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Immobilization of Proteins with Controlled Load and Orientation.

Bednar RM, Golbek TW, Kean KM, Brown WJ, Jana S, Baio JE, Karplus PA, Mehl RA.

ACS Appl Mater Interfaces. 2019 Oct 9;11(40):36391-36398. doi: 10.1021/acsami.9b12746. Epub 2019 Sep 26.


Substrate Specificity in Thiol Dioxygenases.

Aloi S, Davies CG, Karplus PA, Wilbanks SM, Jameson GNL.

Biochemistry. 2019 May 14;58(19):2398-2407. doi: 10.1021/acs.biochem.9b00079. Epub 2019 May 2.


Structure and role for active site lid of lactate monooxygenase from Mycobacterium smegmatis.

Kean KM, Karplus PA.

Protein Sci. 2019 Jan;28(1):135-149. doi: 10.1002/pro.3506. Epub 2018 Oct 3.


Differential Kinetics of Two-Cysteine Peroxiredoxin Disulfide Formation Reveal a Novel Model for Peroxide Sensing.

Portillo-Ledesma S, Randall LM, Parsonage D, Dalla Rizza J, Karplus PA, Poole LB, Denicola A, Ferrer-Sueta G.

Biochemistry. 2018 Jun 19;57(24):3416-3424. doi: 10.1021/acs.biochem.8b00188. Epub 2018 Mar 30.


Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra.

Evangelidis T, Nerli S, Nováček J, Brereton AE, Karplus PA, Dotas RR, Venditti V, Sgourakis NG, Tripsianes K.

Nat Commun. 2018 Jan 26;9(1):384. doi: 10.1038/s41467-017-02592-z.


Correction to: NMR structure of the HIV-1 reverse transcriptase thumb subdomain.

Sharaf NG, Brereton AE, Byeon IL, Karplus PA, Gronenborn AM.

J Biomol NMR. 2017 Dec;69(4):247. doi: 10.1007/s10858-017-0139-0.


Structural insights into a thermostable variant of human carbonic anhydrase II.

Kean KM, Porter JJ, Mehl RA, Karplus PA.

Protein Sci. 2018 Feb;27(2):573-577. doi: 10.1002/pro.3347. Epub 2017 Nov 27.


High-resolution studies of hydride transfer in the ferredoxin:NADP+ reductase superfamily.

Kean KM, Carpenter RA, Pandini V, Zanetti G, Hall AR, Faber R, Aliverti A, Karplus PA.

FEBS J. 2017 Oct;284(19):3302-3319. doi: 10.1111/febs.14190. Epub 2017 Aug 29.


Ensemblator v3: Robust atom-level comparative analyses and classification of protein structure ensembles.

Brereton AE, Karplus PA.

Protein Sci. 2018 Jan;27(1):41-50. doi: 10.1002/pro.3249. Epub 2017 Aug 11.


The sedoheptulose 7-phosphate cyclases and their emerging roles in biology and ecology.

Osborn AR, Kean KM, Karplus PA, Mahmud T.

Nat Prod Rep. 2017 Aug 2;34(8):945-956. doi: 10.1039/c7np00017k. Review.


Experimentally Dissecting the Origins of Peroxiredoxin Catalysis.

Nelson KJ, Perkins A, Van Swearingen AED, Hartman S, Brereton AE, Parsonage D, Salsbury FR Jr, Karplus PA, Poole LB.

Antioxid Redox Signal. 2018 Mar 1;28(7):521-536. doi: 10.1089/ars.2016.6922. Epub 2017 Apr 4.


Evolution and Distribution of C7-Cyclitol Synthases in Prokaryotes and Eukaryotes.

Osborn AR, Kean KM, Alseud KM, Almabruk KH, Asamizu S, Lee JA, Karplus PA, Mahmud T.

ACS Chem Biol. 2017 Apr 21;12(4):979-988. doi: 10.1021/acschembio.7b00066. Epub 2017 Feb 17.


The mitotic kinesin-14 KlpA contains a context-dependent directionality switch.

Popchock AR, Tseng KF, Wang P, Karplus PA, Xiang X, Qiu W.

Nat Commun. 2017 Jan 4;8:13999. doi: 10.1038/ncomms13999.


NMR structure of the HIV-1 reverse transcriptase thumb subdomain.

Sharaf NG, Brereton AE, Byeon IL, Karplus PA, Gronenborn AM.

J Biomol NMR. 2016 Dec;66(4):273-280. doi: 10.1007/s10858-016-0077-2. Epub 2016 Nov 17. Erratum in: J Biomol NMR. 2017 Dec 12;:.


Peroxiredoxin Catalysis at Atomic Resolution.

Perkins A, Parsonage D, Nelson KJ, Ogba OM, Cheong PH, Poole LB, Karplus PA.

Structure. 2016 Oct 4;24(10):1668-1678. doi: 10.1016/j.str.2016.07.012. Epub 2016 Sep 1.


Structure-Based Insights into the Role of the Cys-Tyr Crosslink and Inhibitor Recognition by Mammalian Cysteine Dioxygenase.

Driggers CM, Kean KM, Hirschberger LL, Cooley RB, Stipanuk MH, Karplus PA.

J Mol Biol. 2016 Oct 9;428(20):3999-4012. doi: 10.1016/j.jmb.2016.07.012. Epub 2016 Jul 29.


Beyond basins: φ,ψ preferences of a residue depend heavily on the φ,ψ values of its neighbors.

Hollingsworth SA, Lewis MC, Karplus PA.

Protein Sci. 2016 Sep;25(9):1757-62. doi: 10.1002/pro.2973. Epub 2016 Jul 11.


A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream.

Moriarty NW, Tronrud DE, Adams PD, Karplus PA.

Acta Crystallogr D Struct Biol. 2016 Jan;72(Pt 1):176-9. doi: 10.1107/S2059798315022408. Epub 2016 Jan 1.


On the reliability of peptide nonplanarity seen in ultra-high resolution crystal structures.

Brereton AE, Karplus PA.

Protein Sci. 2016 Apr;25(4):926-32. doi: 10.1002/pro.2883. Epub 2016 Feb 8.


The Anchored Flexibility Model in LC8 Motif Recognition: Insights from the Chica Complex.

Clark S, Nyarko A, Löhr F, Karplus PA, Barbar E.

Biochemistry. 2016 Jan 12;55(1):199-209. doi: 10.1021/acs.biochem.5b01099. Epub 2015 Dec 22.


Native proteins trap high-energy transit conformations.

Brereton AE, Karplus PA.

Sci Adv. 2015 Oct 16;1(9):e1501188. doi: 10.1126/sciadv.1501188. eCollection 2015 Oct.


Backbone chemical shift assignments for Xanthomonas campestris peroxiredoxin Q in the reduced and oxidized states: a dramatic change in backbone dynamics.

Buchko GW, Perkins A, Parsonage D, Poole LB, Karplus PA.

Biomol NMR Assign. 2016 Apr;10(1):57-61. doi: 10.1007/s12104-015-9637-8. Epub 2015 Sep 15.


Assessing and maximizing data quality in macromolecular crystallography.

Karplus PA, Diederichs K.

Curr Opin Struct Biol. 2015 Oct;34:60-8. doi: 10.1016/ Epub 2015 Jul 24. Review.


Peroxiredoxins: guardians against oxidative stress and modulators of peroxide signaling.

Perkins A, Nelson KJ, Parsonage D, Poole LB, Karplus PA.

Trends Biochem Sci. 2015 Aug;40(8):435-45. doi: 10.1016/j.tibs.2015.05.001. Epub 2015 Jun 9. Review.


Residue-level global and local ensemble-ensemble comparisons of protein domains.

Clark SA, Tronrud DE, Karplus PA.

Protein Sci. 2015 Sep;24(9):1528-42. doi: 10.1002/pro.2714. Epub 2015 Jun 22.


ChSeq: A database of chameleon sequences.

Li W, Kinch LN, Karplus PA, Grishin NV.

Protein Sci. 2015 Jul;24(7):1075-86. doi: 10.1002/pro.2689. Epub 2015 Jun 16. Review.


De novo synthesis of a sunscreen compound in vertebrates.

Osborn AR, Almabruk KH, Holzwarth G, Asamizu S, LaDu J, Kean KM, Karplus PA, Tanguay RL, Bakalinsky AT, Mahmud T.

Elife. 2015 May 12;4. doi: 10.7554/eLife.05919.


Kinetic mechanism of L-α-glycerophosphate oxidase from Mycoplasma pneumoniae.

Maenpuen S, Watthaisong P, Supon P, Sucharitakul J, Parsonage D, Karplus PA, Claiborne A, Chaiyen P.

FEBS J. 2015 Aug;282(16):3043-59. doi: 10.1111/febs.13247. Epub 2015 Mar 20.


Structure and proposed mechanism of L-α-glycerophosphate oxidase from Mycoplasma pneumoniae.

Elkhal CK, Kean KM, Parsonage D, Maenpuen S, Chaiyen P, Claiborne A, Karplus PA.

FEBS J. 2015 Aug;282(16):3030-42. doi: 10.1111/febs.13233. Epub 2015 Mar 14.


Dissecting peroxiredoxin catalysis: separating binding, peroxidation, and resolution for a bacterial AhpC.

Parsonage D, Nelson KJ, Ferrer-Sueta G, Alley S, Karplus PA, Furdui CM, Poole LB.

Biochemistry. 2015 Feb 24;54(7):1567-75. doi: 10.1021/bi501515w. Epub 2015 Feb 10.


Rationally engineered flavin-dependent oxidase reveals steric control of dioxygen reduction.

Zafred D, Steiner B, Teufelberger AR, Hromic A, Karplus PA, Schofield CJ, Wallner S, Macheroux P.

FEBS J. 2015 Aug;282(16):3060-74. doi: 10.1111/febs.13212. Epub 2015 Feb 24.


A primer on peroxiredoxin biochemistry.

Karplus PA.

Free Radic Biol Med. 2015 Mar;80:183-90. doi: 10.1016/j.freeradbiomed.2014.10.009. Epub 2014 Oct 19. Review.


Tuning of peroxiredoxin catalysis for various physiological roles.

Perkins A, Poole LB, Karplus PA.

Biochemistry. 2014 Dec 16;53(49):7693-705. doi: 10.1021/bi5013222. Epub 2014 Dec 1. Review.


Structures of Arg- and Gln-type bacterial cysteine dioxygenase homologs.

Driggers CM, Hartman SJ, Karplus PA.

Protein Sci. 2015 Jan;24(1):154-61. doi: 10.1002/pro.2587. Epub 2014 Nov 17.


Gleaning unexpected fruits from hard-won synthetases: probing principles of permissivity in non-canonical amino acid-tRNA synthetases.

Cooley RB, Karplus PA, Mehl RA.

Chembiochem. 2014 Aug 18;15(12):1810-9. doi: 10.1002/cbic.201402180. Epub 2014 Jul 11.


Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement.

Moriarty NW, Tronrud DE, Adams PD, Karplus PA.

FEBS J. 2014 Sep;281(18):4061-71. doi: 10.1111/febs.12860. Epub 2014 Jun 17.


Structure of a sedoheptulose 7-phosphate cyclase: ValA from Streptomyces hygroscopicus.

Kean KM, Codding SJ, Asamizu S, Mahmud T, Karplus PA.

Biochemistry. 2014 Jul 8;53(26):4250-60. doi: 10.1021/bi5003508. Epub 2014 Jun 25. Erratum in: Biochemistry. 2014 Jul 8;53(26):4316.


Crystal structure of Escherichia coli SsuE: defining a general catalytic cycle for FMN reductases of the flavodoxin-like superfamily.

Driggers CM, Dayal PV, Ellis HR, Karplus PA.

Biochemistry. 2014 Jun 3;53(21):3509-19. doi: 10.1021/bi500314f. Epub 2014 May 21.


Structural basis of improved second-generation 3-nitro-tyrosine tRNA synthetases.

Cooley RB, Feldman JL, Driggers CM, Bundy TA, Stokes AL, Karplus PA, Mehl RA.

Biochemistry. 2014 Apr 1;53(12):1916-24. doi: 10.1021/bi5001239. Epub 2014 Mar 20.


The sensitive balance between the fully folded and locally unfolded conformations of a model peroxiredoxin.

Perkins A, Nelson KJ, Williams JR, Parsonage D, Poole LB, Karplus PA.

Biochemistry. 2013 Dec 3;52(48):8708-21. doi: 10.1021/bi4011573. Epub 2013 Nov 20.


Evaluating peroxiredoxin sensitivity toward inactivation by peroxide substrates.

Nelson KJ, Parsonage D, Karplus PA, Poole LB.

Methods Enzymol. 2013;527:21-40. doi: 10.1016/B978-0-12-405882-8.00002-7.


Better models by discarding data?

Diederichs K, Karplus PA.

Acta Crystallogr D Biol Crystallogr. 2013 Jul;69(Pt 7):1215-22. doi: 10.1107/S0907444913001121. Epub 2013 Jun 15.


Cysteine dioxygenase structures from pH4 to 9: consistent cys-persulfenate formation at intermediate pH and a Cys-bound enzyme at higher pH.

Driggers CM, Cooley RB, Sankaran B, Hirschberger LL, Stipanuk MH, Karplus PA.

J Mol Biol. 2013 Sep 9;425(17):3121-36. doi: 10.1016/j.jmb.2013.05.028. Epub 2013 Jun 7.


Mapping the active site helix-to-strand conversion of CxxxxC peroxiredoxin Q enzymes.

Perkins A, Gretes MC, Nelson KJ, Poole LB, Karplus PA.

Biochemistry. 2012 Sep 25;51(38):7638-50. doi: 10.1021/bi301017s. Epub 2012 Sep 14.


Linking crystallographic model and data quality.

Karplus PA, Diederichs K.

Science. 2012 May 25;336(6084):1030-3. doi: 10.1126/science.1218231.


The tumor suppressor merlin controls growth in its open state, and phosphorylation converts it to a less-active more-closed state.

Sher I, Hanemann CO, Karplus PA, Bretscher A.

Dev Cell. 2012 Apr 17;22(4):703-5. doi: 10.1016/j.devcel.2012.03.008. No abstract available.


Peroxiredoxins as molecular triage agents, sacrificing themselves to enhance cell survival during a peroxide attack.

Karplus PA, Poole LB.

Mol Cell. 2012 Feb 10;45(3):275-8. doi: 10.1016/j.molcel.2012.01.012.


Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites.

Berkholz DS, Driggers CM, Shapovalov MV, Dunbrack RL Jr, Karplus PA.

Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):449-53. doi: 10.1073/pnas.1107115108. Epub 2011 Dec 23.


(φ,ψ)₂ motifs: a purely conformation-based fine-grained enumeration of protein parts at the two-residue level.

Hollingsworth SA, Lewis MC, Berkholz DS, Wong WK, Karplus PA.

J Mol Biol. 2012 Feb 10;416(1):78-93. doi: 10.1016/j.jmb.2011.12.022. Epub 2011 Dec 16.

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