Karen N. Allen, PhD
Boston University College of Arts and Sciences
Dept of Chemistry

PhD, Brandeis University

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.

Associate Professor
Boston University School of Medicine
Physiology & Biophysics

Molecular Mechanism of the NFkappaB Essential Modulator (NEMO) Scaffold Protein Mutated in Human Immunodeficiencies
08/15/2016 - 06/30/2020 (Co-PI)
PI: Adrian Whitty, PhD
NIH/National Institute of General Medical Sciences

A Multidisciplinary Approach for the Treatment of Botulinum Intoxication
08/26/2016 - 06/30/2019 (PI)
The Scripps Research Institute NIH NIAID

Trehalose-6-phosphate phosphatase inhibitors as anti-helminthics
09/12/2016 - 11/30/2018 (PI)
NIH/National Institute of Allergy & Infectious Diseases

Collaborative research: Development of a platform enabling analysis of membrane protein interactions
08/01/2016 - 07/31/2018 (PI)
National Science Foundation

Structure and Function of HAD Phosphatase Partners Dullard and Lipin
09/01/2012 - 05/31/2017 (PI)
NIH/National Institute of General Medical Sciences

05/01/2010 - 04/30/2016 (PI)
University of Illinois NIH NIGMS

Trehalose-6-Phosphate Phosphatase: A Target for Anti-Onchocerciasis Therapeutics
01/18/2013 - 12/31/2015 (PI)
NIH/National Institute of Allergy & Infectious Diseases

PGT Inhibitors Mapped From A Tunicamycin Blueprint
02/01/2013 - 01/31/2015 (PI)
Massachusetts Institute of Technology NIH

MRI: Acquisition of Circular Dichroism (CD) Spectrometer
09/15/2011 - 08/31/2014 (PI)
National Science Foundation

Biochemical Studies of Oxalate Decarboxylase
07/01/2012 - 06/30/2014 (PI)
Trustees of Indiana University NIH

Showing 10 of 23 results. Show All Results

Yr Title Project-Sub Proj Pubs
2019 Structure and function of the monotopic phosphoglycosyl transferase superfamily: Initiators of biosynthesis of complex bacterial glycoconjugates 1R01GM131627-01
2018 Trehalose-6-phosphate phosphatase inhibitors as anti-helminthics 5R21AI127623-02
2017 Trehalose-6-phosphate phosphatase inhibitors as anti-helminthics 1R21AI127623-01
2015 Structure and Function of HAD Phosphatase Partners Dullard and Lipin 5R01GM098760-04 2
2014 Trehalose-6-phosphate phosphatase: a target for anti-onchocerciasis therapeutics 5R21AI103484-02 1
2014 Structure and Function of HAD Phosphatase Partners Dullard and Lipin 5R01GM098760-03 2
2013 Trehalose-6-phosphate phosphatase: a target for anti-onchocerciasis therapeutics 1R21AI103484-01 1
2013 Structure and Function of HAD Phosphatase Partners Dullard and Lipin 5R01GM098760-02 2
2012 Structure and Function of HAD Phosphatase Partners Dullard and Lipin 1R01GM098760-01A1 2
Showing 10 of 34 results. Show All Results
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

  1. 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.View Related Profiles. PMID: 31116217.
  2. Allen KN, Imperiali B. Structural and mechanistic themes in glycoconjugate biosynthesis at membrane interfaces. Curr Opin Struct Biol. 2019 Apr 16; 59:81-90. PMID: 31003021.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.View Related Profiles. PMID: 29581267.
  9. Latham JA, Ji T, Matthews K, Mariano PS, Allen KN, Dunaway-Mariano D. Catalytic Mechanism of the Hotdog-Fold Thioesterase PA1618 Revealed by X-ray Structure Determination of a Substrate-Bound Oxygen Ester Analogue Complex. Chembiochem. 2017 10 05; 18(19):1935-1943. PMID: 28741300; DOI: 10.1002/cbic.201700322;.
  10. Jacobson AR, Adler M, Silvaggi NR, Allen KN, Smith GM, Fredenburg RA, Stein RL, Park JB, Feng X, Shoemaker CB, Deshpande SS, Goodnough MC, Malizio CJ, Johnson EA, Pellett S, Tepp WH, Tzipori S. Small molecule metalloprotease inhibitor with in vitro, ex vivo and in vivo efficacy against botulinum neurotoxin serotype A. Toxicon. 2017 Oct; 137:36-47. PMID: 28698055.
Showing 10 of 105 results. Show More

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 105 publications over 24 distinct years, with a maximum of 8 publications in 2004 and 2014

In addition to these self-described keywords below, a list of MeSH based concepts is available here.

x-ray crystallographical studies of enzymes
Botulinum Neurotoxins
Haloalkanoic Acid Dehalogenase Superfamily
Hotdog Fold Thioesterases
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