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Items: 1 to 50 of 54

1.

Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme.

Kristofich J, Morgenthaler AB, Kinney WR, Ebmeier CC, Snyder DJ, Old WM, Cooper VS, Copley SD.

PLoS Genet. 2018 Aug 27;14(8):e1007615. doi: 10.1371/journal.pgen.1007615. eCollection 2018 Aug.

2.

Shining a light on enzyme promiscuity.

Copley SD.

Curr Opin Struct Biol. 2017 Dec;47:167-175. doi: 10.1016/j.sbi.2017.11.001. Epub 2017 Nov 21. Review.

PMID:
29169066
3.

A Synonymous Mutation Upstream of the Gene Encoding a Weak-Link Enzyme Causes an Ultrasensitive Response in Growth Rate.

Kershner JP, Yu McLoughlin S, Kim J, Morgenthaler A, Ebmeier CC, Old WM, Copley SD.

J Bacteriol. 2016 Sep 22;198(20):2853-63. doi: 10.1128/JB.00262-16. Print 2016 Oct 15.

4.

Members of a Novel Kinase Family (DUF1537) Can Recycle Toxic Intermediates into an Essential Metabolite.

Thiaville JJ, Flood J, Yurgel S, Prunetti L, Elbadawi-Sidhu M, Hutinet G, Forouhar F, Zhang X, Ganesan V, Reddy P, Fiehn O, Gerlt JA, Hunt JF, Copley SD, de Crécy-Lagard V.

ACS Chem Biol. 2016 Aug 19;11(8):2304-11. doi: 10.1021/acschembio.6b00279. Epub 2016 Jun 24.

PMID:
27294475
5.

An evolutionary biochemist's perspective on promiscuity.

Copley SD.

Trends Biochem Sci. 2015 Feb;40(2):72-8. doi: 10.1016/j.tibs.2014.12.004. Epub 2015 Jan 5.

6.

An evolutionary perspective on protein moonlighting.

Copley SD.

Biochem Soc Trans. 2014 Dec;42(6):1684-91. doi: 10.1042/BST20140245. Review.

7.

A versatile and highly efficient method for scarless genome editing in Escherichia coli and Salmonella enterica.

Kim J, Webb AM, Kershner JP, Blaskowski S, Copley SD.

BMC Biotechnol. 2014 Sep 25;14:84. doi: 10.1186/1472-6750-14-84.

8.

Differential effects of a mutation on the normal and promiscuous activities of orthologs: implications for natural and directed evolution.

Khanal A, Yu McLoughlin S, Kershner JP, Copley SD.

Mol Biol Evol. 2015 Jan;32(1):100-8. doi: 10.1093/molbev/msu271. Epub 2014 Sep 21.

9.

A radical intermediate in the conversion of pentachlorophenol to tetrachlorohydroquinone by Sphingobium chlorophenolicum.

Rudolph J, Erbse AH, Behlen LS, Copley SD.

Biochemistry. 2014 Oct 21;53(41):6539-49. doi: 10.1021/bi5010427. Epub 2014 Oct 6.

10.

CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes.

Rokicki J, Knox D, Dowell RD, Copley SD.

BMC Genomics. 2014 Jan 24;15:65. doi: 10.1186/1471-2164-15-65.

11.

Reactivity landscape of pyruvate under simulated hydrothermal vent conditions.

Novikov Y, Copley SD.

Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13283-8. doi: 10.1073/pnas.1304923110. Epub 2013 Jul 19.

12.

Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol.

Yadid I, Rudolph J, Hlouchova K, Copley SD.

Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):E2182-90. doi: 10.1073/pnas.1214052110. Epub 2013 May 15.

13.

The orphan protein bis-γ-glutamylcystine reductase joins the pyridine nucleotide disulfide reductase family.

Kim J, Copley SD.

Biochemistry. 2013 Apr 30;52(17):2905-13. doi: 10.1021/bi4003343. Epub 2013 Apr 19.

14.

Inhibitory cross-talk upon introduction of a new metabolic pathway into an existing metabolic network.

Kim J, Copley SD.

Proc Natl Acad Sci U S A. 2012 Oct 16;109(42):E2856-64. doi: 10.1073/pnas.1208509109. Epub 2012 Sep 14.

15.

Moonlighting is mainstream: paradigm adjustment required.

Copley SD.

Bioessays. 2012 Jul;34(7):578-88. doi: 10.1002/bies.201100191. Review.

PMID:
22696112
16.

Pentachlorophenol hydroxylase, a poorly functioning enzyme required for degradation of pentachlorophenol by Sphingobium chlorophenolicum.

Hlouchova K, Rudolph J, Pietari JM, Behlen LS, Copley SD.

Biochemistry. 2012 May 8;51(18):3848-60. doi: 10.1021/bi300261p. Epub 2012 Apr 27.

17.

A Simple Route for Synthesis of 4-Phospho-D-Erythronate.

Novikov Y, Copley SD, Eaton BE.

Tetrahedron Lett. 2011 Apr 20;52(16):1913-1915.

18.

The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway.

Copley SD, Rokicki J, Turner P, Daligault H, Nolan M, Land M.

Genome Biol Evol. 2012;4(2):184-98. doi: 10.1093/gbe/evr137. Epub 2011 Dec 16.

19.

Toward a systems biology perspective on enzyme evolution.

Copley SD.

J Biol Chem. 2012 Jan 2;287(1):3-10. doi: 10.1074/jbc.R111.254714. Epub 2011 Nov 8. Review.

20.

A dimethyl ketal-protected benzoin-based linker suitable for photolytic release of unprotected peptides.

Chumachenko N, Novikov Y, Shoemaker RK, Copley SD.

J Org Chem. 2011 Nov 18;76(22):9409-16. doi: 10.1021/jo2017263. Epub 2011 Oct 18.

PMID:
21950361
21.

Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5'-phosphate synthesis.

Kim J, Kershner JP, Novikov Y, Shoemaker RK, Copley SD.

Mol Syst Biol. 2010 Nov 30;6:436. doi: 10.1038/msb.2010.88.

22.

Multiple turnovers of the nicotino-enzyme PdxB require α-keto acids as cosubstrates.

Rudolph J, Kim J, Copley SD.

Biochemistry. 2010 Nov 2;49(43):9249-55. doi: 10.1021/bi101291d.

23.

Evolution of efficient pathways for degradation of anthropogenic chemicals.

Copley SD.

Nat Chem Biol. 2009 Aug;5(8):559-66. doi: 10.1038/nchembio.197. Review.

24.

Prediction of function in protein superfamilies.

Copley SD.

F1000 Biol Rep. 2009 Dec 9;1:91. doi: 10.3410/B1-91.

25.

A compromise required by gene sharing enables survival: Implications for evolution of new enzyme activities.

McLoughlin SY, Copley SD.

Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13497-502. doi: 10.1073/pnas.0804804105. Epub 2008 Aug 29.

26.

MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs.

Hamady M, Widmann J, Copley SD, Knight R.

Genome Biol. 2008;9(8):R128. doi: 10.1186/gb-2008-9-8-r128. Epub 2008 Aug 15.

27.

A trade-off between catalytic power and substrate inhibition in TCHQ dehalogenase.

Warner JR, Behlen LS, Copley SD.

Biochemistry. 2008 Mar 11;47(10):3258-65. doi: 10.1021/bi702431n. Epub 2008 Feb 15.

PMID:
18275157
28.

Pre-steady-state kinetic studies of the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase.

Warner JR, Copley SD.

Biochemistry. 2007 Nov 13;46(45):13211-22. Epub 2007 Oct 23.

PMID:
17956123
29.

Why metabolic enzymes are essential or nonessential for growth of Escherichia coli K12 on glucose.

Kim J, Copley SD.

Biochemistry. 2007 Nov 6;46(44):12501-11. Epub 2007 Oct 13. Review.

PMID:
17935357
30.

The origin of the RNA world: co-evolution of genes and metabolism.

Copley SD, Smith E, Morowitz HJ.

Bioorg Chem. 2007 Dec;35(6):430-43. Epub 2007 Sep 25.

PMID:
17897696
31.

Mechanism of the severe inhibition of tetrachlorohydroquinone dehalogenase by its aromatic substrates.

Warner JR, Copley SD.

Biochemistry. 2007 Apr 10;46(14):4438-47. Epub 2007 Mar 14.

PMID:
17355122
32.
33.
34.

A mechanism for the association of amino acids with their codons and the origin of the genetic code.

Copley SD, Smith E, Morowitz HJ.

Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4442-7. Epub 2005 Mar 11.

35.
37.

Enzymes with extra talents: moonlighting functions and catalytic promiscuity.

Copley SD.

Curr Opin Chem Biol. 2003 Apr;7(2):265-72. Review.

PMID:
12714060
39.

Lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes.

Copley SD, Dhillon JK.

Genome Biol. 2002;3(5):research0025. Epub 2002 Apr 29.

40.
41.

The reaction catalyzed by tetrachlorohydroquinone dehalogenase does not involve nucleophilic aromatic substitution.

Kiefer PM Jr, McCarthy DL, Copley SD.

Biochemistry. 2002 Jan 29;41(4):1308-14.

PMID:
11802731
42.

Bacterial sources and sinks of isoprene, a reactive atmospheric hydrocarbon.

Fall R, Copley SD.

Environ Microbiol. 2000 Apr;2(2):123-30. Review. No abstract available.

PMID:
11220299
43.

Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach.

Copley SD.

Trends Biochem Sci. 2000 Jun;25(6):261-5. Review.

PMID:
10838562
44.

Recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol.

Anandarajah K, Kiefer PM Jr, Donohoe BS, Copley SD.

Biochemistry. 2000 May 9;39(18):5303-11.

PMID:
10820000
46.

Microbial dehalogenases: enzymes recruited to convert xenobiotic substrates.

Copley SD.

Curr Opin Chem Biol. 1998 Oct;2(5):613-7. Review.

PMID:
9818187
47.

In vivo levels of chlorinated hydroquinones in a pentachlorophenol-degrading bacterium.

McCarthy DL, Claude AA, Copley SD.

Appl Environ Microbiol. 1997 May;63(5):1883-8.

49.

Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione S-transferase superfamily.

McCarthy DL, Navarrete S, Willett WS, Babbitt PC, Copley SD.

Biochemistry. 1996 Nov 19;35(46):14634-42.

PMID:
8931562

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