Professor of Biochemistry
HHMI Investigator
Volen 444
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2354
dkern (at) scripps.edu
Education
- 1988 - BSc Biochemistry, Martin-Luther University of Halle, Germany
- 1989 - MSc Biochemistry, Martin-Luther University of Halle, Germany
- 1994 - PhD Biochemistry, Martin-Luther University of Halle, Germany
- 1998 - Postdoc Structural Biology, Dept. of Chemistry, University of California, Berkeley & Structural Biology Division, Lawrence Berkeley National Laboratory
Motions are the basis for the function of biological macromolecules. Whereas for many enzymes the structures have been solved, very little is known about dynamic processes, which trigger catalysis. Our main goal is to characterize these motions in enzymes to provide a better understanding of the atomic events in enzyme catalysis as a function of time. We use NMR as a primary tool because it is an excellent method to measure dynamic processes ranging from picoseconds to days. We complement our experiments by computational techniques, namely, molecular dynamics simulations, which provide atomistic insight into the dynamics of macromolecules. Our aim is to reveal the physical mechanism of transitions by combining experimental to computational methods. Click here for more details about our current research and/or read our published work.
Postdoctoral Fellow
Joined the lab in: 2015
Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2326
rpadua (at) scripps.edu
Education
- 2008 - BSc Pharmacy and Biochemistry, Universidade de São Paulo, Ribeirão Preto, Brazil
- 2014 - PhD in Sciences, Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo (Brazil) and Queen Mary - University of London (England)
- 2015 - Postdoctoral Fellow at Laboratory of Protein Crystallography of Ribeirão Preto - FCFRP-USP, Brazil
Publications
From the Kern Lab:
Pitsawong W, Pádua RAP, Grant T, Hoemberger M, Otten R, Bradshaw N, Grigorieff N & Kern D. From primordial clocks to circadian oscillators. Nature 2023
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
Other:
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
Postdoctoral Fellow
Joined the lab in: 2020
Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2326
hludewig (at) scripps.edu
Education
- 2012 - B.Sc. Biochemistry, University of Bayreuth, Germany
- 2014 - M.Sc. Biochemistry & Molecular Biology, University of Bayreuth, Germany
- 2020 - Ph.D. Chemistry, Centre for Doctoral Training in Critical Resource Catalysis, School of Chemistry, University of St Andrews, United Kingdom (Scotland)
Publications
From the Kern Lab:
Stadnicki EJ, Ludewig H, Ramasamy PK, Wang X, Qiao Y, Kern D & Bradshaw N. Dual-Action Kinase Inhibitors Control p38α MAP Kinase Threonine Dephosphorylation. Proc. Natl. Acad. Sci. US 2024
Kim C, Ludewig H, Hadzipasic A, Kutter S, Nguyen V & Kern D. A biophysical framework for double-drugging kinases. Proc. Natl. Acad. Sci. US 2023
Other:
Ludewig H, Molyneux S, Ferrinho S, Guo K, Lynch R, Gkotsi DS & Goss RJMG. Halogenases: structures and functions. Curr. Opin. Struct. Biol. 2020
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
Postdoctoral Fellow
Joined the lab in: 2022
Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2326
hwayment (at) scripps.edu
Education
- 2015 - B.A. Chemistry & Mathematics, Pomona College, USA
- 2016 - M.Phil. Chemistry, Cambridge University, UK
- 2021 - PhD Chemistry, Stanford, USA
Publications
From the Kern Lab:
Wayment-Steele HK#, El Nesr G#, Hettiarachchi R, Kariyawasam H, Ovchinnikov S, & Kern D. Learning millisecond protein dynamics from what is missing in NMR spectra. bioRxiv 2025
Wayment-Steele HK, Ovchinnikov S, Colwell L, Kern D. Sequence clustering enhances AlphaFold2. bioRxiv 2025
Wayment-Steele HK#, Otten R#, Pitsawong W#, Ojoawo A#, Glaser A, Calderone LA & Kern D. The conformational landscape of fold-switcher KaiB is tuned to the circadian rhythm timescale. Proc. Natl. Acad. Sci. US 2024
Zhang Z, Wayment-Steele HK, Brixi G, Wang H, Dal Peraro M, Kern D & Ovchinnikov S. Protein language models learn evolutionary statistics of interacting sequence motifs. Proc. Natl. Acad. Sci. US 2024
Wayment-Steele HK#, Ojoawo A#, Otten R, Apitz JM, Pitsawong W, Hoemberger M, Ovchinnikov S, Colwell L & Kern D. Predicting multiple conformations via sequence clustering and AlphaFold2. Nature 2023
Other:
Wayment-Steele HK, Kladwang W, Strom AI, Becka A, Lee J, Treuille A, Eterna Participants, Das R. RNA secondary structure packages evaluated and improved by high-throughput experiments. bioRxiv 2022
Wayment-Steele HK, Kladwang W, Watkins AM, Kim DS, Tunguz B, … Das R. Deep learning models for predicting RNA degradation via dual crowdsourcing. Arxiv 2022
Leppek K, Byeon GW, Kladwang W, Wayment-Steele HK, Kerr CH, … Barna M & Das R. Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics. Nature Communications 2021
Wayment-Steele HK, Kim DS, Choe CA, Nicol JJ, Wellington-Oguri R, Sperberg RAP, Huang P, Eterna Participants & Das R. Theoretical basis for stabilizing messenger RNA through secondary structure design. Nucleic Acids Research 2021
Wayment-Steele HK, Wu M, Gotrik M & Das R. Evaluating riboswitch optimality. Methods in Enzymology 2019
Kostrz D, Wayment-Steele HK, Wang JL, Follenfant M, Pande VS, Strick TR & Gosse C. A modular DNA scaffold to study protein–protein interactions at single-molecule resolution. Nature Nanotechnology 2019
Wayment-Steele HK & Pande VS. Variational encoding of protein dynamics benefits from maximizing latent autocorrelation. The Journal of Chemical Physics 2018
Hernandez CX, Wayment-Steele HK, Sultan MM, Husic BE & Pande VS. Variational Encoding of Complex Dynamics. Physical Review E 2018
Sultan MM, Wayment-Steele HK & Pande VS. Transferable neural networks for enhanced sampling of protein dynamics. Journal of Chemical Theory and Computation 2018
Postdoctoral Fellow
Joined the lab in: 2022
Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2326
aojoawo (at) scripps.edu
Education
- 2015 - B.Sc. Chemistry, Saint Catherine University, USA
- 2020 - Ph.D. Biochemistry, University of Illinois at Urbana Champaign, USA
- 2022 - Postdoctoral fellow at Saint Jude Children's Hospital Structural Biology Department, USA
Publications
From the Kern Lab:
Wayment-Steele HK#, Otten R#, Pitsawong W#, Ojoawo A#, Glaser A, Calderone LA & Kern D. The conformational landscape of fold-switcher KaiB is tuned to the circadian rhythm timescale. Proc. Natl. Acad. Sci. US 2024
Wayment-Steele HK#, Ojoawo A#, Otten R, Apitz JM, Pitsawong W, Hoemberger M, Ovchinnikov S, Colwell L & Kern D. Predicting multiple conformations via sequence clustering and AlphaFold2. Nature 2023
Other:
Sekar G, Ojoawo A & Moldoveanu T. Protein–protein and protein–lipid interactions of pore-forming BCL-2 family proteins in apoptosis initiation. Biochem Soc Trans 2022
Ojoawo A & Moldoveanu T. A killer metamorphosis: catching BAK in action at the membrane. The EMBO Journal 2021
McClain SM, Ojoawo A, Lin W, Rienstra MC & Murphy CJ. Interaction of Alpha-Synuclein and Its Mutants with Rigid Lipid Vesicle Mimics of Varying Surface Curvature. ACS Nano 2020
Postdoctoral Fellow
Joined the lab in: 2025
Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2326
wantaek (at) scripps.edu
Education
- 2019 - B.S. Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
- 2024 - Ph.D. Chemical Engineering, University of Texas at Austin, USA
Publications
Miller LG#, Kim W#, Schowe S#, Taylor K, Han R, Jain V, Park R, Sherman M, Fang J, Ramirez H, Ellington AD, Tamamis P, Resendiz M, Zhang YJ, Contreras L. Selective 8-oxoG stalling occurs in the catalytic core of polynucleotide phosphorylase during degradation. Proc Natl Acad Sci USA 2024
Zhang Q# Kim W# Panina S, Mayfield JE, Portz B, Zhang YJ. Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription. Nature Communications 2024
Reed KB, Kim W, Lu H, Larue CT, Guo S, Brooks SM, Montez M, Wagner JM, Zhang Y, Alper HS. Evolving dual-trait EPSP synthase variants using a synthetic yeast selection system. Proc Natl Acad Sci USA 2024
D'Oelsnitz S, Diaz D, Kim W, Acosta D, Schechter M, Minus M, Howard J, Do H, Dangerfield T, Loy J, Alper HS, Zhang Y, Ellington AD. Biosensor and machine learning-aided engineering of an Amaryllidaceae enzyme. Nature Communications 2024
Kim W#, Chen T#, Cha L, Zhou G, Xing K, Canty N, Zhang YJ, Chang W. Elucidation of divergent desaturation pathways in the formation of vinyl isonitrile and isocyanoacrylate. Nature Communications 2022
D'Oelsnitz S, Kim W, Burkholder NT, Javanmardi K, Thyer R, Zhang YJ, Alper HS, Ellington AD. Using structurally fungible biosensors to evolve improved alkaloid biosynthesis. Nature Chemical Biology 2022
Lu H, Diaz DJ, Czarnecki NJ, Zhu C, Kim W, Shroff R, Acosta DJ, Alexander B, Cole H, Zhang YJ, Lynd N, Ellington AD, Alper HS. Machine learning-aided engineering of hydrolases for PET depolymerization. Nature 2022
Kim W, LeBlanc B, Matthews WL, Zhang Z-Y, Zhang YJ. Advancements in chemical biology targeting the kinases and phosphatases of RNA polymerase II-mediated transcription. Current Opinion in Chemical Biology 2021
Postdoctoral Fellow
Joined the lab in: 2025
Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2326
mmassari (at) scripps.edu
Education
- 2015 - Bachelor Degree in Biotechnology, University of Pavia, Italy 2017 - Master Degree in Advanced Biotechnology, University of Pavia, Italy 2021 - Ph.D. in Genetics, Molecular and Cellular Biology, University of Pavia, Italy 2025 - Postdoctoral Fellow, University of Pavia, Italy
Publications
Ogboo BC, Patel KB, Massari M, Marchese S, Reis J, Joyce E, Lin M-CJ, Rabb JD, Abidakun OA, Lin Q, van der Vliet A, Mattevi A, Heppner DE. 2025. Enhancing Selectivity and Potency of SNAr Covalent Inhibitors of NADPH Oxidase Enzymes. J Med Chem 2025
Noce B#, Marchese S#, Massari M#, Lambona C, Reis J, Fiorentino F, Raucci A, Fioravanti R, Castelôa M, Mormino A, Garofalo S, Limatola C, Basile L, Gottinger A, Binda C, Mattevi A, Mai A, Valente S. Design of Benzyl-triazolopyrimidine-Based NADPH Oxidase Inhibitors Leads to the Discovery of a Potent Dual Covalent NOX2/MAOB Inhibitor. J Med Chem 2025
Reis J#, Gorgulla C#, Massari M#, Marchese S#, Valente S, Noce B, Basile L, Törner R, Cox H, Viennet T, Yang MH, Ronan MM, Rees MG, Roth JA, Capasso L, Nebbioso A, Altucci L, Mai A, Arthanari H, Mattevi A. Targeting ROS production through inhibition of NADPH oxidases. Nat Chem Biol 2023
Nicoll CR, Massari M, Fraaije MW, Mascotti ML, Mattevi A. Impact of ancestral sequence reconstruction on mechanistic and structural enzymology. Curr Opin Struct Biol 2023
Massari M, Nicoll CR, Marchese S, Mattevi A, Mascotti ML. Evolutionary and structural analyses of the NADPH oxidase family in eukaryotes reveal an initial calcium dependency. Redox Biol 2022
Massari M, Nicoll CR, Mattevi A. A lonely electron blocks incoming pairs. J Biol Chem 2021
Reis J, Massari M, Marchese S, Ceccon M, Aalbers FS, Corana F, Valente S, Mai A, Magnani F, Mattevi A. A closer look into NADPH oxidase inhibitors: Validation and insight into their mechanism of action. Redox Biol 2020
Postdoctoral Fellow
Joined the lab in: 2025
Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2326
cnicoll (at) scripps.edu
Education
- 2017 - MChem Chemistry, Biological and Medicinal Chemistry, University of York, UK 2021 - Ph.D. Biomolecular Sciences and Biotechnology, University of Pavia, Italy 2025 - Postdoctoral Fellow, University of Pavia, Italy
Publications
Wang D, Gottinger A, Jeong J, Nicoll CR, Liu J, Kadavá T, Cecchini D, Malatesta M, Heck AJR, Mattevi A, Shakhnovich EI. Complete Enzyme Clustering Enhances Coenzyme Q Biosynthesis via Substrate Channeling. bioRxiv 2025
Nicoll CR#, Alvigini L#, Gottinger A#. In vitro construction of the COQ metabolon unveils the molecular determinants of coenzyme Q biosynthesis. Nat Catal 2024
Nicoll CR, Mascotti ML. Investigating the biochemical signatures and physiological roles of the FMO family using molecular phylogeny. BBA Adv 2023
Nicoll CR#, Massari M#, et al. Impact of ancestral sequence reconstruction on mechanistic and structural enzymology. Curr Opin Struct Biol 2023
Bailleul G, Yang G, Nicoll CR et al. Evolution of enzyme functionality in the flavin-containing monooxygenases. Nat Commun 2023
Massari M, Nicoll CR et al. Evolutionary and structural analyses of the NADPH oxidase family in eukaryotes reveal an initial calcium dependency. Redox Biol 2022
Fiorentini F, Nicoll CR, Mattevi A. Baeyer–Villiger Monooxygenases and Their Mechanism of Oxygen Activation: From Microbes to Humans. Biochemistry 2021
Massari M, Nicoll CR, Mattevi A. A lonely electron blocks incoming pairs. J Biol Chem 2021
Bailleul G, Nicoll CR et al. Ancestral reconstruction of mammalian FMO1 enables structural determination, revealing unique features that explain its catalytic properties. J Biol Chem 2021
Nicoll CR et al. Ancestral Sequence Reconstruction Unveils the Structural Basis of Catalysis and Membrane Binding in Mammalian Flavin-Containing Monooxygenases. Nat Struct Mol Biol 2020
Paradisi A, Johnston EM, Tovborg M, Nicoll CR et al. Evidence for a hole-hopping mechanism in lytic polysaccharide monooxygenases: characterization of an active site copper(II)-tyrosyl complex following oxidation by H₂O₂. J Am Chem Soc 2019
Graduate Student
Joined the lab in: 2019
Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2326
aglaser (at) scripps.edu
Education
- 2016 - BSc Biochemistry, Union College, Schenectady, NY, USA
Publications
From the Kern Lab:
Wayment-Steele HK#, Otten R#, Pitsawong W#, Ojoawo A#, Glaser A, Calderone LA & Kern D. The conformational landscape of fold-switcher KaiB is tuned to the circadian rhythm timescale. Proc. Natl. Acad. Sci. US 2024
Graduate Student
Joined the lab in: 2019
Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2326
mpatterson (at) scripps.edu
Education
- 2018 - BSc Biochemistry, University of Massachusetts Boston, Boston, MA, USA
Publications
From the Kern Lab:
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
Other:
Ramasamy PK, Matos JO, Black BY, Ellenburg WH, Chen J, Patterson M, Gehtman J, Theoblad DL, Krauss IJ & Oprian DD. Crystal Structure of Caryolan-1-ol Synthase, a Sesquiterpene Synthase Catalyzing an Initial Anti-Markovnikov Cyclization Reaction. bioRxiv 2024
Webb J, Lieu JJM, Gnann AD, Patterson M, Paul S, Forés M, Jiménez G, Veraksa A & Downling DP. Molecular Basis of DNA recognition by the HMG=box-C1 module of Capicua. bioRxiv 2022
Matos JO, Ramasamy PK, Ma AC, Patterson M, Krauss IJ & Oprian DD. Mechanism Underlying Anti-Markovnikov Addition in the Reaction of Pentalenene Synthase. Biochemistry 2020
Graduate Student
Joined the lab in: 2021
Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2326
cntangka (at) scripps.edu
Education
- 2020 - BS in Biochemistry, Old Dominion University, Norfolk, VA, USA
Publications
Bowitch A, Sahoo A, Clark AM, Ntangka C, Raut KK, Gollnick I, Yu MC, Pascal SM, Walker SE & Ferkey DM. Methylation of the D2 dopamine receptor affects binding with the human regulatory proteins Par-4 and Calmodulin. MicroPubl Biol. 2021
Graduate Student
Joined the lab in: 2022
Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2326
lxiao (at) scripps.edu
Education
- 2021 - BS Biochemistry, University of California San Diego, USA
- 2023 - MS Biochemistry, Brandeis University, USA
Graduate Student
Joined the lab in: 2022
Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2326
camillesullivan (at) brandeis.edu
Education
- 2018 - BA Molecular Biology, Princeton University, USA
Graduate Student
Joined the lab in: 2024
Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2326
bokyungk (at) scripps.edu
Education
- 2020 - BS Bioscience & Biotechnology, Hankuk University of Foreign Studies, Yongin, Republic of Korea
- 2022 - MS Biochemistry, Korea University, Seoul, Republic of Korea
Publications
Ames A, Seman M, Larkin A, Raiymbek G, Chen Z, Levashkevich A, Kim B, Biteen JS & Ragunathan K. Epigenetic memory is governed by an effector recruitment specificity toggle in Heterochromatin Protein I. bioRxiv 2024
Undergraduate Student
Joined the lab in: 2023
Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2326
aedanusing (at) brandeis.edu
Undergraduate Student
Joined the lab in: 2024
Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728
tel: 781 736 2326
gotoo (at) brandeis.edu