My Bibliography

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Lopez KE, Rizo AN, Tse E, Lin J, Scull NW, Thwin AC, Lucius AL, Shorter J, Southworth DR. Conformational plasticity of the ClpAP AAA+ protease couples protein unfolding and proteolysis. Nat Struct Mol Biol. 2020 May;27(5):406-416. doi: 10.1038/s41594-020-0409-5. Epub 2020 Apr 20. PubMed PMID: 32313240; PubMed Central PMCID: PMC7529148.

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Scull CE, Clarke AM, Lucius AL, Schneider DA. Downstream sequence-dependent RNA cleavage and pausing by RNA polymerase I. J Biol Chem. 2020 Jan 31;295(5):1288-1299. doi: 10.1074/jbc.RA119.011354. Epub 2019 Dec 16. PubMed PMID: 31843971; PubMed Central PMCID: PMC6996881.

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Duran EC, Lucius AL. Examination of the nucleotide-linked assembly mechanism of E. coli ClpA. Protein Sci. 2019 Jul;28(7):1312-1323. doi: 10.1002/pro.3638. Epub 2019 Jun 3. PubMed PMID: 31054177; PubMed Central PMCID: PMC6567684.

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Durie CL, Lin J, Scull NW, Mack KL, Jackrel ME, Sweeny EA, Castellano LM, Shorter J, Lucius AL. Hsp104 and Potentiated Variants Can Operate as Distinct Nonprocessive Translocases. Biophys J. 2019 May 21;116(10):1856-1872. doi: 10.1016/j.bpj.2019.03.035. Epub 2019 Apr 5. PubMed PMID: 31027887; PubMed Central PMCID: PMC6531783.

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Scull CE, Ingram ZM, Lucius AL, Schneider DA. A Novel Assay for RNA Polymerase I Transcription Elongation Sheds Light on the Evolutionary Divergence of Eukaryotic RNA Polymerases. Biochemistry. 2019 Apr 23;58(16):2116-2124. doi: 10.1021/acs.biochem.8b01256. Epub 2019 Apr 5. PubMed PMID: 30912638; PubMed Central PMCID: PMC6600827.

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Duran EC, Lucius AL. ATP hydrolysis inactivating Walker B mutation perturbs E. coli ClpA self-assembly energetics in the absence of nucleotide. Biophys Chem. 2018 Nov;242:6-14. doi: 10.1016/j.bpc.2018.08.005. Epub 2018 Aug 27. PubMed PMID: 30173103.

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Durie CL, Duran EC, Lucius AL. Escherichia coli DnaK Allosterically Modulates ClpB between High- and Low-Peptide Affinity States. Biochemistry. 2018 Jul 3;57(26):3665-3675. doi: 10.1021/acs.biochem.8b00045. Epub 2018 Jun 11. PubMed PMID: 29812913.

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Appling FD, Scull CE, Lucius AL, Schneider DA. The A12.2 Subunit Is an Intrinsic Destabilizer of the RNA Polymerase I Elongation Complex. Biophys J. 2018 Jun 5;114(11):2507-2515. doi: 10.1016/j.bpj.2018.04.015. PubMed PMID: 29874602; PubMed Central PMCID: PMC6129170.

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Appling FD, Lucius AL, Schneider DA. Quantifying the influence of 5'-RNA modifications on RNA polymerase I activity. Biophys Chem. 2017 Nov;230:84-88. doi: 10.1016/j.bpc.2017.08.010. Epub 2017 Sep 1. PubMed PMID: 28893424; PubMed Central PMCID: PMC5626657.

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Appling FD, Schneider DA, Lucius AL. Multisubunit RNA Polymerase Cleavage Factors Modulate the Kinetics and Energetics of Nucleotide Incorporation: An RNA Polymerase I Case Study. Biochemistry. 2017 Oct 24;56(42):5654-5662. doi: 10.1021/acs.biochem.7b00370. Epub 2017 Oct 11. PubMed PMID: 28846843; PubMed Central PMCID: PMC6400273.

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Duran EC, Weaver CL, Lucius AL. Comparative Analysis of the Structure and Function of AAA+ Motors ClpA, ClpB, and Hsp104: Common Threads and Disparate Functions. Front Mol Biosci. 2017;4:54. doi: 10.3389/fmolb.2017.00054. eCollection 2017. Review. PubMed PMID: 28824920; PubMed Central PMCID: PMC5540906.

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Weaver CL, Duran EC, Mack KL, Lin J, Jackrel ME, Sweeny EA, Shorter J, Lucius AL. Avidity for Polypeptide Binding by Nucleotide-Bound Hsp104 Structures. Biochemistry. 2017 Apr 18;56(15):2071-2075. doi: 10.1021/acs.biochem.7b00225. Epub 2017 Apr 10. PubMed PMID: 28379007; PubMed Central PMCID: PMC5649362.

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Wang P, Li J, Weaver C, Lucius A, Sha B. Crystal structures of Hsp104 N-terminal domains from Saccharomyces cerevisiae and Candida albicans suggest the mechanism for the function of Hsp104 in dissolving prions. Acta Crystallogr D Struct Biol. 2017 Apr 1;73(Pt 4):365-372. doi: 10.1107/S2059798317002662. Epub 2017 Mar 31. PubMed PMID: 28375147; PubMed Central PMCID: PMC6688567.

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Martin J, Cagle E, Lucius A, Gray G. Correlating the Activity of Rhodium(I)-Phosphite-Lariat Ether Styrene Hydroformylation Catalysts with Alkali Metal Cation Binding through NMR Spectroscopic Titration Methods. Organometallics. 2016 August; :-. doi: 10.1021/acs.organomet.6b00325.

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Lin J, Lucius AL. Examination of ClpB Quaternary Structure and Linkage to Nucleotide Binding. Biochemistry. 2016 Mar 29;55(12):1758-71. doi: 10.1021/acs.biochem.6b00122. Epub 2016 Mar 15. PubMed PMID: 26891079.

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Appling FD, Lucius AL, Schneider DA. Transient-State Kinetic Analysis of the RNA Polymerase I Nucleotide Incorporation Mechanism. Biophys J. 2015 Dec 1;109(11):2382-93. doi: 10.1016/j.bpj.2015.10.037. PubMed PMID: 26636949; PubMed Central PMCID: PMC4675888.

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Lin J, Lucius AL. Examination of the dynamic assembly equilibrium for E. coli ClpB. Proteins. 2015 Nov;83(11):2008-24. doi: 10.1002/prot.24914. Epub 2015 Sep 10. PubMed PMID: 26313457.

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Martin JR, Lucius AL, Gray GM. Metallathiacrown Ethers: Synthesis and Characterization of Transition-Metal Complexes Containing α,ω-Bis(phosphite)-Polythioether Ligands and an Evaluation of Their Soft Metal Binding Capabilities. Organometallics. 2015 September; doi: 10.1021/acs.organomet.5b00693.

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Li T, Weaver CL, Lin J, Duran EC, Miller JM, Lucius AL. Escherichia coli ClpB is a non-processive polypeptide translocase. Biochem J. 2015 Aug 15;470(1):39-52. doi: 10.1042/BJ20141457. Epub 2015 Jun 11. PubMed PMID: 26251445; PubMed Central PMCID: PMC4692069.

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Lin J, Lucius AL. Analysis of Linked Equilibria. Methods Enzymol. 2015;562:161-86. doi: 10.1016/bs.mie.2015.07.003. Epub 2015 Aug 13. PubMed PMID: 26412651.

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Li T, Lin J, Lucius AL. Examination of polypeptide substrate specificity for Escherichia coli ClpB. Proteins. 2015 Jan;83(1):117-34. doi: 10.1002/prot.24710. Epub 2014 Nov 28. PubMed PMID: 25363713.

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Fancy RM, Wang L, Napier T, Lin J, Jing G, Lucius AL, McDonald JM, Zhou T, Song Y. Characterization of calmodulin-Fas death domain interaction: an integrated experimental and computational study. Biochemistry. 2014 Apr 29;53(16):2680-8. doi: 10.1021/bi500228h. Epub 2014 Apr 18. PubMed PMID: 24702583; PubMed Central PMCID: PMC4007977.

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Miller JM, Lucius AL. ATPγS competes with ATP for binding at Domain 1 but not Domain 2 during ClpA catalyzed polypeptide translocation. Biophys Chem. 2014 Jan;185:58-69. doi: 10.1016/j.bpc.2013.11.002. Epub 2013 Nov 13. PubMed PMID: 24362308; PubMed Central PMCID: PMC3966025.

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Miller JM, Lin J, Li T, Lucius AL. E. coli ClpA catalyzed polypeptide translocation is allosterically controlled by the protease ClpP. J Mol Biol. 2013 Aug 9;425(15):2795-812. doi: 10.1016/j.jmb.2013.04.019. Epub 2013 Apr 29. PubMed PMID: 23639359; PubMed Central PMCID: PMC3918674.

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Li T, Lucius AL. Examination of the polypeptide substrate specificity for Escherichia coli ClpA. Biochemistry. 2013 Jul 23;52(29):4941-54. doi: 10.1021/bi400178q. Epub 2013 Jul 10. PubMed PMID: 23773038.

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Lucius AL, Veronese PK, Stafford RP. Dynamic light scattering to study allosteric regulation. Methods Mol Biol. 2012;796:175-86. doi: 10.1007/978-1-61779-334-9_9. PubMed PMID: 22052490.

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Veronese PK, Rajendar B, Lucius AL. Activity of E. coli ClpA bound by nucleoside diphosphates and triphosphates. J Mol Biol. 2011 Jun 10;409(3):333-47. doi: 10.1016/j.jmb.2011.02.018. Epub 2011 Mar 2. PubMed PMID: 21376057.

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Lucius AL, Miller JM, Rajendar B. Application of the sequential n-step kinetic mechanism to polypeptide translocases. Methods Enzymol. 2011;488:239-64. doi: 10.1016/B978-0-12-381268-1.00010-0. PubMed PMID: 21195231.

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Sheff JT, Lucius AL, Owens SB, Gray GM. Generally Applicable NMR Titration Methods for the Determination of Equilibrium Constants for Coordination Complexes: Syntheses and Characterizations of Metallacrown Ethers with α,ω-Bis(phosphite)-polyether Ligands and Determination of Equilibrium Binding Constants to Li+. Organometallics. 2011; 30(21):5695. doi: 10.1021/om200580t.

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Veronese PK, Lucius AL. Effect of temperature on the self-assembly of the Escherichia coli ClpA molecular chaperone. Biochemistry. 2010 Nov 16;49(45):9820-9. doi: 10.1021/bi101136d. Epub 2010 Oct 22. PubMed PMID: 20964444.

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Chenna BC, King JR, Shinkre BA, Glover AL, Lucius AL, Velu SE. Synthesis and structure activity relationship studies of novel Staphylococcus aureus Sortase A inhibitors. Eur J Med Chem. 2010 Sep;45(9):3752-61. doi: 10.1016/j.ejmech.2010.05.024. Epub 2010 May 20. PubMed PMID: 20541848; PubMed Central PMCID: PMC4346195.

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Rajendar B, Lucius AL. Molecular mechanism of polypeptide translocation catalyzed by the Escherichia coli ClpA protein translocase. J Mol Biol. 2010 Jun 25;399(5):665-79. doi: 10.1016/j.jmb.2010.03.061. Epub 2010 Apr 7. PubMed PMID: 20380838.

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McClure CP, Lucius AL. Implementing and Evaluating a Chemistry Course in Chemical Ethics and Civic Responsibility. Journal of chemical education. 2010; 87(11):1171. doi: 10.1021/ed1005135.

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Veronese PK, Stafford RP, Lucius AL. The Escherichia coli ClpA molecular chaperone self-assembles into tetramers. Biochemistry. 2009 Oct 6;48(39):9221-33. doi: 10.1021/bi900935q. PubMed PMID: 19650643.

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Chenna BC, Shinkre BA, King JR, Lucius AL, Narayana SV, Velu SE. Identification of novel inhibitors of bacterial surface enzyme Staphylococcus aureus Sortase A. Bioorg Med Chem Lett. 2008 Jan 1;18(1):380-5. doi: 10.1016/j.bmcl.2007.10.051. Epub 2007 Oct 18. PubMed PMID: 18023345.

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Lucius AL, Jezewska MJ, Bujalowski W. The Escherichia coli PriA helicase has two nucleotide-binding sites differing dramatically in their affinities for nucleotide cofactors. 1. Intrinsic affinities, cooperativities, and base specificity of nucleotide cofactor binding. Biochemistry. 2006 Jun 13;45(23):7202-16. doi: 10.1021/bi051826m. PubMed PMID: 16752911.

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Lucius AL, Jezewska MJ, Roychowdhury A, Bujalowski W. Kinetic mechanisms of the nucleotide cofactor binding to the strong and weak nucleotide-binding site of the Escherichia coli PriA helicase. 2. Biochemistry. 2006 Jun 13;45(23):7217-36. doi: 10.1021/bi051827e. PubMed PMID: 16752912.

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Lucius AL, Jezewska MJ, Bujalowski W. Allosteric interactions between the nucleotide-binding sites and the ssDNA-binding site in the PriA helicase-ssDNA complex. 3. Biochemistry. 2006 Jun 13;45(23):7237-55. doi: 10.1021/bi0518287. PubMed PMID: 16752913.

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Jezewska MJ, Marcinowicz A, Lucius AL, Bujalowski W. DNA polymerase X from African swine fever virus: quantitative analysis of the enzyme-ssDNA interactions and the functional structure of the complex. J Mol Biol. 2006 Feb 10;356(1):121-41. doi: 10.1016/j.jmb.2005.10.061. Epub 2005 Nov 10. PubMed PMID: 16337650.

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Wong CJ, Lucius AL, Lohman TM. Energetics of DNA end binding by E.coli RecBC and RecBCD helicases indicate loop formation in the 3'-single-stranded DNA tail. J Mol Biol. 2005 Sep 30;352(4):765-82. doi: 10.1016/j.jmb.2005.07.056. PubMed PMID: 16126227.

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Jezewska MJ, Lucius AL, Bujalowski W. Binding of six nucleotide cofactors to the hexameric helicase RepA protein of plasmid RSF1010. 2. Base specificity, nucleotide structure, magnesium, and salt effect on the cooperative binding of the cofactors. Biochemistry. 2005 Mar 15;44(10):3877-90. doi: 10.1021/bi048036h. PubMed PMID: 15751963.

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Jezewska MJ, Lucius AL, Bujalowski W. Binding of six nucleotide cofactors to the hexameric helicase RepA protein of plasmid RSF1010. 1. Direct evidence of cooperative interactions between the nucleotide-binding sites of a hexameric helicase. Biochemistry. 2005 Mar 15;44(10):3865-76. doi: 10.1021/bi048037+. PubMed PMID: 15751962.

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Lucius AL, Lohman TM. Effects of temperature and ATP on the kinetic mechanism and kinetic step-size for E.coli RecBCD helicase-catalyzed DNA unwinding. J Mol Biol. 2004 Jun 11;339(4):751-71. doi: 10.1016/j.jmb.2004.04.010. PubMed PMID: 15165848.

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Lucius AL, Wong CJ, Lohman TM. Fluorescence stopped-flow studies of single turnover kinetics of E.coli RecBCD helicase-catalyzed DNA unwinding. J Mol Biol. 2004 Jun 11;339(4):731-50. doi: 10.1016/j.jmb.2004.04.009. PubMed PMID: 15165847.

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Lucius AL, Maluf NK, Fischer CJ, Lohman TM. General methods for analysis of sequential "n-step" kinetic mechanisms: application to single turnover kinetics of helicase-catalyzed DNA unwinding. Biophys J. 2003 Oct;85(4):2224-39. doi: 10.1016/S0006-3495(03)74648-7. PubMed PMID: 14507688; PubMed Central PMCID: PMC1303449.

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Lohman TM, Hsieh J, Maluf NK, Cheng W, Lucius AL, Fischer CJ, Brendza KM, Korolev S, Waksman G. DNA helicases, motors that move along nucleic acids: Lessons from the SF1 helicase superfamily. The Enzymes. 2003; 23. doi: 10.1016/S1874-6047(04)80008-8.

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Lucius AL, Vindigni A, Gregorian R, Ali JA, Taylor AF, Smith GR, Lohman TM. DNA unwinding step-size of E. coli RecBCD helicase determined from single turnover chemical quenched-flow kinetic studies. J Mol Biol. 2002 Nov 29;324(3):409-28. doi: 10.1016/s0022-2836(02)01067-7. PubMed PMID: 12445778.