Cooperative Institute for Research in Environmental Sciences

Journal Article Total: 45

Citations

References

Copley, SD (2012), Moonlighting is mainstream: Paradigm adjustment required. Bioessays, 34 (7) 578-588, issn: 0265-9247, ids: 958KG, doi: 10.1002/bies.201100191, Published JUL 2012
Times Cited: 3

Copley, SD, J Rokicki, P Turner, H Daligault, M Nolan and M Land (2012), The Whole Genome Sequence of Sphingobium chlorophenolicum L-1: Insights into the Evolution of the Pentachlorophenol Degradation Pathway. Genome Biol. Evol., 4 (2) 184-198, issn: 1759-6653, ids: 914VJ, doi: 10.1093/gbe/evr137
Times Cited: 2

Hlouchova, K, J Rudolph, JMH Pietari, LS Behlen and SD Copley (2012), Pentachlorophenol Hydroxylase, a Poorly Functioning Enzyme Required for Degradation of Pentachlorophenol by Sphingobium chlorophenolicum. Biochemistry, 51 (18) 3848-3860, issn: 0006-2960, ids: 936ZG, doi: 10.1021/bi300261p, Published 8-May 2012
Times Cited: 1

Kim, J and SD Copley (2012), Inhibitory cross-talk upon introduction of a new metabolic pathway into an existing metabolic network. Proc. Natl. Acad. Sci. U. S. A., 109 (42) E2856-E2864, issn: 0027-8424, ids: 029SK, doi: 10.1073/pnas.1208509109, Published 16-Oct 2012

Chumachenko, N, Y Novikov, RK Shoemaker and SD Copley (2011), A Dimethyl Ketal-Protected Benzoin-Based Linker Suitable for Photolytic Release of Unprotected Peptides. J. Org. Chem., 76 (22) 9409-9416, issn: 0022-3263, ids: 844NN, doi: 10.1021/jo2017263, Published 18-Nov 2011
Times Cited: 2

Novikov, Y, SD Copley and BE Eaton (2011), A simple route for synthesis of 4-phospho-D-erythronate. Tetrahedron Lett., 52 (16) 1913-1915, issn: 0040-4039, ids: 765YV, doi: 10.1016/j.tetlet.2011.02.045, Published 20-Apr 2011
Times Cited: 1

Copley, S. D., Smith, E. and Morowitz, H. J. (2010), The Emergence of Sparse Metabolic Networks. Journal of Cosmology, 10 3345-3361

Kim, JH, JP Kershner, Y Novikov, RK Shoemaker and SD Copley (2010), Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5 '-phosphate synthesis. Mol. Syst. Biol., 6 , Art. No. 436, issn: 1744-4292, ids: 691GI, doi: 10.1038/msb.2010.88, Published NOV 2010
Times Cited: 11

Rudolph, J, J Kim and SD Copley (2010), Multiple Turnovers of the Nicotino-Enzyme PdxB Require alpha-Keto Acids as Cosubstrates. Biochemistry, 49 (43) 9249-9255, issn: 0006-2960, ids: 670GL, doi: 10.1021/bi101291d, Published 2-Nov 2010
Times Cited: 3

Copley, S. D. (2009), Prediction of Function in Enzyme Superfamilies. F1000 Biology Reports, 1 (Report 91)

Hamady, M, J Widmann, SD Copley and R Knight (2008), MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs. Genome Biol., 9 (8) , Art. No. R128, issn: 1474-760X, ids: 355IA, doi: 10.1186/gb-2008-9-8-r128

McLoughlin, SY and SD Copley (2008), A compromise required by gene sharing enables survival: Implications for evolution of new enzyme activities. Proc. Natl. Acad. Sci. U. S. A., 105 (36) 13497-13502, issn: 0027-8424, ids: 349AR, doi: 10.1073/pnas.0804804105, Published 9-Sep 2008
Times Cited: 15

Warner, JR, LS Behlen and SD Copley (2008), A trade-off between catalytic power and substrate inhibition in TCHQ dehalogenase. Biochemistry, 47 (10) 3258-3265, issn: 0006-2960, ids: 270NG, doi: 10.1021/bi702431n, Published 11-Mar 2008
Times Cited: 5

Copley, SD, E Smith and HJ Morowitz (2007), The origin of the RNA world: Co-evolution of genes and metabolism. Bioorganic Chem., 35 (6) 430-443, issn: 0045-2068, ids: 237GV, doi: 10.1016/j.bioorg.2007.08.001, Published DEC 2007
Times Cited: 26

Kim, J and SD Copley (2007), Why metabolic enzymes are essential or nonessential for growth of Escherichia coli k12 on glucose. Biochemistry, 46 (44) 12501-12511, issn: 0006-2960, ids: 226FA, doi: 10.1021/bi7014629, Published 6-Nov 2007
Times Cited: 14

Warner, JR and SD Copley (2007), Pre-steady-state kinetic studies of the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase. Biochemistry, 46 (45) 13211-13222, issn: 0006-2960, ids: 228XT, doi: 10.1021/bi701069n, Published 13-Nov 2007
Times Cited: 9

Warner, JR and SD Copley (2007), Mechanism of the severe inhibition of tetrachlorohydroquinone dehalogenase by its aromatic substrates. Biochemistry, 46 (14) 4438-4447, issn: 0006-2960, ids: 152OD, doi: 10.1021/bi0620104, Published 10-Apr 2007
Times Cited: 5

Cleland, C. E.. and Copley, S. D. (2005), The Possibility of Alternative Microbial Life on Earth. International Journal of Astrobiology, 4 165-173,doi: 10.1017/S147355040500279X

Copley, SD, E Smith and HJ Morowitz (2005), A mechanism for the association of amino acids with their codons and the origin of the genetic code. Proc. Natl. Acad. Sci. U. S. A., 102 (12) 4442-4447, issn: 0027-8424, ids: 909IY, doi: 10.1073/pnas.0501049102, Published 22-Mar 2005
Times Cited: 39

Dai, MH, S Ziesman, T Ratcliffe, RT Gill and SD Copley (2005), Visualization of protoplast fusion and quantitation of recombination in fused protoplasts of auxotrophic strains of Escherichia coli. Metab. Eng., 7 (1) 45-52, issn: 1096-7176, ids: 904LI, doi: 10.1016/j.ymben.2004.09.002, Published JAN 2005
Times Cited: 23

Warner, JR, SL Lawson and SD Copley (2005), A mechanistic investigation of the thiol-disulfide exchange step in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase. Biochemistry, 44 (30) 10360-10368, issn: 0006-2960, ids: 950TG, doi: 10.1021/bi050666b, Published 2-Aug 2005
Times Cited: 13

Copley, SD, WRP Novak and PC Babbitt (2004), Divergence of function in the thioredoxin fold suprafamily: Evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor. Biochemistry, 43 (44) 13981-13995, issn: 0006-2960, ids: 868UV, doi: 10.1021/bi048947r, Published 9-Nov 2004
Times Cited: 63

Dai, MH and SD Copley (2004), Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723. Appl. Environ. Microbiol., 70 (4) 2391-2397, issn: 0099-2240, ids: 811SS, doi: 10.1128/AEM.70.4.2391-2397.2004, Published APR 2004
Times Cited: 92

Dai, MH, JB Rogers, JR Warner and SD Copley (2003), A previously unrecognized step in pentachlorophenol degradation in Sphingobium chlorophenolicum is catalyzed by tetrachlorobenzoquinone reductase (PcpD). J. Bacteriol., 185 (1) 302-310, issn: 0021-9193, ids: 629LJ, doi: 10.1128/JB.185.1.302-310.2003, Published JAN 2003
Times Cited: 39

Copley, S. D. and Dhillon, J. K (2002), Lateral Gene Transfer and Parallel. Genome, 3, research 0025.1-0025.16

Kiefer, PM and SD Copley (2002), Characterization of the initial steps in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase. Biochemistry, 41 (4) 1315-1322, issn: 0006-2960, ids: 517LM, doi: 10.1021/bi0117504, Published 29-Jan 2002
Times Cited: 21

Kiefer, PM, DL McCarthy and SD Copley (2002), The reaction catalyzed by tetrachlorohydroquinone dehalogenase does not involve nucleophilic aromatic substitution. Biochemistry, 41 (4) 1308-1314, issn: 0006-2960, ids: 517LM, doi: 10.1021/bi0117495, Published 29-Jan 2002
Times Cited: 15

Anandarajah, K, PM Kiefer, BS Donohoe and SD Copley (2000), Recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol. Biochemistry, 39 (18) 5303-5311, issn: 0006-2960, ids: 312PD, doi: 10.1021/bi9923813, Published 9-May 2000
Times Cited: 64

Copley, SD (2000), Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. Trends Biochem.Sci., 25 (6) 261-265, issn: 0968-0004, ids: 322UU, doi: 10.1016/S0968-0004(00)01562-0, Published JUN 2000
Times Cited: 95

Xu, L, K Resing, SL Lawson, PC Babbitt and SD Copley (1999), Evidence that pcpA encodes 2,6-dichlorohydroquinone dioxygenase, the ring cleavage enzyme required for pentachlorophenol degradation in Sphingomonas chlorophenolica strain ATCC 39723. Biochemistry, 38 (24) 7659-7669, issn: 0006-2960, ids: 208XB, doi: 10.1021/bi990103y, Published 15-Jun 1999
Times Cited: 47

Copley, SD (1997), Diverse mechanistic approaches to difficult chemical transformations: Microbial dehalogenation of chlorinated aromatic compounds. Chem. Biol., 4 (3) 169-174, issn: 1074-5521, ids: WV743, doi: 10.1016/S1074-5521(97)90285-4, Published MAR 1997
Times Cited: 14

McCarthy, DL, AA Claude and SD Copley (1997), In vivo levels of chlorinated hydroquinones in a pentachlorophenol-degrading bacterium. Appl. Environ. Microbiol., 63 (5) 1883-1888, issn: 0099-2240, ids: WX361, Published MAY 1997
Times Cited: 42

McCarthy, DL, DF Louie and SD Copley (1997), Identification of a covalent intermediate between glutathione and cysteine13 formed during catalysis by tetrachlorohydroquinone dehalogenase. J. Am. Chem. Soc., 119 (46) 11337-11338, issn: 0002-7863, ids: YG901, doi: 10.1021/ja9726365, Published 19-Nov 1997
Times Cited: 21

McCarthy, DL, S Navarrete, WS Willett, PC Babbitt and SD Copley (1996), Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione S-transferase superfamily. Biochemistry, 35 (46) 14634-14642, issn: 0006-2960, ids: VU224, doi: 10.1021/bi961730f, Published 19-Nov 1996
Times Cited: 52

Willett, WS and SD Copley (1996), Identification and localization of a stable sulfenic acid in peroxide-treated tetrachlorohydroquinone dehalogenase using electrospray mass spectrometry. Chem. Biol., 3 (10) 851-857, issn: 1074-5521, ids: VR145, Published OCT 1996
Times Cited: 21

CROOKS, GP, L XU, RM BARKLEY and SD COPLEY (1995), EXPLORATION OF POSSIBLE MECHANISMS FOR 4-CHLOROBENZOYL COA DEHALOGENASE - EVIDENCE FOR AN ARYL-ENZYME INTERMEDIATE. J. Am. Chem. Soc., 117 (44) 10791-10798, issn: 0002-7863, ids: TD410, doi: 10.1021/ja00149a001, Published 8-Nov 1995
Times Cited: 25

CROOKS, GP and SD COPLEY (1994), PURIFICATION AND CHARACTERIZATION OF 4-CHLOROBENZOYL COA DEHALOGENASE FROM ARTHROBACTER SP STRAIN 4-CB1. Biochemistry, 33 (38) 11645-11649, issn: 0006-2960, ids: PJ293, doi: 10.1021/bi00204a028, Published 27-Sep 1994
Times Cited: 18

CROOKS, GP and SD COPLEY (1993), A SURPRISING EFFECT OF LEAVING GROUP ON THE NUCLEOPHILIC AROMATIC-SUBSTITUTION REACTION CATALYZED BY 4-CHLOROBENZOYL-COA DEHALOGENASE. J. Am. Chem. Soc., 115 (14) 6422-6423, issn: 0002-7863, ids: LT173, doi: 10.1021/ja00067a072, Published 14-Jul 1993
Times Cited: 17

COPLEY, SD and GP CROOKS (1992), ENZYMATIC DEHALOGENATION OF 4-CHLOROBENZOYL COENZYME-A IN ACINETOBACTER SP STRAIN 4-CB1. Appl. Environ. Microbiol., 58 (4) 1385-1387, issn: 0099-2240, ids: HM121, Published APR 1992
Times Cited: 23

COPLEY, SD, E FRANK, WM KIRSCH and TH KOCH (1992), DETECTION AND POSSIBLE ORIGINS OF AMINOMALONIC ACID IN PROTEIN HYDROLYSATES. Anal. Biochem., 201 (1) 152-157, issn: 0003-2697, ids: HE336, doi: 10.1016/0003-2697(92)90188-D, Published 14-Feb 1992
Times Cited: 11

COPLEY, SD and JR KNOWLES (1987), THE CONFORMATIONAL EQUILIBRIUM OF CHORISMATE IN SOLUTION - IMPLICATIONS FOR THE MECHANISM OF THE NONENZYMATIC AND THE ENZYME-CATALYZED REARRANGEMENT OF CHORISMATE TO PREPHENATE. J. Am. Chem. Soc., 109 (16) 5008-5013, issn: 0002-7863, ids: J5208, doi: 10.1021/ja00250a040, Published 5-Aug 1987
Times Cited: 150

GUILFORD, WJ, SD COPLEY and JR KNOWLES (1987), ON THE MECHANISM OF THE CHORISMATE MUTASE REACTION. J. Am. Chem. Soc., 109 (16) 5013-5019, issn: 0002-7863, ids: J5208, doi: 10.1021/ja00250a041, Published 5-Aug 1987
Times Cited: 92

COPLEY, SD and JR KNOWLES (1985), THE UNCATALYZED CLAISEN REARRANGEMENT OF CHORISMATE TO PREPHENATE PREFERS A TRANSITION-STATE OF CHAIRLIKE GEOMETRY. J. Am. Chem. Soc., 107 (18) 5306-5308, issn: 0002-7863, ids: AQE67, doi: 10.1021/ja00304a064
Times Cited: 80

GRIMSHAW, CE, SG SOGO, SD COPLEY and JR KNOWLES (1984), SYNTHESIS OF STEREOSELECTIVELY LABELED [9-H-2,H-3] CHORISMATE AND THE STEREOCHEMICAL COURSE OF "5-ENOLPYRUVOYLSHIKIMATE-3-PHOSPHATE SYNTHETASE. J. Am. Chem. Soc., 106 (9) 2699-2700, issn: 0002-7863, ids: SP772, doi: 10.1021/ja00321a037
Times Cited: 39

KOVACHY, RJ, SD COPLEY and RH ALLEN (1983), RECOGNITION, ISOLATION, AND CHARACTERIZATION OF RAT-LIVER D-METHYLMALONYL COENZYME-A HYDROLASE. J. Biol. Chem., 258 (18) 1415-1421, issn: 0021-9258, ids: RH492
Times Cited: 33

Chapter in a Book Total: 4

Citations

References

Copley, S. D. (2010), Evolution and the Enzyme. Comprehensive Natural Products Chemistry, vol. 8, (Enzymes and Enzyme Mechanisms), , Elsevier

Smith, E., Morowitz, H. J., and Copley, S. D. (2009), Core Metabolism as a Self-Organized System. Protocells: Bridging Nonliving and Living Matter, , MIT Press, doi: 10.1162/106454603322392479, Rasmussen, S. et al. (Ed.)

Copley, Shelley D (2007), Glutathione Transferases. Redox Biology, , Wiley, R. Banarjee (Ed.)

Copley, S. D. (2002), Aromatic Dehalogenases: Insights into Structures,. Dehalogenation: Microbial, , Kluwer Academic Publishers

Conference Preprints/Proceedings/Extended Abstracts Total: 14

Citations

References

Copley, SD (2011), Mechanisms gone awry: Catalytic errors committed by enzymes recruited to serve novel functions in pentachlorophenol degradation. Abstr. Pap. Am. Chem. Soc., 242nd National Meeting of the American-Chemical-Society (ACS), 242 , Denver, CO, AUG 28-SEP 01, 2011, AMER CHEMICAL SOC, WASHINGTON, Art. No. 188-BIOL, issn: 0065-7727, ids: 880BE, Published 28-Aug 2011

Gill, RT, M Lynch, T Warnecke, JM Bonomo, S Ziesman, MH Dai and S Copley (2005), Tools and applications for directed genome evolution: Combining inverse and constructive metabolic engineering.. Abstr. Pap. Am. Chem. Soc., 229 Part 1 U197-U198, Published 13-Mar 2005

Gill, RT, S Copley and M Lynch (2003), Metabolic and evolutionary engineering in the era of genomics: Antibiotic resistance as a model for engineering new microbial behaviors.. Abstr. Pap. Am. Chem. Soc., 225 Part 1 U204-U205, Published MAR 2003

Chu, XZ, C Yamashita, PJ Espy, GJ Nott, EJ Jensen, HL Liu, WT Huang and JP Thayer (2001), Responses of polar mesospheric cloud brightness to stratospheric gravity waves at the South Pole and Rothera, Antarctica. Chem.-Biol. Interact., 8th International Workshop on Layered Phenomena in the Mesopause Region (LPMR-8), 133 3-Jan (SI) 200-203, UPPSALA, SWEDEN, MAY 19-23, 2000, ELSEVIER SCI IRELAND LTD, CLARE, issn: 0009-2797, ids: 424QY, Published 28-Feb 2001
Times Cited: 1

TOLBERT, MA (1997), HETEROGENEOUS PROCESSES IN THE STRATOSPHERE. Protein Eng., 10 (S) 69-69, OXFORD UNIV PRESS, OXFORD, issn: 0269-2139, ids: XD832

VELTKAMP, PR, SA BEATON, RC GREAVES, RM BARKLEY and RE SIEVERS (1994), SYNCHRONOUS CHANGES OF OXYGEN-CONTAINING ORGANICS IN ATMOSPHERIC AEROSOLS. Abstr. Pap. Am. Chem. Soc., 207 (Part 2) 192-ORGN, AMER CHEMICAL SOC, WASHINGTON, issn: 0065-7727, ids: MY955, Published 13-Mar 1994

SIEVERS, RE and SA NYARADY (1993), REDOX CHEMI-LUMINESCENCE - A NEW APPROACH TO CHROMATOGRAPHY DETECTION. Abstr. Pap. Am. Chem. Soc., 205 (Part 1) 12-IEC, AMER CHEMICAL SOC, WASHINGTON, issn: 0065-7727, ids: KQ981, Published 28-Mar 1993

SIEVERS, RE, JM ROBERTS and FC FEHSENFELD (1993), MEASUREMENT OF MONOTERPENE HYDROCARBONS IN RURAL ATMOSPHERES. Abstr. Pap. Am. Chem. Soc., 205 (Part 1) 2-IEC, AMER CHEMICAL SOC, WASHINGTON, issn: 0065-7727, ids: KQ981, Published 28-Mar 1993

WEBB, SP, SW YEH, LA PHILIPS, LM TOLBERT, MA TOLBERT and JH CLARK (1993), EXCITED-STATE PROTON-TRANSFER DYNAMICS IN HYDROXYBIPHENYLS AND NAPHTHOLS. Abstr. Pap. Am. Chem. Soc., 205 (Part 2) 83-NUCL, AMER CHEMICAL SOC, WASHINGTON, issn: 0065-7727, ids: KQ983, Published 28-Mar 1993

BROOKS, KC and RE SIEVERS (1991), NMR LANTHANIDE SHIFT-REAGENTS WITH POLYDENTATE CAGE LIGANDS. Faseb J., 5 4 (Part 1) A533-A533, FEDERATION AMER SOC EXP BIOL, BETHESDA, issn: 0892-6638, ids: FC207, Published 11-Mar 1991

PICKER, JE and RE SIEVERS (1991), SELECTIVE SORPTION OF NUCLEOPHILES USING LANTHANIDE METAL-COMPLEXES. Faseb J., 5 4 (Part 1) A533-A533, FEDERATION AMER SOC EXP BIOL, BETHESDA, issn: 0892-6638, ids: FC207, Published 11-Mar 1991

SIEVERS, RE, HF WALTON, JW BIRKS and CA KOVAL (1991), THE RENAISSANCE OF ANALYTICAL-CHEMISTRY AT THE UNIV-OF-COLORADO. Faseb J., 5 4 (Part 1) A534-A534, FEDERATION AMER SOC EXP BIOL, BETHESDA, issn: 0892-6638, ids: FC207, Published 11-Mar 1991

STANLEY, JS, DD SWANSON, MK CONDITT and RE SIEVERS (1991), THE ROLE OF ORGANIC-LIGANDS ON THE MOBILITY OF TRACE-ELEMENTS IN OIL-SHALE WASTES. Faseb J., 5 4 (Part 1) A533-A533, FEDERATION AMER SOC EXP BIOL, BETHESDA, issn: 0892-6638, ids: FC207, Published 11-Mar 1991

Volkamer, RM, S Coburn, B Dix, R Sinreich, R Thalman and E Waxman (1982), Novel chemistry at the air-sea interface: Role of the organic microlayer in activating iodine. Clin. Res., 242nd National Meeting of the American-Chemical-Society (ACS), 30 2 A505-A505, SLACK INC, THOROFARE, issn: 0009-9279, ids: NJ707

Correction Total: 1

Citations

References

COPLEY, SD (1992), CORRECTION. Appl. Environ. Microbiol., 58 (8) 2709-2709, AMER SOC MICROBIOLOGY, WASHINGTON, issn: 0099-2240, ids: JF839, Published AUG 1992

Editorial Material Total: 1

Citations

References

Morowitz, HJ, V Shinivasan, S Copley and E Smith (2005), The simplest enzyme revisited - The chicken and egg argument solved. Complexity, 10 (5) 12-13, Published MAY-JUN 2005

Review Total: 5

Citations

References

Copley, SD (2012), Toward a Systems Biology Perspective on Enzyme Evolution. J. Biol. Chem., 287 (1) 3-10, AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC, BETHESDA, issn: 0021-9258, ids: 870PW, doi: 10.1074/jbc.R111.254714, Published 2-Jan 2012
Times Cited: 7

Copley, SD (2009), Evolution of efficient pathways for degradation of anthropogenic chemicals. Nat. Chem. Biol., 5 (8) 560-567, NATURE PUBLISHING GROUP, NEW YORK, issn: 1552-4450, ids: 473LV, doi: 10.1038/nchembio.197, Published AUG 2009
Times Cited: 19

Copley, SD (2003), Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr. Opin. Chem. Biol., 7 (2) 265-272, CURRENT BIOLOGY LTD, LONDON, issn: 1367-5931, ids: 676FB, doi: 10.1016/S1367-5931(03)00032-2, Published APR 2003
Times Cited: 235

Fall, R and SD Copley (2000), Bacterial sources and sinks of isoprene, a reactive atmospheric hydrocarbon. Environ. Microbiol., 2 (2) 123-130, BLACKWELL SCIENCE LTD, OXFORD, issn: 1462-2912, ids: 315HE, doi: 10.1046/j.1462-2920.2000.00095.x, Published APR 2000
Times Cited: 24

Copley, SD (1998), Microbial dehalogenases: enzymes recruited to convert xenobiotic substrates. Curr. Opin. Chem. Biol., 2 (5) 613-617, CURRENT BIOLOGY LTD, LONDON, issn: 1367-5931, ids: 135YT, doi: 10.1016/S1367-5931(98)80092-6, Published OCT 1998
Times Cited: 36