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    Elizabeth Komives

    TitleProfessor
    SchoolUniversity of California, San Diego
    DepartmentChemistry and Biochemistry
    Address9500 Gilman Drive #0378
    CA La Jolla 92093
    Phone858-534-3058
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      Collapse Research 
      Collapse Research Activities and Funding
      Acquisition of an Orbitrap Elite with ETD
      NIH S10OD021724Apr 15, 2016 - Apr 14, 2017
      Role: Principal Investigator
      Functional Dynamics of Thrombin
      NIH/NHLBI R01HL127041Jan 15, 2016 - Dec 31, 2019
      Role: Principal Investigator
      Synapt G2-S System with HXMS Automation
      NIH S10OD016234Sep 1, 2013 - Aug 31, 2014
      Role: Principal Investigator
      2D Nano-flow Mass Spectrometry System
      NIH/NCRR S10RR022420Jul 1, 2006 - Jun 30, 2007
      Role: Principal Investigator
      IkB/NF-kB Recognition in Silico, In Vitro and In Vivo
      NIH/NIGMS P01GM071862Apr 7, 2006 - Feb 28, 2017
      Role: Principal Investigator
      Acquisition of an MALDI TOF-TOF Mass Spectrometer
      NIH/NCRR S10RR019897Jun 1, 2005 - May 31, 2006
      Role: Principal Investigator
      Directed Proteomics of Alzheimer's Related Proteins
      NIH/NIA R01AG025343Sep 30, 2004 - Aug 31, 2009
      Role: Principal Investigator
      The Thrombin-Thrombomodulin Interaction
      NIH/NHLBI R01HL070999Jul 1, 2002 - Feb 28, 2014
      Role: Principal Investigator
      DETECTION AND MODELS OF TOXICANT EXPOSURE
      NIH/NIEHS P42ES010337Jul 1, 2000 - Mar 31, 2022
      Role: Co-Investigator
      BIOPHYSICAL STUDIES OF LRP LIGANDS INTERACTIONS
      NIH/NIA R01AG017992Apr 1, 2000 - Mar 31, 2005
      Role: Principal Investigator
      AQUISITION OF A MALDI TOF DE STR MASS SPECTROMETER
      NIH/NCRR S10RR013800Apr 15, 1999 - Apr 14, 2000
      Role: Principal Investigator
      NMR STUDIES OF MEMBRANE ASSOCIATED PEPTIDES AND PROTEINS
      NIH/NIGMS R01GM054034May 1, 1997 - Apr 30, 2001
      Role: Principal Investigator
      BIOPHYSICAL STUDIES OF THROMBOMODULIN EGF DOMAINS
      NIH/NHLBI R01HL047463Feb 1, 1992 - Aug 31, 2002
      Role: Principal Investigator
      BIOPHYSICAL STUDIES OF THROMBOMODULIN EGF DOMAINS
      NIH/NHLBI R29HL047463Feb 1, 1992 - Sep 29, 1996
      Role: Principal Investigator
      UNIVERSITY OF CALIFORNIA, SAN DIEGO MBRS PROGRAM
      NIH S06GM047165Sep 20, 1991 - Apr 30, 2000
      Role: Co-Investigator
      MOLECULAR BIOPHYSICS TRAINING PROGRAM
      NIH/NIGMS T32GM008326Jul 1, 1989 - Jun 30, 2021
      Role: Principal Investigator
      MECHANISM OF 3-DEOXYHEPTULOSONATE-7-PHOSPHATE SYNTHASE
      NIH/NIGMS F32GM011545Mar 16, 1987
      Role: Principal Investigator
      National Biomedical NMR Resource at Madison
      NIH P41RR002301Jul 1, 1985 - Feb 28, 2015
      Role: Co-Investigator
      HEMOGLOBIN and BLOOD PROTEIN CHEMISTRY
      NIH/NIDDK T32DK007233Jul 1, 1976 - Aug 31, 2013
      Role: Principal Investigator

      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. Kromann-Hansen T, Louise Lange E, Peter Sørensen H, Hassanzadeh-Ghassabeh G, Huang M, Jensen JK, Muyldermans S, Declerck PJ, Komives E, Andreasen PA. Discovery of a novel conformational equilibrium in urokinase-type plasminogen activator. Sci Rep. 2017 Jun 13; 7(1):3385. PMID: 28611361.
        View in: PubMed
      2. Carvajal AI, Vallejos G, Komives E, Castro-Fernández V, Leonardo DA, Garratt RC, Ramírez-Sarmiento CA, Babul J. Unusual dimerization of a BcCsp mutant leads to reduced conformational dynamics. FEBS J. 2017 Jun; 284(12):1882-1896. PMID: 28457014.
        View in: PubMed
      3. Dembinski HE, Wismer K, Vargas JD, Suryawanshi GW, Kern N, Kroon G, Dyson HJ, Hoffmann A, Komives E. Functional importance of stripping in NF?B signaling revealed by a stripping-impaired I?Ba mutant. Proc Natl Acad Sci U S A. 2017 Feb 21; 114(8):1916-1921. PMID: 28167786.
        View in: PubMed
      4. Handley LD, Fuglestad B, Stearns K, Tonelli M, Fenwick RB, Markwick PR, Komives E. NMR reveals a dynamic allosteric pathway in thrombin. Sci Rep. 2017 Jan 06; 7:39575. PMID: 28059082.
        View in: PubMed
      5. Schiffer JM, Malmstrom RD, Parnell J, Ramirez-Sarmiento C, Reyes J, Amaro RE, Komives E. Model of the Ankyrin and SOCS Box Protein, ASB9, E3 Ligase Reveals a Mechanism for Dynamic Ubiquitin Transfer. Structure. 2016 Aug 02; 24(8):1248-56. PMID: 27396830; PMCID: PMC4972691 [Available on 08/02/17].
        View in: PubMed, PubMed Central
      6. Medina E, Córdova C, Villalobos P, Reyes J, Komives E, Ramírez-Sarmiento CA, Babul J. Three-Dimensional Domain Swapping Changes the Folding Mechanism of the Forkhead Domain of FoxP1. Biophys J. 2016 Jun 07; 110(11):2349-2360. PMID: 27276253; PMCID: PMC4922571 [Available on 06/07/17].
        View in: PubMed, PubMed Central
      7. Mukherjee SP, Quintas PO, McNulty R, Komives E, Dyson HJ. Structural characterization of the ternary complex that mediates termination of NF-?B signaling by I?Ba. Proc Natl Acad Sci U S A. 2016 May 31; 113(22):6212-7. PMID: 27185953; PMCID: PMC4896678 [Available on 11/30/16].
        View in: PubMed, PubMed Central
      8. Trelle MB, Ramsey KM, Lee TC, Zheng W, Lamboy J, Wolynes PG, Deniz A, Komives E. Binding of NF?B Appears to Twist the Ankyrin Repeat Domain of I?Ba. Biophys J. 2016 Feb 23; 110(4):887-95. PMID: 26910425; PMCID: PMC4776026 [Available on 02/23/17].
        View in: PubMed, PubMed Central
      9. Potoyan DA, Zheng W, Komives E, Wolynes PG. Molecular stripping in the NF-?B/I?B/DNA genetic regulatory network. Proc Natl Acad Sci U S A. 2016 Jan 05; 113(1):110-5. PMID: 26699500; PMCID: PMC4711861.
        View in: PubMed, PubMed Central
      10. Handley LD, Treuheit NA, Venkatesh VJ, Komives E. Thrombomodulin Binding Selects the Catalytically Active Form of Thrombin. Biochemistry. 2015 Nov 03; 54(43):6650-8. PMID: 26468766; PMCID: PMC4697735 [Available on 11/03/16].
        View in: PubMed, PubMed Central
      11. Ramírez-Sarmiento CA, Baez M, Zamora RA, Balasubramaniam D, Babul J, Komives E, Guixé V. The folding unit of phosphofructokinase-2 as defined by the biophysical properties of a monomeric mutant. Biophys J. 2015 May 05; 108(9):2350-61. PMID: 25954892; PMCID: PMC4423062.
        View in: PubMed, PubMed Central
      12. Mangas I, Taylor P, Vilanova E, Estévez J, França TC, Komives E, Radic Z. Resolving pathways of interaction of mipafox and a sarin analog with human acetylcholinesterase by kinetics, mass spectrometry and molecular modeling approaches. Arch Toxicol. 2016 Mar; 90(3):603-16. PMID: 25743373; PMCID: PMC4833118.
        View in: PubMed, PubMed Central
      13. Balasubramaniam D, Schiffer J, Parnell J, Mir SP, Amaro RE, Komives E. How the ankyrin and SOCS box protein, ASB9, binds to creatine kinase. Biochemistry. 2015 Mar 03; 54(8):1673-80. PMID: 25654263; PMCID: PMC4348336.
        View in: PubMed, PubMed Central
      14. Ferreiro DU, Komives E, Wolynes PG. Frustration in biomolecules. Q Rev Biophys. 2014 Nov; 47(4):285-363. PMID: 25225856; PMCID: PMC4256721.
        View in: PubMed, PubMed Central
      15. Boechi L, Pierce L, Komives E, McCammon JA. Trypsinogen activation as observed in accelerated molecular dynamics simulations. Protein Sci. 2014 Nov; 23(11):1550-8. PMID: 25131668; PMCID: PMC4241106.
        View in: PubMed, PubMed Central
      16. Perera VR, Newton GL, Parnell JM, Komives E, Pogliano K. Purification and characterization of the Staphylococcus aureus bacillithiol transferase BstA. Biochim Biophys Acta. 2014 Sep; 1840(9):2851-61. PMID: 24821014; PMCID: PMC4802972.
        View in: PubMed, PubMed Central
      17. Balasubramaniam D, Komives E. The phylogenetics of dynamics in DNA clamp proteins. Structure. 2014 Apr 08; 22(4):511-2. PMID: 24717558.
        View in: PubMed
      18. Dembinski H, Wismer K, Balasubramaniam D, Gonzalez HA, Alverdi V, Iakoucheva LM, Komives E. Predicted disorder-to-order transition mutations in I?Ba disrupt function. Phys Chem Chem Phys. 2014 Apr 14; 16(14):6480-5. PMID: 24605363; PMCID: PMC4040282.
        View in: PubMed, PubMed Central
      19. Meyer JG, Kim S, Maltby DA, Ghassemian M, Bandeira N, Komives E. Expanding proteome coverage with orthogonal-specificity a-lytic proteases. Mol Cell Proteomics. 2014 Mar; 13(3):823-35. PMID: 24425750; PMCID: PMC3945911.
        View in: PubMed, PubMed Central
      20. Alverdi V, Hetrick B, Joseph S, Komives E. Direct observation of a transient ternary complex during I?Ba-mediated dissociation of NF-?B from DNA. Proc Natl Acad Sci U S A. 2014 Jan 07; 111(1):225-30. PMID: 24367071; PMCID: PMC3890772.
        View in: PubMed, PubMed Central
      21. Li N, Stein RS, He W, Komives E, Wang W. Identification of methyllysine peptides binding to chromobox protein homolog 6 chromodomain in the human proteome. Mol Cell Proteomics. 2013 Oct; 12(10):2750-60. PMID: 23842000; PMCID: PMC3790288.
        View in: PubMed, PubMed Central
      22. Fuglestad B, Gasper PM, McCammon JA, Markwick PR, Komives E. Correlated motions and residual frustration in thrombin. J Phys Chem B. 2013 Oct 24; 117(42):12857-63. PMID: 23621631; PMCID: PMC3808083.
        View in: PubMed, PubMed Central
      23. Ramírez-Sarmiento CA, Baez M, Wilson CA, Babul J, Komives E, Guixé V. Observation of solvent penetration during cold denaturation of E. coli phosphofructokinase-2. Biophys J. 2013 May 21; 104(10):2254-63. PMID: 23708365; PMCID: PMC3660636.
        View in: PubMed, PubMed Central
      24. Lamboy JA, Kim H, Dembinski H, Ha T, Komives E. Single-molecule FRET reveals the native-state dynamics of the I?Ba ankyrin repeat domain. J Mol Biol. 2013 Jul 24; 425(14):2578-90. PMID: 23619335; PMCID: PMC3758917.
        View in: PubMed, PubMed Central
      25. Stein RS, Li N, He W, Komives E, Wang W. Recognition of methylated peptides by Drosophila melanogaster polycomb chromodomain. J Proteome Res. 2013 Mar 01; 12(3):1467-77. PMID: 23320494; PMCID: PMC4258113.
        View in: PubMed, PubMed Central
      26. Schafer NP, Hoffman RM, Burger A, Craig PO, Komives E, Wolynes PG. Discrete kinetic models from funneled energy landscape simulations. PLoS One. 2012; 7(12):e50635. PMID: 23251375; PMCID: PMC3520928.
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      27. Gasper PM, Fuglestad B, Komives E, Markwick PR, McCammon JA. Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities. Proc Natl Acad Sci U S A. 2012 Dec 26; 109(52):21216-22. PMID: 23197839; PMCID: PMC3535651.
        View in: PubMed, PubMed Central
      28. Balasubramaniam D, Komives E. Hydrogen-exchange mass spectrometry for the study of intrinsic disorder in proteins. Biochim Biophys Acta. 2013 Jun; 1834(6):1202-9. PMID: 23099262; PMCID: PMC3600394.
        View in: PubMed, PubMed Central
      29. Fuglestad B, Gasper PM, Tonelli M, McCammon JA, Markwick PR, Komives E. The dynamic structure of thrombin in solution. Biophys J. 2012 Jul 03; 103(1):79-88. PMID: 22828334; PMCID: PMC3388214.
        View in: PubMed, PubMed Central
      30. Guo L, Ghassemian M, Komives E, Russell P. Cadmium-induced proteome remodeling regulated by Spc1/Sty1 and Zip1 in fission yeast. Toxicol Sci. 2012 Sep; 129(1):200-12. PMID: 22610605; PMCID: PMC3713068.
        View in: PubMed, PubMed Central
      31. Dyson HJ, Komives E. Role of disorder in I?B-NF?B interaction. IUBMB Life. 2012 Jun; 64(6):499-505. PMID: 22573609; PMCID: PMC3575514.
        View in: PubMed, PubMed Central
      32. Jobe TO, Sung DY, Akmakjian G, Pham A, Komives E, Mendoza-Cózatl DG, Schroeder JI. Feedback inhibition by thiols outranks glutathione depletion: a luciferase-based screen reveals glutathione-deficient ?-ECS and glutathione synthetase mutants impaired in cadmium-induced sulfate assimilation. Plant J. 2012 Jun; 70(5):783-95. PMID: 22283708; PMCID: PMC4688143.
        View in: PubMed, PubMed Central
      33. Komives E. Consequences of fuzziness in the NF?B/I?Ba interaction. Adv Exp Med Biol. 2012; 725:74-85. PMID: 22399319; PMCID: PMC3603378.
        View in: PubMed, PubMed Central
      34. Guttman M, Komives E. The structure, dynamics, and binding of the LA45 module pair of the low-density lipoprotein receptor suggest an important role for LA4 in ligand release. Biochemistry. 2011 Dec 27; 50(51):11001-8. PMID: 22091758; PMCID: PMC3263374.
        View in: PubMed, PubMed Central
      35. Craig PO, Lätzer J, Weinkam P, Hoffman RM, Ferreiro DU, Komives E, Wolynes PG. Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes. J Am Chem Soc. 2011 Nov 02; 133(43):17463-72. PMID: 21913704; PMCID: PMC3203634.
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      36. Mulvihill MM, Guttman M, Komives E. Protein interactions among Fe65, the low-density lipoprotein receptor-related protein, and the amyloid precursor protein. Biochemistry. 2011 Jul 19; 50(28):6208-16. PMID: 21650223; PMCID: PMC3139566.
        View in: PubMed, PubMed Central
      37. Lamboy JA, Kim H, Lee KS, Ha T, Komives E. Visualization of the nanospring dynamics of the IkappaBalpha ankyrin repeat domain in real time. Proc Natl Acad Sci U S A. 2011 Jun 21; 108(25):10178-83. PMID: 21628581; PMCID: PMC3121830.
        View in: PubMed, PubMed Central
      38. Treuheit NA, Beach MA, Komives E. Thermodynamic compensation upon binding to exosite 1 and the active site of thrombin. Biochemistry. 2011 May 31; 50(21):4590-6. PMID: 21526769; PMCID: PMC3107735.
        View in: PubMed, PubMed Central
      39. DeVries I, Ferreiro DU, Sánchez IE, Komives E. Folding kinetics of the cooperatively folded subdomain of the I?Ba ankyrin repeat domain. J Mol Biol. 2011 Apr 22; 408(1):163-76. PMID: 21329696; PMCID: PMC3081522.
        View in: PubMed, PubMed Central
      40. Ferreiro DU, Hegler JA, Komives E, Wolynes PG. On the role of frustration in the energy landscapes of allosteric proteins. Proc Natl Acad Sci U S A. 2011 Mar 01; 108(9):3499-503. PMID: 21273505; PMCID: PMC3048099.
        View in: PubMed, PubMed Central
      41. Sue SC, Alverdi V, Komives E, Dyson HJ. Detection of a ternary complex of NF-kappaB and IkappaBalpha with DNA provides insights into how IkappaBalpha removes NF-kappaB from transcription sites. Proc Natl Acad Sci U S A. 2011 Jan 25; 108(4):1367-72. PMID: 21220295; PMCID: PMC3029698.
        View in: PubMed, PubMed Central
      42. Cervantes CF, Bergqvist S, Kjaergaard M, Kroon G, Sue SC, Dyson HJ, Komives E. The RelA nuclear localization signal folds upon binding to I?Ba. J Mol Biol. 2011 Jan 21; 405(3):754-64. PMID: 21094161; PMCID: PMC3056351.
        View in: PubMed, PubMed Central
      43. Devries IL, Hampton-Smith RJ, Mulvihill MM, Alverdi V, Peet DJ, Komives E. Consequences of IkappaB alpha hydroxylation by the factor inhibiting HIF (FIH). FEBS Lett. 2010 Dec 01; 584(23):4725-30. PMID: 21056038; PMCID: PMC3034650.
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      44. Mathes E, Wang L, Komives E, Ghosh G. Flexible regions within I{kappa}B{alpha} create the ubiquitin-independent degradation signal. J Biol Chem. 2010 Oct 22; 285(43):32927-36. PMID: 20682784; PMCID: PMC2963393.
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      45. Gertsman I, Fu CY, Huang R, Komives E, Johnson JE. Critical salt bridges guide capsid assembly, stability, and maturation behavior in bacteriophage HK97. Mol Cell Proteomics. 2010 Aug; 9(8):1752-63. PMID: 20332083; PMCID: PMC2938056.
        View in: PubMed, PubMed Central
      46. Guttman M, Prieto JH, Handel TM, Domaille PJ, Komives E. Structure of the minimal interface between ApoE and LRP. J Mol Biol. 2010 Apr 30; 398(2):306-19. PMID: 20303980; PMCID: PMC2880916.
        View in: PubMed, PubMed Central
      47. Ferreiro DU, Komives E. Molecular mechanisms of system control of NF-kappaB signaling by IkappaBalpha. Biochemistry. 2010 Mar 02; 49(8):1560-7. PMID: 20055496; PMCID: PMC2865148.
        View in: PubMed, PubMed Central
      48. Guttman M, Prieto JH, Croy JE, Komives E. Decoding of lipoprotein-receptor interactions: properties of ligand binding modules governing interactions with apolipoprotein E. Biochemistry. 2010 Feb 16; 49(6):1207-16. PMID: 20030366; PMCID: PMC2821871.
        View in: PubMed, PubMed Central
      49. Markwick PR, Cervantes CF, Abel BL, Komives E, Blackledge M, McCammon JA. Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. J Am Chem Soc. 2010 Feb 03; 132(4):1220-1. PMID: 20063881; PMCID: PMC2812018.
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      50. Gertsman I, Komives E, Johnson JE. HK97 maturation studied by crystallography and H/2H exchange reveals the structural basis for exothermic particle transitions. J Mol Biol. 2010 Mar 26; 397(2):560-74. PMID: 20093122; PMCID: PMC2855905.
        View in: PubMed, PubMed Central
      51. Bergqvist S, Alverdi V, Mengel B, Hoffmann A, Ghosh G, Komives E. Kinetic enhancement of NF-kappaBxDNA dissociation by IkappaBalpha. Proc Natl Acad Sci U S A. 2009 Nov 17; 106(46):19328-33. PMID: 19887633; PMCID: PMC2780789.
        View in: PubMed, PubMed Central
      52. Guttman M, Betts GN, Barnes H, Ghassemian M, van der Geer P, Komives E. Interactions of the NPXY microdomains of the low density lipoprotein receptor-related protein 1. Proteomics. 2009 Nov; 9(22):5016-28. PMID: 19771558; PMCID: PMC2862490.
        View in: PubMed, PubMed Central
      53. Cervantes CF, Markwick PR, Sue SC, McCammon JA, Dyson HJ, Komives E. Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance. Biochemistry. 2009 Aug 25; 48(33):8023-31. PMID: 19591507; PMCID: PMC2728578.
        View in: PubMed, PubMed Central
      54. Sung DY, Kim TH, Komives E, Mendoza-Cózatl DG, Schroeder JI. ARS5 is a component of the 26S proteasome complex, and negatively regulates thiol biosynthesis and arsenic tolerance in Arabidopsis. Plant J. 2009 Sep; 59(5):802-13. PMID: 19453443; PMCID: PMC2830867.
        View in: PubMed, PubMed Central
      55. Gertsman I, Gan L, Guttman M, Lee K, Speir JA, Duda RL, Hendrix RW, Komives E, Johnson JE. An unexpected twist in viral capsid maturation. Nature. 2009 Apr 02; 458(7238):646-50. PMID: 19204733; PMCID: PMC2765791.
        View in: PubMed, PubMed Central
      56. Bergqvist S, Ghosh G, Komives E. The IkappaBalpha/NF-kappaB complex has two hot spots, one at either end of the interface. Protein Sci. 2008 Dec; 17(12):2051-8. PMID: 18824506; PMCID: PMC2590914.
        View in: PubMed, PubMed Central
      57. Koeppe JR, Beach MA, Baerga-Ortiz A, Kerns SJ, Komives E. Mutations in the fourth EGF-like domain affect thrombomodulin-induced changes in the active site of thrombin. Biochemistry. 2008 Oct 14; 47(41):10933-9. PMID: 18803401; PMCID: PMC2630536.
        View in: PubMed, PubMed Central
      58. Truhlar SM, Cervantes CF, Torpey JW, Kjaergaard M, Komives E. Rapid mass spectrometric analysis of 15N-Leu incorporation fidelity during preparation of specifically labeled NMR samples. Protein Sci. 2008 Sep; 17(9):1636-9. PMID: 18567787; PMCID: PMC2525515.
        View in: PubMed, PubMed Central
      59. Sue SC, Cervantes C, Komives E, Dyson HJ. Transfer of flexibility between ankyrin repeats in IkappaB* upon formation of the NF-kappaB complex. J Mol Biol. 2008 Jul 25; 380(5):917-31. PMID: 18565540; PMCID: PMC2603615.
        View in: PubMed, PubMed Central
      60. Ferreiro DU, Walczak AM, Komives E, Wolynes PG. The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures. PLoS Comput Biol. 2008 May 16; 4(5):e1000070. PMID: 18483553; PMCID: PMC2366061.
        View in: PubMed, PubMed Central
      61. Truhlar SM, Komives E. LRR domain folding: just put a cap on it! Structure. 2008 May; 16(5):655-7. PMID: 18462667.
        View in: PubMed
      62. Betts GN, van der Geer P, Komives E. Structural and functional consequences of tyrosine phosphorylation in the LRP1 cytoplasmic domain. J Biol Chem. 2008 Jun 06; 283(23):15656-64. PMID: 18381291; PMCID: PMC2414285.
        View in: PubMed, PubMed Central
      63. Truhlar SM, Mathes E, Cervantes CF, Ghosh G, Komives E. Pre-folding IkappaBalpha alters control of NF-kappaB signaling. J Mol Biol. 2008 Jun 27; 380(1):67-82. PMID: 18511071; PMCID: PMC2519148.
        View in: PubMed, PubMed Central
      64. Huang CM, Torpey JW, Liu YT, Chen YR, Williams KE, Komives E, Gallo RL. A peptide with a ProGln C terminus in the human saliva peptidome exerts bactericidal activity against Propionibacterium acnes. Antimicrob Agents Chemother. 2008 May; 52(5):1834-6. PMID: 18285475; PMCID: PMC2346631.
        View in: PubMed, PubMed Central
      65. Barrick D, Ferreiro DU, Komives E. Folding landscapes of ankyrin repeat proteins: experiments meet theory. Curr Opin Struct Biol. 2008 Feb; 18(1):27-34. PMID: 18243686; PMCID: PMC2680087.
        View in: PubMed, PubMed Central
      66. Mendoza-Cózatl DG, Butko E, Springer F, Torpey JW, Komives E, Kehr J, Schroeder JI. Identification of high levels of phytochelatins, glutathione and cadmium in the phloem sap of Brassica napus. A role for thiol-peptides in the long-distance transport of cadmium and the effect of cadmium on iron translocation. Plant J. 2008 Apr; 54(2):249-59. PMID: 18208526; PMCID: PMC2839885.
        View in: PubMed, PubMed Central
      67. Ferreiro DU, Hegler JA, Komives E, Wolynes PG. Localizing frustration in native proteins and protein assemblies. Proc Natl Acad Sci U S A. 2007 Dec 11; 104(50):19819-24. PMID: 18077414; PMCID: PMC2148382.
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      68. Wu X, Li ZF, Brooks R, Komives E, Torpey JW, Engvall E, Gonias SL, Shelton GD. Autoantibodies in canine masticatory muscle myositis recognize a novel myosin binding protein-C family member. J Immunol. 2007 Oct 01; 179(7):4939-44. PMID: 17878394.
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      69. Anand GS, Hotchko M, Brown SH, Ten Eyck LF, Komives E, Taylor SS. R-subunit isoform specificity in protein kinase A: distinct features of protein interfaces in PKA types I and II by amide H/2H exchange mass spectrometry. J Mol Biol. 2007 Nov 23; 374(2):487-99. PMID: 17942118; PMCID: PMC3419600.
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      70. Ferreiro DU, Komives E. The plastic landscape of repeat proteins. Proc Natl Acad Sci U S A. 2007 May 08; 104(19):7735-6. PMID: 17483477; PMCID: PMC1876514.
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      71. Sung DY, Lee D, Harris H, Raab A, Feldmann J, Meharg A, Kumabe B, Komives E, Schroeder JI. Identification of an arsenic tolerant double mutant with a thiol-mediated component and increased arsenic tolerance in phyA mutants. Plant J. 2007 Mar; 49(6):1064-75. PMID: 17335514.
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      72. Lätzer J, Papoian GA, Prentiss MC, Komives E, Wolynes PG. Induced fit, folding, and recognition of the NF-kappaB-nuclear localization signals by IkappaBalpha and IkappaBbeta. J Mol Biol. 2007 Mar 16; 367(1):262-74. PMID: 17257619.
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      73. Truhlar SM, Torpey JW, Komives E. Regions of IkappaBalpha that are critical for its inhibition of NF-kappaB.DNA interaction fold upon binding to NF-kappaB. Proc Natl Acad Sci U S A. 2006 Dec 12; 103(50):18951-6. PMID: 17148610; PMCID: PMC1748158.
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      74. Ferreiro DU, Cervantes CF, Truhlar SM, Cho SS, Wolynes PG, Komives E. Stabilizing IkappaBalpha by "consensus" design. J Mol Biol. 2007 Jan 26; 365(4):1201-16. PMID: 17174335; PMCID: PMC1866275.
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      75. Truhlar SM, Croy CH, Torpey JW, Koeppe JR, Komives E. Solvent accessibility of protein surfaces by amide H/2H exchange MALDI-TOF mass spectrometry. J Am Soc Mass Spectrom. 2006 Nov; 17(11):1490-7. PMID: 16934999.
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      76. Koeppe JR, Komives E. Amide H/2H exchange reveals a mechanism of thrombin activation. Biochemistry. 2006 Jun 27; 45(25):7724-32. PMID: 16784223; PMCID: PMC2535819.
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      77. Bergqvist S, Croy CH, Kjaergaard M, Huxford T, Ghosh G, Komives E. Thermodynamics reveal that helix four in the NLS of NF-kappaB p65 anchors IkappaBalpha, forming a very stable complex. J Mol Biol. 2006 Jul 07; 360(2):421-34. PMID: 16756995; PMCID: PMC2680085.
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      78. Chen A, Komives E, Schroeder JI. An improved grafting technique for mature Arabidopsis plants demonstrates long-distance shoot-to-root transport of phytochelatins in Arabidopsis. Plant Physiol. 2006 May; 141(1):108-20. PMID: 16531489; PMCID: PMC1459314.
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      79. Hotchko M, Anand GS, Komives E, Ten Eyck LF. Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments. Protein Sci. 2006 Mar; 15(3):583-601. PMID: 16501228; PMCID: PMC2249778.
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      80. Shi J, Koeppe JR, Komives E, Taylor P. Ligand-induced conformational changes in the acetylcholine-binding protein analyzed by hydrogen-deuterium exchange mass spectrometry. J Biol Chem. 2006 Apr 28; 281(17):12170-7. PMID: 16484218.
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      81. Koeppe JR, Seitova A, Mather T, Komives E. Thrombomodulin tightens the thrombin active site loops to promote protein C activation. Biochemistry. 2005 Nov 15; 44(45):14784-91. PMID: 16274226.
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      82. Ferreiro DU, Cho SS, Komives E, Wolynes PG. The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family. J Mol Biol. 2005 Dec 02; 354(3):679-92. PMID: 16257414.
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      83. Mandell JG, Baerga-Ortiz A, Croy CH, Falick AM, Komives E. Application of amide proton exchange mass spectrometry for the study of protein-protein interactions. Curr Protoc Protein Sci. 2005 Jun; Chapter 20:Unit20.9. PMID: 18429282.
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      84. Prieto JH, Sampoli Benitez BA, Melacini G, Johnson DA, Wood MJ, Komives E. Dynamics of the fragment of thrombomodulin containing the fourth and fifth epidermal growth factor-like domains correlate with function. Biochemistry. 2005 Feb 01; 44(4):1225-33. PMID: 15667216.
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      85. Wood MJ, Helena Prieto J, Komives E. Structural and functional consequences of methionine oxidation in thrombomodulin. Biochim Biophys Acta. 2005 Jan 17; 1703(2):141-7. PMID: 15680222.
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      86. Mandell JG, Baerga-Ortiz A, Falick AM, Komives E. Measurement of solvent accessibility at protein-protein interfaces. Methods Mol Biol. 2005; 305:65-80. PMID: 15939994.
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      87. Croy CH, Bergqvist S, Huxford T, Ghosh G, Komives E. Biophysical characterization of the free IkappaBalpha ankyrin repeat domain in solution. Protein Sci. 2004 Jul; 13(7):1767-77. PMID: 15215520; PMCID: PMC2279933.
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      88. Croy JE, Brandon T, Komives E. Two apolipoprotein E mimetic peptides, ApoE(130-149) and ApoE(141-155)2, bind to LRP1. Biochemistry. 2004 Jun 15; 43(23):7328-35. PMID: 15182176.
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      89. Croy CH, Koeppe JR, Bergqvist S, Komives E. Allosteric changes in solvent accessibility observed in thrombin upon active site occupation. Biochemistry. 2004 May 11; 43(18):5246-55. PMID: 15122890.
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      90. Baerga-Ortiz A, Bergqvist S, Mandell JG, Komives E. Two different proteins that compete for binding to thrombin have opposite kinetic and thermodynamic profiles. Protein Sci. 2004 Jan; 13(1):166-76. PMID: 14691232; PMCID: PMC2286536.
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      91. Croy JE, Shin WD, Knauer MF, Knauer DJ, Komives E. All three LDL receptor homology regions of the LDL receptor-related protein bind multiple ligands. Biochemistry. 2003 Nov 11; 42(44):13049-57. PMID: 14596620.
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      92. Anand GS, Law D, Mandell JG, Snead AN, Tsigelny I, Taylor SS, Ten Eyck LF, Komives E. Identification of the protein kinase A regulatory RIalpha-catalytic subunit interface by amide H/2H exchange and protein docking. Proc Natl Acad Sci U S A. 2003 Nov 11; 100(23):13264-9. PMID: 14583592; PMCID: PMC263775.
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      93. Wood MJ, Becvar LA, Prieto JH, Melacini G, Komives E. NMR structures reveal how oxidation inactivates thrombomodulin. Biochemistry. 2003 Oct 21; 42(41):11932-42. PMID: 14556624.
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      94. Jennings LL, Malecki M, Komives E, Taylor P. Direct analysis of the kinetic profiles of organophosphate-acetylcholinesterase adducts by MALDI-TOF mass spectrometry. Biochemistry. 2003 Sep 23; 42(37):11083-91. PMID: 12974645.
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      95. Huxford T, Mishler D, Phelps CB, Huang DB, Sengchanthalangsy LL, Reeves R, Hughes CA, Komives E, Ghosh G. Solvent exposed non-contacting amino acids play a critical role in NF-kappaB/IkappaBalpha complex formation. J Mol Biol. 2002 Dec 06; 324(4):587-97. PMID: 12460563.
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      96. Anand GS, Hughes CA, Jones JM, Taylor SS, Komives E. Amide H/2H exchange reveals communication between the cAMP and catalytic subunit-binding sites in the R(I)alpha subunit of protein kinase A. J Mol Biol. 2002 Oct 18; 323(2):377-86. PMID: 12381327.
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      97. Whiles JA, Glover KJ, Vold RR, Komives E. Methods for studying transmembrane peptides in bicelles: consequences of hydrophobic mismatch and peptide sequence. J Magn Reson. 2002 Sep-Oct; 158(1-2):149-56. PMID: 12419680.
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      98. Baerga-Ortiz A, Hughes CA, Mandell JG, Komives E. Epitope mapping of a monoclonal antibody against human thrombin by H/D-exchange mass spectrometry reveals selection of a diverse sequence in a highly conserved protein. Protein Sci. 2002 Jun; 11(6):1300-8. PMID: 12021429; PMCID: PMC2373625.
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      99. Glover KJ, Whiles JA, Wood MJ, Melacini G, Komives E, Vold RR. Conformational dimorphism and transmembrane orientation of prion protein residues 110-136 in bicelles. Biochemistry. 2001 Nov 06; 40(44):13137-42. PMID: 11683621.
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      100. Glover KJ, Whiles JA, Wu G, Yu N, Deems R, Struppe JO, Stark RE, Komives E, Vold RR. Structural evaluation of phospholipid bicelles for solution-state studies of membrane-associated biomolecules. Biophys J. 2001 Oct; 81(4):2163-71. PMID: 11566787; PMCID: PMC1301688.
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      101. Hughes CA, Mandell JG, Anand GS, Stock AM, Komives E. Phosphorylation causes subtle changes in solvent accessibility at the interdomain interface of methylesterase CheB. J Mol Biol. 2001 Apr 06; 307(4):967-76. PMID: 11286548.
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      102. Mandell JG, Baerga-Ortiz A, Akashi S, Takio K, Komives E. Solvent accessibility of the thrombin-thrombomodulin interface. J Mol Biol. 2001 Feb 23; 306(3):575-89. PMID: 11178915.
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      103. Whiles JA, Brasseur R, Glover KJ, Melacini G, Komives E, Vold RR. Orientation and effects of mastoparan X on phospholipid bicelles. Biophys J. 2001 Jan; 80(1):280-93. PMID: 11159401; PMCID: PMC1301232.
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      104. Sampoli Benitez BA, Komives E. Disulfide bond plasticity in epidermal growth factor. Proteins. 2000 Jul 01; 40(1):168-74. PMID: 10813841.
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      105. Wood MJ, Sampoli Benitez BA, Komives E. Solution structure of the smallest cofactor-active fragment of thrombomodulin. Nat Struct Biol. 2000 Mar; 7(3):200-4. PMID: 10700277.
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      106. Baerga-Ortiz A, Rezaie AR, Komives E. Electrostatic dependence of the thrombin-thrombomodulin interaction. J Mol Biol. 2000 Feb 18; 296(2):651-8. PMID: 10669614.
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      107. Struppe J, Whiles JA, Vold RR. Acidic phospholipid bicelles: a versatile model membrane system. Biophys J. 2000 Jan; 78(1):281-9. PMID: 10620292; PMCID: PMC1300636.
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      108. Glover KJ, Martini PM, Vold RR, Komives E. Preparation of insoluble transmembrane peptides: glycophorin-A, prion (110-137), and FGFR (368-397). Anal Biochem. 1999 Aug 01; 272(2):270-4. PMID: 10415099.
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      109. Zhang Z, Komives E, Sugio S, Blacklow SC, Narayana N, Xuong NH, Stock AM, Petsko GA, Ringe D. The role of water in the catalytic efficiency of triosephosphate isomerase. Biochemistry. 1999 Apr 06; 38(14):4389-97. PMID: 10194358.
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      110. Mentz S, de Lacalle S, Baerga-Ortiz A, Knauer MF, Knauer DJ, Komives E. Mechanism of thrombin clearance by human astrocytoma cells. J Neurochem. 1999 Mar; 72(3):980-7. PMID: 10037469.
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      111. Wood MJ, Komives E. Production of large quantities of isotopically labeled protein in Pichia pastoris by fermentation. J Biomol NMR. 1999 Feb; 13(2):149-59. PMID: 10070756.
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      112. Mandell JG, Falick AM, Komives E. Identification of protein-protein interfaces by decreased amide proton solvent accessibility. Proc Natl Acad Sci U S A. 1998 Dec 08; 95(25):14705-10. PMID: 9843953; PMCID: PMC24513.
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      113. Greenwald J, Le V, Corrigan A, Fischer W, Komives E, Vale W, Choe S. Characterization of the extracellular ligand-binding domain of the type II activin receptor. Biochemistry. 1998 Nov 24; 37(47):16711-8. PMID: 9843440.
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      114. Struppe J, Komives E, Taylor SS, Vold RR. 2H NMR studies of a myristoylated peptide in neutral and acidic phospholipid bicelles. Biochemistry. 1998 Nov 03; 37(44):15523-7. PMID: 9799515.
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      115. Mandell JG, Falick AM, Komives E. Measurement of amide hydrogen exchange by MALDI-TOF mass spectrometry. Anal Chem. 1998 Oct 01; 70(19):3987-95. PMID: 9784743.
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      116. Gleeson MA, White CE, Meininger DP, Komives E. Generation of protease-deficient strains and their use in heterologous protein expression. Methods Mol Biol. 1998; 103:81-94. PMID: 9680635.
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      117. Sampoli Benitez BA, Hunter MJ, Meininger DP, Komives E. Structure of the fifth EGF-like domain of thrombomodulin: An EGF-like domain with a novel disulfide-bonding pattern. J Mol Biol. 1997 Nov 07; 273(4):913-26. PMID: 9367781.
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      118. Vindigni A, White CE, Komives E, Di Cera E. Energetics of thrombin-thrombomodulin interaction. Biochemistry. 1997 Jun 03; 36(22):6674-81. PMID: 9184147.
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      119. Komives E, Lougheed JC, Zhang Z, Sugio S, Narayana N, Xuong NH, Petsko GA, Ringe D. The structural basis for pseudoreversion of the H95N lesion by the secondary S96P mutation in triosephosphate isomerase. Biochemistry. 1996 Dec 03; 35(48):15474-84. PMID: 8952501.
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      120. White CE, Hunter MJ, Meininger DP, Garrod S, Komives E. The fifth epidermal growth factor-like domain of thrombomodulin does not have an epidermal growth factor-like disulfide bonding pattern. Proc Natl Acad Sci U S A. 1996 Sep 17; 93(19):10177-82. PMID: 8816772; PMCID: PMC38357.
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      121. Hrabal R, Komives E, Ni F. Structural resiliency of an EGF-like subdomain bound to its target protein, thrombin. Protein Sci. 1996 Feb; 5(2):195-203. PMID: 8745396; PMCID: PMC2143349.
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      122. White CE, Hunter MJ, Meininger DP, White LR, Komives E. Large-scale expression, purification and characterization of small fragments of thrombomodulin: the roles of the sixth domain and of methionine 388. Protein Eng. 1995 Nov; 8(11):1177-87. PMID: 8819984.
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      123. Komives E, Lougheed JC, Liu K, Sugio S, Zhang Z, Petsko GA, Ringe D. The structural basis for pseudoreversion of the E165D lesion by the secondary S96P mutation in triosephosphate isomerase depends on the positions of active site water molecules. Biochemistry. 1995 Oct 17; 34(41):13612-21. PMID: 7577950.
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      124. Hunter MJ, Komives E. Thrombin-binding affinities of different disulfide-bonded isomers of the fifth EGF-like domain of thrombomodulin. Protein Sci. 1995 Oct; 4(10):2129-37. PMID: 8535250; PMCID: PMC2142985.
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      125. Meininger DP, Hunter MJ, Komives E. Synthesis, activity, and preliminary structure of the fourth EGF-like domain of thrombomodulin. Protein Sci. 1995 Sep; 4(9):1683-95. PMID: 8528067; PMCID: PMC2143218.
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      126. Hunter MJ, Komives E. Deprotection of S-acetamidomethyl cysteine-containing peptides by silver trifluoromethanesulfonate avoids the oxidation of methionines. Anal Biochem. 1995 Jun 10; 228(1):173-7. PMID: 8572278.
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      127. Lougheed JC, Bowman CL, Meininger DP, Komives E. Thrombin inhibition by cyclic peptides from thrombomodulin. Protein Sci. 1995 Apr; 4(4):773-80. PMID: 7613475; PMCID: PMC2143091.
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      128. Srinivasan J, Hu S, Hrabal R, Zhu Y, Komives E, Ni F. Thrombin-bound structure of an EGF subdomain from human thrombomodulin determined by transferred nuclear Overhauser effects. Biochemistry. 1994 Nov 22; 33(46):13553-60. PMID: 7947766.
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      129. White CE, Kempi NM, Komives E. Expression of highly disulfide-bonded proteins in Pichia pastoris. Structure. 1994 Nov 15; 2(11):1003-5. PMID: 7881900.
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      130. Fanuel L, Granier B, Wilkin JM, Bellefroid-Bourguignon C, Joris B, Knowles J, Komives E, Van Beeumen J, Ghuysen JM, Frère JM. The precursor of the Streptomyces R61 DD-peptidase containing a C-terminal extension is inactive. FEBS Lett. 1994 Aug 29; 351(1):49-52. PMID: 8076692.
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      131. Joseph-McCarthy D, Rost LE, Komives E, Petsko GA. Crystal structure of the mutant yeast triosephosphate isomerase in which the catalytic base glutamic acid 165 is changed to aspartic acid. Biochemistry. 1994 Mar 15; 33(10):2824-9. PMID: 7907502.
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      132. Zhang Z, Sugio S, Komives E, Liu KD, Knowles JR, Petsko GA, Ringe D. Crystal structure of recombinant chicken triosephosphate isomerase-phosphoglycolohydroxamate complex at 1.8-A resolution. Biochemistry. 1994 Mar 15; 33(10):2830-7. PMID: 8130195.
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      133. Joseph-McCarthy D, Lolis E, Komives E, Petsko GA. Crystal structure of the K12M/G15A triosephosphate isomerase double mutant and electrostatic analysis of the active site. Biochemistry. 1994 Mar 15; 33(10):2815-23. PMID: 8130194.
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      134. Lodi PJ, Chang LC, Knowles JR, Komives E. Triosephosphate isomerase requires a positively charged active site: the role of lysine-12. Biochemistry. 1994 Mar 15; 33(10):2809-14. PMID: 8130193.
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      135. Warn-Cramer BJ, Broze GJ, Komives E. cDNA sequence of rabbit tissue factor pathway inhibitor. Nucleic Acids Res. 1992 Jul 11; 20(13):3548. PMID: 1630940; PMCID: PMC312531.
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      136. Komives E, Chang LC, Lolis E, Tilton RF, Petsko GA, Knowles JR. Electrophilic catalysis in triosephosphate isomerase: the role of histidine-95. Biochemistry. 1991 Mar 26; 30(12):3011-9. PMID: 2007138.
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      137. Komives E, Ortiz de Montellano PR. Mechanism of oxidation of pi bonds by cytochrome P-450. Electronic requirements of the transition state in the turnover of phenylacetylenes. J Biol Chem. 1987 Jul 15; 262(20):9793-802. PMID: 3597438.
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      138. Kaden DA, Call KM, Leong PM, Komives E, Thilly WG. Killing and mutation of human lymphoblast cells by aflatoxin B1: evidence for an inducible repair response. Cancer Res. 1987 Apr 15; 47(8):1993-2001. PMID: 3103909.
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      139. Ortiz de Montellano PR, Komives E. Branchpoint for heme alkylation and metabolite formation in the oxidation of arylacetylenes by cytochrome P-450. J Biol Chem. 1985 Mar 25; 260(6):3330-6. PMID: 3972828.
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      140. DeLuca JG, Kaden DA, Komives E, Thilly WG. Mutation of xeroderma pigmentosum lymphoblasts by far-ultraviolet light. Mutat Res. 1984 Aug; 128(1):47-57. PMID: 6472306.
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      141. Komives E, Weiss ST, Rosa RM. The applicant interview as a predictor of resident performance. J Med Educ. 1984 May; 59(5):425-6. PMID: 6716433.
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      142. Penman BW, Crespi CL, Komives E, Liber HL, Thilly WG. Mutation of human lymphoblasts exposed to low concentrations of chemical mutagens for long periods of time. Mutat Res. 1983 Mar; 108(1-3):417-36. PMID: 6403847.
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