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Items: 1 to 50 of 58

1.

Revised mechanism of carboxylation of ribulose-1,5-biphosphate by rubisco from large scale quantum chemical calculations.

Cummins PL, Kannappan B, Gready JE.

J Comput Chem. 2018 Aug 5;39(21):1656-1665. doi: 10.1002/jcc.25343. Epub 2018 May 14.

PMID:
29756365
2.

Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All.

Cummins PL, Kannappan B, Gready JE.

Front Plant Sci. 2018 Mar 1;9:183. doi: 10.3389/fpls.2018.00183. eCollection 2018.

3.

Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5.

Abraham MJ, Gready JE.

J Comput Chem. 2011 Jul 15;32(9):2031-40. doi: 10.1002/jcc.21773. Epub 2011 Apr 5.

PMID:
21469158
4.

Methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase (MeTr): protonation state of the ligand and active-site residues.

Alonso H, Cummins PL, Gready JE.

J Phys Chem B. 2009 Nov 5;113(44):14787-96. doi: 10.1021/jp900181g.

PMID:
19827815
5.

Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.

Worden AZ, Lee JH, Mock T, Rouzé P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KF, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough UW, Van de Peer Y, Grigoriev IV.

Science. 2009 Apr 10;324(5924):268-72. doi: 10.1126/science.1167222.

6.

Putative functional role for the invariant aspartate 263 residue of Rhodospirillum rubrum Rubisco.

Liggins JR, Gready JE.

Biochemistry. 2009 Mar 17;48(10):2226-36. doi: 10.1021/bi802159e.

PMID:
19231887
7.

Redefinition of rubisco carboxylase reaction reveals origin of water for hydration and new roles for active-site residues.

Kannappan B, Gready JE.

J Am Chem Soc. 2008 Nov 12;130(45):15063-80. doi: 10.1021/ja803464a. Epub 2008 Oct 15.

PMID:
18855361
8.

Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations.

Abraham MJ, Gready JE.

J Chem Theory Comput. 2008 Jul;4(7):1119-28. doi: 10.1021/ct800016r.

PMID:
26636365
9.

Identification of the RGG box motif in Shadoo: RNA-binding and signaling roles?

Corley SM, Gready JE.

Bioinform Biol Insights. 2008 Nov 19;2:383-400.

10.

Calculation of a Complete Enzymic Reaction Surface:  Reaction and Activation Free Energies for Hydride-Ion Transfer in Dihydrofolate Reductase.

Cummins PL, Rostov IV, Gready JE.

J Chem Theory Comput. 2007 May;3(3):1203-11. doi: 10.1021/ct600313b.

PMID:
26627439
11.

Evaluating the stability of disulfide bridges in proteins: a torsional potential energy surface for diethyl disulfide.

Haworth NL, Gready JE, George RA, Wouters MA.

Mol Simul. 2007 May;33(6-8):475-485. Epub 2007 Aug 15.

12.

Combining docking and molecular dynamic simulations in drug design.

Alonso H, Bliznyuk AA, Gready JE.

Med Res Rev. 2006 Sep;26(5):531-68. Review.

PMID:
16758486
13.

Integron-sequestered dihydrofolate reductase: a recently redeployed enzyme.

Alonso H, Gready JE.

Trends Microbiol. 2006 May;14(5):236-42. Epub 2006 Apr 3. Review.

PMID:
16584884
14.

The C-type lectin-like domain superfamily.

Zelensky AN, Gready JE.

FEBS J. 2005 Dec;272(24):6179-217. Review.

15.

Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase.

Alonso H, Gillies MB, Cummins PL, Bliznyuk AA, Gready JE.

J Comput Aided Mol Des. 2005 Mar;19(3):165-87.

PMID:
16059670
16.

The prion protein gene: identifying regulatory signals using marsupial sequence.

Premzl M, Delbridge M, Gready JE, Wilson P, Johnson M, Davis J, Kuczek E, Marshall Graves JA.

Gene. 2005 Apr 11;349:121-34.

PMID:
15777726
18.

An efficient Z-score algorithm for assessing sequence alignments.

Booth HS, Maindonald JH, Wilson SR, Gready JE.

J Comput Biol. 2004;11(4):616-25.

PMID:
15579234
19.

Evolution of vertebrate genes related to prion and Shadoo proteins--clues from comparative genomic analysis.

Premzl M, Gready JE, Jermiin LS, Simonic T, Marshall Graves JA.

Mol Biol Evol. 2004 Dec;21(12):2210-31. Epub 2004 Sep 1.

PMID:
15342797
20.

31P MAS-NMR of human erythrocytes: independence of cell volume from angular velocity.

Kuchel PW, Bubb WA, Ramadan S, Chapman BE, Philp DJ, Coen M, Gready JE, Harvey PJ, McLean AJ, Hook J.

Magn Reson Med. 2004 Sep;52(3):663-8.

21.

C-type lectin-like domains in Fugu rubripes.

Zelensky AN, Gready JE.

BMC Genomics. 2004 Aug 1;5(1):51.

22.

Conformation of prion protein repeat peptides probed by FRET measurements and molecular dynamics simulations.

Gustiananda M, Liggins JR, Cummins PL, Gready JE.

Biophys J. 2004 Apr;86(4):2467-83.

23.

Shadoo, a new protein highly conserved from fish to mammals and with similarity to prion protein.

Premzl M, Sangiorgio L, Strumbo B, Marshall Graves JA, Simonic T, Gready JE.

Gene. 2003 Sep 18;314:89-102.

PMID:
14527721
24.
25.

Comparative analysis of structural properties of the C-type-lectin-like domain (CTLD).

Zelensky AN, Gready JE.

Proteins. 2003 Aug 15;52(3):466-77.

PMID:
12866057
26.

Hepatic phospholipid changes induced by sustained oxygen supplementation.

Harvey PJ, Gready JE, Yin Z, Le Couteur DG, McLean AJ.

Pharmacol Toxicol. 2002 Sep;91(3):150-2. Review. No abstract available.

PMID:
12427116
27.
28.

Copper-induced conformational change in a marsupial prion protein repeat peptide probed using FTIR spectroscopy.

Gustiananda M, Haris PI, Milburn PJ, Gready JE.

FEBS Lett. 2002 Feb 13;512(1-3):38-42.

29.

CO(2) fixation by Rubisco: computational dissection of the key steps of carboxylation, hydration, and C-C bond cleavage.

Mauser H, King WA, Gready JE, Andrews TJ.

J Am Chem Soc. 2001 Nov 7;123(44):10821-9.

PMID:
11686683
30.
31.

Identification of active-site residues of the pro-metastatic endoglycosidase heparanase.

Hulett MD, Hornby JR, Ohms SJ, Zuegg J, Freeman C, Gready JE, Parish CR.

Biochemistry. 2000 Dec 26;39(51):15659-67.

PMID:
11123890
32.
34.

Acute oxygen supplementation restores markers of hepatocyte energy status and hypoxia in cirrhotic rats.

Harvey PJ, Gready JE, Yin Z, Le Couteur DG, McLean AJ.

J Pharmacol Exp Ther. 2000 May;293(2):641-5.

PMID:
10773039
35.

Enzyme polarization of substrates of dihydrofolate reductase by different theoretical methods.

Greatbanks SP, Gready JE, Limaye AC, Rendell AP.

Proteins. 1999 Nov 1;37(2):157-65.

PMID:
10584062
36.
37.

31P and 1H NMR spectroscopic studies of liver extracts of carbon tetrachloride-treated rats.

Harvey PJ, Gready JE, Hickey HM, Le Couteur DG, McLean AJ.

NMR Biomed. 1999 Oct;12(6):395-401.

PMID:
10516622
38.
39.

Identification and energetic ranking of possible docking sites for pterin on dihydrofolate reductase.

Bliznyuk AA, Gready JE.

J Comput Aided Mol Des. 1998 Jul;12(4):325-33.

PMID:
9777491
40.
41.
44.
45.
46.

Ionization state and pKa of pterin-analogue ligands bound to dihydrofolate reductase.

Jeong SS, Gready JE.

Eur J Biochem. 1994 May 1;221(3):1055-62.

49.

Development of a spectrofluorimetric method for determining the pKa of pterin-analogue ligands bound to DHFR.

Jeong SS, Gready JE.

Adv Exp Med Biol. 1993;338:529-32. No abstract available.

PMID:
8304173
50.

Comparison of binding and activity of 8-alkyl-pterins and 8-alkyl-N5-deaza-pterins with dihydrofolate reductase.

Ivery MT, Gready JE.

Adv Exp Med Biol. 1993;338:525-8. No abstract available.

PMID:
8304172

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