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Arieh Warshel
Department of Chemistry & Biochemistry, University of Southern California, Los Angeles, United States of America

Faculty Member: CHEMICAL BIOLOGY > Biocatalysis [ since 4 July 2001 ]
[ Homepage ] [ Evaluations ]
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http://laetro.usc.edu/

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Evaluations

Formation and stability of a vinyl carbanion at the active site of orotidine 5'-monophosphate decarboxylase: pKa of the C-6 proton of enzyme-bound UMP.
Amyes TL, Wood BM, …, Gerlt JA, Richard JP
J Am Chem Soc 2008 Feb 6 130(5):1574-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Arieh Warshel
Evaluated 24 Jan 2008

Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase.
Luo G, Wang M, Konigsberg WH, Xie XS
Proc Natl Acad Sci U S A 2007 Jul 31 104(31):12610-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Arieh Warshel
Evaluated 17 Dec 2007

The mechanism of rate-limiting motions in enzyme function.
Watt ED, Shimada H, Kovrigin EL, Loria JP
Proc Natl Acad Sci U S A 2007 Jul 17 104(29):11981-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Arieh Warshel / Mikael Akke
Evaluated 2 Aug 2007

A new paradigm for DNA polymerase specificity.
Tsai YC, Johnson KA
Biochemistry 2006 Aug 15 45(32):9675-87 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Karen Allen / Arieh Warshel
Evaluated 1 Mar 2007

Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole.
Kraut DA, Sigala PA, …, Petsko GA, Herschlag D
PLoS Biol 2006 Apr 4(4):e99 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Arieh Warshel
Evaluated 12 Jun 2006

Activation of orotidine 5'-monophosphate decarboxylase by phosphite dianion: the whole substrate is the sum of two parts.
Amyes TL, Richard JP, Tait JJ
J Am Chem Soc 2005 Nov 16 127(45):15708-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Karen Allen / Arieh Warshel
Evaluated 24 Mar 2006

Intrinsic dynamics of an enzyme underlies catalysis.
Eisenmesser EZ, Millet O, …, Kay LE, Kern D
Nature 2005 Nov 3 438(7064):117-21 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Kristina Downing / Gottfried Otting / David Cowburn / Arieh Warshel / Laura Itzhaki
Evaluated 22 Nov 2005

Slow solvation dynamics at the active site of an enzyme: implications for catalysis.
Guha S, Sahu K, …, Roy S, Bhattacharyya K
Biochemistry 2005 Jun 28 44(25):8940-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Arieh Warshel
Evaluated 1 Sep 2005

A theoretical DFT investigation of the lysozyme mechanism: computational evidence for a covalent intermediate pathway.
Bottoni A, Miscione GP, De Vivo M
Proteins 2005 Apr 1 59(1):118-30 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Arieh Warshel
Evaluated 1 Apr 2005

Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site.
Bjelic S, Aqvist J
Biochemistry 2004 Nov 23 43(46):14521-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Arieh Warshel
Evaluated 21 Mar 2005

Substrate-assisted catalysis of peptide bond formation by the ribosome.
Weinger JS, Parnell KM, …, Green R, Strobel SA
Nat Struct Mol Biol 2004 Nov 11(11):1101-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Reinhard Luehrmann / Arieh Warshel / Samuel Gunderson / Andrea Barta / Shelley Copley / Alfred Wittinghofer
Evaluated 1 Dec 2004

The ribosome as an entropy trap.
Sievers A, Beringer M, Rodnina MV, Wolfenden R
Proc Natl Acad Sci U S A 2004 May 25 101(21):7897-901 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Ada Yonath / Arieh Warshel
Evaluated 3 Sep 2004

High-energy intermediate or stable transition state analogue: theoretical perspective of the active site and mechanism of beta-phosphoglucomutase.
Webster CE
J Am Chem Soc 2004 Jun 9 126(22):6840-1 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Arieh Warshel
Evaluated 21 Jul 2004

Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein.
Groenhof G, Bouxin-Cademartory M, …, Mark AE, Robb MA
J Am Chem Soc 2004 Apr 7 126(13):4228-33 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Arieh Warshel
Evaluated 25 May 2004

Dynamics of an enzymatic substitution reaction in haloalkane dehalogenase.
Nam K, Prat-Resina X, …, Devi-Kesavan LS, Gao J
J Am Chem Soc 2004 Feb 11 126(5):1369-76 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Arieh Warshel
Evaluated 23 Feb 2004

Metaphosphate in the active site of fructose-1,6-bisphosphatase.
Choe JY, Iancu CV, Fromm HJ, Honzatko RB
J Biol Chem 2003 May 2 278(18):16015-20 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Karen Allen / Arieh Warshel
Evaluated 20 Feb 2004

Barriers to Hydride Transfer in Wild Type and Mutant Dihydrofolate Reductase from E. coli.
Thorpe IF, Brooks CL
J Phys Chem B 2003 107:14042-14051 [order article]
Selected by | Arieh Warshel
Evaluated 22 Dec 2003

The near attack conformation approach to the study of the chorismate to prephenate reaction.
Hur S, Bruice TC
Proc Natl Acad Sci U S A 2003 Oct 14 100(21):12015-20 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Ruma Banerjee / Arieh Warshel
Evaluated 31 Oct 2003

The first experimental test of the hypothesis that enzymes have evolved to enhance hydrogen tunneling.
Doll KM, Bender BR, Finke RG
J Am Chem Soc 2003 Sep 10 125(36):10877-84 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Joan Broderick / Arieh Warshel / Wolfgang Buckel
Evaluated 2 Oct 2003

Theoretical modeling of enzyme catalytic power: analysis of "cratic" and electrostatic factors in catechol O-methyltransferase.
Roca M, Martí S, …, Bertrán J, Williams IH
J Am Chem Soc 2003 Jun 25 125(25):7726-37 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Arieh Warshel
Evaluated 10 Sep 2003

The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction.
Lahiri SD, Zhang G, Dunaway-Mariano D, Allen KN
Science 2003 Mar 28 299(5615):2067-71 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Wolfgang Buckel / Arieh Warshel / Alfred Wittinghofer / Janet Morrow
Evaluated 22 Apr 2003

Selective stabilization of the chorismate mutase transition state by a positively charged hydrogen bond donor.
Kienhöfer A, Kast P, Hilvert D
J Am Chem Soc 2003 Mar 19 125(11):3206-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Arieh Warshel / Benjamin Cravatt
Evaluated 4 Apr 2003

The catalytic power of ketosteroid isomerase investigated by computer simulation.
Feierberg I, Aqvist J
Biochemistry 2002 Dec 31 41(52):15728-35 [abstract on PubMed] [related articles] [order article]
Selected by | Arieh Warshel
Evaluated 16 Jan 2003

Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study.
Zhang Y, Kua J, McCammon JA
J Am Chem Soc 2002 Sep 4 124(35):10572-7 [abstract on PubMed] [related articles] [order article]
Selected by | Arieh Warshel
Evaluated 11 Oct 2002

Electrostatic contributions to site specific DNA cleavage by EcoRV endonuclease.
Horton NC, Otey C, …, Ananthnarayan V, Perona JJ
Biochemistry 2002 Sep 3 41(35):10754-63 [abstract on PubMed] [related articles] [order article]
Selected by | Arieh Warshel
Evaluated 28 Aug 2002

Probing protein electrostatics with a synthetic fluorescent amino acid.
Cohen BE, McAnaney TB, …, Boxer SG, Jan LY
Science 2002 May 31 296(5573):1700-3 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Deborah Leckband / Peter Qin / Yu-Li Wang / Volkhard Helms / Arieh Warshel / Mario Amzel / Ross Weatherman / Robert Kelley
Evaluated 20 Jun 2002

RanGAP mediates GTP hydrolysis without an arginine finger.
Seewald MJ, Körner C, Wittinghofer A, Vetter IR
Nature 2002 Feb 7 415(6872):662-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Lindsley / Elena Conti / Arieh Warshel
Evaluated 27 Feb 2002

Site-bound water and the shortcomings of a less than perfect transition state analogue.
Snider MJ, Wolfenden R
Biochemistry 2001 Sep 25 40(38):11364-71 [abstract on PubMed] [related articles] [order article]
Selected by | John Ladbury / Arieh Warshel
Evaluated 18 Jan 2002

Ribozyme catalysis via orbital steering.
Scott WG
J Mol Biol 2001 Aug 31 311(5):989-99 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Thorsten Dieckmann / Arieh Warshel
Evaluated 21 Nov 2001

Role of enzyme-ribofuranosyl contacts in the ground state and transition state for orotidine 5'-phosphate decarboxylase: a role for substrate destabilization?
Miller BG, Butterfoss GL, Short SA, Wolfenden R
Biochemistry 2001 May 29 40(21):6227-32 [abstract on PubMed] [related articles] [order article]
Selected by | Arieh Warshel
Evaluated 4 Sep 2001

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