Publications
171 results found
Clay EH, Gould IR, 2005, A combined QM and MM investigation into guanine quadruplexes, JOURNAL OF MOLECULAR GRAPHICS & MODELLING, Vol: 24, Pages: 138-146, ISSN: 1093-3263
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- Citations: 21
Gould IR, 2005, Molecular modeling of Lysl_tRNA synthetase: Simulation meets experiment, 230th National Meeting of the American-Chemical-Society, Publisher: AMER CHEMICAL SOC, Pages: U1393-U1393, ISSN: 0065-7727
Gould IR, 2005, Investigations of light harvesting complexes, 230th National Meeting of the American-Chemical-Society, Publisher: AMER CHEMICAL SOC, Pages: U1298-U1298, ISSN: 0065-7727
Gould IR, 2005, Linear and non-linear spectroscopy of biological systems: Theory and experiment, 230th National Meeting of the American-Chemical-Society, Publisher: AMER CHEMICAL SOC, Pages: U2948-U2948, ISSN: 0065-7727
Cho BM, Walker RC, Amer H, et al., 2005, Effect of adiabaticity on electron dynamics in zinc myoglobin, JOURNAL OF PHYSICAL CHEMISTRY B, Vol: 109, Pages: 5954-5961, ISSN: 1520-6106
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- Citations: 6
Cho BM, Walker RC, Mercer IP, et al., 2005, Ultrafast relaxation inside proteins: calculation and measurement of electron-vibration coupling in enzymes, Berlin, 14th international conference on ultrafast phenomena, Niigata, Japan, 25 - 30 July 2004, Publisher: Springer-Verlag Berlin, Pages: 622-624
Rais D, Gould IR, Vilar R, et al., 2004, Structural and theoretical studies of new ruthenium-amidato complexes with phenanthroline ligands containing H-bonding groups, EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Pages: 1865-1872, ISSN: 1434-1948
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- Citations: 9
Cho BM, Walker RC, Mercer IP, et al., 2004, Ultrafast relaxation inside proteins: Calculation and measurement of electron-vibration coupling in enzymes, Pages: 622-624, ISSN: 0172-6218
Electron-vibration coupling in alcohol dehydrogenase and zinc substituted myoglobin was calculated using a quantum mechanics/molecular mechanics method. Good agreement with experimental measurements demonstrates the viability of the method.
Hughes SJ, Tanner JA, Hindley AD, et al., 2003, Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment., BMC Struct Biol, Vol: 3
BACKGROUND: Charging of transfer-RNA with cognate amino acid is accomplished by the aminoacyl-tRNA synthetases, and proceeds through an aminoacyl adenylate intermediate. The lysyl-tRNA synthetase has evolved an active site that specifically binds lysine and ATP. Previous molecular dynamics simulations of the heat-inducible Escherichia coli lysyl-tRNA synthetase, LysU, have revealed differences in the binding of ATP and aspects of asymmetry between the nominally equivalent active sites of this dimeric enzyme. The possibility that this asymmetry results in different binding affinities for the ligands is addressed here by a parallel computational and biochemical study. RESULTS: Biochemical experiments employing isothermal calorimetry, steady-state fluorescence and circular dichroism are used to determine the order and stoichiometries of the lysine and nucleotide binding events, and the associated thermodynamic parameters. An ordered mechanism of substrate addition is found, with lysine having to bind prior to the nucleotide in a magnesium dependent process. Two lysines are found to bind per dimer, and trigger a large conformational change. Subsequent nucleotide binding causes little structural rearrangement and crucially only occurs at a single catalytic site, in accord with the simulations. Molecular dynamics based free energy calculations of the ATP binding process are used to determine the binding affinities of each site. Significant differences in ATP binding affinities are observed, with only one active site capable of realizing the experimental binding free energy. Half-of-the-sites models in which the nucleotide is only present at one active site achieve their full binding potential irrespective of the subunit choice. This strongly suggests the involvement of an anti-cooperative mechanism. Pathways for relaying information between the two active sites are proposed. CONCLUSIONS: The asymmetry uncovered here appears to be a common feature of oligomeric aminoacyl-t
Walker RC, de Souza MM, Mercer IP, et al., 2002, Large and fast relaxations inside a protein: Calculation and measurement of reorganization energies in alcohol dehydrogenase, JOURNAL OF PHYSICAL CHEMISTRY B, Vol: 106, Pages: 11658-11665, ISSN: 1520-6106
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- Citations: 76
Kwok WM, Gould I, Ma C, et al., 2001, Vibrational studies of ground state 4-dimethylaminobenzonitrile (DMABN) and its ring deuterated isotopomer DMABN-d<sub>4</sub>, International Discussion Meeting of the Deutsche-Bunsen-Gesellschaft-fur-Physikalische-Chemie, Publisher: ROYAL SOC CHEMISTRY, Pages: 2424-2432, ISSN: 1463-9076
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- Citations: 17
Gould IR, 2001, Computational chemistry: Application to biological systems, MOLECULAR SIMULATION, Vol: 26, Pages: 73-+, ISSN: 0892-7022
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- Citations: 2
Ostler RB, Scully AD, Taylor AG, et al., 2000, The effect of pH on the photophysics and photochemistry of disulphonated aluminium phthalocyanine, Photochemistry and Photobiology, Vol: 71, Pages: 397-404, ISSN: 0031-8655
de Souza MM, Rumbles G, Gould IR, et al., 2000, A theoretical and experimental study of cyano- and alkoxy- substituted phenylenevinylene model compounds, Synthetic Metals, Vol: 111, Pages: 539-543, ISSN: 0379-6779
de Souza MM, Rumbles G, Gould IR, et al., 2000, A theoretical and experimental study of cyano- and alkoxy- substituted phenylenevinylene model compounds, Synthetic Metals, Vol: 111, Pages: 539-543, ISSN: 0379-6779
Ostler RB, Scully AD, Taylor AG, et al., 2000, The effect of pH on the photophysics and photochemistry of disulphonated aluminium phthalocyanine, Photochemistry and Photobiology, Vol: 71, Pages: 397-404, ISSN: 0031-8655
Griffiths EAH, Britovsek GJP, Gibson VC, et al., 1999, Full ab initio calculations on bis(imino)pyridine iron catalysts for ethylene polymerization., ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, Vol: 218, Pages: U762-U762, ISSN: 0065-7727
Griffiths EAH, Britovsek GJP, Gibson VC, et al., 1999, Highly active ethylene polymerisation catalysts based on iron: an ab initio study, Chemical Communications, Pages: 1333-1334, ISSN: 1359-7345
Eggeling J, Griffiths EAH, Gould IR, et al., 1999, Negative ion resonances and vibrational mode selectivity in inelastic electron scattering studies of hydrogen and diethylsilane adsorbed on Si(100), Chemical Physics Letters, Vol: 313, Pages: 805-811, ISSN: 0009-2614
Mercer IP, Gould IR, King DR, 1999, ARTICLES-BIOPHYSICAL CHEMISTRY-A Quantum Mechanical/Molecular Mechanical Approach to Relaxation Dynamics: Calculation of the Optical Properties of Solvated Bacteriochlorophyll-a, Journal of Physical Chemistry B-Condensed Phase, Vol: 103, Pages: 7720-7727
Templer RH, Klug DR, Gould IR, et al., 1999, Mathematics Laboratories for Science Undergraduates, Rethinking the Mathematics Curriculum, Editors: Hoyles, Morgan, Woodhouse, Hoyles, Morgan, Woodhouse, Hoyles, Morgan, Woodhouse, Publisher: Falmer Press, Pages: 140-154
Mulcahy CPA, Eggeling J, Gould I, et al., 1999, ARTICLES-PHYSICAL CHEMISTRY OF SURFACES AND INTERFACES-Resonant and Nonresonant Vibrational and Electronic Excitations in Trimethylaluminum Adsorbed on GaAs, Journal of Physical Chemistry B-Condensed Phase, Vol: 103, Pages: 3187-3194
Scholes GD, Gould IR, Cogdell RJ, et al., 1999, ARTICLES-BIOPHYSICAL CHEMISTRY-Ab Initio Molecular Orbital Calculations of Electronic Couplings in the LH2 Bacterial Light-Harvesting Complex of Rps Acidophila, Journal of Physical Chemistry B-Condensed Phase, Vol: 103, Pages: 2543-2553
Mulcahy CPA, Eggeling J, Gould I, et al., 1999, Resonant and nonresonant vibrational and electronic excitations in trimethylaluminum adsorbed on GaAs, Journal of Physical Chemistry B, Vol: 103, Pages: 3187-3194, ISSN: 1089-5647
Scholes GD, Gould IR, Cogdell RJ, et al., 1999, Ab initio molecular orbital calculations of electronic couplings in the LH2 bacterial light-harvesting complex of Rps. Acidophila, Journal of Physical Chemistry B, Vol: 103, Pages: 2543-2553, ISSN: 1089-5647
Krueger BP, Scholes GD, Gould IR, et al., 1999, Carotenoid mediated B8000-B850 coupling in LH2, Chemical Communications, Vol: 8, ISSN: 1359-7345
Mercer IP, Gould IR, Klug DR, 1999, A quantum mechanical/molecular mechanical approach to relaxation dynamics: Calculation of the optical properties of solvated bacteriochlorophyll-a, Journal of Physical Chemistry B, Vol: 103, Pages: 7720-7727, ISSN: 1089-5647
Fournier T, Scholes GD, Gould IR, et al., 1999, Triplet 1-nitronaphthalene and competitive energy and electron transfer reactions with trans-stilbene, Laser Chemistry, Vol: 19, Pages: 397-401, ISSN: 0278-6273
Griffiths EAH, Britovsek GJP, Gibson VC, et al., 1999, Highly active ethylene polymerisation catalysts based on iron: an ab initio study, Chemical Communications, Pages: 1333-1334, ISSN: 1359-7345
Rumbles G, Miller PF, deSouza MM, et al., 1999, Photoluminescence studies of the light-emitting species in new materials for polymer devices., Conference on Organic Light-Emitting Materials and Devices III, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, Pages: 101-108, ISSN: 0277-786X
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