Department of Chemistry & Biochemistry
U.C. San Diego
La Jolla, CA 92093-0378
Telephone: (858) 534-3058
Email: ekomives@ucsd.edu




Assistant Professor of Chemistry & Biochemistry, 1990 – 1996
Associate Professor of Chemistry & Biochemistry, 1996 – 2000
Professor of Chemistry & Biochemistry, 2000 – present


M.S. in Toxicology, B.S. in Chemistry, 1982

Ph.D. in Pharmaceutical Chemistry with Paul R. Ortiz de Montellano 1982 – 1987
Research Topic: The Mechanism of p-Bond Oxidation by Cytochrome P-450

NIH Postdoctoral Fellow with Jeremy R. Knowles 1987 – 1990
Research Topics: Analysis of Triosephosphate Isomerase Mutants using FTIR and X-ray crystallography

Academic Honors

  • Regents Fellowship (1982 – 1983)
  • Graduate Opportunity Fellowship (1983 – 1984)
  • NIH Graduate Traineeship (1984 – 1986)
  • NIH Postdoctoral Traineeship (1987 – 1989)
  • Long Award for Excellence in Teaching (1983)
  • Rita Allen Scholar (1991 – 1996)
  • Searle Scholar (1992 – 1995)
  • Kaiser Award for Excellence in Teaching, First Year Medical Students (1999)
  • Brown and Williamson Scholar, University of Louisville (2000)
  • Barany Award for Outstanding Contributions to Biophysics, Biophysical Society (2000)
  • Bruno Zimm Scholar (first awardee, 2010)

Professional Activities

  • Advisory Committee, UCSF Mass Spectrometry Resource (1999 – present)
  • Nominating Committee, Protein Society, (2001 – 2004)
  • Session Chair, Biophysics of Protein Binding Events, ACS National Meeting (2002)
  • Council, Biophysical Society (2002 – 2006)
  • Minority Affairs Committee, Biophysical Society (2006-9)
  • Session Chair, Protein Binding and Conformation, ASMS Meeting Montreal (2003)
  • Editorial Board, Molecular and Cellular Proteomics (2002 – 2008)
  • Associate Editor, Molecular and Cellular Proteomics (2008-present)
  • Editorial Advisory Board, Biochemistry (2007-present)
  • Chair, Molecular Biophysics Subgroup, Biophysical Society (2008)
  • Awards Committee, Biophysical Society (2015-present, Chair, 2016-2017)
  • Chair, Intrinsically Disordered Proteins Subgroup, Biophysical Society (2014)
  • Executive Council, Protein Society (2017-present)
  • Manuscript Review: Proceedings of the National Academy of Sciences, Protein Science, Journal of Molecular Biology, Journal of Biological Chemistry, Biochemistry, Nature Structure and Molecular Biology

University Service


Visit the publications section for PDF files of recent publications.

  1. Penman, B. W.; Crespi, C. L.; Liber, H. L.; Komives, E. A. and Thilly, W. G. (1983) “Mutation of Human Lymphoblasts Exposed to Low Concentrations of Chemical Mutagens for Long Periods of Time”. Mutat. Res. 108: 417 – 436.
  2. DeLuca, J. G.; Kaden, D. A.; Komives, E. A. and Thilly, W.G. (1984) “Mutation of Xeroderma Pigmentosum Lymphoblasts by Far-ultraviolet Light”. Mutat. Res. 128: 47 – 57.
  3. Kaden, D. A.; Call, K. M.; Leong, P. M.; Komives, E. A. and Thilly, W.G. (1987) “Killing and Mutation of Human Lymphoblast Cells by Aflatoxin B1: Evidence for an Inducible Repair Response”. Can. Res. 47: 1993 – 2001.
  4. Ortiz de Montellano, P. R. and Komives, E. A. (1985) “Branchpoint for Heme Alkylation and Metabolite Formation in the Oxidation of Arylacetylenes by Cytochrome P-450”. J. Biol. Chem. 260: 3330 – 3336.
  5. Komives, E. A. and Ortiz de Montellano, P. R. (1987) “Mechanism of Oxidation of -Bonds by Cytochrome P-450: Electronic Requirements of the Transition State in the Turnover of Phenylacetylenes”. J. Biol. Chem. 262: 9793 – 9802.
  6. Komives, E. A., Tew, D., Olmstead, M. M. and Ortiz de Montellano, P. R. (1988) “Models for Cytochrome P-450 Prosthetic Heme Alkylation. Reaction of Diazoacetophenone with (Tetraphenylporphyrinato)iron(II) Chloride” Inorganic Chem. 27: 3112 – 3117.
  7. Komives, E. A., Chang. L. C., Lolis, E., Tilton, R. F., Petsko, G. and Knowles, J. R. (1991) “Electrophilic Catalysis in Triosephosphate Isomerase: The Role of Histidine-95” Biochemistry 30, 3011 – 3019.
  8. Warn-Cramer, B. J., Broze, G. J. and Komives, E. A. (1992) “cDNA Sequence of Rabbit Tissue Factor Pathway Inhibitor” Nucleic Acids Research 20: 3548. Corrigendum.
  9. Fanuel, L., Granier, B., Wilkin, JM., Bellefroid-Bourguignon, C., Joris, B., Knowles, J., Komives, E., Van Beeumen, J., Ghuysen, JM., Frere, J. M. (1994) “The precursor of the Streptomyces R61 DD-peptidase containing a C-terminal extension is inactive” Febs Letters 351: 49-52.
  10. Lodi, P. J., Chang. L. C., Knowles, J. R. and Komives, E. A. (1994) “Triosephosphtae Isomerase Requires a Positively Charged Active Site: The Role of Lysine-12” Biochemistry 33: 2809 – 2814.
  11. Joseph-McCarthy, D., Rost, L. E., Komives, E. A. and Petsko, G. A. (1994) “Crystal Structure of the Mutant Yeast Triosephosphate Isomerase in which the Catalytic Base Glu-165 is Changed to Asp” Biochemistry 33: 2824 – 2830.
  12. Joseph-McCarthy, D., Lolis, E., Komives, E. A. and Petsko, G. A. (1994) “Crystal Structure of the K12M/G15A Triosephosphate Isomerase Double Mutant and Electrostatic Analysis of the Active Site” Biochemistry 33: 2815 – 2823.
  13. Zhang, Z., Sugio, S., Komives, E. A., Liu, K. D., Knowles, J. R., Petsko, G. A. and Ringe, D. (1994) “Crystal Structure of Recombinant Chicken Triosephosphate Isomerase-Phosphoglycolohydroxamate Complex at 1.8-Å Resolution” Biochemistry 33: 2830 – 2837.
  14. White, C. E., Kempi, N. M. and Komives, E. A. (1994) “Expression of Highly Disulfide-Bonded Proteins in Pichia Pastoris” Structure 2: 1003 – 1005.
  15. Srinivasan, J., Hu, S., Hrabal, R., Zhu, Y., Komives, E. A. and Ni, F. (1994) “Thrombin-Bound Structure of an EGF Subdomain from Thrombomodulin Determined by Transferred Nuclear Overhauser Effects” Biochemistry 33: 13553 – 13560.
  16. Lougheed, J. L., Bowman, C. A. Meininger, D. P.and Komives, E. A. (1995) “Thrombin Inhibition by Cyclic Peptides from Thrombomodulin” Protein Science. 4:773-780.
  17. Hunter, M. J. and Komives, E. A. (1995) “Deprotection of S-Acetamidomethyl Cysteine Containing Peptides by Silver Trifluoromethanesulfonate Avoids the Oxidation of Methionines” Anal. Biochem. 228:173 – 177.
  18. Komives, E. A., Lougheed, J. C., Liu, K., Zhang, Z., Petsko, G. A. and Ringe, D. (1995) “The Structural Basis for Pseudoreversion of the E165D Lesion by the Secondary S96P Mutation in Triosephosphate Isomerase Depends on the Position of Bound Water Molecules” Biochemistry 34: 13612-21.
  19. Meininger, D. P., Hunter, M. J. and Komives, E. A. (1995) “Synthesis and Preliminary Structure of the Fourth EGF-like Domain of Thrombomodulin” Protein Science 4, 1683 – 1695 .
  20. Hunter, M. J. and Komives, E. A. (1995) “Thrombin-Binding Affinities of Different Disulfide Bonding Isomers of the Fifth EGF-like Domain of Thrombomodulin” Protein Science 4: 2129 – 2137.
  21. Blackmar, C., Healy, V. L., Narendra, U., Hrabal, R., Ni, F. and Komives, E. A. (1995) “Structure/Activity of the Region of Thrombomodulin that binds to Thrombin” Bioorganic Chemistry 23, 519 – 527.
  22. White, C. E., Hunter, M. J., Meininger, D. P., White, L. R. and Komives, E. A. (1995) “Large Scale Expression, Purification and Characterization of the Smallest Active Fragment of Thrombomodulin: The Roles of the Sixth Domain and of Methionine-388” Protein Engineering 8, 1177 – 1187.
  23. Komives, E. A., Hunter, M. J., Meininger, D. P., White, L. R. and White, C. E. (1995) “Structure/Function of the Fourth and Fifth EGF Domains of Thrombomodulin” Techniques in Protein Chemistry VII 391 – 400.
  24. Hrabal, R., Komives, E. A. and Ni, F. (1996) “Structural Resiliency of an EGF-like Subdomain Bound to its Target Protein, Thrombin” Protein Science 5, 195 – 203.
  25. Chen, Y. L., Cino, J.,White, C. E. and Komives, E. A. (1996) “Continuous Production of Thrombomodulin from a Pichia pastoris in Fermentation” Journal of Chemical Technology and Biotechnology 67, 143 – 148.
  26. White, C. E., Hunter, M. J., Meininger, D. P., Garrod, S. and Komives, E. A. (1996) “The Fifth EGF-like domain of Thrombomodulin Does Not Have An EGF-like Disulfide Bonding Pattern” Proc. Nat. Acad. Sci. U. S. A. 93, 10177 – 82.
  27. Komives, E. A., Lougheed, J. C., Zhang, Z., Sugio, S., Narayana, N., Xuong, N. H., Petsko, G. and Ringe, D. (1996)”The Structural Basis for Pseudoreversion of the H95N Lesion by the Secondary S96P Mutation in Triosephosphate Isomerase” Biochemistry 35, 15474-484.
  28. Chen, Y. L., Cino, J., Hart, G., Freedman, D., White, C. E. and Komives, E. A. (1997) “High Protein Expression in Fermentation of Recombinant Pichia Pastoris by Fed Batch Process” Process Biochemistry 32, 107 – 111.
  29. Gleeson, M.A. G., White. C. E., Meininger, D. P. and Komives, E. A. (1997) “Generation of Protease Deficient Strains of Pichia pastoris and Their Use in Heterologous Protein Expression” Methods in Molecular Biology 103, 81 – 94.
  30. Sampoli Benitez B., Hunter, M. J., Meininger D. P. and Komives, E. A. (1997) “Structure of the Fifth EGF-like Domain of Thrombomodulin: An EGF-like Domain with a Novel Disulfide Bonding Pattern” (1997) J. Mol. Biol. 273, 913 – 926.
  31. Vindigni, A., White, C. E., Komives, E. A. and Di Cera, E. (1997) “Energetics of Thrombin-Thrombomodulin Interaction” Biochemistry 36, 6674 – 6681.
  32. Mandell, J. G., Falick, A. M. and Komives, E. A. (1998) “Measurement of Amide Hydrogen Exchange by MALDI-TOF Mass Spectrometry” Analytical Chemistry 70, 3987 – 3995.
  33. Mandell, J. G., Falick, A. M. and Komives, E. A. (1998) “Identification of Protein-Protein Interfaces by Decreased Amide Proton Solvent Accessibility” Proc. Nat. Acad. Sci. U. S. A. 95, 14705 – 14710.
  34. Struppe, J., Komives, E. A., Taylor, S. S. and Vold, R. R. (1998) “2H NMR Studies of a Myristoylated Peptide in Neutral and Acidic Phospholipid Bicelles.” Biochemistry 37, 15523 – 15527.
  35. Greenwald, J., Le, V., Corrigan, A., Fischer, W., Komives, E., Vale, W., Choe, S. (1998) Characterization of the extracellular ligand-binding domain of the type II activin receptor. Biochemistry 37, 16711 – 16718.
  36. Mentz, S., DeLacalle, S. Baerga-Ortiz, A. J., Knauer, M. F., Knauer, D. J. and Komives, E. A. (1999) “Binding and Internalization of Thrombin by Human Astrocyte Cells” J. Neurochemistry 72, 980 – 987.
  37. Wood, M. J. and Komives, E. A. (1999) “Production of Large Quantities of Isotopically-Labeled Protein in Pichia pastoris by Fermentation” J. Biomolecular NMR 13, 149 – 159.
  38. Zhang, Z., Komives, E. A. Sugio, S., Blacklow, S. C., Narayana, N., Xuong, N. H., Stock, A. M., Petsko, G. and Ringe, D. (1999) “The role of water in the catalytic efficiency of triosephosphate isomerase”. Biochemistry 38, 4389 – 4397.
  39. Mandell, J. G., Falick, A. M. and Komives, E. A. (1999) “Identification of Protein-Protein Interfaces by Amide Proton Exchange Coupled to MALDI-TOF Mass Spectrometry” in Mass Spectrometry in Biology and Medicine, A. L. Burlingame, ed. Humana Press pgs 91 – 109.
  40. Glover, K. J., Martini, P. M., Vold. R. R. and Komives, E. A. (1999) “Preparation of insoluble transmembrane peptides: Glycophorin-A, Prion (110-137), FGFR (368-397). Anal. Biochem. 272, 270 – 4.
  41. Baerga-Ortiz, A. J., Rezaie, A. R. and Komives, E. A. (2000) “Electrostatic Dependence of the Thrombin-Thrombomodulin interaction” J. Mol. Biol. 296: 651 – 658.
  42. Wood, M. J., Sampoli Benitez, B., Komives, E. A. (2000) “Solution structure of the smallest cofactor-active fragment of thrombomodulin” Nature Structural Biology 7: 200 – 204.
  43. Sampoli Benitez, B.and Komives, E. A. (2000) Disulfide bond plasticity in EGF” Proteins, Structure, Function and Genetics 40, 168 – 174.
  44. Whiles, J. A., Brasseur, R., Glover, K. J., Melacini, G., Komives, E. A. and Vold, R. R. (2001) “The Orientation and the Effects of Mastoparan X on Phospholipid Bicelles.” Biophys. J. 80, 280 – 293.
  45. Mandell, J. G. Baerga-Ortiz, A., Akashi, S., Takio, K. and Komives, E. A. (2001) “Solvent Accessibility of the Thrombin-Thrombomodulin Interface” J. Mol. Biol. 306, 575-589.
  46. Hughes, C. A., Mandell, J. G., Anand, G. S., Stock, A. M. and Komives, E. A. (2001) “Phosphorylation Causes Subtle Changes in Solvent Accessibility at the Interdomain Interface of Methylesterase CheB” J. Mol. Biol. 307, 967-976.
  47. Glover, K. J., Whiles, J. A., Wu, G., Yu, N., Deems, R., Struppe, J. O., Stark, R. E., Komives, E. A. and Vold, R. R. (2001) “Structural Evaluation of Phospholipid Bicelles for Solution-State Studies of Membrane Associated Biomolecules” Biophys. J. 81, 2163 – 2171.
  48. Glover, K. J., Whiles, J. A., Wood, M. J., Melacini, G., Komives, E. A. and Vold, R. R. (2001) “Conformational dimorphism and transmembrane orientation of Prion protein residues 110-136 in bicelles” Biochemistry 40, 13137-13142.
  49. Baerga-Ortiz, A., Hughes, C. A., Mandell, J. G. and Komives, E. A. (2002) “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 Science 11, 1300-1308.
  50. Anand, G. S., Hughes, C. A., Jones, J. M., Taylor, S. S. and Komives, E. A. (2002) “Amide H/2H exchange reveals communication between the cAMP- and catalytic subunit-binding sites in the regulatory subunit of protein kinase A” Journal of Molecular Biology 323, 377-386.
  51. Whiles, J. A. Glover, K. J., Vold, R. R. and Komives, E. A. (2002) “Methods for studying transmembrane peptides in bicelles: Consequences of hydrophobic mismatch and peptide sequence.” Journal of Magnetic Resonance 158, 149-156.
  52. Huxford, T. Mischler, D., Reeves, R. Sengchanthalangsy, L. L. Huang, D.-B., Phelps, C. B., Hughes, C. A., Komives, E. A. and Ghosh, G. (2002) “Solvent exposed non-contacting amino acids play a critical role in the NF-kB/IkBa complex formation” Journal of Molecular Biology 324, 587-597.
  53. Wood, M. J., Becvar, L. A., Prieto, J. H., Melacini, G., and Komives, E. A. (2003) “NMR Structures Reveal How Oxidation Inactivates Thrombomodulin” Biochemistry 42, 11932-42.
  54. Jennings, L. L., Malecki, M., Komives, E. A. and Taylor, P. (2003) “Direct Analysis of the Kinetic Profiles of Organophosphate-Acetycholinesterase Adducts by MALDI-TOF Mass Spectrometry” Biochemistry 42, 11083-91.
  55. Croy, J. E., Shin, W. D., Knauer, M. F., Knauer, D. J., and Komives, E. A. (2003) “All three LDL receptor homology regions of the LDL receptor-related protein (LRP) bind multiple ligands” Biochemistry 42, 13049-57.
  56. Anand, G. S., Law, D., Mandell, J. G., Snead, A. N., Tsigelny, I., Taylor, S. S., Ten Eyck, L., andKomives, E. A. (2003) “Identification of the Protein Kinase A Regulatory RI-Catalytic Subunit Interface by Amide H/2H Exchange and Protein Docking” Proc. Nat. Acad. Sci. U. S. A. 100, 13264-13269.
  57. Baerga-Ortiz, A., Bergqvist, S. P., Mandell, J. G. and Komives, E. A. (2004) “Two different proteins that compete for binding to thrombin have opposite kinetic and thermodynamic profiles”. Protein Science 13, 166-176.
  58. Croy, C. H., Koeppe, J. R., Bergqvist, S. P.and Komives, E. A. (2004) “Allosteric Changes in Solvent Accessibility Observed in Thrombin upon Active Site Occupation” Biochemistry 43, 5346-55.
  59. Croy, J. E., Brandon, T. and Komives, E. A. (2004) “Two apolipoprotein E mimetic peptides, apoE(130-149) and apoE(141-155)2, bind to LRP1” Biochemistry 43, 7328-35.
  60. Croy, C. H, Bergqvist, S. P., Huxford, T., Ghosh, G. and Komives, E. A. (2004) “Biophysical Characterization of Free IB in Solution” Protein Science 13, 1767-77.
  61. Prieto, J. H., Sampoli Benitez, B. A., Melacini, G., Johnson, D. A., Wood, M. A. and Komives, E. A.(2005) “Dynamics of the Fragment of Thrombomodulin containing the fourth and fifth EGF-like domains correlate with function” Biochemistry 44, 1225-1233.
  62. Komives, E. A. (2005) “Protein-protein interaction dynamics by amide H/2H exchange mass spectrometry”, International Journal of Mass Spectrometry 240, 285-290.
  63. Wood, M. J., Prieto, J. H. and Komives, E. A. (2005) “Structural and functional consequences of methionine oxidation in thrombomodulin” Biochim. Biophys. Acta 1703, 141-147.
  64. Mandell, J. G., Baerga-Ortiz, A., Falick, A. H. and Komives, E. A. (2005) “Measurement of Solvent Accessibility at Protein-protein Interfaces”. Methods in Molecular Biology, vol. 305 “Protein-Ligand Interactions”, Chapter 4, pgs 65-80, G. U. Nienhaus, Ed.
  65. Mandell, J. G., Baerga-Ortiz, A., Croy, C. H., Falick, A. H. and Komives, E. A. (2005) “Application of Hydrogen-Exchange- Mass Spectrometry for the Study of Protein-Protein Interactions” Current Protocols in Protein Science vol. 20.
  66. Koeppe, J. R., Seitova, A., Mather, T. and Komives, E. A. (2005) “Thrombomodulin tightens the thrombin active site loops to promote protein C activation” Biochemistry 44, 14784-91.
  67. Ferreiro, D. U., Cho, S. S. Komives, E. A. and Wolynes, P. G. (2005) “The energy landscape of modular repeat proteins: Topology determines folding mechanism in the ankyrin family” J. Mol. Biol. 354, 679-92.
  68. Hotchko, M., Anand, G., Komives, E. A., and Ten Eyck, L. (2006) “Automated extraction of backbone deuteration levels from amide H/2H exchange mass spectrometry experiments” Protein Science 15, 583 – 601. PMC2249778
  69. Shi, J., Koeppe, J. R., Komives, E. A. and Taylor, P. (2006) Ligand-induced conformational changes in the acetylcholine binding protein analyzed by hydrogen-deuterium exchange mass spectrometry. J Biol Chem. 281, 12170-7.
  70. Chen, A., Komives, E. A. and Schroeder, J. I. (2006) An improved grafting technique for mature Arabidopsis plants demonstrates long-distance shoot-to-root transport of phytochelatins in Arabidopsis. Plant Physiol. 141, 108-20.
  71. Koeppe, J. R. and Komives, E. A. (2006) Amide H/2H Exchange Reveals a Mechanism of Thrombin Activation. Biochemistry 45, 7724-32. PMC2535819
  72. Bergqvist, S., Croy, C. H., Kjaergaard, M., Huxford, T., Ghosh, G. and Komives, E. A. (2006) Thermodynamics reveal that helix four in the NLS of NF-kappaB p65 anchors IkappaBalpha, forming a very stable complex. J. Mol. Biol. 360, 421-34.
  73. Truhlar, S. M. E., Croy, C. H., Torpey, J. W., Koeppe, J. R. and Komives, E. A. (2006) Solvent Accessibility of Protein Surfaces by Amide H/2H Exchange MALDI-TOF Mass Spectrometry. J. Am. Soc. Mass Spectrom. 17, 1490 – 97.
  74. Truhlar, S. M. E., Torpey, J. W., and Komives, E. A. (2006) Regions of IB that are critical for its inhibition of NF B•DNA interaction fold upon binding to NF-B. Proc. Nat. Acad. Sci. U. S. A. 103, 18951-6. PMC1748158
  75. Ferreiro, D. U., Cervantes, C. F., Truhlar, S. M. E., Cho, S. S., Wolynes, P. G., and Komives, E. A.(2007) Stabilizing IB by ‘consensus’ design. J. Mol. Biol. 365, 1201-16. PMC1866275
  76. Latzer, J., Papoian, G. A., Prentiss, M. C., Komives, E. A., Wolynes, P. G. (2007) Induced fit, folding, and recognition of the NF-kappaB-nuclear localization signals by IkappaBalpha and IkappaBbeta. J Mol Biol. 367, 262-74.
  77. Wu, X., Li, Z. F., Brooks, R., Komives, E. A., Torpey, J. W., Engvall, E., Gonias, S. L. and Shelton, G. D. (2007) Autoantibodies in canine masticatory muscle myositis recognize a novel myosin binding protein-C family member. J. Immunol. 179, 4939-44.
  78. Sung, D. Y., Lee, D., Harris, H., Raab, A., Feldmann, J., Meharg, A., Kumabe, B., Komives, E. A. and Schroeder, J. I. (2007) Identification of an arsenic tolerant double mutant with a thiol-mediated component and increased arsenic tolerance in phyA mutants. Plant J. 49, 1064-75.
  79. Ferreiro, D. U. and Komives, E. A. (2007) The plastic landscape of repeat proteins. Proc Natl Acad Sci U S A. 104, 7735-6.PMC1876514
  80. Anand, G. S., Hotchko, M., Brown, S. H., Ten Eyck, L. F., Komives, E. A. and Taylor, S. S. (2007) R-subunit Isoform Specificity in Protein Kinase A: Distinct Features of Protein Interfaces in PKA Types I and II by Amide H/(2)H Exchange Mass Spectrometry. J Mol Biol. 374, 487-99.
  81. Ferreiro, D. U., Hegler, J. A., Komives, E. A. and Wolynes, P. G. (2007) Localizing Frustration in native proteins and protein assemblies. Proc. Nat. Acad. Sci. U. S. A. 104, 19819-24. PMC2148382
  82. Barrick, D., Ferreiro, D. U., Komives, E. A. (2008) Folding landscapes of ankyrin repeat proteins: experiments meet theory. Curr. Opp. Struct. Biol. 18, 27-34.PMC2680087
  83. Truhlar, S. M. E., Cervantes, Torpey, J., Kjaergaard, M., Komives, E. A. (2008) Rapid mass spectrometric analysis of 15N-Leu incorporation fidelity during preparation of specifically labeled NMR samples. Protein Sci 17, 1636–1639. PMC2525515
  84. Truhlar, S. M. E., Mathes, E., Cervantes, C. F., Ghosh, G., Komives, E. A. (2008) Pre-folding IB alters control of NF-B signaling. J. Mol. Biol. 380, 67-82.PMC2519148
  85. Huang CM, Torpey JW, Liu YT, Chen YR, Williams KE, Komives EA, Gallo RL. (2008) A Peptide with ProGln C-terminus in the Human Saliva Peptidome Exerts Bactericidal Activity Against Propionibacterium acnes. Antimicrob Agents Chemother. 52, 1834-6. PMC2346631
  86. Betts, G. N, van der Geer, P., and Komives, E. A. (2008) Structural and Functional Consequences of Tyrosine Phosphorylation in the LRP1 Cytoplasmic Domain. J Biol Chem. 283, 15656-64. PMC2414285
  87. Mendoza-Cózatl DG, Butko E, Springer F, Torpey JW, Komives EA, Kehr J, Schroeder JI. (2008) 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. 54, 249-59.
  88. Ferreiro, D.U., Walczak, A. M., Komives, E. A. and Wolynes, P. G. (2008) The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures. PLoS Comput Biol. 16, 4(5):e1000070. PMC2366061
  89. Truhlar, S. M., Komives, E. A. (2008) LRR Domain Folding: Just Put a Cap on It! Structure. 16, 655-7.
  90. Sue, S.C., Cervantes, C., Komives, E.A., Dyson, H.J. (2008) Transfer of flexibility between ankyrin repeats in IkappaBalpha upon formation of the NF-kappaB complex. J Mol Biol. 380, 917-931.PMC2603615
  91. Koeppe, J. R., Beach, M. A., Baerga-Ortiz, A., Kerns, S. J. and Komives, E. A. (2008) Mutations in the fourth EGF-like domain affect thrombomodulin-induced changes in the active site of thrombin. Biochemistry 47, 10933-9. PMC2630536
  92. Bergqvist, S., Ghosh, G. and Komives, E. A. (2008) The IB /NF-B complex has two hot-spots, one at either end of the interface. Prot. Sci. 17, 2051-8.PMCID: PMC2590914
  93. Gertsman, I., Gan, L., Guttman, M., Lee, K., Duda, R. L., Hendrix, R. W., Komives, E. A., Johnson, J. E. (2009) “Tertiary transitions about quaternary staples guides viral capsid maturation in Bacteriophage HK97” Nature 458, 646-50.PMC2765791
  94. Cervantes, C. F., Markwick, P. R. L., Sue, S. C., McCammon, J. A., Dyson, H. J., Komives, E. A. (2009) Functional dynamics of the folded ankyrin repeats of IkappaB alpha revealed by nuclear magnetic resonance. Biochemistry 48, 8023-31. PMCID: PMC2728578
  95. Guttman, M., Betts, G. N., Ghassemian, M., Barnes, H., van der Geer, P. and Komives, E. A. (2009) Interactions of the NPXY microdomains of the LDL Receptor-Related Protein 1. Proteomics 9, 5016-28. PMCID: PMC2862490
  96. Bergqvist, S., Alverdi, V., Mengel, B., Hoffmann, A., Ghosh, G., and Komives, E. A. (2009) Kinetic enhancement of NF-B•DNA dissociation by IB. Proc. Nat. Acad. Sci. U. S. A. 106, 19328-33. PMC2780789
  97. Markwick, P. R., Cervantes, C. F., Abel, B. L., Komives, E. A., Blackledge, M. , McCammon, J. A. (2010) Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. J Am Chem Soc. 132, 1220-1.PMC2812018
  98. Guttman, M., Prieto, J. H., Croy, J. E., Komives, E. A. (2010) Decoding of Lipoprotein-Receptor Interactions: Properties of Ligand Binding Modules Governing Interactions with Apolipoprotein E. Biochemistry 49, 1207-16.PMC2821871
  99. Ferreiro, D. U., Komives, E.A. (2010) Molecular Mechanisms of System Control of NF-kappaB Signaling by IkappaBalpha. Biochemistry 49, 1560-7. PMC2865148
  100. Gertsman, I., Komives, E. A., Johnson, J. E. (2010) HK97 Maturation Studied by Crystallography and H/(2)H Exchange Reveals the Structural Basis for Exothermic Particle Transitions. J Mol Biol. 397, 560-574. PMC2938056.
  101. Guttman, M., Prieto, J. H., Handel. T., Domaille, P., Komives, E. A. (2010) Structure of the Minimal Interface Between ApoE and LRP. J. Mol. Biol. 398, 306-19. PMC2880916.
  102. Gertsman, I., Fu, C., Huang, R., Komives, E. A., Johnson, J. E. (2010) Critical salt bridges guide capsid assembly, stability, and maturation behavior in Bacteriophage HK97. (2010) Mol Cell Proteomics 9, 1752-63. PMC2938056.
  103. Mathes E, Wang L, Komives E, Ghosh G. (2010) Flexible regions within IkappaBalpha create the ubiquitin-independent degradation signal. J Biol Chem. 285, 32927-36. PMCID: PMC2963393.
  104. Devries, I., Hampton-Smith, R. J., Mulvihill, M., Alverdi, V., Peet, D. J., and Komives, E. A., (2010) Consequences of IkappaB alpha hydroxylation by the factor inhibiting HIF (FIH) FEBS Lett. 584, 4725-30. PMC3034650.
  105. Cervantes, C. F., Bergqvist, S., Kjaergaard, M., Kroon, G., Sue, S-C., Dyson, H. J., and Komives, E. A.(2010) The RelA nuclear localization signal folds upon binding to IkBa. J Mol Biol 405, 754-64. PMC3056351
  106. Sue SC, Alverdi V, Komives, E. A., Dyson HJ. (2011) 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. 108, 1367-72. PMC3029698.
  107. Ferreiro DU, Hegler JA, Komives, E. A., Wolynes PG. (2011) On the role of frustration in the energy landscapes of allosteric proteins. Proc Natl Acad Sci U S A. 108, 3499-503. PMC3048099.
  108. Devries, I., Ferreiro, D. U., Sánchez, I. E. and Komives, E. A. (2011) Folding Kinetics of the Cooperatively Folded Subdomain of the IκBα Ankyrin Repeat Domain. J. Mol. Biol. 408, 163-76. PMC3081522
  109. Lamboy, J. A., Kim, H., Lee, K. S., Ha, T. and Komives, E. A. (2011) Visualization of the nanospring dynamics of the IB ankyrin repeat domain in real time Proc. Nat. Acad. Sci. U S A. 108, 10178-83. PMC3121830
  110. Treuheit, NA, Beach, MA. and Komives, E. A.(2011) Thermodynamic compensation upon binding to exosite 1 and the active site of thrombin Biochemistry 50, 4590-6. PMC3107735
  111. Mulvihill, M, Guttman, M. and Komives, E. A. (2011) Protein Interactions among Fe65, the Low-Density Lipoprotein Receptor-Related Protein, and the Amyloid Precursor Protein Biochemistry 50(28):6208-16. PMC3139566
  112. Guttman, M. and Komives, EA (2011) 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 50(51):11001-8. PMC3263374
  113. Craig PO, Lätzer J, Weinkam P, Hoffman RM, Ferreiro DU, Komives, EA Wolynes PG. (2011) Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes. J Am Chem Soc. 133(43):17463-72. PMC3203634
  114. Jobe TO, Sung DY, Akmakjian G, Pham A, Komives, EA, Mendoza-Cózatl DG, Schroeder JI. (2012) Feedback inhibition by thiols outranks glutathione depletion: a luciferase-based screen reveals glutathione-deficient γ-ECS and glutathione synthetase mutants impaired in cadmium-induced sulfate assimilation. Plant J. 70(5):783-795 doi: 10.1111/j.1365-313X.2012.04924.x
  115. Komives, EA. (2012) Consequences of Fuzziness in the NFκB/IκBα Interaction. Adv Exp Med Biol. 725:74-85. PMC3603378
  116. Dyson HJ, Komives, EA (2012) Role of disorder in IkB-NFkB interaction. IUBMB Life 64(6):499-505. doi: 10.1002/iub.1044. PMC3575514
  117. Meyer JG, Komives, EA (2012) Charge state coalescence during electrospray ionization improves peptide identification by tandem mass spectrometry. J Am Soc Mass Spec 23, 1390-1399. doi: 10.1007/s13361-012-0404-0.
  118. Guo L, Ghassemian M, Komives, EA, Russell P. (2012) Cadmium-Induced Proteome Remodeling Regulated by Spc1/Sty1 and Zip1 in Fission Yeast. Toxicol Sci. 129(1):200-212.
  119. Fuglestad B, Gasper PM, Tonelli M, McCammon JA, Markwick PR, Komives, EA. (2012) The dynamic structure of thrombin in solution. Biophys J. 103(1):79-88. PMC3388214
  120. Gasper, PM, Fuglestad, B., Komives, EA, Markwick, PRL, McCammon, JA. (2012) Allosteric networks in thrombin distinguish procoagulant and anticoagulant activities. Proc Natl Acad Sci USA 109(52):21216-22. PMC3535651
  121. Balasubramaniam D, Komives, EA. (2012) Hydrogen-exchange mass spectrometry for the study of intrinsic disorder in proteins. Biochim Biophys Acta. doi:pii: S1570-9639(12)00250-6. 10.1016/j.bbapap.2012.10.009. PMC3600394
  122. Schafer NP, Hoffman RM, Burger A, Craig PO, Komives, EA, Wolynes PG. (2012) Discrete kinetic models from funneled energy landscape simulations. PLoS One. 2012;7(12):e50635. doi: 10.1371/journal.pone.0050635. PMC3520928
  123. Cervantes CF, Handley LD, Sue SC, Dyson HJ, Komives, EA. (2012) Long-range effects and functional consequences of stabilizing mutations in the ankyrin repeat domain of IκBα J Mol Biol. 425(5):902-13. PMC3744861
  124. Balasubramaniam D, Komives, EA. (2013) Hydrogen-exchange mass spectrometry for the study of intrinsic disorder in proteins. Biochim Biophys Acta. doi:pii: S1570-9639(12)00250-6. 10.1016/j.bbapap.2012.10.009. PMC3600394
  125. Fuglestad B, Gasper PM, McCammon JA, Markwick PR, Komives, EA. (2013) Correlated Motions and Residual Frustration in Thrombin. J Phys Chem B. 117(42):12857-63. PMC3808083
  126. Lamboy-Gonzalez, J., Kim, H., Dembinski, H., Ha, T.J., Komives, EA. (2013) Single molecule FRET reveals the native state dynamics of the IκBα ankyrin repeat domain. J Mol Biol. 425(14):2578-90. PMC3758917
  127. Ramirez-Sarmiento C, Baez M, Wilson CAM, Babul J, Komives, EA, Guixé V. (2013) Observation of solvent penetration during cold denaturation of E. coli phosphofructokinase-2. Biophys J 104, 2254-2263. PMC3660636
  128. Stein RS, Li N, He W, Komives, EA, Wang W. (2013) Recognition of methylated peptides by Drosophila melanogaster polycomb chromodomain. J Proteome Res. 12(3):1467-77. PMC4258113
  129. Li N, Stein RS, He W, Komives, EA, Wang W. (2013) Identification of methyllysine peptides binding to CBX6 chromodomain in the human proteome. Mol Cell Proteomics. 12(10):2750-60. PMC3790288
  130. Alverdi V, Hetrick B, Joseph S, Komives, EA (2014) Direct observation of a transient ternary complex during IκBα-mediated dissociation of NFκB from DNA. Proc Nat Acad Sci USA 111(1):225-30. PMC3890772
  131. Meyer JG, Kim S, Maltby DA, Ghassemian M, Bandeira N, Komives, EA (2014) Expanding proteome coverage with orthogonal-specificity alpha-lytic proteases. Mol Cell Proteomics 13, 823-35. doi: 10.1074/mcp.M113.034710 PMC3945911
  132. Dembinski H, Wismer K, Balasubramaniam D, Gonzalez HA, Alverdi V, Iakoucheva L, Komives, EA (2014) Predicted disorder-to-order transition mutations in IκBα disrupt function. Phys. Chem. Chem. Phys., 2014, 16 (14), 6480 – 6485. PMC4040282
  133. Perera VR, Newton GL, Parnell JM, Komives, EA, Pogliano K.(2014) Purification and characterization of the Staphylococcus aureus bacillithiol transferase BstA. Biochim Biophys Acta. 1840(9):2851-2861 doi: 10.1016/j.bbagen.2014
  134. Boechi L, Pierce L, Komives, EA, McCammon JA. (2014) Trypsinogen activation as observed in accelerated molecular dynamics simulations. Protein Sci. 23(11):1550-8. doi: 10.1002/pro.2532 PMC4241106
  135. Balasubramaniam D, Schiffer J, Parnell J, Mir SP, Amaro RE, Komives, EA (2015) How the Ankyrin and SOCS Box Protein, ASB9, Binds to Creatine Kinase. Biochemistry 108(9):2350-61. doi: 10.1021/bi501420n. PMC4348336
  136. Ramírez-Sarmiento CA, Baez M, Zamora RA, Balasubramaniam D, Babul J, Komives, EA, Guixé V. (2015) The folding unit of phosphofructokinase-2 as defined by the biophysical properties of a monomeric mutant. Biophys J. 108(9):2350-61. doi: 10.1016/j.bpj.2015.04.001.
  137. Handley LD, Treuheit NA, Venkatesh VJ, Komives, EA. (2015) Thrombomodulin binding selects the catalytically active form of thrombin. Biochemistry. 2015 54(43):6650-8. PMC4697735
  138. Mangas I, Taylor P, Vilanova E, Estévez J, França TC, Komives, EA, Radić Z. (2016) Resolving pathways of interaction of mipafox and a sarin analog with human acetylcholinesterase by kinetics, mass spectrometry and molecular modeling approaches. Arch Toxicol. 90(3):603-16. PMC4833118
  139. Potoyan DA, Zheng W, Komives, EA, Wolynes PG. (2016) Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network. Proc Natl Acad Sci U S A. 113(1):110-115. PMC4711861
  140. Trelle MB, Ramsey KM, Lee TC, Zheng W, Lamboy J, Wolynes PG, Deniz A, Komives, EA. (2016) Binding of NFκB Appears to Twist the Ankyrin Repeat Domain of IκBα. Biophys J. 110(4):887-95. PMC4776026
  141. Potoyan DA, Zheng W, Ferreiro DU, Wolynes PG, Komives, EA. (2016) PEST Control of Molecular Stripping of NFκB from DNA Transcription Sites. J Phys Chem B. 120(33):8532-8538.
  142. Mukherjee SP, Quintas PO, McNulty R, Komives, EA, Dyson HJ. (2016) Structural characterization of the ternary complex that mediates termination of NF-κB signaling by IκBα. Proc Natl Acad Sci U S A 113(22):6212-7. PMC4896678
  143. Medina E, Córdova C, Villalobos P, Reyes J, Komives, EA, Ramírez-Sarmiento CA, Babul J. (2016) Three-Dimensional Domain Swapping Changes the Folding Mechanism of the Forkhead Domain of FoxP1. Biophys J. 110(11):2349-60.
  144. Schiffer JM, Malmstrom RD, Parnell J, Ramirez-Sarmiento C, Reyes J, Amaro RE, Komives, EA. (2016) Model of the Ankyrin and SOCS Box Protein, ASB9, E3 Ligase Reveals a Mechanism for Dynamic Ubiquitin Transfer. Structure 2;24(8):1248-56). PMC4972691
  145. Handley, LD, Fuglestad, B, Stearns, K, Tonelli, M, Fenwick, RB, Markwick, PRL, Komives, EA. (2017) NMR reveals a dynamic allosteric pathway in thrombin. Scientific Reports 7:39575. PMC5216386
  146. Dembinski, HD, Wismer, K, Vargas, JD, Suryawanshi, GW, Kern, N, Kroon, GJA, Dyson, HJ, Hoffmann, A, Komives, EA. (2017) Functional importance of stripping in NFκB signaling revealed by a stripping-impaired IκBα mutant. Proc Natl Acad Sci U S A Feb 6. pii: 201610192.
  147. Ramsey, KM, Dembinski, HD, Chen, W, Ricci, CG, Komives, EA. (2017) DNA and IκBα both induce long range conformational changes in NFκB. J Mol Biol. pii: S0022-2836(17)30094-3.