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Elizabeth Komives

Title(s)Professor, Chemistry and Biochemistry
SchoolAcademic Aff
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.
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    1. Markwick PRL, Peacock RB, Komives EA. Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery. Biophys J. 2019 Jan 08; 116(1):49-56. PMID: 30558884.
      View in: PubMed
    2. Hard R, Li N, He W, Ross B, Mo GCH, Peng Q, Stein RSL, Komives E, Wang Y, Zhang J, Wang W. Deciphering and engineering chromodomain-methyllysine peptide recognition. Sci Adv. 2018 Nov; 4(11):eaau1447. PMID: 30417094.
      View in: PubMed
    3. Gudlur A, Zeraik AE, Hirve N, Rajanikanth V, Bobkov AA, Ma G, Zheng S, Wang Y, Zhou Y, Komives EA, Hogan PG. Calcium sensing by the STIM1 ER-luminal domain. Nat Commun. 2018 10 31; 9(1):4536. PMID: 30382093.
      View in: PubMed
    4. Ramsey KM, Narang D, Komives EA. Prediction of the presence of a seventh ankyrin repeat in I?Be from homology modeling combined with hydrogen-deuterium exchange mass spectrometry (HDX-MS). Protein Sci. 2018 Sep; 27(9):1624-1635. PMID: 30133030.
      View in: PubMed
    5. Rahnamoun H, Lee J, Sun Z, Lu H, Ramsey KM, Komives EA, Lauberth SM. RNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation. Nat Struct Mol Biol. 2018 Aug; 25(8):687-697. PMID: 30076409.
      View in: PubMed
    6. Peacock RB, Davis JR, Markwick PRL, Komives EA. Dynamic Consequences of Mutation of Tryptophan 215 in Thrombin. Biochemistry. 2018 05 08; 57(18):2694-2703. PMID: 29634247.
      View in: PubMed
    7. Ramirez-Sarmiento CA, Komives EA. Hydrogen-deuterium exchange mass spectrometry reveals folding and allostery in protein-protein interactions. Methods. 2018 07 15; 144:43-52. PMID: 29627358.
      View in: PubMed
    8. Narang D, Chen W, Ricci CG, Komives EA. RelA-Containing NF?B Dimers Have Strikingly Different DNA-Binding Cavities in the Absence of DNA. J Mol Biol. 2018 May 11; 430(10):1510-1520. PMID: 29625198.
      View in: PubMed
    9. Kromann-Hansen T, Lange EL, Lund IK, Høyer-Hansen G, Andreasen PA, Komives EA. Ligand binding modulates the structural dynamics and activity of urokinase-type plasminogen activator: A possible mechanism of plasminogen activation. PLoS One. 2018; 13(2):e0192661. PMID: 29420634.
      View in: PubMed
    10. West AMV, Komives EA, Corbett KD. Conformational dynamics of the Hop1 HORMA domain reveal a common mechanism with the spindle checkpoint protein Mad2. Nucleic Acids Res. 2018 Jan 09; 46(1):279-292. PMID: 29186573.
      View in: PubMed
    11. Potoyan DA, Bueno C, Zheng W, Komives EA, Wolynes PG. Resolving the NF?B Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors. J Am Chem Soc. 2017 12 27; 139(51):18558-18566. PMID: 29183131.
      View in: PubMed
    12. Kim JK, Liu J, Hu X, Yu C, Roskamp K, Sankaran B, Huang L, Komives EA, Qiao F. Structural Basis for Shelterin Bridge Assembly. Mol Cell. 2017 Nov 16; 68(4):698-714.e5. PMID: 29149597.
      View in: PubMed
    13. Ferreiro DU, Komives EA, Wolynes PG. Frustration, function and folding. Curr Opin Struct Biol. 2018 02; 48:68-73. PMID: 29101782.
      View in: PubMed
    14. Lumpkin RJ, Gu H, Zhu Y, Leonard M, Ahmad AS, Clauser KR, Meyer JG, Bennett EJ, Komives EA. Site-specific identification and quantitation of endogenous SUMO modifications under native conditions. Nat Commun. 2017 10 27; 8(1):1171. PMID: 29079793.
      View in: PubMed
    15. Wong JJW, Young TA, Zhang J, Liu S, Leser GP, Komives EA, Lamb RA, Zhou ZH, Salafsky J, Jardetzky TS. Monomeric ephrinB2 binding induces allosteric changes in Nipah virus G that precede its full activation. Nat Commun. 2017 10 03; 8(1):781. PMID: 28974687.
      View in: PubMed
    16. Kromann-Hansen T, Louise Lange E, Peter Sørensen H, Hassanzadeh-Ghassabeh G, Huang M, Jensen JK, Muyldermans S, Declerck PJ, Komives EA, Andreasen PA. Discovery of a novel conformational equilibrium in urokinase-type plasminogen activator. Sci Rep. 2017 06 13; 7(1):3385. PMID: 28611361.
      View in: PubMed
    17. Carvajal AI, Vallejos G, Komives EA, 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 06; 284(12):1882-1896. PMID: 28457014.
      View in: PubMed
    18. Ramsey KM, Dembinski HE, Chen W, Ricci CG, Komives EA. DNA and I?Ba Both Induce Long-Range Conformational Changes in NF?B. J Mol Biol. 2017 04 07; 429(7):999-1008. PMID: 28249778.
      View in: PubMed
    19. Dembinski HE, Wismer K, Vargas JD, Suryawanshi GW, Kern N, Kroon G, Dyson HJ, Hoffmann A, Komives EA. Functional importance of stripping in NF?B signaling revealed by a stripping-impaired I?Ba mutant. Proc Natl Acad Sci U S A. 2017 02 21; 114(8):1916-1921. PMID: 28167786.
      View in: PubMed
    20. Handley LD, Fuglestad B, Stearns K, Tonelli M, Fenwick RB, Markwick PR, Komives EA. NMR reveals a dynamic allosteric pathway in thrombin. Sci Rep. 2017 01 06; 7:39575. PMID: 28059082.
      View in: PubMed
    21. Schiffer JM, Malmstrom RD, Parnell J, Ramirez-Sarmiento C, Reyes J, Amaro RE, Komives EA. Model of the Ankyrin and SOCS Box Protein, ASB9, E3 Ligase Reveals a Mechanism for Dynamic Ubiquitin Transfer. Structure. 2016 08 02; 24(8):1248-1256. PMID: 27396830; PMCID: PMC4972691 [Available on 08/02/17].
      View in: PubMed, PubMed Central
    22. Medina E, Córdova C, Villalobos P, Reyes J, Komives EA, Ramírez-Sarmiento CA, Babul J. Three-Dimensional Domain Swapping Changes the Folding Mechanism of the Forkhead Domain of FoxP1. Biophys J. 2016 06 07; 110(11):2349-2360. PMID: 27276253.
      View in: PubMed
    23. Mukherjee SP, Quintas PO, McNulty R, Komives EA, 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
    24. Potoyan DA, Zheng W, Ferreiro DU, Wolynes PG, Komives EA. PEST Control of Molecular Stripping of NF?B from DNA Transcription Sites. J Phys Chem B. 2016 08 25; 120(33):8532-8. PMID: 27098223.
      View in: PubMed
    25. Trelle MB, Ramsey KM, Lee TC, Zheng W, Lamboy J, Wolynes PG, Deniz A, Komives EA. 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.
      View in: PubMed
    26. Potoyan DA, Zheng W, Komives EA, 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
    27. Handley LD, Treuheit NA, Venkatesh VJ, Komives EA. 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
    28. Ramírez-Sarmiento CA, Baez M, Zamora RA, Balasubramaniam D, Babul J, Komives EA, 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.
      View in: PubMed
    29. Balasubramaniam D, Schiffer J, Parnell J, Mir SP, Amaro RE, Komives EA. 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
    30. Ferreiro DU, Komives EA, Wolynes PG. Frustration in biomolecules. Q Rev Biophys. 2014 Nov; 47(4):285-363. PMID: 25225856; PMCID: PMC4256721.
      View in: PubMed, PubMed Central
    31. Boechi L, Pierce L, Komives EA, 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
    32. Perera VR, Newton GL, Parnell JM, Komives EA, 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
    33. Balasubramaniam D, Komives EA. The phylogenetics of dynamics in DNA clamp proteins. Structure. 2014 Apr 08; 22(4):511-2. PMID: 24717558.
      View in: PubMed
    34. Dembinski H, Wismer K, Balasubramaniam D, Gonzalez HA, Alverdi V, Iakoucheva LM, Komives EA. 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
    35. Meyer JG, Kim S, Maltby DA, Ghassemian M, Bandeira N, Komives EA. 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
    36. Alverdi V, Hetrick B, Joseph S, Komives EA. 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
    37. 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
    38. Fuglestad B, Gasper PM, McCammon JA, Markwick PR, Komives EA. 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
    39. Ramírez-Sarmiento CA, Baez M, Wilson CA, Babul J, Komives EA, 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
    40. Lamboy JA, Kim H, Dembinski H, Ha T, Komives EA. 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
    41. 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
    42. Cervantes CF, Handley LD, Sue SC, Dyson HJ, Komives EA. Long-range effects and functional consequences of stabilizing mutations in the ankyrin repeat domain of I?Ba. J Mol Biol. 2013 Mar 11; 425(5):902-13. PMID: 23274114; PMCID: PMC3744861.
      View in: PubMed, PubMed Central
    43. Schafer NP, Hoffman RM, Burger A, Craig PO, Komives EA, Wolynes PG. Discrete kinetic models from funneled energy landscape simulations. PLoS One. 2012; 7(12):e50635. PMID: 23251375; PMCID: PMC3520928.
      View in: PubMed, PubMed Central
    44. Gasper PM, Fuglestad B, Komives EA, 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
    45. Balasubramaniam D, Komives EA. 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
    46. Fuglestad B, Gasper PM, Tonelli M, McCammon JA, Markwick PR, Komives EA. 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
    47. Guo L, Ghassemian M, Komives EA, 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
    48. Dyson HJ, Komives EA. 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
    49. Jobe TO, Sung DY, Akmakjian G, Pham A, Komives EA, 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
    50. Komives EA. 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
    51. Guttman M, Komives EA. 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.
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    52. Craig PO, Lätzer J, Weinkam P, Hoffman RM, Ferreiro DU, Komives EA, 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.
      View in: PubMed, PubMed Central
    53. Mulvihill MM, Guttman M, Komives EA. 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
    54. Lamboy JA, Kim H, Lee KS, Ha T, Komives EA. 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
    55. Treuheit NA, Beach MA, Komives EA. 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
    56. DeVries I, Ferreiro DU, Sánchez IE, Komives EA. 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
    57. Ferreiro DU, Hegler JA, Komives EA, 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
    58. Sue SC, Alverdi V, Komives EA, 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
    59. Cervantes CF, Bergqvist S, Kjaergaard M, Kroon G, Sue SC, Dyson HJ, Komives EA. 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
    60. Devries IL, Hampton-Smith RJ, Mulvihill MM, Alverdi V, Peet DJ, Komives EA. Consequences of IkappaB alpha hydroxylation by the factor inhibiting HIF (FIH). FEBS Lett. 2010 Dec 01; 584(23):4725-30. PMID: 21056038; PMCID: PMC3034650.
      View in: PubMed, PubMed Central
    61. 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.
      View in: PubMed, PubMed Central
    62. Gertsman I, Fu CY, Huang R, Komives EA, 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
    63. Guttman M, Prieto JH, Handel TM, Domaille PJ, Komives EA. 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
    64. Ferreiro DU, Komives EA. 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
    65. Guttman M, Prieto JH, Croy JE, Komives EA. 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
    66. Markwick PR, Cervantes CF, Abel BL, Komives EA, 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.
      View in: PubMed, PubMed Central
    67. Gertsman I, Komives EA, 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.
      View in: PubMed
    68. Bergqvist S, Alverdi V, Mengel B, Hoffmann A, Ghosh G, Komives EA. 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
    69. Guttman M, Betts GN, Barnes H, Ghassemian M, van der Geer P, Komives EA. 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
    70. Cervantes CF, Markwick PR, Sue SC, McCammon JA, Dyson HJ, Komives EA. 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
    71. Sung DY, Kim TH, Komives EA, 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
    72. Gertsman I, Gan L, Guttman M, Lee K, Speir JA, Duda RL, Hendrix RW, Komives EA, Johnson JE. An unexpected twist in viral capsid maturation. Nature. 2009 Apr 02; 458(7238):646-50. PMID: 19204733; PMCID: PMC2765791.
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    73. Bergqvist S, Ghosh G, Komives EA. 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
    74. Koeppe JR, Beach MA, Baerga-Ortiz A, Kerns SJ, Komives EA. 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
    75. Truhlar SM, Cervantes CF, Torpey JW, Kjaergaard M, Komives EA. 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.
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    76. Sue SC, Cervantes C, Komives EA, 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.
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    77. Ferreiro DU, Walczak AM, Komives EA, 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.
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    78. Truhlar SM, Komives EA. LRR domain folding: just put a cap on it! Structure. 2008 May; 16(5):655-7. PMID: 18462667.
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    79. Betts GN, van der Geer P, Komives EA. 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
    80. Truhlar SM, Mathes E, Cervantes CF, Ghosh G, Komives EA. 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
    81. Huang CM, Torpey JW, Liu YT, Chen YR, Williams KE, Komives EA, 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.
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    82. Barrick D, Ferreiro DU, Komives EA. Folding landscapes of ankyrin repeat proteins: experiments meet theory. Curr Opin Struct Biol. 2008 Feb; 18(1):27-34. PMID: 18243686; PMCID: PMC2680087.
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    83. Mendoza-Cózatl DG, Butko E, Springer F, Torpey JW, Komives EA, 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.
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    84. Ferreiro DU, Hegler JA, Komives EA, 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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    85. Wu X, Li ZF, Brooks R, Komives EA, 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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    86. Anand GS, Hotchko M, Brown SH, Ten Eyck LF, Komives EA, 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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    87. Ferreiro DU, Komives EA. 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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    88. Sung DY, Lee D, Harris H, Raab A, Feldmann J, Meharg A, Kumabe B, Komives EA, 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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    89. Lätzer J, Papoian GA, Prentiss MC, Komives EA, 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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    90. Truhlar SM, Torpey JW, Komives EA. 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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    91. Ferreiro DU, Cervantes CF, Truhlar SM, Cho SS, Wolynes PG, Komives EA. Stabilizing IkappaBalpha by "consensus" design. J Mol Biol. 2007 Jan 26; 365(4):1201-16. PMID: 17174335; PMCID: PMC1866275.
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    92. Truhlar SM, Croy CH, Torpey JW, Koeppe JR, Komives EA. 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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    93. Koeppe JR, Komives EA. 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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    94. Bergqvist S, Croy CH, Kjaergaard M, Huxford T, Ghosh G, Komives EA. 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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    95. Chen A, Komives EA, 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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    96. Hotchko M, Anand GS, Komives EA, 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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    97. Shi J, Koeppe JR, Komives EA, 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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    98. Koeppe JR, Seitova A, Mather T, Komives EA. 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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    99. Ferreiro DU, Cho SS, Komives EA, 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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    100. Mandell JG, Baerga-Ortiz A, Croy CH, Falick AM, Komives EA. 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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    101. Prieto JH, Sampoli Benitez BA, Melacini G, Johnson DA, Wood MJ, Komives EA. 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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    102. Wood MJ, Helena Prieto J, Komives EA. 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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    103. Mandell JG, Baerga-Ortiz A, Falick AM, Komives EA. Measurement of solvent accessibility at protein-protein interfaces. Methods Mol Biol. 2005; 305:65-80. PMID: 15939994.
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    104. Croy CH, Bergqvist S, Huxford T, Ghosh G, Komives EA. 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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    105. Croy JE, Brandon T, Komives EA. 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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    106. Croy CH, Koeppe JR, Bergqvist S, Komives EA. 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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    107. Baerga-Ortiz A, Bergqvist S, Mandell JG, Komives EA. 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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    108. Croy JE, Shin WD, Knauer MF, Knauer DJ, Komives EA. 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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    109. Anand GS, Law D, Mandell JG, Snead AN, Tsigelny I, Taylor SS, Ten Eyck LF, Komives EA. 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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    110. Wood MJ, Becvar LA, Prieto JH, Melacini G, Komives EA. NMR structures reveal how oxidation inactivates thrombomodulin. Biochemistry. 2003 Oct 21; 42(41):11932-42. PMID: 14556624.
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    111. Jennings LL, Malecki M, Komives EA, 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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    112. Huxford T, Mishler D, Phelps CB, Huang DB, Sengchanthalangsy LL, Reeves R, Hughes CA, Komives EA, 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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    113. Anand GS, Hughes CA, Jones JM, Taylor SS, Komives EA. 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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    114. Whiles JA, Glover KJ, Vold RR, Komives EA. 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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    115. Baerga-Ortiz A, Hughes CA, Mandell JG, Komives EA. 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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    116. 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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    117. Mandell JG, Falick AM, Komives EA. 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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