Karen N. Allen, PhD
Professor
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
3R01GM117350-03S1

A MULTIDISCIPLINARY APPROACH FOR THE TREATMENT OF BOTULINUM INTOXICATION
08/26/2016 - 06/30/2019 (PI)
The Scripps Research Institute NIH NIAID
5R01AI19564-03

TREHALOSE-6-PHOSPHATE PHOSPHATASE INHIBITORS AS ANTI-HELMINTHICS
09/12/2016 - 11/30/2018 (PI)
NIH/National Institute of Allergy & Infectious Diseases
5R21AI127623-02

COLLABORATIVE RESEARCH: DEVELOPMENT OF A PLATFORM ENABLING ANALYSIS OF MEMBRANE PROTEIN INTERACTIONS
08/01/2016 - 07/31/2018 (PI)
National Science Foundation
MCB-1614608

STRUCTURE AND FUNCTION OF HAD PHOSPHATASE PARTNERS DULLARD AND LIPIN
09/01/2012 - 05/31/2017 (PI)
NIH/National Institute of General Medical Sciences
5R01GM098760-04

COLLABORATIVE CENTER FOR AN ENZYME FUNCTION INITIATIVE
05/01/2010 - 04/30/2016 (PI)
University of Illinois NIH NIGMS
5U54GM093342-05

TREHALOSE-6-PHOSPHATE PHOSPHATASE: A TARGET FOR ANTI-ONCHOCERCIASIS THERAPEUTICS
01/18/2013 - 12/31/2015 (PI)
NIH/National Institute of Allergy & Infectious Diseases
5R21AI103484-02

PGT INHIBITORS MAPPED FROM A TUNICAMYCIN BLUEPRINT
02/01/2013 - 01/31/2015 (PI)
Massachusetts Institute of Technology NIH
1R21AI101807-01A1

MRI: ACQUISITION OF CIRCULAR DICHROISM (CD) SPECTROMETER
09/15/2011 - 08/31/2014 (PI)
National Science Foundation
CHE-1126545

BIOCHEMICAL STUDIES OF OXALATE DECARBOXYLASE
07/01/2012 - 06/30/2014 (PI)
Trustees of Indiana University NIH
7R01DK061666-08

Showing 10 of 23 results. Show All Results



Yr Title Project-Sub Proj Pubs
2018 Trehalose-6-phosphate phosphatase inhibitors as anti-helminthics 5R21AI127623-02
2017 Trehalose-6-phosphate phosphatase inhibitors as anti-helminthics 1R21AI127623-01
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
2009 2-KETO-3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE 5P41RR012408-13-7497 122
2009 STRUCTURE-FUNCTION DETEMINATION OF THE TYPE III HALOACID DEHALOGENASE (HAD) SUPE 5P41RR012408-13-7534 122
2009 Mechanisms and Function in HAD Phosphotransferases 7R01GM061099-09 27
Showing 10 of 32 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. Zhang C, Allen KN, Dunaway-Mariano D. Mechanism of Substrate Recognition and Catalysis of the Haloalkanoic Acid Dehalogenase Family Member a-Phosphoglucomutase. Biochemistry. 2018 Jul 31; 57(30):4504-4517. PMID: 29952545.
     
  2. 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.
     
  3. 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.
     
  4. 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 Jun 26; 57(25):3480-3492. PMID: 29695157.
     
  5. 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.
     
  6. 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;.
     
  7. 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.
     
  8. Barthelmes D, Barthelmes K, Schnorr K, Jonker HRA, Bodmer B, Allen KN, Imperiali B, Schwalbe H. Conformational dynamics and alignment properties of loop lanthanide-binding-tags (LBTs) studied in interleukin-1ß. J Biomol NMR. 2017 Jul; 68(3):187-194. PMID: 28534082; DOI: 10.1007/s10858-017-0118-5;.
     
  9. Bremer PT, Pellett S, Carolan JP, Tepp WH, Eubanks LM, Allen KN, Johnson EA, Janda KD. Metal Ions Effectively Ablate the Action of Botulinum Neurotoxin A. J Am Chem Soc. 2017 05 31; 139(21):7264-7272. PMID: 28475321; DOI: 10.1021/jacs.7b01084;.
     
  10. Koo BM, Kritikos G, Farelli JD, Todor H, Tong K, Kimsey H, Wapinski I, Galardini M, Cabal A, Peters JM, Hachmann AB, Rudner DZ, Allen KN, Typas A, Gross CA. Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis. Cell Syst. 2017 Mar 22; 4(3):291-305.e7. PMID: 28189581.
     
Showing 10 of 102 results. Show More

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

Bar chart showing 102 publications over 23 distinct years, with a maximum of 8 publications in 2004 and 2014

YearPublications
19892
19943
19952
19992
20002
20011
20025
20034
20048
20055
20066
20075
20086
20093
20104
20117
20124
20135
20148
20157
20163
20175
20185
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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