactions, seriously influences the results obtained. A simple correction for the use of cutoff radii cannot be made. Results are compared to experimental values.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.455539
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  • 7
    Electronic Resource
    Electronic Resource
    Treatment of rotational isomers in free energy calculations. II. Molecular dynamics simulation study of 18-crown-6 in aqueous solution as an example of systems with large numbers of rotational isomeric states (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 3631-3637 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The evaluation of free energy differences using the perturbation method or thermodynamic integration method requires special caution if multiple rotational isomeric states may exist in the system under investigation. In this article a recently suggested procedure to properly treat rotational isomeric states is illustrated with a molecular dynamics simulation of an aqueous solution of uncomplexed 18-crown-6 crown ether, as an example of a system in which large numbers of isomeric states may exist. By using very long molecular dynamics simulations, thermodynamic perturbation methods and symmetry arguments, the free energy of host organization into the conformation required to form the complex with K+ is estimated to be 2.6 kJ mol−1. It has also been found that the lowest energy conformations of 18-crown-6 in vacuo do not necessarily correspond to the most populated conformations in aqueous solution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.456896
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  • 8
    Electronic Resource
    Electronic Resource
    Treatment of rotational isomers in free energy evaluations. Analysis of the evaluation of free energy differences by molecular dynamics simulations of systems with rotational isomeric states (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 90 (1989), S. 3300-3304 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Using 1,2-dimethoxy ethane in aqueous solution as an example, the applicability of the perturbation method and the thermodynamic integration technique to evaluate free energy differences is considered for systems with multiple rotational isomeric states. It is shown that the naive application of these methods to evaluate free energy differences for such systems, even in a simple case such as the free energy of hydration of 1,2-dimethoxy ethane, may lead to unreasonable results. This problem is due to the fact that, in a conventional simulation, it is unlikely that all isomeric states will be sampled with the appropriate equilibrium probabilities. A procedure is proposed to estimate the contributions of isomeric states in free energy difference calculations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.456651
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  • 9
    Electronic Resource
    Electronic Resource
    Treatment of rotational isomeric states. III. The use of biasing potentials (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 5032-5039 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A technique is described to determine umbrella biasing potentials that can be used to enhance sampling of rotational isomeric states in molecular simulations of polypeptides in water. The analytical biasing potential functions are obtained through fitting of potentials of mean force obtained by thermodynamic integration simulations to a small number of functions used to describe dihedral torsion. The resulting dramatic increase in efficiency of sampling is illustrated by comparison of molecular simulations of the alanine–dipeptide molecule in aqueous solution, with and without the use of the biasing potentials. The same biasing potentials were used in simulations of the alanine–tripeptide and the alanine–heptapeptide in aqueous solution. Similar dramatic increases in sampling efficiency were observed for these simulations, when the biasing potentials were applied, which suggests that these biasing potentials, although determined for the dipeptide, may be transferable to larger peptide chains. It is illustrated how the biasing potentials can be used in biasing potential annealing simulations, leading to rapid folding of peptide chains into aqueous solution structures with low energy.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468409
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  • 10
    Electronic Resource
    Electronic Resource
    The missing term in effective pair potentials (1987)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 91 (1987), S. 6269-6271 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100308a038
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