RESEARCH and review articles

 

Niekamp S, Coudray N, Zhang N, Vale RD, Bhabha G. Coupling of ATPase activity, microtubule binding, and mechanics in the dynein motor domain. EMBO J. 2019 May 31. pii: e101414. doi: 10.15252/embj.2018101414.[Epub ahead of print] PubMed PMID: 31152008.

Niekamp S, Sung J, Huynh W, Bhabha G, Vale RD, Stuurman N. Nanometer-accuracy distance measurements between fluorophores at the single-molecule level. Proc Natl Acad Sci U S A. 2019 Feb 15. pii: 201815826. doi: 10.1073/pnas.1815826116. [Epub ahead of print] PubMed PMID: 30770448; PubMed Central PMCID: PMC6410877.

Ekiert DC, Bhabha G, Isom GL, Greenan G, Ovchinnikov S, Henderson IR, Cox JS, Vale RD. Architectures of Lipid Transport Systems for the Bacterial Outer Membrane. Cell. 2017 Apr 6;169(2):273-285.e17. doi: 10.1016/j.cell.2017.03.019.PubMed PMID: 28388411; PubMed Central PMCID: PMC5467742.

Bhabha G, Johnson GT, Schroeder CM, Vale RD. How Dynein Moves Along Microtubules. Trends Biochem Sci. 2016 Jan;41(1):94-105. doi:10.1016/j.tibs.2015.11.004. Epub 2015 Dec 9. Review. PubMed PMID: 26678005; PubMed Central PMCID: PMC4706479.

Brunette TJ, Parmeggiani F, Huang PS, Bhabha G, Ekiert DC, Tsutakawa SE, Hura GL, Tainer JA, Baker D. Exploring the repeat protein universe through computational protein design. Nature. 2015 Dec 24;528(7583):580-4. doi:10.1038/nature16162. Epub 2015 Dec 16. PubMed PMID: 26675729; PubMed Central PMCID: PMC4845728.

Bhabha G, Biel JT, Fraser JS. Keep on moving: discovering and perturbing the conformational dynamics of enzymes. Acc Chem Res. 2015 Feb 17;48(2):423-30. doi: 10.1021/ar5003158. Epub 2014 Dec 24. Review. PubMed PMID: 25539415; PubMed Central PMCID: PMC4334266.

Ekiert DC, Cox JS. Structure of a PE-PPE-EspG complex from Mycobacterium tuberculosis reveals molecular specificity of ESX protein secretion. Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):14758-63. doi: 10.1073/pnas.1409345111. Epub 2014 Oct 1. PubMed PMID: 25275011; PubMed Central PMCID: PMC4205667.

Bhabha G, Cheng HC, Zhang N, Moeller A, Liao M, Speir JA, Cheng Y, Vale RD. Allosteric communication in the dynein motor domain. Cell. 2014 Nov 6;159(4):857-68. doi: 10.1016/j.cell.2014.10.018. PubMed PMID: 25417161; PubMed Central PMCID: PMC4269335.

Liu Y, Zhang X, Tan YL, Bhabha G, Ekiert DC, Kipnis Y, Bjelic S, Baker D, Kelly JW. De novo-designed enzymes as small-molecule-regulated fluorescence imaging tags and fluorescent reporters. J Am Chem Soc. 2014 Sep 24;136(38):13102-5. doi: 10.1021/ja5056356. Epub 2014 Sep 11. PubMed PMID:25209927; PubMed Central PMCID: PMC4183642.

McKenney RJ, Huynh W, Tanenbaum ME, Bhabha G, Vale RD. Activation of cytoplasmic dynein motility by dynactin-cargo adapter complexes. Science. 2014 Jul 18;345(6194):337-41. doi: 10.1126/science.1254198. Epub 2014 Jun 19. PubMed PMID: 25035494; PubMed Central PMCID: PMC4224444.

Liu Y, Tan YL, Zhang X, Bhabha G, Ekiert DC, Genereux JC, Cho Y, Kipnis Y, Bjelic S, Baker D, Kelly JW. Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts. Proc Natl Acad Sci U S A. 2014 Mar 25;111(12):4449-54. doi:10.1073/pnas.1323268111. Epub 2014 Mar 3. PubMed PMID: 24591605; PubMed Central PMCID: PMC3970509.

Friesen RH, Lee PS, Stoop EJ, Hoffman RM, Ekiert DC, Bhabha G, Yu W, Juraszek J, Koudstaal W, Jongeneelen M, Korse HJ, Ophorst C, Brinkman-van der Linden EC, Throsby M, Kwakkenbos MJ, Bakker AQ, Beaumont T, Spits H, Kwaks T, Vogels R, Ward AB, Goudsmit J, Wilson IA. A common solution to group 2 influenza virus neutralization. Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):445-50. doi:10.1073/pnas.1319058110. Epub 2013 Dec 11. PubMed PMID: 24335589; PubMed Central PMCID: PMC3890827.

Bhabha G, Ekiert DC, Jennewein M, Zmasek CM, Tuttle LM, Kroon G, Dyson HJ, Godzik A, Wilson IA, Wright PE. Divergent evolution of protein conformational dynamics in dihydrofolate reductase. Nat Struct Mol Biol. 2013 Nov;20(11):1243-9. doi: 10.1038/nsmb.2676. Epub 2013 Sep 29. PubMed PMID: 24077226; PubMed Central PMCID: PMC3823643.

van den Bedem H, Bhabha G, Yang K, Wright PE, Fraser JS. Automated identification of functional dynamic contact networks from X-ray crystallography. Nat Methods. 2013 Sep;10(9):896-902. doi: 10.1038/nmeth.2592. Epub 2013 Aug 4. PubMed PMID: 23913260; PubMed Central PMCID: PMC3760795.

Wang F, Ekiert DC, Ahmad I, Yu W, Zhang Y, Bazirgan O, Torkamani A, Raudsepp T, Mwangi W, Criscitiello MF, Wilson IA, Schultz PG, Smider VV. Reshaping antibody diversity. Cell. 2013 Jun 6;153(6):1379-93. doi: 10.1016/j.cell.2013.04.049. PubMed PMID: 23746848; PubMed Central PMCID:PMC4007204.

Dreyfus C, Ekiert DC, Wilson IA. Structure of a classical broadly neutralizing stem antibody in complex with a pandemic H2 influenza virus hemagglutinin. J Virol. 2013 Jun;87(12):7149-54. doi: 10.1128/JVI.02975-12. Epub 2013 Apr 3. PubMed PMID: 23552413; PubMed Central PMCID: PMC3676097.

Tsibane T, Ekiert DC, Krause JC, Martinez O, Crowe JE Jr, Wilson IA, Basler CF. Influenza human monoclonal antibody 1F1 interacts with three major antigenic sites and residues mediating human receptor specificity in H1N1 viruses. PLoS Pathog. 2012;8(12):e1003067. doi: 10.1371/journal.ppat.1003067. Epub 2012 Dec 6. PubMed PMID: 23236279; PubMed Central PMCID: PMC3516549.

Schneemann A, Speir JA, Tan GS, Khayat R, Ekiert DC, Matsuoka Y, Wilson IA. A virus-like particle that elicits cross-reactive antibodies to the conserved stem of influenza virus hemagglutinin. J Virol. 2012 Nov;86(21):11686-97. doi: 10.1128/JVI.01694-12. Epub 2012 Aug 15. PubMed PMID: 22896619; PubMed Central PMCID: PMC3486276.

Lee PS, Yoshida R, Ekiert DC, Sakai N, Suzuki Y, Takada A, Wilson IA. Heterosubtypic antibody recognition of the influenza virus hemagglutinin receptor binding site enhanced by avidity. Proc Natl Acad Sci U S A. 2012 Oct 16;109(42):17040-5. doi: 10.1073/pnas.1212371109. Epub 2012 Oct 1. PubMed PMID: 23027945; PubMed Central PMCID: PMC3479480.

Dreyfus C, Laursen NS, Kwaks T, Zuijdgeest D, Khayat R, Ekiert DC, Lee JH, Metlagel Z, Bujny MV, Jongeneelen M, van der Vlugt R, Lamrani M, Korse HJ, Geelen E, Sahin Ö, Sieuwerts M, Brakenhoff JP, Vogels R, Li OT, Poon LL, Peiris M, Koudstaal W, Ward AB, Wilson IA, Goudsmit J, Friesen RH. Highly conserved protective epitopes on influenza B viruses. Science. 2012 Sep 14;337(6100):1343-8. doi: 10.1126/science.1222908. Epub 2012 Aug 9. PubMed PMID: 22878502; PubMed Central PMCID: PMC3538841.

Ekiert DC, Kashyap AK, Steel J, Rubrum A, Bhabha G, Khayat R, Lee JH, Dillon MA, O'Neil RE, Faynboym AM, Horowitz M, Horowitz L, Ward AB, Palese P, Webby R, Lerner RA, Bhatt RR, Wilson IA. Cross-neutralization of influenza A viruses mediated by a single antibody loop. Nature. 2012 Sep 27;489(7417):526-32. doi: 10.1038/nature11414. Epub 2012 Sep 16. PubMed PMID: 22982990; PubMed Central PMCID: PMC3538848.

Buck-Koehntop BA, Stanfield RL, Ekiert DC, Martinez-Yamout MA, Dyson HJ, Wilson IA, Wright PE. Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso. Proc Natl Acad Sci U S A. 2012 Sep 18;109(38):15229-34. Epub 2012 Sep 4. PubMed PMID: 22949637; PubMed Central PMCID: PMC3458336.

Nycholat CM, McBride R, Ekiert DC, Xu R, Rangarajan J, Peng W, Razi N, Gilbert M, Wakarchuk W, Wilson IA, Paulson JC. Recognition of sialylated poly-N-acetyllactosamine chains on N- and O-linked glycans by human and avian influenza A virus hemagglutinins. Angew Chem Int Ed Engl. 2012 May 14;51(20):4860-3. doi: 10.1002/anie.201200596. Epub 2012 Apr 13. PubMed PMID:22505324; PubMed Central PMCID: PMC3517101.

Ekiert DC, Wilson IA. Broadly neutralizing antibodies against influenza virus and prospects for universal therapies. Curr Opin Virol. 2012 Apr;2(2):134-41. doi: 10.1016/j.coviro.2012.02.005. Epub 2012 Mar 21. Review. PubMed PMID:22482710; PubMed Central PMCID: PMC3368890.

Bhabha G, Tuttle L, Martinez-Yamout MA, Wright PE. Identification of endogenous ligands bound to bacterially expressed human and E. coli dihydrofolate reductase by 2D NMR. FEBS Lett. 2011 Nov 16;585(22):3528-32. doi: 10.1016/j.febslet.2011.10.014. Epub 2011 Oct 20. PubMed PMID: 22024482; PubMed Central PMCID: PMC3215841.

Ekiert DC, Friesen RH, Bhabha G, Kwaks T, Jongeneelen M, Yu W, Ophorst C, Cox F, Korse HJ, Brandenburg B, Vogels R, Brakenhoff JP, Kompier R, Koldijk MH, Cornelissen LA, Poon LL, Peiris M, Koudstaal W, Wilson IA, Goudsmit J. A highly conserved neutralizing epitope on group 2 influenza A viruses. Science. 2011 Aug 12;333(6044):843-50. doi: 10.1126/science.1204839. Epub 2011 Jul 7. PubMed PMID: 21737702; PubMed Central PMCID: PMC3210727.

Fleishman SJ, Whitehead TA, Ekiert DC, Dreyfus C, Corn JE, Strauch EM, Wilson IA, Baker D. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science. 2011 May 13;332(6031):816-21. doi: 10.1126/science.1202617. PubMed PMID: 21566186; PubMed Central PMCID: PMC3164876.

Bhabha G, Lee J, Ekiert DC, Gam J, Wilson IA, Dyson HJ, Benkovic SJ, Wright PE. A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science. 2011 Apr 8;332(6026):234-8. doi: 10.1126/science.1198542. PubMed PMID: 21474759; PubMed Central PMCID: PMC3151171.

Krause JC, Ekiert DC, Tumpey TM, Smith PB, Wilson IA, Crowe JE Jr. An insertion mutation that distorts antibody binding site architecture enhances function of a human antibody. MBio. 2011 Feb 8;2(1):e00345-10. doi: 10.1128/mBio.00345-10. Print 2011. PubMed PMID: 21304166; PubMed Central PMCID: PMC3037006.

Wang TT, Tan GS, Hai R, Pica N, Ngai L, Ekiert DC, Wilson IA, García-Sastre A, Moran TM, Palese P. Vaccination with a synthetic peptide from the influenza virus hemagglutinin provides protection against distinct viral subtypes. Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):18979-84. doi: 10.1073/pnas.1013387107. Epub 2010 Oct 18. PubMed PMID: 20956293; PubMed Central PMCID: PMC2973924.

Xu R, Ekiert DC, Krause JC, Hai R, Crowe JE Jr, Wilson IA. Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus. Science. 2010 Apr 16;328(5976):357-60. doi: 10.1126/science.1186430. Epub 2010 Mar 25. PubMed PMID: 20339031; PubMed Central PMCID: PMC2897825.

Fuller AA, Du D, Liu F, Davoren JE, Bhabha G, Kroon G, Case DA, Dyson HJ, Powers ET, Wipf P, Gruebele M, Kelly JW. Evaluating beta-turn mimics as beta-sheet folding nucleators. Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11067-72. doi: 10.1073/pnas.0813012106. Epub 2009 Jun 18. PubMed PMID: 19541614; PubMed Central PMCID: PMC2708776.

Ekiert DC, Bhabha G, Elsliger MA, Friesen RH, Jongeneelen M, Throsby M, Goudsmit J, Wilson IA. Antibody recognition of a highly conserved influenza virus epitope. Science. 2009 Apr 10;324(5924):246-51. doi: 10.1126/science.1171491. Epub 2009 Feb 26. PubMed PMID: 19251591; PubMed Central PMCID: PMC2758658.

Yao Y, Bhabha G, Kroon G, Landes M, Dyson HJ. Structure discrimination for the C-terminal domain of Escherichia coli trigger factor in solution. J Biomol NMR. 2008 Jan;40(1):23-30. Epub 2007 Nov 28. PubMed PMID: 18043871.

Allikian MJ, Bhabha G, Dospoy P, Heydemann A, Ryder P, Earley JU, Wolf MJ, Rockman HA, McNally EM. Reduced life span with heart and muscle dysfunction in Drosophila sarcoglycan mutants. Hum Mol Genet. 2007 Dec 1;16(23):2933-43. Epub 2007 Sep 12. PubMed PMID: 17855453.