ANU - The John Curtin School of Medical Research

Computational Proteomics and Therapy Design

Publications-Professor Jill Gready

2008

Abraham, M.J. and Gready, J.E., 2008, Ensuring mixing efficiency of replica-exchange molecular dynamics simulations. Journal of Chemical Theory and Computation 4(7), 1119-1128.

Kannappan, B. and Gready, J.E., 2008, Redefinition of Rubisco Carboxylase Reaction Reveals Origin of Water for Hydration and New Roles for Active-Site Residues. Journal of the American Chemical Society 130(45), 15063-15080.

2007

Cummins, P., Rostov, I., and Gready, J. (2007). Calculation of a complete enzymic reaction surface: Reaction and activation free energies for hydride-ion transfer in dihyrofolate reductase. Journal of Chemical Theory and Computation 3((3)), 1203-1211.

Gready, JE, Rostov, I and Cummins, PL (2007). Simulations of enzyme reaction mechanisms in active sites: accounting for an environment which is much more than a solvent perturbation. In: Modelling Molecular Structure and Reactivity in Biological Systems, Eds: KJ Naidoo, M Hann, J Gao, M Field and J Brady, Royal Society of Chemistry, London, pp. 101-118

Haworth, N.L., Gready, J.E., George, R.A., and Wouters, M.A., 2007, Evaluating the stability of disulfide bridges in proteins: a torsional potential energy surface for diethyl disulfide. Molecular Simulation 33(6), 475-485.

2006

Alonso, H., Bliznyuk, A. A., and Gready, J. E. (2006). Combining docking and molecular dynamic simulations in drug design. Med Res Rev 26(5), 531-68.

Alonso, H., and Gready, J. E. (2006). Integron-sequestered dihydrofolate reductase: a recently redeployed enzyme. Trends Microbiol 14(5), 236-42.

Strumbo, B., Sangiorgio, L., Ronchi, S., Gready, J. E., and Simonic, T. (2006). Cloning and analysis of transcripts and genes encoding fish-specific proteins related to PrP. Fish Physiology and Biochemistry 32, 339-353.

2005

Gready, J. E. (2005). "Defining the Inefficiencies in the Chemical Mechanismsof the Photosynthetic Enzyme Rubisco by Computational Simulation." Artificial Photosynthesis - From Basic Biology to Industrial Application (A. F. C. a. C. Critchely, Ed.) Wiley-VCH.

Zelensky, A. N., and Gready, J. E. (2005). The C-type lectin-like domain superfamily. Febs J 272(24), 6179-217.

Alonso, H., Gillies, M. B., Cummins, P. L., Bliznyuk, A. A., and Gready, J. E. (2005). Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase. J Comput Aided Mol Des 19(3), 165-87.

Cummins, P.L. and Gready, J.E., (2005). Computational methods for the study of enzymic reaction mechanisms III: a perturbation plus QM/MM approach for calculating relative free energies of protonation. J Comput Chem 26(6), 561-568.

Premzl, M., Delbridge, M., Gready, J.E., Wilson, P., Johnson, M., Davis, J., Kuczek, E., and Graves, J.A.M., 2005, The prion protein gene: Identifying regulatory signals using marsupial sequence. Gene 349, 121-134.

2004

Gustiananda, M; Liggins,JR.; Cummins, PL and Gready, JE. (2004) Conformation of prion protein repeat peptides probed by FRET measurements and MD simulations. Biophys. J. 86, 2467-2483.

Kuchel, PW; Bubb, WA; Ramadan, S; Chapman, BE; Philp, DJ; Coen, M; Gready, JE; Harvey, PJ; McLean, AJ and Hook, J.
(2004). 31P MAS-NMR of human erythrocytes; independence of cell volume on spin rate. Mag. Res. Med. 52, 663-668.

Booth, HS; Maindonald, JH; Wilson, SR and Gready, JE. (2004). An efficient Z-score algorithm for assessing sequence alignments.
J. Comput. Biol. 11, 616-625.

Zelensky, AN and Gready, JE. (2004). C-type-lectin-like domains in Fugu rubripes. BMC Genomics 5:51 (22 pages).

Premzl, M; Gready, JE.; Jermiin,L.S; Simonic,T and Marshall Graves J.A. (2004) Evolution of vertebrate genes related to Prion and Shadoo proteins - clues from comparative genomic analysis. Mol. Biol. Evol., published online 1/9/04.

Gready, JE. (2004). Defining the inefficiencies in the chemical mechanism of the photosynthetic enzyme Rubisco by computational simulation. In Artificial Photosynthesis, A. Collings, ed., Wiley-VCH, Weinheim, in press.

2003

Premzl, M; Sangiorgio, L; Strumbo, B; Graves, JAM; Simonic, T; Gready, JE. 2003. Shadoo, a new protein highly conserved from fish to mammals and with similarity to prion protein. GENE 314C: 89-102.

Cummins PL, Bliznyuk AA and Gready JE (2003). Solvent simulation. in Computational Medicinal Chemistry and Drug Discovery, J. P.Tollenaere, P. Bultnink, H. de Winter and W. Langenaeker, eds., Marcel Dekker, New York,pp. 259-294.

Cummins PL and Gready JE (2003). Computational methods for the study of enzymic reaction mechanisms II: An overlapping mechanically embedded method for hybrid semiempirical-QM/MM calculations. Theochem 632, 245-255.

Gebauer MG, McKinlay C and Gready JE (2003). Synthesis of quaternised 2- aminopyrimido[4,5-d]pyrimidin-4(3H)-ones and their biological activity with dihydrofolate reductase. Eur J MedChem, 38, 719-728.

Zelensky AN and Gready JE (2003). Comparative analysis of structural properties of the C-type-lectin-like domain (CTLD). Proteins 52, 466-477.

Zuegg J, Bliznyuk AA and Gready JE (2003). Comparison of electrostatic potential around proteins calculated from Amber and AM1 charges: Application to mutants of prion protein. Mol Phys. 101, 2437-2450.

2002

Cummins PL, Greatbanks SP, Rendell AP, Gready JE. (2002). Computational methods for the study of enzymic reaction mechanisms. 1. Application to the hydride transfer step in the catalysis of Dihydrofolate reductase. Journal of Phys. Chem. 106, 9934-9944

Harvey PJ, Gready JE, Yin ZL, Le Couteur DG, McLean AJ. (2002). Hepatic phospholipid changes induced by sustained oxygen supplementation. Pharmacol Toxicol. 91, 150-152

Titmuss SJ, Cummins PL, Rendel AP, Bliznyuk AA and Gready JE (2002). Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis. J Comp Chem 23, 1314-1322.

Cummins PL, Titmuss SJ, Jayatilaka D, Bliznyuk AA, Rendell AP, Gready JE (2002). Comparison of semiempirical and ab initio QM decomposition analyses for the interaction energy between molecules. Chemical Physics Letters. 352, 245-251

Gustiananda M, Haris P, Milburn PJ and Gready JE. (2002). Copper-induced conformational change in a marsupial prion protein repeat peptide probed using FTIR spectroscopy. FEBS Letters. 512, 38-42

2001

Cummins PL and Gready JE (2001). Energetically most likely substrate and active-site protonation sites and pathways in the catalytic mechanism of dihydrofolate reductase. J. Am. Chem. Soc. 123, 3418-3428

Gready JE and Cummins PL (2001). Dihydrofolate reductase: free energy calculations for the design of mechanism-based inhibitors. "in Free Energy Calulations in Rational Drug Design", M.R.Reddy and M.D. Erion, eds., Kluwer Academic/Plenum Publishers. pp 343-364,

Mauser H, King WA, Gready JE, Andrews TJ. (2001) Co2Fixations by Rubisco: Computational Dissection of the Key Steps of Carboxylation, Hydration, and C-C Bond Cleavage. Journal of the American Chemical Society 123, 10821-10829.

2000

R.K. Schmidt and J.E.Gready (2000) Conformational preferences of the substrates of lactate dehydrogenase. THEOCHEM. 489: 101-112.

S.J. Titmuss, P.L. Cummins, A.A. Bliznyuk, A.P.L. Rendell and J.E. Gready (2000) Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to the study of enzume reactions. Chemical Physics Letters 320: 169-176

P.L. Cummins and J.E. Gready (2000) Combined quantum and molecular mechanics (QM/MM) study of the ionization state of 8-methylpterin substrate bound to dihydrofolate reductase. J. Physical Chem. B. 104: 4503-4510

P.J. Harvey, J.E. Gready, , Z.Yin, D.G. Le Couteur and A.J. McLean (2000) Acute oxygen supplementation restores markers of hepatocyte energy status and hypoxia in cirrhotic rat livers. J. Pharm. & Experi. Therapeutics. 293: 641-645

S.P. Greatbanks, J.E. Gready, A.C. Limaye and A.P. Rendell (2000) Comparison of enzyme polarization of ligands and charge-transfers effects for dihydrofolare reductase using point-charge embedded ab initio QM and linear-scaling semiempirical QM methods. J. Computational Chem. 21: 788-811

P.L. Cummins and J.E. Gready (2000) QM/MM adn SCRF studies of the ionization state of 8-methylpterin substrate bound to dihydrofolate reductase: existance of a low-barrier hydrogen bond. J. Mol. Graph. Modelling. 18: 42-49

Zuegg and J.E.Gready (2000) Molecular dynamics simulations of human prion protein including the N-linked oligosaccharides and GPI anchor. Glycobiology 10: 959-974

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