Publications


Zorba A#, Nguyen V#, Koide A, Hoemberger M, Zheng Y, Kutter S, Kim C, Koide S & Kern D. Allosteric Modulation of a Human Protein Kinase with Monobodies. Proc. Natl. Acad. Sci. USA 2019

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Stiller JB#, Kerns SJ#, Hoemberger M, Cho Y-J, Otten R, Hagan MF & Kern D. Probing the Transition State in Enzyme Catalysis by High-Pressure NMR Dynamics. Nat. Catal. 2019

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  • PDB Structure: 4K46
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Pádua RAP#, Sun Y#, Marko I, Pitsawong W, Stiller JB, Otten R & Kern D. Mechanism of Activating Mutations and Allosteric Drug Inhibition of the Phosphatase SHP2. Nat. Commun. 2018

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Pitsawong W#, Buosi V#, Otten R#, Agafonov RV#, Zorba A, Kern N, Kutter S, Kern G, Pádua RAP, Meniche X & Kern D. Dynamics of Human Protein Kinase Aurora A Linked to Drug Selectivity. eLife 2018

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Otten R#, Liu L#, Kenner LR, Clarkson MW, Mavor D, Tawfik DS, Kern D & Fraser JS. Rescue of Conformational Dynamics in Enzyme Catalysis by Directed Evolution. Nat. Commun. 2018

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Nguyen V#, Wilson C#, Hoemberger M, Stiller JB, Agafonov RV, Kutter S, English J, Theobald D & Kern D. Evolutionary Drivers of Thermoadaptation in Enzyme Catalysis. Science 2017

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Chakrabarti KS#, Agafonov RV#, Pontiggia F, Otten R, Higgins MK, Schertler GF, Oprian DD & Kern D. Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis. Cell Reports 2016

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Wilson C, Agafonov RV & Kern D. Drug targets evolve, and so should the methods. Mol. Cell Oncol. 2016

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Eichner T, Kutter S, Labeikovsky W, Buosi V & Kern D. Molecular Mechanism of Pin1-Tau Recognition and Catalysis. J. Mol. Biol. 2016

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Kutter S, Eichner T, Deaconescu AM & Kern D. Regulation of Microtubule Assembly by Tau and not by Pin1. J. Mol. Biol. 2016

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Pontiggia F, Pachov DV, Clarkson MW, Villali J, Hagan MF, Pande VS & Kern D. Free energy landscape of activation in a signaling protein at atomic resolution. Nat. Commun. 2015

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Agafonov RV, Wilson C & Kern D. Evolution and intelligent design in drug development. Front. Mol. Biosci. 2015

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Wilson C#, Agafonov RV#, Hoemberger M, Kutter S, Zorba A, Halpin J, Buosi V, Otten R, Waterman D, Theobald DL & Kern D. Using ancient protein kinases to unravel a modern cancer drug’s mechanism. Science 2015

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Kerns SJ#, Agafonov RV#, Cho YJ#, Pontiggia F, Otten R, Pachov DV, Kutter S, Phung LA, Murphy PN, Thai V, Alber T, Hagan MF & Kern D. The energy landscape of adenylate kinase during catalysis. Nat. Struct. Mol. Biol. 2015

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Hass MA, Liu WM, Agafonov R.V., Otten R, Phung LA, Schilder JT, Kern D & Ubbink M. A minor conformation of a lanthanide tag on adenylate kinase characterized by paramagnetic relaxation dispersion NMR spectroscopy. J. Biomol. NMR. 2015

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Agafonov RV#, Wilson C#, Otten R, Buosi V & Kern D. Energetic dissection of Gleevec’s selectivity toward human tyrosine kinases. Nat. Struct. Mol. Biol. 2014

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Zorba A#, Buosi V#, Kutter S, Kern N, Pontiggia F, Cho YJ & Kern D. Molecular mechanism of Aurora A kinase autophosphorylation and its allosteric activation by TPX2. eLife 2014

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Villali J, Pontiggia F, Clarkson MW, Hagan MF & Kern D. Evidence against the “Y-T coupling” mechanism of activation in the response regulator NtrC. J. Mol. Biol. 2014

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Ranaghan MJ, Kumar RP, Chakrabarti KS, Buosi V, Kern D & Oprian DD. A Highly Conserved Cysteine of Neuronal Calcium-sensing Proteins Controls Cooperative Binding of Ca2+ to Recoverin. J. Biol. Chem. 2013

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Park JM, Hu J-H, Milshteyn A, Zhang, P-W, Moore CG, Park S, Datko MC, Doming RD, Reyes CM, Wang XJ, Etzkorn FA, Xiao B, Szumlinski KK, Kern D, Linden DJ & Worley PF. A Prolyl-isomerase Mediates Dopamine-dependent Plasticity and Cocaine Motor Sensitization. Cell 2013

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Morrison EA, DeKoster GT, Dutta S, Vafabakhsh R, Clarkson MW, Bahl A, Kern D, Ha T & Henzler-Wildman KA. Antiparallel EmrE exports drugs by exchanging between asymmetric structures. Nature 2012

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Otten R, Villali J, Kern D & Mulder FAA. Probing Microsecond Time Scale Dynamics in Proteins by Methyl 1H Carr−Purcell−Meiboom−Gill Relaxation Dispersion NMR Measurements. Application to Activation of the Signaling Protein NtrCr. J. Am. Chem. Soc. 2010

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Villali J & Kern D. Choreographing an enzyme’s dance. Curr. Opin. Chem. Biol. 2010

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Gardino AK, Villali J, Kivenson A, Lei M, Liu CF, Steindel P, Eisenmesser EZ, Labeikovsky W, Wolf-Watz M, Clarkson MW & Kern D. Transient Non-native Hydrogen Bonds Promote Activation of a Signaling Protein. Cell 2009


Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D & Alber T. Hidden alternative structures of proline isomerase essential for catalysis. Nature 2009

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Shim S, Yuan JP, Kim JY, Zeng W, Huang G, Milshteyn A, Kern D, Muallem S, Ming G-L & Worley PF. Peptidyl-Prolyl Isomerase FKBP52 Controls Chemotropic Guidance of Neuronal Growth Cones via Regulation of TRPC1 Channel Opening. Neuron 2009

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Clarkson MW, Lei M, Eisenmesser EZ, Labeikovsky W, Redfield A & Kern D. Mesodynamics in the SARS nucleocapsid measured by NMR field cycling. J. Biomol. NMR. 2009

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Lei M, Velos J, Gardino A, Kivenson A, Karplus M & Kern D. Segmented Transition Pathway of the Signaling Protein Nitrogen Regulatory Protein C. J. Mol. Biol. 2009

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Thai V, Renesto P, Fowler CA, Brown DJ, Davis T, Gu W, Pollock DD, Kern D, Raoult D & Eisenmesser EZ. Structural, Biochemical, and in Vivo Characterization of the First Virally Encoded Cyclophilin from the Mimivirus. J. Mol. Biol. 2008

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  • PDB Structure: 2OAO
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Henzler-Wildman KA & Kern D. Dynamic personalities of proteins. Nature 2007

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Henzler-Wildman KA, Vu T, Lei M, Ott M, Wolf-Watz M, Fenn T, Pozharski E, Wilson MA, Petsko GA, Karplus M, Hübner CG & Kern D. Intrinsic motions along an enzymatic reaction trajectory. Nature 2007

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Henzler-Wildman KA, Lei M, Thai V, Kerns SJ, Karplus M & Kern D. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 2007

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Gardino AK & Kern D. Functional Dynamics of Response Regulators Using NMR Relaxation Techniques. Methods Enzymol. 2007

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Labeikovsky W, Eisenmesser EZ, Bosco DA & Kern D. Structure and Dynamics of Pin1 During Catalysis by NMR. J. Mol. Biol. 2007

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Wemmer DE & Kern D. Beryllofluoride Binding Mimics Phosphorylation of Aspartate in Response Regulators. J. Bacteriol. 2005

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Eisenmesser EZ, Millet O, Labeikovsky W, Korzhnev DM, Wolf-Watz M, Bosco DA, Skalicky JJ, Kay LE & Kern D. Intrinsic dynamics of an enzyme underlies catalysis. Nature 2005


Tittmann K, Neef H, Golbik R, Hübner G & Kern D. Kinetic Control of Thiamin Diphosphate Activation in Enzymes Studied by Proton-Nitrogen Correlated NMR Spectroscopy. Biochemistry, 2005

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Kern D, Eisenmesser EZ & Wolf-Watz M. Enzyme Dynamics During Catalysis Measured by NMR Spectroscopy. Methods Enzymol. 2005

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Wolf-Watz M, Thai V, Henzler-Wildman KA, Hadjipavlou G, Eisenmesser EZ & Kern D. Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair. Nat. Struct. Mol. Biol. 2004

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Bosco DA & Kern D. Catalysis and Binding of Cyclophilin A with Different HIV-1 Capsid Constructs. Biochemistry 2004

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Kern D & Zuiderweg ERP. The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 2003

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Gardino AK, Volkman BF, Cho HS, Lee S-Y, Wemmer DE & Kern D. The NMR Solution Structure of BeF3--Activated Spo0F Reveals the Conformational Switch in a Phosphorelay System. J. Mol. Biol. 2003

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  • PDB Structure: 1PUX
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Kern D. Cutting the leash. Nat. Struct. Biol. 2002

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Bosco DA, Eisenmesser E, Pochapsky S, Sundquist WI & Kern D. Catalysis of cis/trans isomerization in native HIV-1 capsid by human cyclophilin A. Proc. Natl. Acad. Sci. USA, 2002

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Eisenmesser EZ, Bosco DA, Akke M & Kern D. Enzyme Dynamics During Catalysis. Science 2002

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Kern G, Pelton J, Marqusee S & Kern D. Structural properties of the histidine-containing loop in HIV-1 Rnase H. Biophys. Chem. 2002

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Volkman BF, Lipson D, Wemmer DE & Kern D. Two-State Allosteric Behavior in a Single-Domain Signaling Protein. Science 2001


Kern D, Volkman BF, Luginbühl P, Nohaile MJ, Kustu S & Wemmer DE. Structure of a transiently phosphorylated “switch” in bacterial signal transduction. Nature 1999

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Kern D, Kern G, Neef H, Tittmann K, Killenberg-Jabs M, Wikner C, Schneider G & Hübner G. How Thiamin Diphosphate is Activated in Enzymes. Science 1997

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