Otten R#, Pádua RAP#, Bunzel HA#, Nguyen V, Pitsawong W, Patterson M, Sui S, Perry SL, Cohen AE, Hilvert D & Kern D. How directed evolution reshapes the energy landscape in an enzyme to boost catalysis. Science 2020
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
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
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
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
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
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
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
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
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
Niklasson M, Otten R, Ahlner A, Andresen C, Schlagnitweit J, Petzhold K & Lundström P. Comprehensive Analysis of NMR Data Using Advanced Line Shape Fitting. J. Biomol. NMR 2017
Oktaviani NA, Risor MW, Lee YH, Megens RP, de Jong DH, Otten R, Scheek RM, Enghild JJ, Nielsen NC, Ikegami T & Mulder FAA. Optimized Co-Solute Paramagnetic Relaxation Enhancement for the Rapid NMR Analysis of a Highly Fibrillogenic Peptide. J. Biomol. NMR 2015
Maeno SJ, Sindhikara D, Hirata F, Otten R, Dahlquist FW, Yokoyama S, Akasaka K, Mulder FAA & Kitahara R. Cavity as a Source of Conformational Fluctuation and High-Energy State: High-Pressure NMR Study of a Cavity-Enlarged Mutant of T4 Lysozyme. Biophys. J. 2015
Chu BCH, Otten R, Krewulak KD, Mulder FAA & Vogel HJ. The Solution Structure, Binding Properties, and Dynamics of the Bacterial Siderophore-Binding Protein FepB. J. Biol. Chem. 2014
Meniche X, Otten R, Siegrist MS, Baer CE, Murphy KC, Bertozzi CR & Sassetti CM. Subpolar Addition of New Cell Wall Is Directed by DivIVA in Mycobacteria. Proc Natl. Acad. Sci. USA 2014
Wood K#, Gallat FX#, Otten R#, van Heel AJ, Lethier M, van Eijck L, Moulin M, Haertlein M, Weik M & Mulder FAA. Protein Surface and Core Dynamics Show Concerted Hydration-Dependent Activation. Angew. Chem. Int. Ed. 2013
Stockbridge RB, Lim HH, Otten R, Williams C, Shane T, Weinberg Z & Miller C. Fluoride Resistance and Transport by Riboswitch-Controlled CLC Antiporters. Proc Natl. Acad. Sci. USA 2012
Wood K, Paz A, Dijkstra K, Scheek RM, Otten R, Silman I, Sussman JL & Mulder FAA. Backbone and Side Chain NMR Assignments for the Intrinsically Disordered Cytoplasmic Domain of Human neuroligin-3. Biomol. NMR Assign. 2012
Karasawa A, Erkens GB, Berntsson RPA, Otten R, Schuurman-Wolters GK, Mulder FAA & Poolman B. Cystathionine β-Synthase (CBS) Domains 1 and 2 Fulfill Different Roles in Ionic Strength Sensing of the ATP-binding Cassette (ABC) Transporter OpuA. J. Biol. Chem. 2011
Mulder FAA, Otten R & Scheek RM. Origin and Removal of Mixed-Phase Artifacts in Gradient Sensitivity Enhanced Heteronuclear Single Quantum Correlation Spectra. J. Biomol. NMR 2011
Meinema AC#, Laba JK#, Hapsari RA#, Otten R, Mulder FAA, Kralt A, van den Bogaart G, Lusk CP, Poolman B & Veenhoff LM. Long Unfolded Linkers Facilitate Membrane Protein Import Through the Nuclear Pore Complex. Science 2011
Oktaviani NA, Otten R, Dijkstra K, Scheek RM, Thulin E, Akke M & Mulder FAA. 100% Complete Assignment of Non-Labile 1H, 13C, and 15N Signals for Calcium-Loaded Calbindin D9k P43G. Biomol. NMR Assign. 2011
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
Otten R, Chu B, Krewulak KD, Vogel HJ & Mulder FAA. Comprehensive and Cost-Effective NMR Spectroscopy of Methyl Groups in Large Proteins. J. Am. Chem. Soc. 2010
Otten R#, Wood K# & Mulder FAA. Comprehensive Determination of 3JHNHα for Unfolded Proteins Using 13C′-Resolved Spin-Echo Difference Spectroscopy. J. Biomol. NMR 2009
Louhivuori M, Otten R, Salminen T & Annila A. Evidence of Molecular Alignment Fluctuations in Aqueous Dilute Liquid Crystalline Media. J. Biomol. NMR 2007
Louhivuori M, Otten R, Lindorff-Larsen K & Annila A. Conformational Fluctuations Affect Protein Alignment in Dilute Liquid Crystal Media. J. Am. Chem. Soc. 2006
Otten R, van Lune FS, Dijkstra K & Scheek RM. Letter to the Editor: 1H, 13C, and 15N Resonance Assignments of the Phosphorylated Enzyme IIB of the Mannitol-Specific Phophoenolpyruvate-Dependent Phosphotransferase System of Escherichia coli. J. Biomol. NMR 2004
Otten R#, Pádua RAP#, Bunzel HA#, Nguyen V, Pitsawong W, Patterson M, Sui S, Perry SL, Cohen AE, Hilvert D & Kern D. How directed evolution reshapes the energy landscape in an enzyme to boost catalysis. Science 2020
Hoemberger M, Pitsawong W & Kern D. Cumulative mechanism of several major imatinib-resistant mutations in Abl kinase. PNAS 2020
Hadzipasic A, Wilson C, Nguyen V, Kern N, Kim C, Pitsawong W, Villali J, Zheng Y & Kern D. Ancient origins of allosteric activation in a Ser-Thr kinase. Science 2020
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
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
Pitsawong W, Chenprakhon P, Dhammaraj T, Medhanavyn D, Sucharitakul J, Tonsook C, van Berkel WJH, Chaiyen P & Miller A-F. Tuning of pKas activates substrates in flavin-dependent aromatic hydroxylases. J. Biol. Chem. 2020
Miller A-F, Park JT, Ferguson KL, Pitsawong W & Bommarius AS. Informing Efforts to Develop Nitroreductase for Amine Production. Molecules 2018
Pitsawong W, Haynes CA, Koder RL, Rodgers DW & Miller A-F. Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase. Structure 2017
Pitsawong W, Hoben JP & Miller A-F. Understanding and Exploiting the Broad Substrate Repertoire of Nitroreductase via Kinetic Mechanism. J. Biol. Chem. 2014
Tinikul R#, Pitsawong W#, Sucharitakul J, Nijvipakul S, Ballou DP & Chaiyen P. The Transfer of Reduced Flavin Mononucleotide from LuxG Oxidoreductase to Luciferase Occurs via Free Diffusion. Biochemistry 2013
Tan T-C, Pitsawong W, Wongnate T, Spadiut O, Haltrich D, Chaiyen P & Divne C. H-bonding and Positive Charge at the N(5)/O(4) Locus Are Critical for Covalent Flavin Attachment in Trametes Pyranose 2-Oxidase. J. Mol. Biol. 2010
Pitsawong W, Sucharitakul J, Prongjit M, Tan T-C, Spadiut O, Haltrich D, Divne C, & Chaiyen P. A Conserved Active-site Threonine Is Important for Both Sugar and Flavin Oxidation of Pyranose 2-Oxidase. J. Biol. Chem. 2010
Otten R#, Pádua RAP#, Bunzel HA#, Nguyen V, Pitsawong W, Patterson M, Sui S, Perry SL, Cohen AE, Hilvert D & Kern D. How directed evolution reshapes the energy landscape in an enzyme to boost catalysis. Science 2020
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
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
Sartim MA, Pinheiro MP, Pádua RAP, Sampaio SV & Nonato MC. Structural and Binding Studies of a C-type Galactose-Binding Lectin from Bothrops jararacussu Snake Venom. Toxicon 2017
Pádua RAP, Kia AM, Costa-Filho AJ, Wilkinson SR & Nonato MC. Characterisation of the Fumarate Hydratase Repertoire in Trypanosoma cruzi. Int. J. Biol. Macromol. 2017
Pádua RAP, Tomaleri GP, Reis RAG, David JS, Silva V, Pinheiro MP & Nonato MC. ThermoFMN - a Thermofluor Assay Developed for Ligand-Screening as an Alternative Strategy for Drug Discovery. J. Braz. Chem. Soc. 2014
Pádua RAP & Nonato MC. Cloning, Expression, Purification, Crystallization and Preliminary X-ray Diffraction Analysis of Recombinant Human Fumarase. Acta Crystallogr. F. Struct. Biol. Commun. 2014
Gkotsi DS, Ludewig H, Sharma SV, Connolly JA, Dhaliwal J, Wang Y, Unsworth WP, Taylor RJK, McLachlan MWM, Shanahan S, Naismith JH & Goss RJM. A marine viral halogenase that iodinates divers substrates. Nat. Chem. 2019
Ludewig H, Czekster CM, Oueis E, Munday ES, Arshad M, Synowsky SA, Bent AF & Naismith JH. Characterization of the Fast and Promiscuous Macrocyclase from Plant PCY1 Enables the Use of Simple Substrates. ACS Chem. Biol. 2018
Czekster CM, Ludewig H, McMahon SA & Naismith JH. Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates. Nat. Commun. 2017
Oueis E, Adamson C, Mann G, Ludewig H, Redpath P, Migaud M, Westwood NJ & Naismith JH. Derivatisable Cyanobactin Analogues: A Semisynthetic Approach. ChemBioChem 2015
Koehnke J, Mann G, Bent AF, Ludewig H, Shirran S, Botting C, Lebl T, Houssen WE, Jaspars M & Naismith JH. Structural analysis of leader peptide binding enables leader-free cyanobactin processing. Nat. Chem. Biol. 2015
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
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
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
Boswell ZK, Canny MD, Buschmann TA, Sang J & Latham, MP. Adjacent mutations in the archaeal Rad50 ABC ATPase D-loop disrupt allosteric regulation of ATP hydrolysis through different mechanisms. Nucleic Acids Res. 2020
Boswell ZK & Latham MP. Methyl-Based NMR Spectroscopy Methods for Uncovering Structural Dynamics in Large Proteins and Protein Complexes. Biochemistry 2019
Boswell ZK, Rahman S, Canny, MD & Latham MP. A dynamic allosteric pathway underlies Rad50 ABC ATPase function in DNA repair. Sci. Rep. 2018
Kretschmer PM, Bannister AM, MacManus-Spencer LA & Paulick MG. A Liquid Chromatography Tandem Mass Spectrometry Assay for the Detection and Quantification of Trehalose in Biological Samples. J. Chromatogr. B 2016
Hadzipasic A, Wilson C, Nguyen V, Kern N, Kim C, Pitsawong W, Villali J, Zheng Y & Kern D. Ancient origins of allosteric activation in a Ser-Thr kinase. Science 2020
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
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
Otten R#, Pádua RAP#, Bunzel HA#, Nguyen V, Pitsawong W, Patterson M, Sui S, Perry SL, Cohen AE, Hilvert D & Kern D. How directed evolution reshapes the energy landscape in an enzyme to boost catalysis. Science 2020