Karen Allen


Professor Karen N. Allen

Karen Allen investigates protein structure and function through X-ray diffraction and enzyme kinetic studies. Prior to joining the Department of Chemistry in 2008, she was Professor of Physiology and Biophysics at the Boston University School of Medicine. A leader in the American Chemical Society, she is currently an Associate Editor of the ACS journal, Biochemistry.

Degrees and Positions

  • B.S., cum laude in Biology, Tufts University, 1984
  • Ph.D. in Biochemistry, Brandeis University, 1989
  • American Cancer Society Postdoctoral Fellow in X-ray Crystallography, Massachusetts Institute of Technology, 1989 and Brandeis University, 1990


  • Program Chair, XXI Enzyme Mechanism Conference
  • Program Chair, American Chemical Society National Meeting, Biological Chemistry Division
  • Faculty of 1000, contributor
  • Gordon Research Conference, Enzymes, Coenzymes and Metabolic Pathways, Co-Chair


Prof. Allen recently published a paper in Nature revising the long-held view of how the enzyme acetoacetate decarboxylase (AADase) functions in the cell environment.

The Allen Group investigates the structure, function, and catalytic properties of enzymes. Their insights into these essential proteins guide the design of specialized molecules and enzymes to aid in drug discovery and in the development of tools that assist in protein studies. The Allen Group researchers conduct their studies using X-ray crystallography and spectroscopy, enzymology, and bioinformatics and routinely collaborate with leading laboratories at other universities.

Nature Magazine Molecular Transformation

The AADase tertiary structure depicted as a ribbon diagram.

  • Structure/Function/Catalytic Studies investigate the properties of specific enzymes in the haloalkanoic acid dehalogenase (HAD) Superfamily and the Hot Dog Thioesterase Superfamily. The HAD studies aim to develop an understanding of enzyme evolution. The Hot Dog thioestearse (found in eukaryotes, bacteria, and archea) studies focus on the biological functions of this pervasive domain. (With the Dunaway-Mariano Group, University of New Mexico)
  • Drug Discovery Studies aim to develop inhibitors against the potent neurotoxin produced by the soil-dwelling bacterium Clostridium botulinum (BoNT). These inhibitors are crucial because these toxins have high potential for use in biological weapons. (With the Tzipori Group, Tufts University)
  • Tool Discovery Studies develop multi-tasking, easy-to-use Lanthanide Binding Tags (LBTs). LBTs consist of 17 amino-acids which have minimal impact on the structures and functions of the proteins they help study. (With the Imperiali Group, Massachusetts Institute of Technology)

Techniques & Resources

  • X-Ray Crystallography – the University runs a state-of-the-art X-ray crystallographic suite, including a rotating anode generator, with a CCD detector, capable of collecting data on both macro and small molecules. A dedicated X-Ray technician assists with data collection, processing, and troubleshooting.
  • The Crystal Farm – stores and visualizes 96-well trays of crystal, allowing automated tracking of crystal growth, remote viewing of crystals, optimized formulation of new crystal conditions, and enhanced temperature control.
  • Bioinformatics – lab utilizes the Scientific Computing and Visualization (SCV) supercomputers to create an approximation of the potential energy of molecules. These calculations are entered into CHARMM force fields in order to characterize the conformational changes of various members of the HAD superfamily.
  • Spectroscopy – lab performs Mass Spectrometry and CD Spectroscopy using CIC instrumentation.


Members of the Allen Group regularly visit national research centers to take advantage of unique facilities and expertise in x-ray crystallography. Brookhaven and Argonne National Laboratories allow students and post-doctoral fellows to collect high-quality data on samples too small to analyze on home sources. By attending workshops and classes at these facilities, the lab also exchanges ideas with users from all over the world.

What’s Next for Graduates of the Allen Group?

Enzymology and rational drug design skills are in great demand at academic institutions, pharmaceutical companies, and structural genomics consortiums such as the Protein Structure Initiative. Recent graduates include:

  • Marc Morais, The University of Texas Medical Branch
  • Sushmita Lahiri, AstraZeneca
  • Nicholas Silvaggi, University of Wisconsin, Milwaukee

SCI 394A
Phone 617.358.5544
Fax 617.353.6466
Office hours: By appointment
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