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 Chobanian and Avedisian 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

  • Chair, Chemistry, Boston University College of Arts and Sciences
  • Associate Professor, Pharmacology, Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine
  • Member, Evans Center for Interdisciplinary Biomedical Research, Boston University
  • Graduate Faculty (Primary Mentor of Grad Students), Boston University Chobanian & Avedisian School of Medicine, Graduate Medical Sciences


  • Brandeis University, PhD
  • Tufts University, BS


  • Published on 1/19/2021

    Tararina MA, Dam KK, Dhingra M, Janda KD, Palfey BA, Allen KN. Fast Kinetics Reveals Rate-Limiting Oxidation and the Role of the Aromatic Cage in the Mechanism of the Nicotine-Degrading Enzyme NicA2. Biochemistry. 2021 02 02; 60(4):259-273. PMID: 33464876.

    Read at: PubMed
  • Published on 3/19/2020

    Tararina MA, Allen KN. Bioinformatic Analysis of the Flavin-Dependent Amine Oxidase Superfamily: Adaptations for Substrate Specificity and Catalytic Diversity. J Mol Biol. 2020 05 01; 432(10):3269-3288. PMID: 32198115.

    Read at: PubMed
  • Published on 6/5/2019

    Tazhigulov RN, Gurunathan PK, Kim Y, Slipchenko LV, Bravaya KB. Polarizable embedding for simulating redox potentials of biomolecules. Phys Chem Chem Phys. 2019 Jun 05; 21(22):11642-11650. PMID: 31116217.

    Read at: PubMed
  • Published on 4/16/2019

    Allen KN, Imperiali B. Structural and mechanistic themes in glycoconjugate biosynthesis at membrane interfaces. Curr Opin Struct Biol. 2019 12; 59:81-90. PMID: 31003021.

    Read at: PubMed
  • Published on 10/15/2018

    Allen KN, Entova S, Ray LC, Imperiali B. Monotopic Membrane Proteins Join the Fold. Trends Biochem Sci. 2019 01; 44(1):7-20. PMID: 30337134.

    Read at: PubMed
  • Published on 7/13/2018

    Zhang C, Allen KN, Dunaway-Mariano D. Mechanism of Substrate Recognition and Catalysis of the Haloalkanoic Acid Dehalogenase Family Member a-Phosphoglucomutase. Biochemistry. 2018 07 31; 57(30):4504-4517. PMID: 29952545.

    Read at: PubMed
  • 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 07 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 06; 14(6):538-541. PMID: 29769739.

    Read at: PubMed
  • Published on 5/11/2018

    Ji T, Zhang C, Zheng L, Dunaway-Mariano D, Allen KN. Structural Basis of the Molecular Switch between Phosphatase and Mutase Functions of Human Phosphomannomutase 1 under Ischemic Conditions. Biochemistry. 2018 06 26; 57(25):3480-3492. PMID: 29695157.

    Read at: PubMed
  • Published on 3/26/2018

    Beglov D, Hall DR, Wakefield AE, Luo L, Allen KN, Kozakov D, Whitty A, Vajda S. Exploring the structural origins of cryptic sites on proteins. Proc Natl Acad Sci U S A. 2018 04 10; 115(15):E3416-E3425. PMID: 29581267.

    Read at: PubMed

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