Dorothee Kern - Principal Investigator

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) brandeis.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.

Ricardo Pádua
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) brandeis.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:

  • 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


Hannes Ludewig
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
hannesludewig (at) brandeis.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

  • 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


Hannah Wayment-Steele
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
wayment (at) brandeis.edu




Education
  • 2015 - B.A. Chemistry & Mathematics, Pomona College, USA
  • 2016 - M.Phil. Chemistry, Cambridge University, UK
  • 2021 - PhD Chemistry, Stanford, USA


Publications

  • 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


Adedolapo Ojoawo
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
ojoawoa (at) brandeis.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

  • 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


Chansik Kim

Chansik Kim
Graduate Student
Joined the lab in: 2017

Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728

tel: 781 736 2326
kva0987 (at) brandeis.edu




Education
  • 2016 - BSc Biochemistry, Texas A&M University, College Station, TX, USA


Publications

From the Kern Lab:

  • 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



Ingrid Marko

Ingrid Marko
Graduate Student
Joined the lab in: 2017

Volen 443
Department of Biochemistry, MS 009
Brandeis University
415 South Street
Waltham, MA 02453-2728

tel: 781 736 2326
imarko (at) brandeis.edu




Education
  • 2016 - BSc Biochemistry, Worcester Polytechnic Institute, Worcester, MA, USA


Publications

From the Kern Lab:

  • 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



Andrew Glaser

Andrew Glaser
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
andrewglaser (at) brandeis.edu




Education
  • 2016 - BSc Biochemistry, Union College, Schenectady, NY, USA


MacKenzie Patterson

MacKenzie Patterson
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) brandeis.edu




Education
  • 2018 - BSc Biochemistry, University of Massachusetts Boston, Boston, MA, USA

Adenylate kinase (ADK) is a phosphotransferase that regulates energy homeostasis by controlling intracellular nucleotide levels. ADK is an essential enzyme that is found across all domains of life, and its stability is correlated to organismal growth. This stability/fitness relationship imposes that ancestral ADK evolved modern sequences that are stable in the same environments occupied by their native organisms. I am interested in studying how ADK evolved by investigating the effects of mutations on the structural and dynamic properties of the enzyme using biophysical techniques such as X-ray crystallography and NMR spectroscopy.

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



Christiana Ntangka

Christiana Ntangka
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) brandeis.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


Camille Sullivan

Camille Sullivan
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


Carolyn Morningstar

Carolyn Morningstar
Master 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
cmorningstar (at) brandeis.edu




Education
  • 2021 - BS in Biochemistry, Juniata College, Huntingdon PA, USA


Lufan Xiao

Lufan Xiao
Master 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
lux011 (at) brandeis.edu




Education
  • 2021 - BS Biochemistry, University of California San Diego, USA


Nicholas Greco

Nicholas Greco
Master 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
nicholasgreco (at) brandeis.edu




Education
  • 2022 - BS Biochemistry, Brandeis University, USA


Nick Buongiorno

Nick Buongiorno
Undergraduate 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
nbuongiorno (at) brandeis.edu