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Charles Craik, PhD

TitleProfessor
InstitutionUniversity of California San Francisco
DepartmentPharmaceutical Chemistry
Address600 16th St
San Francisco CA 94158
Phone415-476-8146
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    Collapse Biography 
    Collapse Awards and Honors
    National Honor Society1972  - 1975Alden Scholar
    Phi Beta Kappa1974  - 1975Doane Distinguished Scholar
    1975  - 1975Richard Edwin Lee Scholar
    The Amer. Assoc. for the Advan. of Science1978  - 1978Member, The Amer. Chem. Soc
    American Cancer Society 1982  - 1983Postdoctoral Fellow
    American Society of Biological Chemists1983  - 1983Member
    National Institutes of Health1983  - 1984Postdoctoral Fellow
    Science Digest1985  - 1986Top 100 Innovators
    BioTechniques1987  - 1997Editorial Board Member
    DNA1988  - 1988Editorial Board Member
    Protein Engineering1988  - 1988Associate Editor
    Applied Biocatalysis1989  - 1989Editorial Board Member
    Member, The Protein Society1989  - 1990Nominating Committee
    Sigma Xi1991  - 1994Distinguished Lecturer
    National Science Foundation Molecular Biochemistry1993  - 1996Advisory Panel
    Gordon Conference on Proteolytic Enzymes and Inhibitors1996  - 1996Vice Chair
    Gordon Conference on Proteolytic Enzymes and Inhibitors1998  - 1998Chair
    Cold Spring Harbor Meeting on the Biology of Proteolysis1997  - 1997Co-organizer
    Cold Spring Harbor Meeting on the Biology of Proteolysis1999  - 1999Co-organizer
    Cold Spring Harbor Meeting on the Biology of Proteolysis2001  - 2001Co-organizer
    Immunex Corporation (Seattle, WA)2000  - 2000POSH Lecturer
    United States Pharmacopeia2009Council of Experts
    Allegheney College (Meadville, PA)2010  - 2010Lord Lecturer
    American Association for the Advancement of Science2011  - 2011Fellow
    Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic2013  - 2013Institute Medal Lecture and Award

    Collapse Overview 
    Collapse Overview
    My research focuses on structure-function analysis of proteases and their inhibitors. In my lab we use a combination of genetic, biochemical, and biophysical methods, with particular emphasis on identifying the roles and regulating the activity of proteases associated with infectious diseases, cancer, and development.

    Proteases are directly or indirectly involved in virtually every biological function or dysfunction. The omnipresence of proteases and their natural inhibitors has placed them among the most studied proteins in biochemistry. The research efforts of the lab focus primarily on the structure-function analysis of proteases and their inhibitors using a combination of genetic, biochemical and biophysical methods. Chemical biological approaches are used or are being developed to study the substrate specificity, catalytic mechanism and biological role of proteases and their macromolecular inhibitors. The genes for serine (trypsin, serine collagenase, easter, prostate specific antigen, T-cell specific granzymes, MT-SP1 and 2, KSHV protease), cysteine (cruzain and falcipain) and aspartyl (HIV1 & HIV2 & SIV) proteases and macromolecular inhibitors such as ecotin and single chain antibodies are manipulated and expressed in heterologous expression systems. Targeted, region specific or random substitutions are introduced recombinantly to create variants that provide insight into the structure and activity of the target protein. A particular emphasis of our work is on identifying the roles and regulating the activity of proteases associated with infectious diseases, cancer and development. These studies are providing a better understanding of both the chemical make-up and the biological importance of these critical proteins. This in turn is leading to the development of strategies for regulating proteolytic activity as a means of therapeutic intervention. Further study of these proteins holds promise for better understanding, rapid detection and eventual control of infectious diseases and cancer.


    Collapse Research 
    Collapse Research Activities and Funding
    Mapping the conformational cycle of transmembrane transporters
    NIH/NIGMS P01GM111126Aug 1, 2015 - Jul 31, 2020
    Role: Co-Investigator
    Non-invasive Differentiation of Benign Lesions from Aggressive Pancreatic Cancer
    NIH/NCI R21CA185689Jan 1, 2015 - Dec 31, 2016
    Role: Principal Investigator
    Antibody Research Technology Center
    NIH/NCI P41CA196276Sep 24, 2014 - Aug 31, 2019
    Role: Co-Investigator
    Extracellular Proteolysis as a Molecular Stratification Tool for Cancer
    NIH/NCI R21CA186077Apr 1, 2014 - Mar 31, 2016
    Role: Principal Investigator
    Allosteric Inhibition of a Family of Proteolytic Enzymes
    NIH/NIGMS R01GM104659Jul 10, 2013 - Mar 31, 2017
    Role: Principal Investigator
    A Technological Platform for the Identification of Serine Proteases in Cancer
    NIH/NCI R01CA128765Jul 17, 2009 - Jun 30, 2014
    Role: Principal Investigator
    HARC Center: HIV Accessory and Regulatory Complexes
    NIH/NIGMS P50GM082250Aug 27, 2007 - Aug 31, 2022
    Role: Co-Investigator
    Targeting Allosteric Studies to Modulate Protein Interactions and Function
    NIH/NIAID R01AI067423Apr 17, 2007 - Mar 31, 2012
    Role: Principal Investigator
    Research Training in Chemistry and Chemical Biology
    NIH/NIGMS T32GM064337Jul 1, 2002 - Jun 30, 2022
    Role: Principal Investigator
    SFSU/UCSF Comprehensive Cancer Partnership Program
    NIH/NCI U56CA096216Jul 1, 2002 - Jun 30, 2010
    Role: Co-Investigator
    Structure Biology and Targeted Drug Design for AIDS
    NIH/NIGMS P01GM056531Sep 1, 1997 - Aug 31, 2007
    Role: Co-Investigator
    Proteases in Cancer Biology and Drug Development
    NIH/NCI P01CA072006Jun 10, 1997 - Jun 30, 2010
    Role: Co-Principal Investigator
    Targeting Cysteine Proteases: Antiparasitic Chemotherapy
    NIH P01AI035707May 1, 1995 - May 31, 2010
    Role: Co-Investigator
    STRUCTURAL BIOLOGY AND TARGETED DRUG DESIGN FOR AIDS
    NIH/NIGMS P01GM039552Sep 1, 1987 - Aug 31, 1997
    Role: Principal Investigator
    Bio-Organic Biomedical Mass Spectrometry Resource
    NIH P41RR001614Mar 1, 1982 - May 31, 2015
    Role: Co-Investigator
    Resource for Biocomputing, Visualization, and Informatics
    NIH/NCRR P41RR001081Jun 1, 1976 - Sep 14, 2012
    Role: Co-Investigator

    Collapse ORNG Applications 
    Collapse Global Health
    Collapse Websites
    Collapse In The News

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. Leontovyc A, Ulrychová L, O'Donoghue AJ, Vondrášek J, Marešová L, Hubálek M, Fajtová P, Chanová M, Jiang Z, Craik C, Caffrey CR, Mareš M, Dvorák J, Horn M. SmSP2: A serine protease secreted by the blood fluke pathogen Schistosoma mansoni with anti-hemostatic properties. PLoS Negl Trop Dis. 2018 Apr; 12(4):e0006446. PMID: 29677188.
      View in: PubMed
    2. Corvo I, Ferraro F, Merlino A, Zuberbühler K, O'Donoghue AJ, Pastro L, Pi-Denis N, Basika T, Roche L, McKerrow JH, Craik C, Caffrey CR, Tort JF. Substrate Specificity of Cysteine Proteases Beyond the S2 Pocket: Mutagenesis and Molecular Dynamics Investigation of Fasciola hepatica Cathepsins L. Front Mol Biosci. 2018; 5:40. PMID: 29725596.
      View in: PubMed
    3. Binning JM, Smith AM, Hultquist JF, Craik C, Caretta Cartozo N, Campbell MG, Burton L, La Greca F, McGregor MJ, Ta HM, Bartholomeeusen K, Peterlin BM, Krogan NJ, Sevillano N, Cheng Y, Gross JD. Fab-based inhibitors reveal ubiquitin independent functions for HIV Vif neutralization of APOBEC3 restriction factors. PLoS Pathog. 2018 Jan; 14(1):e1006830. PMID: 29304101.
      View in: PubMed
    4. Dang S, Feng S, Tien J, Peters CJ, Bulkley D, Lolicato M, Zhao J, Zuberbühler K, Ye W, Qi L, Chen T, Craik C, Jan YN, Minor DL, Cheng Y, Jan LY. Cryo-EM structures of the TMEM16A calcium-activated chloride channel. Nature. 2017 12 21; 552(7685):426-429. PMID: 29236684.
      View in: PubMed
    5. Ivry SL, Meyer NO, Winter MB, Bohn MF, Knudsen GM, O'Donoghue AJ, Craik C. Global substrate specificity profiling of post-translational modifying enzymes. Protein Sci. 2018 Mar; 27(3):584-594. PMID: 29168252.
      View in: PubMed
    6. Winter MB, La Greca F, Arastu-Kapur S, Caiazza F, Cimermancic P, Buchholz TJ, Anderl JL, Ravalin M, Bohn MF, Sali A, O'Donoghue AJ, Craik C. Immunoproteasome functions explained by divergence in cleavage specificity and regulation. Elife. 2017 Nov 28; 6. PMID: 29182146.
      View in: PubMed
    7. Isaac RS, Sanulli S, Tibble R, Hornsby M, Ravalin M, Craik C, Gross JD, Narlikar GJ. Biochemical Basis for Distinct Roles of the Heterochromatin Proteins Swi6 and Chp2. J Mol Biol. 2017 Nov 24; 429(23):3666-3677. PMID: 28942089.
      View in: PubMed
    8. Acker TM, Gable JE, Bohn MF, Jaishankar P, Thompson MC, Fraser JS, Renslo AR, Craik C. Allosteric Inhibitors, Crystallography, and Comparative Analysis Reveal Network of Coordinated Movement across Human Herpesvirus Proteases. J Am Chem Soc. 2017 Aug 30; 139(34):11650-11653. PMID: 28759216.
      View in: PubMed
    9. Wilkinson DJ, Habgood A, Lamb HK, Thompson P, Hawkins AR, Désilets A, Leduc R, Steinmetzer T, Hammami M, Lee MS, Craik C, Watson S, Lin H, Milner JM, Rowan AD. Matriptase Induction of Metalloproteinase-Dependent Aggrecanolysis In Vitro and In Vivo: Promotion of Osteoarthritic Cartilage Damage by Multiple Mechanisms. Arthritis Rheumatol. 2017 08; 69(8):1601-1611. PMID: 28464560.
      View in: PubMed
    10. Roncase EJ, Moon C, Chatterjee S, González-Páez GE, Craik C, O'Donoghue AJ, Wolan DW. Substrate Profiling and High Resolution Co-complex Crystal Structure of a Secreted C11 Protease Conserved across Commensal Bacteria. ACS Chem Biol. 2017 06 16; 12(6):1556-1565. PMID: 28414448.
      View in: PubMed
    11. Ivry SL, Sharib JM, Dominguez DA, Roy N, Hatcher SE, Yip-Schneider MT, Schmidt CM, Brand RE, Park WG, Hebrok M, Kim GE, O'Donoghue AJ, Kirkwood KS, Craik C. Global Protease Activity Profiling Provides Differential Diagnosis of Pancreatic Cysts. Clin Cancer Res. 2017 Aug 15; 23(16):4865-4874. PMID: 28424202.
      View in: PubMed
    12. Meyer NO, O'Donoghue AJ, Schulze-Gahmen U, Ravalin M, Moss SM, Winter MB, Knudsen GM, Craik C. Multiplex Substrate Profiling by Mass Spectrometry for Kinases as a Method for Revealing Quantitative Substrate Motifs. Anal Chem. 2017 Apr 18; 89(8):4550-4558. PMID: 28322550.
      View in: PubMed
    13. Clarke SC, Dumesic PA, Homer CM, O'Donoghue AJ, La Greca F, Pallova L, Majer P, Madhani HD, Craik C. Integrated Activity and Genetic Profiling of Secreted Peptidases in Cryptococcus neoformans Reveals an Aspartyl Peptidase Required for Low pH Survival and Virulence. PLoS Pathog. 2016 Dec; 12(12):e1006051. PMID: 27977806.
      View in: PubMed
    14. Barkan DT, Cheng XL, Celino H, Tran TT, Bhandari A, Craik C, Sali A, Smythe ML. Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23. BMC Bioinformatics. 2016 Nov 23; 17(1):481. PMID: 27881076.
      View in: PubMed
    15. Winter MB, Salcedo EC, Lohse MB, Hartooni N, Gulati M, Sanchez H, Takagi J, Hube B, Andes DR, Johnson AD, Craik C, Nobile CJ. Global Identification of Biofilm-Specific Proteolysis in Candida albicans. MBio. 2016 09 13; 7(5). PMID: 27624133; PMCID: PMC5021810.
    16. O'Donoghue AJ, Ivry SL, Chaudhury C, Hostetter DR, Hanahan D, Craik C. Procathepsin E is highly abundant but minimally active in pancreatic ductal adenocarcinoma tumors. Biol Chem. 2016 09 01; 397(9):871-81. PMID: 27149201.
      View in: PubMed
    17. Goupil LS, Ivry SL, Hsieh I, Suzuki BM, Craik C, O'Donoghue AJ, McKerrow JH. Cysteine and Aspartyl Proteases Contribute to Protein Digestion in the Gut of Freshwater Planaria. PLoS Negl Trop Dis. 2016 Aug; 10(8):e0004893. PMID: 27501047; PMCID: PMC4976874.
    18. Duan C, Alibakhshi MA, Kim DK, Brown CM, Craik C, Majumdar A. Label-Free Electrical Detection of Enzymatic Reactions in Nanochannels. ACS Nano. 2016 Aug 23; 10(8):7476-84. PMID: 27472431.
      View in: PubMed
    19. Lentz CS, Ordonez AA, Kasperkiewicz P, La Greca F, O'Donoghue AJ, Schulze CJ, Powers JC, Craik C, Drag M, Jain SK, Bogyo M. Design of Selective Substrates and Activity-Based Probes for Hydrolase Important for Pathogenesis 1 (HIP1) from Mycobacterium tuberculosis. ACS Infect Dis. 2016 Nov 11; 2(11):807-815. PMID: 27739665.
      View in: PubMed
    20. Homer CM, Summers DK, Goranov AI, Clarke SC, Wiesner DL, Diedrich JK, Moresco JJ, Toffaletti D, Upadhya R, Caradonna I, Petnic S, Pessino V, Cuomo CA, Lodge JK, Perfect J, Yates JR, Nielsen K, Craik C, Madhani HD. Intracellular Action of a Secreted Peptide Required for Fungal Virulence. Cell Host Microbe. 2016 Jun 08; 19(6):849-64. PMID: 27212659.
      View in: PubMed
    21. Le Gall SM, Szabo R, Lee M, Kirchhofer D, Craik C, Bugge TH, Camerer E. Matriptase activation connects tissue factor-dependent coagulation initiation to epithelial proteolysis and signaling. Blood. 2016 06 23; 127(25):3260-9. PMID: 27114461; PMCID: PMC4920024 [Available on 06/23/17].
    22. Drake CR, Sevillano N, Truillet C, Craik C, VanBrocklin HF, Evans MJ. Site-Specific Radiofluorination of Biomolecules with 8-[(18)F]-Fluorooctanoic Acid Catalyzed by Lipoic Acid Ligase. ACS Chem Biol. 2016 06 17; 11(6):1587-94. PMID: 27008570.
      View in: PubMed
    23. Julien O, Zhuang M, Wiita AP, O'Donoghue AJ, Knudsen GM, Craik C, Wells JA. Quantitative MS-based enzymology of caspases reveals distinct protein substrate specificities, hierarchies, and cellular roles. Proc Natl Acad Sci U S A. 2016 Apr 05; 113(14):E2001-10. PMID: 27006500; PMCID: PMC4833263 [Available on 10/05/16].
    24. Li H, O'Donoghue AJ, van der Linden WA, Xie SC, Yoo E, Foe IT, Tilley L, Craik C, da Fonseca PC, Bogyo M. Structure- and function-based design of Plasmodium-selective proteasome inhibitors. Nature. 2016 Feb 11; 530(7589):233-6. PMID: 26863983; PMCID: PMC4755332.
    25. Gable JE, Lee GM, Acker TM, Hulce KR, Gonzalez ER, Schweigler P, Melkko S, Farady CJ, Craik C. Fragment-Based Protein-Protein Interaction Antagonists of a Viral Dimeric Protease. ChemMedChem. 2016 Apr 19; 11(8):862-9. PMID: 26822284; PMCID: PMC4838516 [Available on 04/19/17].
    26. Bibo-Verdugo B, O'Donoghue AJ, Rojo-Arreola L, Craik C, García-Carreño F. Complementary Proteomic and Biochemical Analysis of Peptidases in Lobster Gastric Juice Uncovers the Functional Role of Individual Enzymes in Food Digestion. Mar Biotechnol (NY). 2016 Apr; 18(2):201-14. PMID: 26613762.
      View in: PubMed
    27. Jones SK, Clarke SC, Craik C, Bennett RJ. Evolutionary Selection on Barrier Activity: Bar1 Is an Aspartyl Protease with Novel Substrate Specificity. MBio. 2015 Nov 24; 6(6):e01604-15. PMID: 26604258; PMCID: PMC4669382.
    28. Wong KR, Menendez E, Craik C, Kavanaugh WM, Vasiljeva O. In vivo imaging of protease activity by Probody therapeutic activation. Biochimie. 2016 Mar; 122:62-7. PMID: 26546838.
      View in: PubMed
    29. Page MJ, Lourenço AL, David T, LeBeau AM, Cattaruzza F, Castro HC, VanBrocklin HF, Coughlin SR, Craik C. Non-invasive imaging and cellular tracking of pulmonary emboli by near-infrared fluorescence and positron-emission tomography. Nat Commun. 2015 Oct 01; 6:8448. PMID: 26423607; PMCID: PMC4593073.
    30. Dvorák J, Fajtová P, Ulrychová L, Leontovyc A, Rojo-Arreola L, Suzuki BM, Horn M, Mareš M, Craik C, Caffrey CR, O'Donoghue AJ. Excretion/secretion products from Schistosoma mansoni adults, eggs and schistosomula have unique peptidase specificity profiles. Biochimie. 2016 Mar; 122:99-109. PMID: 26409899; PMCID: PMC4747843 [Available on 03/01/17].
    31. O'Donoghue AJ, Knudsen GM, Beekman C, Perry JA, Johnson AD, DeRisi JL, Craik C, Bennett RJ. Destructin-1 is a collagen-degrading endopeptidase secreted by Pseudogymnoascus destructans, the causative agent of white-nose syndrome. Proc Natl Acad Sci U S A. 2015 Jun 16; 112(24):7478-83. PMID: 25944934.
      View in: PubMed
    32. Wermelinger LS, Frattani FS, Carneiro-Lobo TC, Craik C, Castro HC, Zingali RB. Ecotin: Exploring a feasible antithrombotic profile. Int J Biol Macromol. 2015 Jul; 78:296-303. PMID: 25881959.
      View in: PubMed
    33. LeBeau AM, Sevillano N, Markham K, Winter MB, Murphy ST, Hostetter DR, West J, Lowman H, Craik C, VanBrocklin HF. Imaging active urokinase plasminogen activator in prostate cancer. Cancer Res. 2015 Apr 01; 75(7):1225-35. PMID: 25672980; PMCID: PMC4383704.
    34. Sharma V, Panwar P, O'Donoghue AJ, Cui H, Guido RV, Craik C, Brömme D. Structural requirements for the collagenase and elastase activity of cathepsin K and its selective inhibition by an exosite inhibitor. Biochem J. 2015 Jan 01; 465(1):163-73. PMID: 25279554.
      View in: PubMed
    35. Kim J, Wu S, Tomasiak TM, Mergel C, Winter MB, Stiller SB, Robles-Colmanares Y, Stroud RM, Tampé R, Craik C, Cheng Y. Subnanometre-resolution electron cryomicroscopy structure of a heterodimeric ABC exporter. Nature. 2015 Jan 15; 517(7534):396-400. PMID: 25363761; PMCID: PMC4372080.
    36. Skala W, Utzschneider DT, Magdolen V, Debela M, Guo S, Craik C, Brandstetter H, Goettig P. Structure-function analyses of human kallikrein-related peptidase 2 establish the 99-loop as master regulator of activity. J Biol Chem. 2014 Dec 05; 289(49):34267-83. PMID: 25326387; PMCID: PMC4256358.
    37. Mahon C, Krogan NJ, Craik C, Pick E. Cullin E3 ligases and their rewiring by viral factors. Biomolecules. 2014 Oct 13; 4(4):897-930. PMID: 25314029; PMCID: PMC4279162.
    38. Gable JE, Acker TM, Craik C. Current and potential treatments for ubiquitous but neglected herpesvirus infections. Chem Rev. 2014 Nov 26; 114(22):11382-412. PMID: 25275644; PMCID: PMC4254030.
    39. Tajon CA, Seo D, Asmussen J, Shah N, Jun YW, Craik C. Sensitive and selective plasmon ruler nanosensors for monitoring the apoptotic drug response in leukemia. ACS Nano. 2014 Sep 23; 8(9):9199-208. PMID: 25166742; PMCID: PMC4174091.
    40. Lucas JM, Heinlein C, Kim T, Hernandez SA, Malik MS, True LD, Morrissey C, Corey E, Montgomery B, Mostaghel E, Clegg N, Coleman I, Brown CM, Schneider EL, Craik C, Simon JA, Bedalov A, Nelson PS. The androgen-regulated protease TMPRSS2 activates a proteolytic cascade involving components of the tumor microenvironment and promotes prostate cancer metastasis. Cancer Discov. 2014 Nov; 4(11):1310-25. PMID: 25122198; PMCID: PMC4409786.
    41. Gable JE, Lee GM, Jaishankar P, Hearn BR, Waddling CA, Renslo AR, Craik C. Broad-spectrum allosteric inhibition of herpesvirus proteases. Biochemistry. 2014 Jul 22; 53(28):4648-60. PMID: 24977643; PMCID: PMC4108181.
    42. Grove LM, Southern BD, Jin TH, White KE, Paruchuri S, Harel E, Wei Y, Rahaman SO, Gladson CL, Ding Q, Craik C, Chapman HA, Olman MA. Urokinase-type plasminogen activator receptor (uPAR) ligation induces a raft-localized integrin signaling switch that mediates the hypermotile phenotype of fibrotic fibroblasts. J Biol Chem. 2014 May 02; 289(18):12791-804. PMID: 24644284; PMCID: PMC4007467.
    43. LeBeau AM, Sevillano N, King ML, Duriseti S, Murphy ST, Craik C, Murphy LL, VanBrocklin HF. Imaging the urokinase plasminongen activator receptor in preclinical breast cancer models of acquired drug resistance. Theranostics. 2014; 4(3):267-79. PMID: 24505235; PMCID: PMC3915090.
    44. Tajon C, Jun YW, Craik C. Single-molecule sensing of caspase activation in live cells via plasmon coupling nanotechnology. Methods Enzymol. 2014; 544:271-97. PMID: 24974294.
      View in: PubMed
    45. Asmussen J, Lasater EA, Tajon C, Oses-Prieto J, Jun YW, Taylor BS, Burlingame A, Craik C, Shah NP. MEK-dependent negative feedback underlies BCR-ABL-mediated oncogene addiction. Cancer Discov. 2014 Feb; 4(2):200-15. PMID: 24362263; PMCID: PMC4248023.
    46. Du X, Chen NL, Wong A, Craik C, Brömme D. Elastin degradation by cathepsin V requires two exosites. J Biol Chem. 2013 Nov 29; 288(48):34871-81. PMID: 24121514; PMCID: PMC3843099.
    47. O'Donoghue AJ, Jin Y, Knudsen GM, Perera NC, Jenne DE, Murphy JE, Craik C, Hermiston TW. Global substrate profiling of proteases in human neutrophil extracellular traps reveals consensus motif predominantly contributed by elastase. PLoS One. 2013; 8(9):e75141. PMID: 24073241; PMCID: PMC3779220.
    48. Corvo I, O'Donoghue AJ, Pastro L, Pi-Denis N, Eroy-Reveles A, Roche L, McKerrow JH, Dalton JP, Craik C, Caffrey CR, Tort JF. Dissecting the active site of the collagenolytic cathepsin L3 protease of the invasive stage of Fasciola hepatica. PLoS Negl Trop Dis. 2013; 7(7):e2269. PMID: 23875031; PMCID: PMC3708847.
    49. Small JL, O'Donoghue AJ, Boritsch EC, Tsodikov OV, Knudsen GM, Vandal O, Craik C, Ehrt S. Substrate specificity of MarP, a periplasmic protease required for resistance to acid and oxidative stress in Mycobacterium tuberculosis. J Biol Chem. 2013 May 03; 288(18):12489-99. PMID: 23504313; PMCID: PMC3642297.
    50. Raman K, Trivedi NN, Raymond WW, Ganesan R, Kirchhofer D, Verghese GM, Craik C, Schneider EL, Nimishakavi S, Caughey GH. Mutational tail loss is an evolutionary mechanism for liberating marapsins and other type I serine proteases from transmembrane anchors. J Biol Chem. 2013 Apr 12; 288(15):10588-98. PMID: 23447538; PMCID: PMC3624440.
    51. LeBeau AM, Duriseti S, Murphy ST, Pepin F, Hann B, Gray JW, VanBrocklin HF, Craik C. Targeting uPAR with antagonistic recombinant human antibodies in aggressive breast cancer. Cancer Res. 2013 Apr 01; 73(7):2070-81. PMID: 23400595; PMCID: PMC3618559.
    52. LeBeau AM, Lee M, Murphy ST, Hann BC, Warren RS, Delos Santos R, Kurhanewicz J, Hanash SM, VanBrocklin HF, Craik C. Imaging a functional tumorigenic biomarker in the transformed epithelium. Proc Natl Acad Sci U S A. 2013 Jan 02; 110(1):93-8. PMID: 23248318; PMCID: PMC3538269.
    53. Lee GM, Balouch E, Goetz DH, Lazic A, McKerrow JH, Craik C. Mapping inhibitor binding modes on an active cysteine protease via nuclear magnetic resonance spectroscopy. Biochemistry. 2012 Dec 18; 51(50):10087-98. PMID: 23181936; PMCID: PMC3566641.
    54. O'Donoghue AJ, Eroy-Reveles AA, Knudsen GM, Ingram J, Zhou M, Statnekov JB, Greninger AL, Hostetter DR, Qu G, Maltby DA, Anderson MO, Derisi JL, McKerrow JH, Burlingame AL, Craik C. Global identification of peptidase specificity by multiplex substrate profiling. Nat Methods. 2012 Nov; 9(11):1095-100. PMID: 23023596; PMCID: PMC3707110.
    55. Nimishakavi S, Besprozvannaya M, Raymond WW, Craik C, Gruenert DC, Caughey GH. Activity and inhibition of prostasin and matriptase on apical and basolateral surfaces of human airway epithelial cells. Am J Physiol Lung Cell Mol Physiol. 2012 Jul; 303(2):L97-106. PMID: 22582115; PMCID: PMC3404626.
    56. Sojka D, Franta Z, Frantová H, Bartosová P, Horn M, Váchová J, O'Donoghue AJ, Eroy-Reveles AA, Craik C, Knudsen GM, Caffrey CR, McKerrow JH, Mares M, Kopácek P. Characterization of gut-associated cathepsin D hemoglobinase from tick Ixodes ricinus (IrCD1). J Biol Chem. 2012 Jun 15; 287(25):21152-63. PMID: 22539347; PMCID: PMC3375538.
    57. Wu S, Avila-Sakar A, Kim J, Booth DS, Greenberg CH, Rossi A, Liao M, Li X, Alian A, Griner SL, Juge N, Yu Y, Mergel CM, Chaparro-Riggers J, Strop P, Tampé R, Edwards RH, Stroud RM, Craik C, Cheng Y. Fabs enable single particle cryoEM studies of small proteins. Structure. 2012 Apr 04; 20(4):582-92. PMID: 22483106; PMCID: PMC3322386.
    58. Ingram JR, Rafi SB, Eroy-Reveles AA, Ray M, Lambeth L, Hsieh I, Ruelas D, Lim KC, Sakanari J, Craik C, Jacobson MP, McKerrow JH. Investigation of the proteolytic functions of an expanded cercarial elastase gene family in Schistosoma mansoni. PLoS Negl Trop Dis. 2012; 6(4):e1589. PMID: 22509414; PMCID: PMC3317910.
    59. Norbury LJ, Hung A, Beckham S, Pike RN, Spithill TW, Craik C, Choe Y, Fecondo JV, Smooker PM. Analysis of Fasciola cathepsin L5 by S2 subsite substitutions and determination of the P1-P4 specificity reveals an unusual preference. Biochimie. 2012 May; 94(5):1119-27. PMID: 22285967.
      View in: PubMed
    60. Craik C, Shahian T. A screening strategy for trapping the inactive conformer of a dimeric enzyme with a small molecule inhibitor. Methods Mol Biol. 2012; 928:119-31. PMID: 22956137; PMCID: PMC3739972.
    61. Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik C, Burlingame A, Sali A, Frankel AD, Krogan NJ. Global landscape of HIV-human protein complexes. Nature. 2011 Dec 21; 481(7381):365-70. PMID: 22190034; PMCID: PMC3310911.
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    74. Swenerton RK, Zhang S, Sajid M, Medzihradszky KF, Craik C, Kelly BL, McKerrow JH. The oligopeptidase B of Leishmania regulates parasite enolase and immune evasion. J Biol Chem. 2011 Jan 07; 286(1):429-40. PMID: 20961853; PMCID: PMC3013002.
    75. Na BK, Bae YA, Zo YG, Choe Y, Kim SH, Desai PV, Avery MA, Craik C, Kim TS, Rosenthal PJ, Kong Y. Biochemical properties of a novel cysteine protease of Plasmodium vivax, vivapain-4. PLoS Negl Trop Dis. 2010 Oct 12; 4(10):e849. PMID: 20967286; PMCID: PMC2953480.
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    77. Cruz CE, Fogaça AC, Nakayasu ES, Angeli CB, Belmonte R, Almeida IC, Miranda A, Miranda MT, Tanaka AS, Braz GR, Craik C, Schneider E, Caffrey CR, Daffre S. Characterization of proteinases from the midgut of Rhipicephalus (Boophilus) microplus involved in the generation of antimicrobial peptides. Parasit Vectors. 2010 Jul 27; 3:63. PMID: 20663211; PMCID: PMC2921360.
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    79. Duriseti S, Goetz DH, Hostetter DR, LeBeau AM, Wei Y, Craik C. Antagonistic anti-urokinase plasminogen activator receptor (uPAR) antibodies significantly inhibit uPAR-mediated cellular signaling and migration. J Biol Chem. 2010 Aug 27; 285(35):26878-88. PMID: 20501655; PMCID: PMC2930687.
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    81. LeBeau AM, Kostova M, Craik C, Denmeade SR. Prostate-specific antigen: an overlooked candidate for the targeted treatment and selective imaging of prostate cancer. Biol Chem. 2010 Apr; 391(4):333-43. PMID: 20180648; PMCID: PMC3454521.
    82. Stoop AA, Joshi RV, Eggers CT, Craik C. Analysis of an engineered plasma kallikrein inhibitor and its effect on contact activation. Biol Chem. 2010 Apr; 391(4):425-33. PMID: 20180651.
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    84. Sun C, Su KH, Valentine J, Rosa-Bauza YT, Ellman JA, Elboudwarej O, Mukherjee B, Craik C, Shuman MA, Chen FF, Zhang X. Time-resolved single-step protease activity quantification using nanoplasmonic resonator sensors. ACS Nano. 2010 Feb 23; 4(2):978-84. PMID: 20121209; PMCID: PMC2884196.
    85. Darragh MR, Schneider EL, Lou J, Phojanakong PJ, Farady CJ, Marks JD, Hann BC, Craik C. Tumor detection by imaging proteolytic activity. Cancer Res. 2010 Feb 15; 70(4):1505-12. PMID: 20145119; PMCID: PMC2823079.
    86. Camerer E, Barker A, Duong DN, Ganesan R, Kataoka H, Cornelissen I, Darragh MR, Hussain A, Zheng YW, Srinivasan Y, Brown C, Xu SM, Regard JB, Lin CY, Craik C, Kirchhofer D, Coughlin SR. Local protease signaling contributes to neural tube closure in the mouse embryo. Dev Cell. 2010 Jan 19; 18(1):25-38. PMID: 20152175; PMCID: PMC2822780.
    87. Jun YW, Sheikholeslami S, Hostetter DR, Tajon C, Craik C, Alivisatos AP. Continuous imaging of plasmon rulers in live cells reveals early-stage caspase-3 activation at the single-molecule level. Proc Natl Acad Sci U S A. 2009 Oct 20; 106(42):17735-40. PMID: 19805121; PMCID: PMC2764940.
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    90. Kerr ID, Lee JH, Farady CJ, Marion R, Rickert M, Sajid M, Pandey KC, Caffrey CR, Legac J, Hansell E, McKerrow JH, Craik C, Rosenthal PJ, Brinen LS. Vinyl sulfones as antiparasitic agents and a structural basis for drug design. J Biol Chem. 2009 Sep 18; 284(38):25697-703. PMID: 19620707; PMCID: PMC2757971.
    91. Mahon CS, O'Donoghue AJ, Goetz DH, Murray PG, Craik C, Tuohy MG. Characterization of a multimeric, eukaryotic prolyl aminopeptidase: an inducible and highly specific intracellular peptidase from the non-pathogenic fungus Talaromyces emersonii. Microbiology. 2009 Nov; 155(Pt 11):3673-82. PMID: 19556294; PMCID: PMC2888130.
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    97. Lilla JN, Joshi RV, Craik C, Werb Z. Active plasma kallikrein localizes to mast cells and regulates epithelial cell apoptosis, adipocyte differentiation, and stromal remodeling during mammary gland involution. J Biol Chem. 2009 May 15; 284(20):13792-803. PMID: 19297327; PMCID: PMC2679480.
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    128. Bhatt AS, Erdjument-Bromage H, Tempst P, Craik C, Moasser MM. Adhesion signaling by a novel mitotic substrate of src kinases. Oncogene. 2005 Aug 11; 24(34):5333-43. PMID: 16007225; PMCID: PMC3023961.
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    140. Na BK, Shenai BR, Sijwali PS, Choe Y, Pandey KC, Singh A, Craik C, Rosenthal PJ. Identification and biochemical characterization of vivapains, cysteine proteases of the malaria parasite Plasmodium vivax. Biochem J. 2004 Mar 01; 378(Pt 2):529-38. PMID: 14629194; PMCID: PMC1223978.
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    148. Mackewicz CE, Craik C, Levy JA. The CD8+ cell noncytotoxic anti-HIV response can be blocked by protease inhibitors. Proc Natl Acad Sci U S A. 2003 Mar 18; 100(6):3433-8. PMID: 12624186; PMCID: PMC152310.
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    153. Singh A, Shenai BR, Choe Y, Gut J, Sijwali PS, Craik C, Rosenthal PJ. Critical role of amino acid 23 in mediating activity and specificity of vinckepain-2, a papain-family cysteine protease of rodent malaria parasites. Biochem J. 2002 Nov 15; 368(Pt 1):273-81. PMID: 12169096; PMCID: PMC1222974.
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    155. Lecaille F, Choe Y, Brandt W, Li Z, Craik C, Brömme D. Selective inhibition of the collagenolytic activity of human cathepsin K by altering its S2 subsite specificity. Biochemistry. 2002 Jul 02; 41(26):8447-54. PMID: 12081494.
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    156. Salter JP, Choe Y, Albrecht H, Franklin C, Lim KC, Craik C, McKerrow JH. Cercarial elastase is encoded by a functionally conserved gene family across multiple species of schistosomes. J Biol Chem. 2002 Jul 05; 277(27):24618-24. PMID: 11986325.
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    157. Mathieu MA, Bogyo M, Caffrey CR, Choe Y, Lee J, Chapman H, Sajid M, Craik C, McKerrow JH. Substrate specificity of schistosome versus human legumain determined by P1-P3 peptide libraries. Mol Biochem Parasitol. 2002 Apr 30; 121(1):99-105. PMID: 11985866.
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    158. Laboissière MC, Young MM, Pinho RG, Todd S, Fletterick RJ, Kuntz I, Craik C. Computer-assisted mutagenesis of ecotin to engineer its secondary binding site for urokinase inhibition. J Biol Chem. 2002 Jul 19; 277(29):26623-31. PMID: 11959867.
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    159. Reiling KK, Endres NF, Dauber DS, Craik C, Stroud RM. Anisotropic dynamics of the JE-2147-HIV protease complex: drug resistance and thermodynamic binding mode examined in a 1.09 A structure. Biochemistry. 2002 Apr 09; 41(14):4582-94. PMID: 11926820.
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    161. Maly DJ, Leonetti F, Backes BJ, Dauber DS, Harris JL, Craik C, Ellman JA. Expedient solid-phase synthesis of fluorogenic protease substrates using the 7-amino-4-carbamoylmethylcoumarin (ACC) fluorophore. J Org Chem. 2002 Feb 08; 67(3):910-5. PMID: 11856036.
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    162. Pray TR, Reiling KK, Demirjian BG, Craik C. Conformational change coupling the dimerization and activation of KSHV protease. Biochemistry. 2002 Feb 05; 41(5):1474-82. PMID: 11814340.
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    163. Dauber DS, Ziermann R, Parkin N, Maly DJ, Mahrus S, Harris JL, Ellman JA, Petropoulos C, Craik C. Altered substrate specificity of drug-resistant human immunodeficiency virus type 1 protease. J Virol. 2002 Feb; 76(3):1359-68. PMID: 11773410; PMCID: PMC135855.
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    165. K.K. Reiling, T.R. Pray, C.S. Craik, R.M. Stroud. Structure: Regulation of Activity and Dimerization by Conserved Structural Elements. Biochemistry.2000; 24:12796-803 .
    166. T.T. Baird Jr., B. Wang, M. Lodder, S.M. Hecht and C.S. Craik. Generation of Active Trypsin by Chemical Cleavage. Tetrahedron Letters.2000; 556:9477-9485 .
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    169. S. Halfon & C.S. Craik. Regulation of Proteolytic Activity by Engineered Tridentate Metal Binding Loops. J. Am. Chem. Soc. 118.1996; 1227-1228 .
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    174. A.E. Eakin, J.H. McKerrow & C.S.Craik. A Cysteine Protease is a Target for the Enzyme Structure-based Design of Antiparasitic Drugs. Drug Information Journal 29.1995; 29:1501S-1517S.
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    176. J.J. Perona, C.A. Tsu, M.E. McGrath, C.S. Craik & R.J. Fletterick. Relocating a Negative Charge in the Binding Pocket of Trypsin. J. Mol. Bio. 230.1993; 934-949.
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    181. Z. Sui, R. Salto, C.S. Craik, P. Ortiz de Montellano. Inhibition of the HIV1 and the HIV2 Proteases by Curcumin and Curcumin Boron Complexes. Bioorg. & Med. Chem. Let. 1 .1993; 415-422 .
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    196. T.L. Burgess, C.S. Craik, L. Matsuuchi & R.B. Kelly. In Vitro Mutagenesis of Trypsinogen: The Role of the N-Terminus in Intracellular Protein Targeting to Secretory Granules. J. Cell Bio. 105, 659-668 .1987.
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