My Bibliography

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Jaramillo-Martinez V, Sennoune SR, Tikhonova EB, Karamyshev AL, Ganapathy V, Urbatsch IL. Molecular Phenotypes Segregate Missense Mutations in SLC13A5 Epilepsy. J Mol Biol. 2024 Nov 15;436(22):168820. doi: 10.1016/j.jmb.2024.168820. Epub 2024 Oct 22. PubMed PMID: 39442909; PubMed Central PMCID: PMC11929159.

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Gewering T, Waghray D, Parey K, Jung H, Tran NNB, Zapata J, Zhao P, Chen H, Januliene D, Hummer G, Urbatsch I, Moeller A, Zhang Q. Tracing the substrate translocation mechanism in P-glycoprotein. Elife. 2024 Jan 23;12. doi: 10.7554/eLife.90174. PubMed PMID: 38259172; PubMed Central PMCID: PMC10945689.

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Tran NNB, Bui ATA, Jaramillo-Martinez V, Weber J, Zhang Q, Urbatsch IL. Lipid environment determines the drug-stimulated ATPase activity of P-glycoprotein. Front Mol Biosci. 2023;10:1141081. doi: 10.3389/fmolb.2023.1141081. eCollection 2023. PubMed PMID: 36911528; PubMed Central PMCID: PMC9995911.

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Jaramillo-Martinez V, Ganapathy V, Urbatsch IL. Peptide Tags and Domains for Expression and Detection of Mammalian Membrane Proteins at the Cell Surface. Methods Mol Biol. 2022;2507:337-358. doi: 10.1007/978-1-0716-2368-8_18. PubMed PMID: 35773591; PubMed Central PMCID: PMC11929158.

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Kielkopf CL, Bauer W, Urbatsch IL. Analysis of Proteins by Immunoblotting. Cold Spring Harb Protoc. 2021 Dec 1;2021(12). doi: 10.1101/pdb.prot102251. PubMed PMID: 34853123.

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Kielkopf CL, Bauer W, Urbatsch IL. Staining Sodium Dodecyl Sulfate-Polyacrylamide Gels with Silver Salts. Cold Spring Harb Protoc. 2021 Dec 1;2021(12). doi: 10.1101/pdb.prot102244. PubMed PMID: 34853122.

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Kielkopf CL, Bauer W, Urbatsch IL. Variations of Staining Sodium Dodecyl Sulfate-Polyacrylamide Gels with Coomassie Brilliant Blue. Cold Spring Harb Protoc. 2021 Dec 1;2021(12). doi: 10.1101/pdb.prot102236. PubMed PMID: 34853121.

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Kielkopf CL, Bauer W, Urbatsch IL. Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis of Proteins. Cold Spring Harb Protoc. 2021 Dec 1;2021(12). doi: 10.1101/pdb.prot102228. PubMed PMID: 34853120.

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Jaramillo-Martinez V, Sivaprakasam S, Ganapathy V, Urbatsch IL. Drosophila INDY and Mammalian INDY: Major Differences in Transport Mechanism and Structural Features despite Mostly Similar Biological Functions. Metabolites. 2021 Sep 29;11(10). doi: 10.3390/metabo11100669. Review. PubMed PMID: 34677384; PubMed Central PMCID: PMC8537002.

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Jaramillo-Martinez V, Ganapathy V, Urbatsch IL. A home run for human NaCT/SLC13A5/INDY: cryo-EM structure and homology model to predict transport mechanisms, inhibitor interactions and mutational defects. Biochem J. 2021 Jun 11;478(11):2051-2057. doi: 10.1042/BCJ20210211. PubMed PMID: 34101804; PubMed Central PMCID: PMC8203205.

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Kielkopf CL, Bauer W, Urbatsch IL. Solubilization of Expressed Proteins from Inclusion Bodies. Cold Spring Harb Protoc. 2021 Feb 1;2021(2). doi: 10.1101/pdb.prot102210. PubMed PMID: 33526420.

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Kielkopf CL, Bauer W, Urbatsch IL. Preparation of Cell Extracts for Purification of Soluble Proteins Expressed in E. coli. Cold Spring Harb Protoc. 2021 Feb 1;2021(2). doi: 10.1101/pdb.prot102178. PubMed PMID: 33526419.

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Kielkopf CL, Bauer W, Urbatsch IL. Subcellular Localization of Signal Peptide Fusion Proteins Expressed in E. coli. Cold Spring Harb Protoc. 2021 Feb 1;2021(2). doi: 10.1101/pdb.prot102145. PubMed PMID: 33526418.

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Kielkopf CL, Bauer W, Urbatsch IL. Expression of Cloned Genes in E. coli Using IPTG-Inducible Promoters. Cold Spring Harb Protoc. 2021 Feb 1;2021(2). doi: 10.1101/pdb.prot102137. PubMed PMID: 33526417.

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Kielkopf CL, Bauer W, Urbatsch IL. Expressing Cloned Genes for Protein Production, Purification, and Analysis. Cold Spring Harb Protoc. 2021 Feb 1;2021(2). doi: 10.1101/pdb.top102129. PubMed PMID: 33272973.

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Kielkopf CL, Bauer W, Urbatsch IL. Considerations for Membrane Protein Purification. Cold Spring Harb Protoc. 2021 Jan 4;2021(1). doi: 10.1101/pdb.top102285. PubMed PMID: 33397781.

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Kielkopf CL, Bauer W, Urbatsch IL. Preparation of Cell Extracts for Purification of Proteins Expressed in Pichia pastoris. Cold Spring Harb Protoc. 2021 Jan 4;2021(1). doi: 10.1101/pdb.prot102186. PubMed PMID: 33397780.

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Kielkopf CL, Bauer W, Urbatsch IL. Expression of Cloned Genes in Pichia pastoris Using the Methanol-Inducible Promoter AOX1. Cold Spring Harb Protoc. 2021 Jan 4;2021(1). doi: 10.1101/pdb.prot102160. PubMed PMID: 33397779.

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Higuchi K, Kopel JJ, Sivaprakasam S, Jaramillo-Martinez V, Sutton RB, Urbatsch IL, Ganapathy V. Functional analysis of a species-specific inhibitor selective for human Na+-coupled citrate transporter (NaCT/SLC13A5/mINDY). Biochem J. 2020 Nov 13;477(21):4149-4165. doi: 10.1042/BCJ20200592. PubMed PMID: 33079129; PubMed Central PMCID: PMC7657661.

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Jaramillo-Martinez V, Urbatsch IL, Ganapathy V. Functional Distinction between Human and Mouse Sodium-Coupled Citrate Transporters and Its Biologic Significance: An Attempt for Structural Basis Using a Homology Modeling Approach. Chem Rev. 2021 May 12;121(9):5359-5377. doi: 10.1021/acs.chemrev.0c00529. Epub 2020 Oct 11. Review. PubMed PMID: 33040525.

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Kielkopf CL, Bauer W, Urbatsch IL. Purification of Fusion Proteins by Affinity Chromatography on Glutathione Resin. Cold Spring Harb Protoc. 2020 Jun 1;2020(6):102202. doi: 10.1101/pdb.prot102202. PubMed PMID: 32482903.

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Kielkopf CL, Bauer W, Urbatsch IL. Purification of Polyhistidine-Tagged Proteins by Immobilized Metal Affinity Chromatography. Cold Spring Harb Protoc. 2020 Jun 1;2020(6):102194. doi: 10.1101/pdb.prot102194. PubMed PMID: 32482902.

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Kielkopf CL, Bauer W, Urbatsch IL. Expression of Cloned Genes Using the Baculovirus Expression System. Cold Spring Harb Protoc. 2020 Jun 1;2020(6):102152. doi: 10.1101/pdb.prot102152. PubMed PMID: 32354747.

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Kielkopf CL, Bauer W, Urbatsch IL. Methods for Measuring the Concentrations of Proteins. Cold Spring Harb Protoc. 2020 Apr 1;2020(4):102277. doi: 10.1101/pdb.top102277. PubMed PMID: 32238598.

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Kielkopf CL, Bauer W, Urbatsch IL. Bradford Assay for Determining Protein Concentration. Cold Spring Harb Protoc. 2020 Apr 1;2020(4):102269. doi: 10.1101/pdb.prot102269. PubMed PMID: 32238597.

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Swartz DJ, Singh A, Sok N, Thomas JN, Weber J, Urbatsch IL. Replacing the eleven native tryptophans by directed evolution produces an active P-glycoprotein with site-specific, non-conservative substitutions. Sci Rep. 2020 Feb 21;10(1):3224. doi: 10.1038/s41598-020-59802-w. PubMed PMID: 32081894; PubMed Central PMCID: PMC7035247.

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Sigoillot M, Overtus M, Grodecka M, Scholl D, Garcia-Pino A, Laeremans T, He L, Pardon E, Hildebrandt E, Urbatsch I, Steyaert J, Riordan JR, Govaerts C. Domain-interface dynamics of CFTR revealed by stabilizing nanobodies. Nat Commun. 2019 Jun 14;10(1):2636. doi: 10.1038/s41467-019-10714-y. PubMed PMID: 31201318; PubMed Central PMCID: PMC6572788.

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Yang Z, Hildebrandt E, Jiang F, Aleksandrov AA, Khazanov N, Zhou Q, An J, Mezzell AT, Xavier BM, Ding H, Riordan JR, Senderowitz H, Kappes JC, Brouillette CG, Urbatsch IL. Structural stability of purified human CFTR is systematically improved by mutations in nucleotide binding domain 1. Biochim Biophys Acta Biomembr. 2018 May;1860(5):1193-1204. doi: 10.1016/j.bbamem.2018.02.006. Epub 2018 Feb 7. PubMed PMID: 29425673; PubMed Central PMCID: PMC6319260.

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Zoghbi ME, Mok L, Swartz DJ, Singh A, Fendley GA, Urbatsch IL, Altenberg GA. Substrate-induced conformational changes in the nucleotide-binding domains of lipid bilayer-associated P-glycoprotein during ATP hydrolysis. J Biol Chem. 2017 Dec 15;292(50):20412-20424. doi: 10.1074/jbc.M117.814186. Epub 2017 Oct 9. PubMed PMID: 29018094; PubMed Central PMCID: PMC5733581.

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Xavier BM, Hildebrandt E, Jiang F, Ding H, Kappes JC, Urbatsch IL. Substitution of Yor1p NBD1 residues improves the thermal stability of Human Cystic Fibrosis Transmembrane Conductance Regulator. Protein Eng Des Sel. 2017 Oct 1;30(10):729-741. doi: 10.1093/protein/gzx054. PubMed PMID: 29053845; PubMed Central PMCID: PMC5914393.

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Hildebrandt E, Khazanov N, Kappes JC, Dai Q, Senderowitz H, Urbatsch IL. Specific stabilization of CFTR by phosphatidylserine. Biochim Biophys Acta Biomembr. 2017 Feb;1859(2):289-293. doi: 10.1016/j.bbamem.2016.11.013. Epub 2016 Nov 30. PubMed PMID: 27913277; PubMed Central PMCID: PMC5237360.

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Yang Z, Zhou Q, Mok L, Singh A, Swartz DJ, Urbatsch IL, Brouillette CG. Interactions and cooperativity between P-glycoprotein structural domains determined by thermal unfolding provides insights into its solution structure and function. Biochim Biophys Acta Biomembr. 2017 Jan;1859(1):48-60. doi: 10.1016/j.bbamem.2016.10.009. Epub 2016 Oct 23. PubMed PMID: 27783926; PubMed Central PMCID: PMC8590470.

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Fendley GA, Urbatsch IL, Sutton RB, Zoghbi ME, Altenberg GA. Nucleotide dependence of the dimerization of ATP binding cassette nucleotide binding domains. Biochem Biophys Res Commun. 2016 Nov 11;480(2):268-272. doi: 10.1016/j.bbrc.2016.10.046. Epub 2016 Oct 17. PubMed PMID: 27765627.

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Bianchi F, Klooster JS, Ruiz SJ, Luck K, Pols T, Urbatsch IL, Poolman B. Asymmetry in inward- and outward-affinity constant of transport explain unidirectional lysine flux in Saccharomyces cerevisiae. Sci Rep. 2016 Aug 23;6:31443. doi: 10.1038/srep31443. PubMed PMID: 27550794; PubMed Central PMCID: PMC4993999.

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Lee JY, Kinch LN, Borek DM, Wang J, Wang J, Urbatsch IL, Xie XS, Grishin NV, Cohen JC, Otwinowski Z, Hobbs HH, Rosenbaum DM. Crystal structure of the human sterol transporter ABCG5/ABCG8. Nature. 2016 May 26;533(7604):561-4. doi: 10.1038/nature17666. Epub 2016 May 4. PubMed PMID: 27144356; PubMed Central PMCID: PMC4964963.

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Hildebrandt E, Mulky A, Ding H, Dai Q, Aleksandrov AA, Bajrami B, Diego PA, Wu X, Ray M, Naren AP, Riordan JR, Yao X, DeLucas LJ, Urbatsch IL, Kappes JC. A stable human-cell system overexpressing cystic fibrosis transmembrane conductance regulator recombinant protein at the cell surface. Mol Biotechnol. 2015 May;57(5):391-405. doi: 10.1007/s12033-014-9830-5. PubMed PMID: 25577540; PubMed Central PMCID: PMC4405497.

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Szewczyk P, Tao H, McGrath AP, Villaluz M, Rees SD, Lee SC, Doshi R, Urbatsch IL, Zhang Q, Chang G. Snapshots of ligand entry, malleable binding and induced helical movement in P-glycoprotein. Acta Crystallogr D Biol Crystallogr. 2015 Mar;71(Pt 3):732-41. doi: 10.1107/S1399004715000978. Epub 2015 Feb 26. PubMed PMID: 25760620; PubMed Central PMCID: PMC4356375.

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Moeller A, Lee SC, Tao H, Speir JA, Chang G, Urbatsch IL, Potter CS, Carragher B, Zhang Q. Distinct conformational spectrum of homologous multidrug ABC transporters. Structure. 2015 Mar 3;23(3):450-460. doi: 10.1016/j.str.2014.12.013. Epub 2015 Feb 5. PubMed PMID: 25661651; PubMed Central PMCID: PMC4351144.

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Hildebrandt E, Zhang Q, Cant N, Ding H, Dai Q, Peng L, Fu Y, DeLucas LJ, Ford R, Kappes JC, Urbatsch IL. A survey of detergents for the purification of stable, active human cystic fibrosis transmembrane conductance regulator (CFTR). Biochim Biophys Acta. 2014 Nov;1838(11):2825-37. doi: 10.1016/j.bbamem.2014.07.016. Epub 2014 Jul 24. PubMed PMID: 25065669; PubMed Central PMCID: PMC4170525.

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Swartz DJ, Mok L, Botta SK, Singh A, Altenberg GA, Urbatsch IL. Directed evolution of P-glycoprotein cysteines reveals site-specific, non-conservative substitutions that preserve multidrug resistance. Biosci Rep. 2014 Jun 25;34(3). doi: 10.1042/BSR20140062. PubMed PMID: 24825346; PubMed Central PMCID: PMC4069687.

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Yang Z, Wang C, Zhou Q, An J, Hildebrandt E, Aleksandrov LA, Kappes JC, DeLucas LJ, Riordan JR, Urbatsch IL, Hunt JF, Brouillette CG. Membrane protein stability can be compromised by detergent interactions with the extramembranous soluble domains. Protein Sci. 2014 Jun;23(6):769-89. doi: 10.1002/pro.2460. Epub 2014 May 3. PubMed PMID: 24652590; PubMed Central PMCID: PMC4093953.

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Ward AB, Szewczyk P, Grimard V, Lee CW, Martinez L, Doshi R, Caya A, Villaluz M, Pardon E, Cregger C, Swartz DJ, Falson PG, Urbatsch IL, Govaerts C, Steyaert J, Chang G. Structures of P-glycoprotein reveal its conformational flexibility and an epitope on the nucleotide-binding domain. Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13386-91. doi: 10.1073/pnas.1309275110. Epub 2013 Jul 30. PubMed PMID: 23901103; PubMed Central PMCID: PMC3746859.

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Swartz DJ, Weber J, Urbatsch IL. P-glycoprotein is fully active after multiple tryptophan substitutions. Biochim Biophys Acta. 2013 Mar;1828(3):1159-68. doi: 10.1016/j.bbamem.2012.12.005. Epub 2012 Dec 19. PubMed PMID: 23261390; PubMed Central PMCID: PMC3602414.

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Tao H, Weng Y, Zhuo R, Chang G, Urbatsch IL, Zhang Q. Design and synthesis of Selenazole-containing peptides for cocrystallization with P-glycoprotein. Chembiochem. 2011 Apr 11;12(6):868-73. doi: 10.1002/cbic.201100048. Epub 2011 Mar 8. PubMed PMID: 21387512; PubMed Central PMCID: PMC4814162.

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Schölz C, Parcej D, Ejsing CS, Robenek H, Urbatsch IL, Tampé R. Specific lipids modulate the transporter associated with antigen processing (TAP). J Biol Chem. 2011 Apr 15;286(15):13346-56. doi: 10.1074/jbc.M110.216416. Epub 2011 Feb 25. PubMed PMID: 21357424; PubMed Central PMCID: PMC3075681.

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Bai J, Swartz DJ, Protasevich II, Brouillette CG, Harrell PM, Hildebrandt E, Gasser B, Mattanovich D, Ward A, Chang G, Urbatsch IL. A gene optimization strategy that enhances production of fully functional P-glycoprotein in Pichia pastoris. PLoS One. 2011;6(8):e22577. doi: 10.1371/journal.pone.0022577. Epub 2011 Aug 3. PubMed PMID: 21826197; PubMed Central PMCID: PMC3149604.

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Hoffman AD, Urbatsch IL, Vogel PD. Nucleotide binding to the human multidrug resistance protein 3, MRP3. Protein J. 2010 Jul;29(5):373-9. doi: 10.1007/s10930-010-9262-4. PubMed PMID: 20563633.

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Johnson BJ, Lee JY, Pickert A, Urbatsch IL. Bile acids stimulate ATP hydrolysis in the purified cholesterol transporter ABCG5/G8. Biochemistry. 2010 Apr 27;49(16):3403-11. doi: 10.1021/bi902064g. PubMed PMID: 20210363.

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Gutmann DA, Ward A, Urbatsch IL, Chang G, van Veen HW. Understanding polyspecificity of multidrug ABC transporters: closing in on the gaps in ABCB1. Trends Biochem Sci. 2010 Jan;35(1):36-42. doi: 10.1016/j.tibs.2009.07.009. Epub 2009 Oct 12. Review. PubMed PMID: 19819701; PubMed Central PMCID: PMC4608440.

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Zehnpfennig B, Urbatsch IL, Galla HJ. Functional reconstitution of human ABCC3 into proteoliposomes reveals a transport mechanism with positive cooperativity. Biochemistry. 2009 May 26;48(20):4423-30. doi: 10.1021/bi9001908. PubMed PMID: 19334674.