Keywords
Last Name

Karen N. Allen, PhD

TitleProfessor
InstitutionBoston University College of Arts and Sciences
DepartmentChemistry
Address590 Commonwealth Ave
Boston MA 02215
Phone(617) 353-2500
Other Positions
TitleAssociate Professor
InstitutionBoston University School of Medicine
DepartmentPhysiology & Biophysics

 Research Expertise & Professional Interests
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.

 Publications
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.
List All   |   Timeline
  1. 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.
    View in: PubMed
  2. Allen KN, Dunaway-Mariano D. Catalytic scaffolds for phosphoryl group transfer. Curr Opin Struct Biol. 2016 Dec; 41:172-179. PMID: 27526404.
    View in: PubMed
  3. 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.
    View in: PubMed
  4. 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.
    View in: PubMed
  5. 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.
    View in: PubMed
  6. 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.
    View in: PubMed
  7. 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.
    View in: PubMed
  8. 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.
    View in: PubMed
  9. Huang H, Pandya C, Liu C, Al-Obaidi NF, Wang M, Zheng L, Toews Keating S, Aono M, Love JD, Evans B, Seidel RD, Hillerich BS, Garforth SJ, Almo SC, Mariano PS, Dunaway-Mariano D, Allen KN, Farelli JD. Panoramic view of a superfamily of phosphatases through substrate profiling. Proc Natl Acad Sci U S A. 2015 Apr 21; 112(16):E1974-83. PMID: 25848029.
    View in: PubMed
  10. London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt PC, Almo SC, Allen KN, Shoichet BK. Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases. Biochemistry. 2015 Jan 20; 54(2):528-37. PMID: 25513739.
    View in: PubMed
  11. Zhou L, Yeo AT, Ballarano C, Weber U, Allen KN, Gilmore TD, Whitty A. Disulfide-mediated stabilization of the I?B kinase binding domain of NF-?B essential modulator (NEMO). Biochemistry. 2014 Dec 23; 53(50):7929-44. PMID: 25400026.
    View in: PubMed
  12. Pandya C, Farelli JD, Dunaway-Mariano D, Allen KN. Enzyme promiscuity: engine of evolutionary innovation. J Biol Chem. 2014 Oct 31; 289(44):30229-36. PMID: 25210039.
    View in: PubMed
  13. Wu R, Latham JA, Chen D, Farelli J, Zhao H, Matthews K, Allen KN, Dunaway-Mariano D. Structure and catalysis in the Escherichia coli hotdog-fold thioesterase paralogs YdiI and YbdB. Biochemistry. 2014 Jul 29; 53(29):4788-805. PMID: 25010423.
    View in: PubMed
  14. Latham JA, Chen D, Allen KN, Dunaway-Mariano D. Divergence of substrate specificity and function in the Escherichia coli hotdog-fold thioesterase paralogs YdiI and YbdB. Biochemistry. 2014 Jul 29; 53(29):4775-87. PMID: 24992697.
    View in: PubMed
  15. Farelli JD, Galvin BD, Li Z, Liu C, Aono M, Garland M, Hallett OE, Causey TB, Ali-Reynolds A, Saltzberg DJ, Carlow CK, Dunaway-Mariano D, Allen KN. Structure of the trehalose-6-phosphate phosphatase from Brugia malayi reveals key design principles for anthelmintic drugs. PLoS Pathog. 2014 Jul; 10(7):e1004245. PMID: 24992307.
    View in: PubMed
  16. Barelier S, Cummings JA, Rauwerdink AM, Hitchcock DS, Farelli JD, Almo SC, Raushel FM, Allen KN, Shoichet BK. Substrate deconstruction and the nonadditivity of enzyme recognition. J Am Chem Soc. 2014 May 21; 136(20):7374-82. PMID: 24791931.
    View in: PubMed
  17. Pandya C, Dunaway-Mariano D, Xia Y, Allen KN. Structure-guided approach for detecting large domain inserts in protein sequences as illustrated using the haloacid dehalogenase superfamily. Proteins. 2014 Sep; 82(9):1896-906. PMID: 24577717.
    View in: PubMed
  18. Campomanes P, Kellett WF, Easthon LM, Ozarowski A, Allen KN, Angerhofer A, Rothlisberger U, Richards NG. Assigning the EPR fine structure parameters of the Mn(II) centers in Bacillus subtilis oxalate decarboxylase by site-directed mutagenesis and DFT/MM calculations. J Am Chem Soc. 2014 Feb 12; 136(6):2313-23. PMID: 24444454.
    View in: PubMed
  19. Cote SM, Gilmore TD, Shaffer R, Weber U, Bollam R, Golden MS, Glover K, Herscovitch M, Ennis T, Allen KN, Whitty A. Mutation of nonessential cysteines shows that the NF-?B essential modulator forms a constitutive noncovalent dimer that binds I?B kinase-ß with high affinity. Biochemistry. 2013 Dec 23; 52(51):9141-54. PMID: 24266532.
    View in: PubMed
  20. Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt PC, Xia Y, Allen KN. Consequences of domain insertion on sequence-structure divergence in a superfold. Proc Natl Acad Sci U S A. 2013 Sep 03; 110(36):E3381-7. PMID: 23959887.
    View in: PubMed
  21. Bryan T, González JM, Bacik JP, DeNunzio NJ, Unkefer CJ, Schrader TE, Ostermann A, Dunaway-Mariano D, Allen KN, Fisher SZ. Neutron diffraction studies towards deciphering the protonation state of catalytic residues in the bacterial KDN9P phosphatase. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Sep; 69(Pt 9):1015-9. PMID: 23989152.
    View in: PubMed
  22. Daughtry KD, Huang H, Malashkevich V, Patskovsky Y, Liu W, Ramagopal U, Sauder JM, Burley SK, Almo SC, Dunaway-Mariano D, Allen KN. Structural basis for the divergence of substrate specificity and biological function within HAD phosphatases in lipopolysaccharide and sialic acid biosynthesis. Biochemistry. 2013 Aug 13; 52(32):5372-86. PMID: 23848398.
    View in: PubMed
  23. Wang M, Song F, Wu R, Allen KN, Mariano PS, Dunaway-Mariano D. Co-evolution of HAD phosphatase and hotdog-fold thioesterase domain function in the menaquinone-pathway fusion proteins BF1314 and PG1653. FEBS Lett. 2013 Sep 02; 587(17):2851-9. PMID: 23851007.
    View in: PubMed
  24. Šilhár P, Silvaggi NR, Pellett S, Capková K, Johnson EA, Allen KN, Janda KD. Evaluation of adamantane hydroxamates as botulinum neurotoxin inhibitors: synthesis, crystallography, modeling, kinetic and cellular based studies. Bioorg Med Chem. 2013 Mar 01; 21(5):1344-8. PMID: 23340139.
    View in: PubMed
  25. Daughtry KD, Martin LJ, Sarraju A, Imperiali B, Allen KN. Tailoring encodable lanthanide-binding tags as MRI contrast agents. Chembiochem. 2012 Nov 26; 13(17):2567-74. PMID: 23150430.
    View in: PubMed
  26. Saylor BT, Reinhardt LA, Lu Z, Shukla MS, Nguyen L, Cleland WW, Angerhofer A, Allen KN, Richards NG. A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase. Biochemistry. 2012 Apr 03; 51(13):2911-20. PMID: 22404040.
    View in: PubMed
  27. Daughtry KD, Xiao Y, Stoner-Ma D, Cho E, Orville AM, Liu P, Allen KN. Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance Raman, and UV-visible spectroscopic analysis of a Rieske-type demethylase. J Am Chem Soc. 2012 Feb 8; 134(5):2823-34. PMID: 22224443.
    View in: PubMed
  28. Toteva MM, Silvaggi NR, Allen KN, Richard JP. Binding energy and catalysis by D-xylose isomerase: kinetic, product, and X-ray crystallographic analysis of enzyme-catalyzed isomerization of (R)-glyceraldehyde. Biochemistry. 2011 Nov 22; 50(46):10170-81. PMID: 21995300.
    View in: PubMed
  29. Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt PC, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV. The Enzyme Function Initiative. Biochemistry. 2011 Nov 22; 50(46):9950-62. PMID: 21999478.
    View in: PubMed
  30. Huang H, Patskovsky Y, Toro R, Farelli JD, Pandya C, Almo SC, Allen KN, Dunaway-Mariano D. Divergence of structure and function in the haloacid dehalogenase enzyme superfamily: Bacteroides thetaiotaomicron BT2127 is an inorganic pyrophosphatase. Biochemistry. 2011 Oct 18; 50(41):8937-49. PMID: 21894910.
    View in: PubMed
  31. Lu Z, Dunaway-Mariano D, Allen KN. The X-ray crystallographic structure and specificity profile of HAD superfamily phosphohydrolase BT1666: comparison of paralogous functions in B. thetaiotaomicron. Proteins. 2011 Nov; 79(11):3099-107. PMID: 21989931.
    View in: PubMed
  32. Wu R, Garland M, Dunaway-Mariano D, Allen KN. Homo sapiens dullard protein phosphatase shows a preference for the insulin-dependent phosphorylation site of lipin1. Biochemistry. 2011 Apr 19; 50(15):3045-7. PMID: 21413788.
    View in: PubMed
  33. Barthelmes K, Reynolds AM, Peisach E, Jonker HR, DeNunzio NJ, Allen KN, Imperiali B, Schwalbe H. Engineering encodable lanthanide-binding tags into loop regions of proteins. J Am Chem Soc. 2011 Feb 2; 133(4):808-19. PMID: 21182275.
    View in: PubMed
  34. Salzameda NT, Eubanks LM, Zakhari JS, Tsuchikama K, DeNunzio NJ, Allen KN, Hixon MS, Janda KD. A cross-over inhibitor of the botulinum neurotoxin light chain B: a natural product implicating an exosite mechanism of action. Chem Commun (Camb). 2011 Feb 14; 47(6):1713-5. PMID: 21203627.
    View in: PubMed
  35. Stowe GN, Silhár P, Hixon MS, Silvaggi NR, Allen KN, Moe ST, Jacobson AR, Barbieri JT, Janda KD. Chirality holds the key for potent inhibition of the botulinum neurotoxin serotype a protease. Org Lett. 2010 Feb 19; 12(4):756-9. PMID: 20092262.
    View in: PubMed
  36. Wang L, Huang H, Nguyen HH, Allen KN, Mariano PS, Dunaway-Mariano D. Divergence of biochemical function in the HAD superfamily: D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB). Biochemistry. 2010 Feb 16; 49(6):1072-81. PMID: 20050615.
    View in: PubMed
  37. Nguyen HH, Wang L, Huang H, Peisach E, Dunaway-Mariano D, Allen KN. Structural determinants of substrate recognition in the HAD superfamily member D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB) . Biochemistry. 2010 Feb 16; 49(6):1082-92. PMID: 20050614.
    View in: PubMed
  38. Allen KN, Imperiali B. Lanthanide-tagged proteins--an illuminating partnership. Curr Opin Chem Biol. 2010 Apr; 14(2):247-54. PMID: 20102793.
    View in: PubMed
  39. Allen KN, Dunaway-Mariano D. Markers of fitness in a successful enzyme superfamily. Curr Opin Struct Biol. 2009 Dec; 19(6):658-65. PMID: 19889535.
    View in: PubMed
  40. Ho MC, Ménétret JF, Tsuruta H, Allen KN. The origin of the electrostatic perturbation in acetoacetate decarboxylase. Nature. 2009 May 21; 459(7245):393-7. PMID: 19458715.
    View in: PubMed
  41. Dai J, Finci L, Zhang C, Lahiri S, Zhang G, Peisach E, Allen KN, Dunaway-Mariano D. Analysis of the structural determinants underlying discrimination between substrate and solvent in beta-phosphoglucomutase catalysis. Biochemistry. 2009 Mar 10; 48(9):1984-95. PMID: 19154134.
    View in: PubMed
  42. Lu Z, Wang L, Dunaway-Mariano D, Allen KN. Structure-function analysis of 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphatase defines specificity elements in type C0 haloalkanoate dehalogenase family members. J Biol Chem. 2009 Jan 9; 284(2):1224-33. PMID: 18986982.
    View in: PubMed
  43. Wang L, Lu Z, Allen KN, Mariano PS, Dunaway-Mariano D. Human symbiont Bacteroides thetaiotaomicron synthesizes 2-keto-3-deoxy-D-glycero-D- galacto-nononic acid (KDN). Chem Biol. 2008 Sep 22; 15(9):893-7. PMID: 18804026.
    View in: PubMed
  44. Silvaggi NR, Wilson D, Tzipori S, Allen KN. Catalytic features of the botulinum neurotoxin A light chain revealed by high resolution structure of an inhibitory peptide complex. Biochemistry. 2008 May 27; 47(21):5736-45. PMID: 18457419.
    View in: PubMed
  45. Sherawat M, Tolan DR, Allen KN. Structure of a rabbit muscle fructose-1,6-bisphosphate aldolase A dimer variant. Acta Crystallogr D Biol Crystallogr. 2008 May; 64(Pt 5):543-50. PMID: 18453690.
    View in: PubMed
  46. Lu Z, Dunaway-Mariano D, Allen KN. The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state. Proc Natl Acad Sci U S A. 2008 Apr 15; 105(15):5687-92. PMID: 18398008.
    View in: PubMed
  47. Peisach E, Wang L, Burroughs AM, Aravind L, Dunaway-Mariano D, Allen KN. The X-ray crystallographic structure and activity analysis of a Pseudomonas-specific subfamily of the HAD enzyme superfamily evidences a novel biochemical function. Proteins. 2008 Jan 1; 70(1):197-207. PMID: 17654544.
    View in: PubMed
  48. Pezza JA, Stopa JD, Brunyak EM, Allen KN, Tolan DR. Thermodynamic analysis shows conformational coupling and dynamics confer substrate specificity in fructose-1,6-bisphosphate aldolase. Biochemistry. 2007 Nov 13; 46(45):13010-8. PMID: 17935305.
    View in: PubMed
  49. Allen KN. Form finds function. Nat Chem Biol. 2007 Aug; 3(8):452-3. PMID: 17637773.
    View in: PubMed
  50. Martin LJ, Hähnke MJ, Nitz M, Wöhnert J, Silvaggi NR, Allen KN, Schwalbe H, Imperiali B. Double-lanthanide-binding tags: design, photophysical properties, and NMR applications. J Am Chem Soc. 2007 Jun 6; 129(22):7106-13. PMID: 17497862.
    View in: PubMed
  51. Silvaggi NR, Martin LJ, Schwalbe H, Imperiali B, Allen KN. Double-lanthanide-binding tags for macromolecular crystallographic structure determination. J Am Chem Soc. 2007 Jun 6; 129(22):7114-20. PMID: 17497863.
    View in: PubMed
  52. Silvaggi NR, Boldt GE, Hixon MS, Kennedy JP, Tzipori S, Janda KD, Allen KN. Structures of Clostridium botulinum Neurotoxin Serotype A Light Chain complexed with small-molecule inhibitors highlight active-site flexibility. Chem Biol. 2007 May; 14(5):533-42. PMID: 17524984.
    View in: PubMed
  53. Lahiri SD, Zhang G, Dunaway-Mariano D, Allen KN. Diversification of function in the haloacid dehalogenase enzyme superfamily: The role of the cap domain in hydrolytic phosphoruscarbon bond cleavage. Bioorg Chem. 2006 Dec; 34(6):394-409. PMID: 17070898.
    View in: PubMed
  54. Choi KH, Lai V, Foster CE, Morris AJ, Tolan DR, Allen KN. New superfamily members identified for Schiff-base enzymes based on verification of catalytically essential residues. Biochemistry. 2006 Jul 18; 45(28):8546-55. PMID: 16834328.
    View in: PubMed
  55. Burroughs AM, Allen KN, Dunaway-Mariano D, Aravind L. Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes. J Mol Biol. 2006 Sep 1; 361(5):1003-34. PMID: 16889794.
    View in: PubMed
  56. Dai J, Wang L, Allen KN, Radstrom P, Dunaway-Mariano D. Conformational cycling in beta-phosphoglucomutase catalysis: reorientation of the beta-D-glucose 1,6-(Bis)phosphate intermediate. Biochemistry. 2006 Jun 27; 45(25):7818-24. PMID: 16784233.
    View in: PubMed
  57. Silvaggi NR, Zhang C, Lu Z, Dai J, Dunaway-Mariano D, Allen KN. The X-ray crystal structures of human alpha-phosphomannomutase 1 reveal the structural basis of congenital disorder of glycosylation type 1a. J Biol Chem. 2006 May 26; 281(21):14918-26. PMID: 16540464.
    View in: PubMed
  58. Tremblay LW, Dunaway-Mariano D, Allen KN. Structure and activity analyses of Escherichia coli K-12 NagD provide insight into the evolution of biochemical function in the haloalkanoic acid dehalogenase superfamily. Biochemistry. 2006 Jan 31; 45(4):1183-93. PMID: 16430214.
    View in: PubMed
  59. Zhang G, Dai J, Wang L, Dunaway-Mariano D, Tremblay LW, Allen KN. Catalytic cycling in beta-phosphoglucomutase: a kinetic and structural analysis. Biochemistry. 2005 Jul 12; 44(27):9404-16. PMID: 15996095.
    View in: PubMed
  60. Lu Z, Dunaway-Mariano D, Allen KN. HAD superfamily phosphotransferase substrate diversification: structure and function analysis of HAD subclass IIB sugar phosphatase BT4131. Biochemistry. 2005 Jun 21; 44(24):8684-96. PMID: 15952775.
    View in: PubMed
  61. Tremblay LW, Zhang G, Dai J, Dunaway-Mariano D, Allen KN. Chemical confirmation of a pentavalent phosphorane in complex with beta-phosphoglucomutase. J Am Chem Soc. 2005 Apr 20; 127(15):5298-9. PMID: 15826149.
    View in: PubMed
  62. Ali MH, Taylor CM, Grigoryan G, Allen KN, Imperiali B, Keating AE. Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed alpha/beta structure. Structure. 2005 Feb; 13(2):225-34. PMID: 15698566.
    View in: PubMed
  63. Malay AD, Allen KN, Tolan DR. Structure of the thermolabile mutant aldolase B, A149P: molecular basis of hereditary fructose intolerance. J Mol Biol. 2005 Mar 18; 347(1):135-44. PMID: 15733923.
    View in: PubMed
  64. Arakaki TL, Pezza JA, Cronin MA, Hopkins CE, Zimmer DB, Tolan DR, Allen KN. Structure of human brain fructose 1,6-(bis)phosphate aldolase: linking isozyme structure with function. Protein Sci. 2004 Dec; 13(12):3077-84. PMID: 15537755.
    View in: PubMed
  65. Peisach E, Selengut JD, Dunaway-Mariano D, Allen KN. X-ray crystal structure of the hypothetical phosphotyrosine phosphatase MDP-1 of the haloacid dehalogenase superfamily. Biochemistry. 2004 Oct 12; 43(40):12770-9. PMID: 15461449.
    View in: PubMed
  66. Pezza JA, Allen KN, Tolan DR. Intein-mediated purification of a recombinantly expressed peptide. Chem Commun (Camb). 2004 Nov 7; (21):2412-3. PMID: 15514791.
    View in: PubMed
  67. Allen KN, Dunaway-Mariano D. Phosphoryl group transfer: evolution of a catalytic scaffold. Trends Biochem Sci. 2004 Sep; 29(9):495-503. PMID: 15337123.
    View in: PubMed
  68. Ali MH, Peisach E, Allen KN, Imperiali B. X-ray structure analysis of a designed oligomeric miniprotein reveals a discrete quaternary architecture. Proc Natl Acad Sci U S A. 2004 Aug 17; 101(33):12183-8. PMID: 15302930.
    View in: PubMed
  69. Nitz M, Sherawat M, Franz KJ, Peisach E, Allen KN, Imperiali B. Structural origin of the high affinity of a chemically evolved lanthanide-binding peptide. Angew Chem Int Ed Engl. 2004 Jul 12; 43(28):3682-5. PMID: 15248272.
    View in: PubMed
  70. Zhang G, Morais MC, Dai J, Zhang W, Dunaway-Mariano D, Allen KN. Investigation of metal ion binding in phosphonoacetaldehyde hydrolase identifies sequence markers for metal-activated enzymes of the HAD enzyme superfamily. Biochemistry. 2004 May 4; 43(17):4990-7. PMID: 15109258.
    View in: PubMed
  71. Lahiri SD, Zhang G, Dai J, Dunaway-Mariano D, Allen KN. Analysis of the substrate specificity loop of the HAD superfamily cap domain. Biochemistry. 2004 Mar 16; 43(10):2812-20. PMID: 15005616.
    View in: PubMed
  72. Morais MC, Zhang G, Zhang W, Olsen DB, Dunaway-Mariano D, Allen KN. X-ray crystallographic and site-directed mutagenesis analysis of the mechanism of Schiff-base formation in phosphonoacetaldehyde hydrolase catalysis. J Biol Chem. 2004 Mar 5; 279(10):9353-61. PMID: 14670958.
    View in: PubMed
  73. Zhang G, Allen KN, Dunaway-Mariano D. Enzymatic synthesis of radiolabeled phosphonoacetaldehyde. Anal Biochem. 2003 Nov 15; 322(2):233-7. PMID: 14596832.
    View in: PubMed
  74. Lahiri SD, Zhang G, Dunaway-Mariano D, Allen KN. The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction. Science. 2003 Mar 28; 299(5615):2067-71. PMID: 12637673.
    View in: PubMed
  75. Pezza JA, Choi KH, Berardini TZ, Beernink PT, Allen KN, Tolan DR. Spatial clustering of isozyme-specific residues reveals unlikely determinants of isozyme specificity in fructose-1,6-bisphosphate aldolase. J Biol Chem. 2003 May 9; 278(19):17307-13. PMID: 12611890.
    View in: PubMed
  76. Lahiri SD, Wang PF, Babbitt PC, McLeish MJ, Kenyon GL, Allen KN. The 2.1 A structure of Torpedo californica creatine kinase complexed with the ADP-Mg(2+)-NO(3)(-)-creatine transition-state analogue complex. Biochemistry. 2002 Nov 26; 41(47):13861-7. PMID: 12437342.
    View in: PubMed
  77. Zhang G, Mazurkie AS, Dunaway-Mariano D, Allen KN. Kinetic evidence for a substrate-induced fit in phosphonoacetaldehyde hydrolase catalysis. Biochemistry. 2002 Nov 12; 41(45):13370-7. PMID: 12416981.
    View in: PubMed
  78. Lahiri SD, Zhang G, Dunaway-Mariano D, Allen KN. Caught in the act: the structure of phosphorylated beta-phosphoglucomutase from Lactococcus lactis. Biochemistry. 2002 Jul 2; 41(26):8351-9. PMID: 12081483.
    View in: PubMed
  79. Hopkins CE, O'Connor PB, Allen KN, Costello CE, Tolan DR. Chemical-modification rescue assessed by mass spectrometry demonstrates that gamma-thia-lysine yields the same activity as lysine in aldolase. Protein Sci. 2002 Jul; 11(7):1591-9. PMID: 12070312.
    View in: PubMed
  80. Lahiri SD, Zhang G, Radstrom P, Dunaway-Mariano D, Allen KN. Crystallization and preliminary X-ray diffraction studies of beta-phosphoglucomutase from Lactococcus lactus. Acta Crystallogr D Biol Crystallogr. 2002 Feb; 58(Pt 2):324-6. PMID: 11807265.
    View in: PubMed
  81. Choi KH, Shi J, Hopkins CE, Tolan DR, Allen KN. Snapshots of catalysis: the structure of fructose-1,6-(bis)phosphate aldolase covalently bound to the substrate dihydroxyacetone phosphate. Biochemistry. 2001 Nov 20; 40(46):13868-75. PMID: 11705376.
    View in: PubMed
  82. Morais MC, Zhang W, Baker AS, Zhang G, Dunaway-Mariano D, Allen KN. The crystal structure of bacillus cereus phosphonoacetaldehyde hydrolase: insight into catalysis of phosphorus bond cleavage and catalytic diversification within the HAD enzyme superfamily. Biochemistry. 2000 Aug 29; 39(34):10385-96. PMID: 10956028.
    View in: PubMed
  83. Morais MC, Baker AS, Dunaway-Mariano D, Allen KN. Crystallization and preliminary crystallographic analysis of phosphonoacetaldehyde hydrolase. Acta Crystallogr D Biol Crystallogr. 2000 Feb; 56(Pt 2):206-9. PMID: 10666607.
    View in: PubMed
  84. Choi KH, Mazurkie AS, Morris AJ, Utheza D, Tolan DR, Allen KN. Structure of a fructose-1,6-bis(phosphate) aldolase liganded to its natural substrate in a cleavage-defective mutant at 2.3 A(,). Biochemistry. 1999 Sep 28; 38(39):12655-64. PMID: 10504235.
    View in: PubMed
  85. Choi KH, Laursen RA, Allen KN. The 2.1 A structure of a cysteine protease with proline specificity from ginger rhizome, Zingiber officinale. Biochemistry. 1999 Sep 7; 38(36):11624-33. PMID: 10512617.
    View in: PubMed
  86. Allen KN. Aspirin--now we can see it. Nat Med. 1995 Sep; 1(9):882-3. PMID: 7585209.
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  87. Allen KN, Lavie A, Petsko GA, Ringe D. Design, synthesis, and characterization of a potent xylose isomerase inhibitor, D-threonohydroxamic acid, and high-resolution X-ray crystallographic structure of the enzyme-inhibitor complex. Biochemistry. 1995 Mar 21; 34(11):3742-9. PMID: 7893671.
    View in: PubMed
  88. Lavie A, Allen KN, Petsko GA, Ringe D. X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis. Biochemistry. 1994 May 10; 33(18):5469-80. PMID: 8180169.
    View in: PubMed
  89. Allen KN, Lavie A, Farber GK, Glasfeld A, Petsko GA, Ringe D. Isotopic exchange plus substrate and inhibition kinetics of D-xylose isomerase do not support a proton-transfer mechanism. Biochemistry. 1994 Feb 15; 33(6):1481-7. PMID: 8312268.
    View in: PubMed
  90. Allen KN, Lavie A, Glasfeld A, Tanada TN, Gerrity DP, Carlson SC, Farber GK, Petsko GA, Ringe D. Role of the divalent metal ion in sugar binding, ring opening, and isomerization by D-xylose isomerase: replacement of a catalytic metal by an amino acid. Biochemistry. 1994 Feb 15; 33(6):1488-94. PMID: 7906142.
    View in: PubMed
  91. Allen KN, Abeles RH. Inhibition kinetics of acetylcholinesterase with fluoromethyl ketones. Biochemistry. 1989 Oct 17; 28(21):8466-73. PMID: 2605196.
    View in: PubMed
  92. Allen KN, Abeles RH. Inhibition of pig liver esterase by trifluoromethyl ketones: modulators of the catalytic reaction alter inhibition kinetics. Biochemistry. 1989 Jan 10; 28(1):135-40. PMID: 2706239.
    View in: PubMed
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