Karen Nazaretian Allen, PhD

Professor, Chemistry

Karen Allen
590 Commonwealth Ave


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.

The Allen Research 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.

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 include:

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.

Other Positions

  • Associate Professor, Physiology & Biophysics, Boston University School of Medicine


  • Brandeis University, PhD
  • Tufts University, BS


  • Published on 6/13/2018

    Tararina MA, Xue S, Smith LC, Muellers SN, Miranda PO, Janda KD, Allen KN. Crystallography Coupled with Kinetic Analysis Provides Mechanistic Underpinnings of a Nicotine-Degrading Enzyme. Biochemistry. 2018 Jul 03; 57(26):3741-3751. PMID: 29812904.

    Read at: PubMed
  • Published on 5/16/2018

    Ray LC, Das D, Entova S, Lukose V, Lynch AJ, Imperiali B, Allen KN. Membrane association of monotopic phosphoglycosyl transferase underpins function. Nat Chem Biol. 2018 May 16. PMID: 29769739.

    Read at: PubMed
  • Published on 11/18/2016

    Tararina MA, Janda KD, Allen KN. Structural Analysis Provides Mechanistic Insight into Nicotine Oxidoreductase from Pseudomonas putida. Biochemistry. 2016 Dec 06; 55(48):6595-6598. PMID: 27933790.

    Read at: PubMed
  • Published on 8/13/2016

    Allen KN, Dunaway-Mariano D. Catalytic scaffolds for phosphoryl group transfer. Curr Opin Struct Biol. 2016 Dec; 41:172-179. PMID: 27526404.

    Read at: PubMed
  • Published on 4/4/2016

    Zhu W, Easthon LM, Reinhardt LA, Tu C, Cohen SE, Silverman DN, Allen KN, Richards NG. Substrate Binding Mode and Molecular Basis of a Specificity Switch in Oxalate Decarboxylase. Biochemistry. 2016 Apr 12; 55(14):2163-73. PMID: 27014926.

    Read at: PubMed
  • Published on 12/4/2015

    Lukose V, Luo L, Kozakov D, Vajda S, Allen KN, Imperiali B. Conservation and Covariance in Small Bacterial Phosphoglycosyltransferases Identify the Functional Catalytic Core. Biochemistry. 2015 Dec 22; 54(50):7326-34. PMID: 26600273.

    Read at: PubMed
  • Published on 10/21/2015

    Rago F, Saltzberg D, Allen KN, Tolan DR. Enzyme Substrate Specificity Conferred by Distinct Conformational Pathways. J Am Chem Soc. 2015 Nov 4; 137(43):13876-86. PMID: 26440863.

    Read at: PubMed
  • Published on 9/4/2015

    Barthelmes D, Gränz M, Barthelmes K, Allen KN, Imperiali B, Prisner T, Schwalbe H. Encoded loop-lanthanide-binding tags for long-range distance measurements in proteins by NMR and EPR spectroscopy. J Biomol NMR. 2015 Nov; 63(3):275-82. PMID: 26341230.

    Read at: PubMed
  • Published on 6/10/2015

    Xia B, Mamonov A, Leysen S, Allen KN, Strelkov SV, Paschalidis ICh, Vajda S, Kozakov D. Accounting for observed small angle X-ray scattering profile in the protein-protein docking server ClusPro. J Comput Chem. 2015 Jul 30; 36(20):1568-72. PMID: 26095982.

    Read at: PubMed
  • Published on 4/27/2015

    Kozakov D, Hall DR, Jehle S, Jehle S, Luo L, Ochiana SO, Jones EV, Pollastri M, Allen KN, Whitty A, Vajda S. Ligand deconstruction: Why some fragment binding positions are conserved and others are not. Proc Natl Acad Sci U S A. 2015 May 19; 112(20):E2585-94. PMID: 25918377.

    Read at: PubMed

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