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Detection of Incorporation of p-Coumaric Acid into Photoactive Yellow Protein Variants in Vivo.

Brechun KE, Zhen D, Jaikaran A, Borisenko V, Kumauchi M, Hoff WD, Arndt KM, Woolley GA.

Biochemistry. 2019 Jun 11;58(23):2682-2694. doi: 10.1021/acs.biochem.9b00279. Epub 2019 May 30.


Candidatus Krumholzibacterium zodletonense gen. nov., sp nov, the first representative of the candidate phylum Krumholzibacteriota phyl. nov. recovered from an anoxic sulfidic spring using genome resolved metagenomics.

Youssef NH, Farag IF, Hahn CR, Premathilake H, Fry E, Hart M, Huffaker K, Bird E, Hambright J, Hoff WD, Elshahed MS.

Syst Appl Microbiol. 2019 Jan;42(1):85-93. doi: 10.1016/j.syapm.2018.11.002. Epub 2018 Nov 15.


Spectroscopic ruler for measuring active-site distortions based on Raman optical activity of a hydrogen out-of-plane vibration.

Haraguchi S, Shingae T, Fujisawa T, Kasai N, Kumauchi M, Hanamoto T, Hoff WD, Unno M.

Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):8671-8675. doi: 10.1073/pnas.1806491115. Epub 2018 Aug 13.


Photoreceptors Take Charge: Emerging Principles for Light Sensing.

Kottke T, Xie A, Larsen DS, Hoff WD.

Annu Rev Biophys. 2018 Mar 14. doi: 10.1146/annurev-biophys-070317-033047. [Epub ahead of print]


Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila.

Mix LT, Carroll EC, Morozov D, Pan J, Gordon WR, Philip A, Fuzell J, Kumauchi M, van Stokkum I, Groenhof G, Hoff WD, Larsen DS.

Biochemistry. 2018 Mar 20;57(11):1733-1747. doi: 10.1021/acs.biochem.7b01114. Epub 2018 Mar 6.


In defence of the three-domains of life paradigm.

van der Gulik PTS, Hoff WD, Speijer D.

BMC Evol Biol. 2017 Sep 19;17(1):218. doi: 10.1186/s12862-017-1059-z. Review.


Noncanonical Photocycle Initiation Dynamics of the Photoactive Yellow Protein (PYP) Domain of the PYP-Phytochrome-Related (Ppr) Photoreceptor.

Mix LT, Hara M, Rathod R, Kumauchi M, Hoff WD, Larsen DS.

J Phys Chem Lett. 2016 Dec 15;7(24):5212-5218. Epub 2016 Dec 5.


Draft genome sequence of Staphylococcus hominis strain Hudgins isolated from human skin implicates metabolic versatility and several virulence determinants.

Calkins S, Couger MB, Jackson C, Zandler J, Hudgins GC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N.

Genom Data. 2016 Oct 7;10:91-96. eCollection 2016 Dec.


Bifurcation in the Ultrafast Dynamics of the Photoactive Yellow Proteins from Leptospira biflexa and Halorhodospira halophila.

Mix LT, Kirpich J, Kumauchi M, Ren J, Vengris M, Hoff WD, Larsen DS.

Biochemistry. 2016 Nov 8;55(44):6138-6149. Epub 2016 Oct 26.


Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis.

Moghadam F, Couger MB, Russ B, Ramsey R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N.

Genom Data. 2016 Sep 20;10:63-68. eCollection 2016 Dec.


Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential.

Avramov AP, Couger MB, Hartley EL, Land C, Wellendorf R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N.

Genom Data. 2016 Sep 17;10:54-60. eCollection 2016 Dec.


Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential.

Miller NT, Fuller D, Couger MB, Bagazinski M, Boyne P, Devor RC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N.

Genom Data. 2016 Aug 4;9:154-9. doi: 10.1016/j.gdata.2016.08.004. eCollection 2016 Sep.


Draft genome sequence of Micrococcus luteus strain O'Kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates.

Hanafy RA, Couger MB, Baker K, Murphy C, O'Kane SD, Budd C, French DP, Hoff WD, Youssef N.

Genom Data. 2016 Aug 8;9:148-53. doi: 10.1016/j.gdata.2016.08.006. eCollection 2016 Sep.


Anticodon Modifications in the tRNA Set of LUCA and the Fundamental Regularity in the Standard Genetic Code.

van der Gulik PT, Hoff WD.

PLoS One. 2016 Jul 25;11(7):e0158342. doi: 10.1371/journal.pone.0158342. eCollection 2016.


Draft Genome of the Arthrobacter sp. Strain Edens01.

Couger MB, Hanafy RA, Edens C, Budd C, French DP, Hoff WD, Elshahed MS, Youssef NH.

Genome Announc. 2015 Dec 17;3(6). pii: e01475-15. doi: 10.1128/genomeA.01475-15.


The Draft Genome Sequence of Xanthomonas sp. Strain Mitacek01 Expands the Pangenome of a Genus of Plant Pathogens.

Couger MB, Hanafy RA, Mitacek RM, Budd C, French DP, Hoff WD, Elshahed MS, Youssef NH.

Genome Announc. 2015 Dec 10;3(6). pii: e01450-15. doi: 10.1128/genomeA.01450-15.


Draft Genome Sequence of the Environmental Isolate Chryseobacterium sp. Hurlbut01.

Couger MB, Hurlbut A, Murphy CL, Budd C, French DP, Hoff WD, Elshahed MS, Youssef NH.

Genome Announc. 2015 Sep 17;3(5). pii: e01071-15. doi: 10.1128/genomeA.01071-15.


Experimental Detection of the Intrinsic Difference in Raman Optical Activity of a Photoreceptor Protein under Preresonance and Resonance Conditions.

Haraguchi S, Hara M, Shingae T, Kumauchi M, Hoff WD, Unno M.

Angew Chem Int Ed Engl. 2015 Sep 21;54(39):11555-8. doi: 10.1002/anie.201505466. Epub 2015 Jul 23.


Draft Genome Sequence of the Extremely Halophilic Phototrophic Purple Sulfur Bacterium Halorhodospira halochloris.

Singh KS, Kirksey J, Hoff WD, Deole R.

J Genomics. 2014 Jul 6;2:118-20. doi: 10.7150/jgen.9123. eCollection 2014.


Chromophore dynamics in the PYP photocycle from femtosecond stimulated Raman spectroscopy.

Creelman M, Kumauchi M, Hoff WD, Mathies RA.

J Phys Chem B. 2014 Jan 23;118(3):659-67. doi: 10.1021/jp408584v. Epub 2014 Jan 10.


Strong ionic hydrogen bonding causes a spectral isotope effect in photoactive yellow protein.

Kaledhonkar S, Hara M, Stalcup TP, Xie A, Hoff WD.

Biophys J. 2013 Dec 3;105(11):2577-85. doi: 10.1016/j.bpj.2013.10.017.


Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales.

Youssef NH, Savage-Ashlock KN, McCully AL, Luedtke B, Shaw EI, Hoff WD, Elshahed MS.

ISME J. 2014 Mar;8(3):636-49. doi: 10.1038/ismej.2013.165. Epub 2013 Sep 19.


Complete genome sequence of Halorhodospira halophila SL1.

Challacombe JF, Majid S, Deole R, Brettin TS, Bruce D, Delano SF, Detter JC, Gleasner CD, Han CS, Misra M, Reitenga KG, Mikhailova N, Woyke T, Pitluck S, Nolan M, Land ML, Saunders E, Tapia R, Lapidus A, Ivanova N, Hoff WD.

Stand Genomic Sci. 2013 Apr 15;8(2):206-14. doi: 10.4056/sigs.3677284. eCollection 2013.


Total chemical synthesis of fully functional Photoactive Yellow Protein.

Gordon WR, Bang D, Hoff WD, Kent SB.

Bioorg Med Chem. 2013 Jun 15;21(12):3436-42. doi: 10.1016/j.bmc.2013.03.025. Epub 2013 Mar 27.


An extremely halophilic proteobacterium combines a highly acidic proteome with a low cytoplasmic potassium content.

Deole R, Challacombe J, Raiford DW, Hoff WD.

J Biol Chem. 2013 Jan 4;288(1):581-8. doi: 10.1074/jbc.M112.420505. Epub 2012 Nov 9.


Side-chain specific isotopic labeling of proteins for infrared structural biology: the case of ring-D4-tyrosine isotope labeling of photoactive yellow protein.

Rathod R, Kang Z, Hartson SD, Kumauchi M, Xie A, Hoff WD.

Protein Expr Purif. 2012 Sep;85(1):125-32. doi: 10.1016/j.pep.2012.06.011. Epub 2012 Jul 16.


Unassigned codons, nonsense suppression, and anticodon modifications in the evolution of the genetic code.

van der Gulik PT, Hoff WD.

J Mol Evol. 2011 Oct;73(3-4):59-69. doi: 10.1007/s00239-011-9470-3. Epub 2011 Nov 11.


Light helps bacteria make important lifestyle decisions.

Gomelsky M, Hoff WD.

Trends Microbiol. 2011 Sep;19(9):441-8. doi: 10.1016/j.tim.2011.05.002. Epub 2011 Jun 12. Review.


A conserved helical capping hydrogen bond in PAS domains controls signaling kinetics in the superfamily prototype photoactive yellow protein.

Kumauchi M, Kaledhonkar S, Philip AF, Wycoff J, Hara M, Li Y, Xie A, Hoff WD.

J Am Chem Soc. 2010 Nov 10;132(44):15820-30. doi: 10.1021/ja107716r.


Subpicosecond Excited-State Proton Transfer Preceding Isomerization During the Photorecovery of Photoactive Yellow Protein.

Carroll EC, Song SH, Kumauchi M, van Stokkum IH, Jailaubekov A, Hoff WD, Larsen DS.

J Phys Chem Lett. 2010;1(19):2793-2799.


Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain.

Philip AF, Kumauchi M, Hoff WD.

Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):17986-91. doi: 10.1073/pnas.1004823107. Epub 2010 Oct 1.


Spectral tuning in photoactive yellow protein by modulation of the shape of the excited state energy surface.

Philip AF, Nome RA, Papadantonakis GA, Scherer NF, Hoff WD.

Proc Natl Acad Sci U S A. 2010 Mar 30;107(13):5821-6. doi: 10.1073/pnas.0903092107. Epub 2010 Mar 10.


Modulating native-like residual structure in the fully denatured state of photoactive yellow protein affects its refolding.

Lee BC, Kumauchi M, Hoff WD.

J Biol Chem. 2010 Apr 23;285(17):12579-86. doi: 10.1074/jbc.M109.065821. Epub 2010 Feb 23.


Locked chromophore analogs reveal that photoactive yellow protein regulates biofilm formation in the deep sea bacterium Idiomarina loihiensis.

van der Horst MA, Stalcup TP, Kaledhonkar S, Kumauchi M, Hara M, Xie A, Hellingwerf KJ, Hoff WD.

J Am Chem Soc. 2009 Dec 2;131(47):17443-51. doi: 10.1021/ja9057103.


Prokaryotic phototaxis.

Hoff WD, van der Horst MA, Nudel CB, Hellingwerf KJ.

Methods Mol Biol. 2009;571:25-49. doi: 10.1007/978-1-60761-198-1_2.


Functional tuning of photoactive yellow protein by active site residue 46.

Philip AF, Eisenman KT, Papadantonakis GA, Hoff WD.

Biochemistry. 2008 Dec 30;47(52):13800-10. doi: 10.1021/bi801730y.


Proline 54 trans-cis isomerization is responsible for the kinetic partitioning at the last-step photocycle of photoactive yellow protein.

Lee BC, Hoff WD.

Protein Sci. 2008 Dec;17(12):2101-10. doi: 10.1110/ps.037655.108. Epub 2008 Sep 15.


Single-molecule tour de force: teasing apart a signaling complex.

Hoff WD, Spudich JL.

Structure. 2008 Aug 6;16(8):1149-50. doi: 10.1016/j.str.2008.07.004. No abstract available.


Identification of six new photoactive yellow proteins--diversity and structure-function relationships in a bacterial blue light photoreceptor.

Kumauchi M, Hara MT, Stalcup P, Xie A, Hoff WD.

Photochem Photobiol. 2008 Jul-Aug;84(4):956-69. doi: 10.1111/j.1751-1097.2008.00335.x. Epub 2008 Apr 9.


Axis-dependent anisotropy in protein unfolding from integrated nonequilibrium single-molecule experiments, analysis, and simulation.

Nome RA, Zhao JM, Hoff WD, Scherer NF.

Proc Natl Acad Sci U S A. 2007 Dec 26;104(52):20799-804. Epub 2007 Dec 19.


Single-molecule detection of structural changes during Per-Arnt-Sim (PAS) domain activation.

Zhao JM, Lee H, Nome RA, Majid S, Scherer NF, Hoff WD.

Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11561-6. Epub 2006 Jul 19.


Synchrotron radiation energy-dispersive X-ray diffraction analysis of salt distribution in Lépine limestone.

Ioannou I, Hall C, Hoff WD, Pugsley VA, Jacques SD.

Analyst. 2005 Jul;130(7):1006-8. Epub 2005 May 11.


On the role of organic adlayers in the anomalous water sorptivity of Lépine limestone.

Ioannou I, Hoff WD, Hall C.

J Colloid Interface Sci. 2004 Nov 1;279(1):228-34.


Kinetics of moisture expansion in fired clay ceramics: a (time)(1/4) law.

Wilson MA, Hoff WD, Hall C, McKay B, Hiley A.

Phys Rev Lett. 2003 Mar 28;90(12):125503. Epub 2003 Mar 26.


Mimic of photocycle by a protein folding reaction in photoactive yellow protein.

Lee BC, Croonquist PA, Hoff WD.

J Biol Chem. 2001 Nov 30;276(48):44481-7. Epub 2001 Sep 27.


Folding and signaling share the same pathway in a photoreceptor.

Lee BC, Pandit A, Croonquist PA, Hoff WD.

Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):9062-7. Epub 2001 Jul 24.


Formation of a new buried charge drives a large-amplitude protein quake in photoreceptor activation.

Xie A, Kelemen L, Hendriks J, White BJ, Hellingwerf KJ, Hoff WD.

Biochemistry. 2001 Feb 13;40(6):1510-7.


PAS domain receptor photoactive yellow protein is converted to a molten globule state upon activation.

Lee BC, Croonquist PA, Sosnick TR, Hoff WD.

J Biol Chem. 2001 Jun 15;276(24):20821-3. Epub 2001 Apr 23.


Partial Wetting in Capillary Liquid Absorption by Limestones.

Taylor SC, Hall C, Hoff WD, Wilson MA.

J Colloid Interface Sci. 2000 Apr 15;224(2):351-357.


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