Wintrode:Publications

Research Papers

Wang F., Orioli S., Ianeselli A., Spagnolli G., A Beccara S., Gershenson A., Faccioli P., Wintrode P.L. (2018) All-Atom Simulations Reveal How Single-Point Mutations Promote Serpin Misfolding. Biophys. J. 114 2083-2094.

Bonsor D.A., Zhao Q., Schmidinger B., Weiss E., Wang J., Deredge D., Beadenkopf R., Dow B., Fischer W., Beckett D., Wintrode P.L., Haas R, Sundberg E.J. (2018) The Helicobacter pylori adhesin protein HopQ exploits the dimer interface of human CEACAMs to facilitate translocation of the oncoprotein CagA. EMBO J. e98664.

Klontz, E., Tomich, A., Gunther, S., Lemkul, J., Deredge, D., Silverstein, Z., Shaw, J., McElheny, C., Doi, Y., Wintrode, P.L., MacKerell, A., Sluis-Cremer, N. and Sundberg, E. (2017) Structure and dynamics of FosA-mediated fosfomycin resistance in Klebsiella pneumoniae and Escherichia coli. Antimicrob. Agents Chemother. 61 e01572-17.

Günther, S., Deredge, D., Bowers, A.L., Luchini, A., Bonsor, Beadenkopf, R., Liotta, L., Wintrode, P.L. and Sundberg, E.J. (2017) Molecular Basis of Receptor Sharing in the IL-1 Family. Immunity 47, 510-523.

Deredge, D.J., Huang, W., Hui, C., Matsumura, H., Yue, Z., Moenne-Loccoz, P., Shen, J., Wintrode, P.L. and Wilks, A. (2017) Ligand Induced Allostery in the Interaction of the Pseudomonas aeruginosa Heme Binding Protein (PhuS) with Heme Oxygenase (HemO. Proc. Natl. Acad. Sci. USA 114 3421-3426.

Malik, R., Dau, T., Gonik, M., Sivakumar, A., Deredge, D.J., Edeleva, E.E., Götzfried, J., van der Laan, S.W., Pasterkamp, G., Beaufort, N., Seixas, S., Bevan, S., Lincz, L.F., Holliday, E.G., Burgess, A.I., Rannikmae, K., Minnerup, J., Kriebel, J., Waldenberger, M., Müller-Nurasyid, M., Lichtner, P., Saleheen, D., International Stroke Genetics Consortium, Rothwell, P.M., Levi, C., Attia, J., Sudlow, C.M., Braun, D., Markus, H.S., Wintrode, P.L., Berger, K., Jenne, D.E. and Dichgans, M. (2017) A Common Coding Variant in SERPINA1 Increases the Risk for Large Artery Stroke. Proc. Natl. Acad. Sci. USA 114 3613-3618.

Adhikary, A., Deredge, D., Nagarajan, A., Forrest, L.R., Wintrode, P.L. and Singh, S.K. (2017) Conformational Dynamics of a Neurotransmitter Sodium Symporter in a Lipid Bilayer. Proc. Natl. Acad. Sci. USA 114 1786-1795.

Postel, S., Deredge, D., Bonsor, D.A., Yu, X., Diederichs, K., Helmsing, S., Vromen, A., Friedler, A., Hust, M., Egelman, E.H., Beckett, D., Wintrode, P.L. and Sundberg, E.J. (2016) Bacterial Flagellar Capping Proteins Adopt Diverse Oligomeric States. eLife, 10.7554/eLife.18857.

Wang, F., Cazzolli, G., Wintrode, P.L. and Faccioli, P. (2016) The Folding Mechanism of Proteins Im7 and Im9: Insight from All-Atom Simulations in Implicit and Explicit Solvent. J. Phys. Chem. B, 120 9297-9307.

Tsutsui, Y. Deredge, D., Wintrode, P.L. and Hayes, F.A. (2016) Imatinib binding to human c-Src is coupled to inter-domain allostery and suggests a novel kinase inhibition strategy. Sci. Rep., 6 30832.

Deredge, D., Li, J., Johnson, K.A. and Wintrode, P.L. (2016) Hydrogen/Deuterium Exchange Kinetics Demonstrate Long Range Allosteric Effects of Thumb Site 2 Inhibitors of Hepatitis C Viral RNA-dependent RNA Polymerase. J. Biol. Chem., 291 10078-10088. DOI:10.1074/jbc.M115.708370.

Lupton, C.J., Steer, D.L., Wintrode, P.L., Bottomley, S.P., Hughes, V.A. and Ellison, A.M. (2015) Enhanced Molecular Mobility of Ordinarily Structured Regions Drives Polyglutamine Disease. J. Biol. Chem., 290 24190-24200. DOI:10.1074/jbc.M115.659532

White, M., Khan, M.M., Deredge, D., Ross, C.R., Quintyn, R., Zucconi, B.E., Wysocki, V.H., Wintrode, P.L., Wilson, G.M. and Garcin, E.D. (2015) A dimer interface mutation in glyceraldehyde-3-phosphate dehydrogenase regulates its binding to AU-rich RNA. J. Biol. Chem., 290 1770-1785. DOI:10.1074/jbc.M114.618165.

Cazzolli, G., Wang, F.*, a Beccara, S., Gershenson, A., Faccioli, P. and Wintrode, P.L. (2014) Serpin Latency Transition at Atomic Resolution. Proc. Natl. Acad. Sci. USA, 111, 15414-15419.

Hughes, V.A., Meklemburg, R., Bottomley, S.P. and Wintrode P.L. (2014) The Z mutation alters the global structural dynamics of alpha-1 antitrypsin. PLoS ONE 9(9):e102617. doi:10.1371/journal.pone.0102617.

Snyder, G.A., Deredge, D.*, Waldhuber, A., Fresquez, T., Wilkins, D.Z., Smith, P., Durr, S., Cirl, C., Jian, J., Jennings, W., Luchetti, T., Snyder, N., Sundberg, E.J., Wintrode, P.L., Miethke, T. and Xiao, T.S. (2014) Crystal structures of the TIR domains from the Brucella protein TcpB and the host adaptor protein TIRAP reveal mechanisms of molecular mimicry. J. Biol. Chem. 289 669-679. DOI: 10.1074/jbc.M113.523407

Cheng, J., Karri, S*., Roberts, M.F., Wintrode, P.L. and Gershenson, A. (2013) Do mutations predicted to change the dynamics of a phospholipase C alter activity and membrane binding? Biophys. J. 104 185-195. DOI:10.1016/j.bpj.2012.11.015

Stocks, B.B., Sarkar, A.*, Wintrode, P.L. and Konermann, L. (2012) Early hydrophobic collapse of α1-antitrypsin facilitates formation of a metastable state: Insights from oxidative labeling and mass spectrometry. J. Mol. Biol. 423 789-799. DOI: 10.1016/j.jmb.2012.08.019.

Cheng, I., Nikita, N., Fishovitz, J., Frase, H., Wintrode, P.L. and Lee, I. (2012) Identification of a region in the N-terminus of escherichia coli lon that affects ATPase, substrate translocation and proteolytic activity. J. Mol. Biol. 418 208-225. DOI: 10.1016/j.jmb.2012.02.039

Tsutsui, Y.*, dela Cruz, R.G. and Wintrode, P.L. (2012) Folding mechanism of the metastable serpin a1-antitrypsin. Proc. Natl. Acad. Sci. USA, 109 4467-4472. DOI: 10.1073/pnas.1109125109

Sarkar, A.*, Zhou, C.*, Meklemburg, R.* and Wintrode, P.L. (2011) Local conformational flexibility provides a basis for facile polymer formation in human neuroserpin. Biophys. J. 101 1758-1765. DOI: 10.1016/j.bpj.2011.08.037

Sarkar, A.* and Wintrode, P.L. (2011) Effects of glycosylation on the stability and flexibility of a metastable protein: the human serpin α1-antitrypsin. Int. J. Mass Spectrom. 302, 69-75. DOI: 10.1016/j.ijms.2010.08.003

Seckler, J.M.*, Barkley, M.D. and Wintrode, P.L. (2011) Allosteric suppression of HIV-1 reverse transcriptase structural dynamics upon inhibitor binding. Biophys. J. 100 144-153. DOI: 10.1016/j.bpj.2010.11.004

Braz, V. Barkley, M.D., Jockusch, R. and Wintrode, P.L. (2010) The Efavirenz Binding Site in HIV-1 Reverse Transcriptase Monomers. Biochemistry 49 10565-10573. DOI: 10.1021/bi101480z

Sengupta, T.*, Tsutsui, Y.* and Wintrode, P.L. (2009) Local and global effects of a cavity filling mutation in a metastable serpin. Biochemistry 48 8233-8240. DOI: 10.1021/bi900342d

Seckler, J.M.*, Howard, K.J., Barkley, M.D and Wintrode, P.L. (2009) Solution structural dynamics of HIV-1 reverse transcriptase heterodimer. Biochemistry 48 7646-7655. DOI: 10.1021/bi900790x

Goc, A., Angel, T., Jastrzebska, B. Wang, B. Wintrode, P.L. and Palczewski, K. (2008) Different properties of the native and reconstituted heterotrimeric G protein transducin. Biochemistry 47 12409-12419. DOI: 10.1021/bi8015444

Tsutsui, Y.*, Kuri, B.*, Sengupta, T.* and Wintrode, P.L. (2008) The structural basis of serpin polymerization studied by hydrogen/deuterium exchange and mass spectrometry. J. Biol. Chem. 283 30804-30811. DOI: 10.1074/jbc.M804048200

Zheng, X., Wintrode, P.L. and Chance, M.R. (2008) Complementary structural mass spectrometry techniques reveal local dynamics in functionally important regions of a metastable serpin. Structure 16 1-14. DOI: 10.1016/j.str.2007.10.019

Tsutsui, Y.* and Wintrode, P.L. (2007) Cooperative unfolding of a metastable serpin to a molten globule suggests a link between functional and folding energy landscapes. J. Mol. Biol. 371 245-255. DOI: 10.1016/j.jmb.2007.05.039

Lu, X., Wintrode, P.L. and Surewicz, W.K. (2007) Beta-Sheet core of human prion protein amyloid fibrils as determined by hydrogen/deuterium exchange. Proc. Natl. Acad. Sci. USA 104 1510-1515. DOI: 10.1073/pnas.0608447104

Tsutsui, Y.*, Liu, L., Gershenson, A. and Wintrode, P.L. (2006) The conformational dynamics of a metastable serpin studied by hydrogen exchange and mass spectrometry. Biochemistry 45 6561-6569. DOI: 10.1021/bi060431f

Review Articles

Deredge, D. and Wintrode, P.L. (2017) Remodeling KRAS. Commentary in Structure, 25 1323-1324.

Tsutsui, Y.*, Sarkar, A.* & Wintrode, P.L. (2011) Probing serpin conformational change using mass spectrometry and related methods. Methods in Enzymology, 501 325-350.

Tsutsui, Y.* & Wintrode, P.L.(2007) Hydrogen/deuterium exchange-mass spectrometry: a powerful tool for probing protein structure, dynamics and interactions. Curr. Med. Chem. 22 2344-2358.

Earlier Publications

Wintrode, P.L., Rojsajjakul, T., Varevu, R., Matthews, C.R. and Smith, D.L. (2005) An obligatory intermediate controls the folding of the alpha subunit of tryptophan synthase, a TIM barrel protein. J. Mol. Biol. 347 911-919. DOI: 10.1016/j.jmb.2005.01.064.

Rojsajjakul, T., Wintrode, P.L., Vadrevu, R., Matthews, C.R. and Smith, D.L. (2004) Multi-state unfolding of the alpha subunit of tryptophan synthase, a TIM barrel protein: insights into the secondary structure of the stable equilibrium intermediates by hydrogen exchange mass spectrometry. J. Mol. Biol. 341 241-253. DOI: 10.1016/j.jmb.2004.05.062.

Wintrode, P.L., Friedrich, K., Vierling, E., Smith, J.B. & Smith, D.L. (2003) Solution structure and dynamics of a heat shock protein assembly probed by hydrogen exchange/mass spectrometry. Biochemistry, 42 10667-10673. DOI: 10.1021/bi034117m.

Wintrode, P.L., Zhang, D., Vaidehi, N., Arnold, F.H. & Goddard, W.A. III. (2003) Protein dynamics in a family of laboratory evolved thermophilic enzymes. J. Mol. Biol., 327 745-757. DOI: 10.1016/S0022-2836(03)00147-5.

Wintrode, P.L., Miyazaki, K. & Arnold, F.H. (2001). Patterns of adaptation in a laboratory evolved thermophilic enzyme. Biochem. Biophys. Acta, 1549 1-8. DOI: 10.1016/S0167-4838(01)00226-6.

Arnold, F.H., Wintrode, P.L., Miyazaki, K. & Gershenson, A. (2001). How enzymes adapt: lessons from directed evolution. TIBS 26 100-106.

Wintrode, P.L., Miyazaki, K. & Arnold, F.H. (2000). Cold adaptation of a mesophilic subtilisin-like protease by laboratory evolution. J. Biol. Chem. 275 31635-31640. DOI: 10.1074/jbc.M004503200.

Wintrode, P.L. & Arnold, F.H. (2000). Temperature adaptation of enzymes: lessons from laboratory evolution. Adv. Prot. Chem. 55 161-225.

Miyazaki, K., Wintrode, P.L., Grayling, R.A, Rubingh, D.N. & Arnold, F.H. (2000). Directed evolution study of temperature adaptation in a psychrophilic enzyme. J. Mol. Biol. 297 1015-1026. DOI: 10.1006/jmbi.2000.3612.

Wintrode, P.L. & Privalov, P.L. (1997). Energetics of target peptide recognition by calmodulin: a calorimetric study. J. Mol. Biol. 266 1050-1062. DOI: 10.1006/jmbi.1996.0785.

Wintrode, P.L., Griko, Y.V. & Privalov, P.L. (1995). Structural energetics of barstar studied by differential scanning microcalorimetry. Protein Sci. 4 1528-1534.

Lawson, T.G, Gronos, D.L., Werner, J.A., Wey, A.C., DiGeorge, A.M., Lockhart, J.L., Wilson, J.W. & Wintrode, P.L. (1994). The encephalomyocarditis virus 3C protease is a substrate for the ubiquitin-mediated proteolytic system. J. Biol. Chem. 269 28429-28435.

Wintrode, P.L., Makhatadze, G.I. & Privalov, P.L. (1994). Thermodynamics of ubiquitin unfolding. Proteins: Struct. Funct. & Genet. 18 246-253. DOI: 10.1002/prot.340180305.