Wintrode:Publications

Research Papers

Kaur U, Kihn KC, Ke H, Kuo W, Gierasch LM, Hebert DN, Wintrode PL, Deredge D, Gershenson A. (2023) The conformational landscape of a serpin N-terminal subdomain facilitates folding and in-cell quality control. bioRxiv. 2023.04.24.537978.

Kihn K, Marchiori E, Spagnolli G, Boldrini A, Terruzzi L, Lawrence DA, Gershenson A, Faccioli P, Wintrode PL. (2022) Long-range allostery mediates the regulation of plasminogen activator inhibitor-1 by cell adhesion factor vitronectin. J Biol Chem. 298(12):102652.

Chun H, Kurasawa JH, Olivares P, Marakasova ES, Shestopal SA, Hassink GU, Karnaukhova E, Migliorini M, Obi JO, Smith AK, Wintrode PL, Durai P, Park K, Deredge D, Strickland DK, Sarafanov AG. (2022) Characterization of interaction between blood coagulation factor VIII and LRP1 suggests dynamic binding by alternating complex contacts. J Thromb Haemost. 20(10):2255-2269.

Kihn KC, Wilson T, Smith AK, Bradshaw RT, Wintrode PL, Forrest LR, Wilks A, Deredge DJ. (2021) Modeling the native ensemble of PhuS using enhanced sampling MD and HDX-ensemble reweighting. Biophys J. 120(23):5141-5157.

Lee PS, Bradshaw RT, Marinelli F, Kihn K, Smith A, Wintrode PL, Deredge DJ, Faraldo-Gómez JD, Forrest LR. (2021) Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software [Article v1.0]. Living J Comput Mol Sci. 3(1):1521.

Orlandi C., Deredge D., Ray K., Gohain N., Tolbert W., DeVico A.L., Wintrode P., Pazgier M., Lewis G.K. (2020) Antigen-Induced Allosteric Changes in a Human IgG1 Fc Increase Low-Affinity Fcγ Receptor Binding. Structure 28(5):516-527.

Klontz EH, Li C, Kihn K, Fields JK, Beckett D, Snyder GA, Wintrode PL, Deredge D, Wang LX, Sundberg EJ. (2020) Structure and dynamics of an α-fucosidase reveal a mechanism for highly efficient IgG transfucosylation. Nat Commun. 2020 11(1):6204.

Masson GR, Burke JE, Ahn NG, Anand GS, Borchers C, Brier S, Bou-Assaf GM, Engen JR, Englander SW, Faber J, Garlish R, Griffin PR, Gross ML, Guttman M, Hamuro Y, Heck AJR, Houde D, Iacob RE, Jørgensen TJD, Kaltashov IA, Klinman JP, Konermann L, Man P, Mayne L, Pascal BD, Reichmann D, Skehel M, Snijder J, Strutzenberg TS, Underbakke ES, Wagner C, Wales TE, Walters BT, Weis DD, Wilson DJ, Wintrode PL, Zhang Z, Zheng J, Schriemer DC, Rand KD. (2019) Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods. 16(7):595-602.

Deredge D, Wintrode PL, Tulapurkar ME, Nagarsekar A, Zhang Y, Weber DJ, Shapiro P, Hasday JD. (2019) A temperature-dependent conformational shift in p38α MAPK substrate-binding region associated with changes in substrate phosphorylation profile. J Biol Chem. 294(34):12624-12637.

Hudgens JW, Gallagher ES, Karageorgos I, Anderson KW, Filliben JJ, Huang RY, Chen G, Bou-Assaf GM, Espada A, Chalmers MJ, Harguindey E, Zhang HM, Walters BT, Zhang J, Venable J, Steckler C, Park I, Brock A, Lu X, Pandey R, Chandramohan A, Anand GS, Nirudodhi SN, Sperry JB, Rouse JC, Carroll JA, Rand KD, Leurs U, Weis DD, Al-Naqshabandi MA, Hageman TS, Deredge D, Wintrode PL, Papanastasiou M, Lambris JD, Li S, Urata S. (2019) Interlaboratory Comparison of Hydrogen-Deuterium Exchange Mass Spectrometry Measurements of the Fab Fragment of NISTmAb. Anal Chem. 91(11):7336-7345.

Hudgens JW, Gallagher ES, Karageorgos I, Anderson KW, Huang RY, Chen G, Bou-Assaf GM, Espada A, Chalmers MJ, Harguindey E, Zhang HM, Walters BT, Zhang J, Venable J, Steckler C, Park I, Brock A, Lu X, Pandey R, Chandramohan A, Anand GS, Nirudodhi SN, Sperry JB, Rouse JC, Carroll JA, Rand KD, Leurs U, Weis DD, Al-Naqshabandi MA, Hageman TS, Deredge D, Wintrode PL, Papanastasiou M, Lambris JD, Li S, Urata S. (2019) Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Centroid Data Measured between 3.6 °C and 25.4 °C for the Fab Fragment of NISTmAb. J Res Natl Inst Stand Technol. 124:1-7.

Klontz EH, Trastoy B, Deredge D, Fields JK, Li C, Orwenyo J, Marina A, Beadenkopf R, Günther S, Flores J, Wintrode PL, Wang LX, Guerin ME, Sundberg EJ. (2019) Molecular Basis of Broad Spectrum N-Glycan Specificity and Processing of Therapeutic IgG Monoclonal Antibodies by Endoglycosidase S2. ACS Cent Sci. 5(3):524-538.

Taraban MB, Deredge DJ, Smith ME, Briggs KT, Li Y, Jiang ZX, Wintrode PL, Yu YB. (2019) Monitoring dendrimer conformational transition using 19 F and 1 H2 O NMR. Magn Reson Chem. 57(10):861-872.

Taraban MB, Deredge DJ, Smith ME, Briggs KT, Feng Y, Li Y, Jiang ZX, Wintrode PL, Yu YB. (2019) Conformational transition of a non-associative fluorinated amphiphile in aqueous solution. II. Conformational transition vs. supramolecular assembly. RSC Adv. 9(4):1956-1966.

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

Gershenson A, Gosavi S, Faccioli P, Wintrode PL. (2020) Successes and challenges in simulating the folding of large proteins. J Biol Chem. 295(1):15-33.

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.