Karen Nazaretian Allen, PhD

Professor, Chemistry

Karen Allen
617.353.2500
590 Commonwealth Ave

Biography

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

Education

  • Brandeis University, PhD
  • Tufts University, BS

Publications

  • 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 Jul 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 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 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 Jun 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
  • Published on 8/30/2017

    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.

    Read at: PubMed
  • Published on 7/8/2017

    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.

    Read at: PubMed
  • Published on 5/22/2017

    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.

    Read at: PubMed
  • Published on 5/19/2017

    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.

    Read at: PubMed
  • Published on 2/8/2017

    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.

    Read at: PubMed

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