KomivesLab

Specializing in Biophysics Research

Dr. Elizabeth A. Komives

Distinguished Professor of Chemistry and Biochemistry

Department of Chemistry & Biochemistry

U.C. San Diego
La Jolla, CA 92093-0378
Telephone: (858) 534-3058
email: ekomives@ucsd.edu

Education

MASSACHUSETTS INSTITUTE OF TECHNOLOGY
M.S. in Toxicology, B.S. in Chemistry, 1982

UNIVERSITY OF CALIFORNIA SAN FRANCISCO
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

HARVARD UNIVERSITY
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)
  • Distinguished Professor (2019-present)

Professional Activities

  • Advisory Committee, UCSF Mass Spectrometry Resource (1999 – 2017)
  • 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 (2008-2019)
  • 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 (2017-2019)
  • 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

Publications

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 π-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. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  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. 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 .
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  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” J. Chem. Tech. and Biotech.  67, 143 – 148.
  26. 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.
  27. 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.
  28. 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.
  29. Vindigni, A., White, C. E., Komives, E. A. and Di Cera, E. (1997) “Energetics of Thrombin-Thrombomodulin Interaction” Biochemistry  36, 6674 – 6681.
  30. 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.
  31. 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.
  32. Mandell, J. G., Falick, A. M. and Komives, E. A. (1998) “Measurement of Amide Hydrogen Exchange by MALDI-TOF Mass Spectrometry” Anal. Chem. 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 Struct. Biol. 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) “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” J. Mol. Biol.  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.” J. Mag. Res. 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” J. Mol. Biol. 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., and Komives, E. A. (2003) “Identification of the Protein Kinase A Regulatory RIa-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 IkBa 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”, Int. J. Mass Spectrom. 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. 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
  65. 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.
  66. 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
  67. 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.
  68. 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.
  69. Koeppe, J. R. and Komives, E. A. (2006) Amide H/2H Exchange Reveals a Mechanism of Thrombin Activation. Biochemistry 45, 7724-32. PMC2535819
  70. 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.
  71. 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.
  72. Truhlar, S. M. E., Torpey, J. W., and Komives, E. A. (2006) Regions of IkBa that are critical for its inhibition of NF‑kB•DNA interaction fold upon binding to NF-kB. Proc. Nat. Acad. Sci. U. S. A. 103, 18951-6.  PMC1748158
  73. Ferreiro, D. U., Cervantes, C. F., Truhlar, S. M. E., Cho, S. S., Wolynes, P. G., and Komives, E. A.  (2007) Stabilizing IkBalpha by ‘consensus’ design.  J. Mol. Biol. 365, 1201-16. PMC1866275
  74. 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.
  75. 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.
  76. 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.
  77. 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.
  78. 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
  79. 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
  80. 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
  81. 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
  82. 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
  83. 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.
  84. 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
  85. 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
  86. 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
  87. 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
  88. Bergqvist, S., Ghosh, G. and Komives, E. A. (2008) The IkBa /NF-kB complex has two hot-spots, one at either end of the interface. Prot. Sci. 17, 2051-8.PMCID: PMC2590914
  89. Truhlar, S. M. E., Mathes, E., Cervantes, C. F., Ghosh, G., Komives, E. A. (2008) Pre-folding IkBa alters control of NF-kB signaling. J. Mol. Biol. 380, 67-82.PMC2519148
  90. Sung DY, Kim TH, Komives EA, Mendoza-Cózatl DG, Schroeder JI. (2009) ARS5 is a component of the 26S proteasome complex, and negatively regulates thiol biosynthesis and arsenic tolerance in Arabidopsis. Plant J. 59(5), 802-13. PMC2830867
  91. 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. PMC2862490
  92. Bergqvist, S., Alverdi, V., Mengel, B., Hoffmann, A., Ghosh, G., and Komives, E. A. (2009) Kinetic enhancement of NF-kB•DNA dissociation by IkBa. Proc. Nat. Acad. Sci. U. S. A. 106, 19328-33. PMC2780789
  93. 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. PMC2728578
  94. 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
  95. 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
  96. 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.
  97. 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.
  98. 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.
  99. 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. PMC2963393.
  100. 100. Ferreiro, D. U., Komives, E.A. (2010) Molecular Mechanisms of System Control of NF-kappaB Signaling by IkappaBalpha. Biochemistry 49, 1560-7. PMC2865148
  101. 101.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.
  102. 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
  103. Sue SC, Alverdi V, Komives EA, 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.
  104. 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
  105. Lamboy, J. A., Kim, H., Lee, K. S., Ha, T. and Komives, E. A. (2011) Visualization of the nanospring dynamics of the IkBa ankyrin repeat domain in real time Proc. Nat. Acad. Sci. U S A. 108, 10178-83. PMC3121830
  106. Treuheit, NA, Beach, MA. and Komives, EA. (2011) Thermodynamic compensation upon binding to exosite 1 and the active site of thrombin Biochemistry 50, 4590-6. PMC3107735
  107. Mulvihill, M, Guttman, M. and Komives EA (2011) Protein Interactions among Fe65, the Low-Density Lipoprotein Receptor-Related Protein, and the Amyloid Precursor Protein Biochemistry 50(28):6208-16. PMC3139566
  108. Ferreiro DU, Hegler JA, Komives EA, 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.
  109. 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
  110. 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. doi: 10.1021/ja207506zPMC3203634
  111. 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
  112. Komives EA. (2012) Consequences of Fuzziness in the NFκB/IκBα Interaction. Adv Exp Med Biol. 725:74-85. PMC3603378
  113. Dyson HJ, Komives EA. (2012) Role of disorder in IkB-NFkB interaction. IUBMB Life 64(6):499-505. doi: 10.1002/iub.1044. PMC3575514
  114. 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.
  115. 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. doi: 10.1093/toxsci/kfs179 PMC3713068
  116. 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
  117. 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
  118. 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
  119. 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. doi:pii: S0022-2836(12)00945-X.10.1016/j.jmb.2012.12.012. PMC3744861
  120. 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
  121. 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. doi: 10.1021/jp402107u. PMC3808083
  122. Lamboy, J., Kim, H., Dembinski, H., Ha, T.J., Komives, E. A. (2013) Single molecule FRET reveals the native state dynamics of the IκBα ankyrin repeat domain. J Mol Biol. 425(14):2578-90. doi: 10.1016/j.jmb.2013.04.015 PMC3758917
  123. 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. doi: 10.1016/j.bpj.2013 PMC3660636
  124. Stein RS, Li N, He W, Komives E, Wang W. (2013) Recognition of methylated peptides by Drosophila melanogaster polycomb chromodomain. J Proteome Res. 12(3):1467-77. PMC4258113
  125. Li N, Stein RS, He W, Komives E, Wang W. (2013) Identification of methyllysine peptides binding to CBX6 chromodomain in the human proteome. Mol Cell Proteomics. 12(10):2750-60. PMC3790288
  126. 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. doi: 10.1073/pnas.1318115111 PMC3890772
  127. 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
  128. Dembinski H, Wismer K, Balasubramaniam D, Gonzalez HA, Alverdi V, Iakoucheva L, and Komives EA (2014) Predicted disorder-to-order transition mutations in IκBα disrupt function. Phys. Chem. Chem. Phys., 2014, 16 (14), 6480 – 6485 doi: 10.1039/c3cp54427c PMC4040282
  129. 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
  130. 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
  131. 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
  132. 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
  133. 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.
  134. Handley LD, Treuheit NA, Venkatesh VJ, Komives EA. (2015) Thrombomodulin binding selects the catalytically active form of thrombin. Biochemistry. 2015 54(43):6650-8. doi: 10.1021/acs.biochem.5b00825. PMC4697735
  135. 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
  136. 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
  137. 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. PMC5389414
  138. 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
  139. 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.
  140. 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 24(8):1248-56. PMC4972691
  141. 14 Handley, LD, Fuglestad, B, Stearns, K, Tonelli, M, Fenwick, RB, Markwick, PRL, and Komives, EA (2017) NMR reveals a dynamic allosteric pathway in thrombin. Scientific Reports 7:39575. PMC5216386
  142. Dembinski, HE, 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 114, 1916-1921. PMC5338396
  143. Ramsey KM, Dembinski HE, Chen W, Ricci CG, Komives EA. (2017) DNA and IκBα Both Induce Long-Range Conformational Changes in NFκB. J Mol Biol. 429(7):999-1008. PMC5389416
  144. Carvajal AI, Vallejos G, Komives EA, Castro-Fernández V, Leonardo DA, Garratt RC, Ramírez-Sarmiento CA, Babul J. (2017) Unusual dimerization of a BcCsp mutant leads to reduced conformational dynamics. FEBS J. 284(12):1882-1896.
  145. 144 Kromann-Hansen T, Lange EL, Sørensen HP, Hassanzadeh-Ghassabeh G, Huang M, Jensen JK, Muyldermans S, Declerck PJ, Komives EA, Andreasen PA. (2017) Discovery of a novel conformational equilibrium in urokinase-type plasminogen activator. Sci Rep. 7(1):3385 PMC5469797
  146. Wong J, Young T, Zhang J, Liu S, Leser G, Komives EA, Lamb R, Zhou H, Salafsky J, and Jardetsky T. (2017) Monomeric ephrinB2 binding induces allosteric changes in Nipah virus G that precede its full activation. Nat Comm 8, 781, 1-11. PMC5626764
  147. Lumpkin, RJ, Gu, H, Zhu, Y, Leonard, M, Ahmad, AS, Clauser, KR, Meyer, JR, Bennett, EJ, Komives, EA (2017) Site-specific identification and quantitation of endogenous SUMO modifications under native conditions Nat Comm 8(1):1171. PMC5660086
  148. Ferreiro DU, Komives EA, Wolynes PG. (2017) Frustration, function and folding. Curr Opin Struct Biol. 48:68-73.
  149. Potoyan DA, Bueno C, Zheng W, Komives EA, Wolynes PG. (2017) Resolving the NFκB Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors. J Am Chem Soc. 139(51):18558-18566.  PMC5803749
  150. Kim JK, Liu J, Hu X, Yu C, Roskamp K, Sankaran B, Huang L, Komives EA, Qiao F. (2017) Structural Basis for Shelterin Bridge Assembly. Mol Cell. 68(4):698-714. e5. PMC5698806
  151. West AMV, Komives EA, Corbett KD. (2018) Conformational dynamics of the Hop1 HORMA domain reveal a common mechanism with the spindle checkpoint protein Mad2. Nucleic Acids Res. 46(1):279-292. PMC5758881
  152. Kromann-Hansen T, Lange EL, Lund IK, Høyer-Hansen G, Andreasen PA, Komives EA. (2018) Ligand binding modulates the structural dynamics and activity of urokinase-type plasminogen activator: A possible mechanism of plasminogen activation. PLoS One. 13(2):e0192661.  PMC5805342
  153. Narang D, Chen W, Ricci CG, Komives EA. (2018) RelA-containing NFκB dimers have strikingly different DNA-binding cavities in the absence of DNA. J Mol Biol. 430(10):1510-1520. PMC5951767
  154. Ramirez-Sarmiento C, and Komives EA. (2018) Hydrogen-deuterium exchange mass spectrometry reveals folding and allostery in protein-protein interactions, Methods S1046-2023(17)30457-7. PMC6051914
  155. Peacock R, Davis J, Markwick PRL, Komives EA. (2018) Dynamic Consequences of Mutation of Tryptophan 215 in Thrombin. Biochemistry 57(18):2694-2703. PMC5940494
  156. Rahnamoun H, Lee J, Sun X, Lu H, Ramsey KH, Komives EA, Lauberth SM (2018) RNAs Interact with BRD4 to Promote Enhanced Chromatin Engagement and Transcription Activation. Nat Struct Mol Biol 25(8):687-697.
  157. Ramsey KM, Narang D, Komives EA (2018) Prediction of the Presence of a Seventh Ankyrin Repeat in IκBε from Homology Modeling Combined with Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS). Protein Sci 27(9):1624-1635. PMC6194264.
  158. Gudlur A, Zeraik AE, Hirve N, Rajanikanth V, Bobkov AA, Ma G, Zheng S, Wang Y, Zhou Y, Komives EA, Hogan PG. (2018) Calcium sensing by the STIM1 ER-luminal domain. Nat Commun. 9(1):4536. PMC6208404
  159. Hard R, Li N, He W, Ross B, Mo GCH, Peng Q, Stein RSL, Komives E, Wang Y, Zhang J, Wang W. (2018) Deciphering and engineering chromodomain-methyllysine peptide recognition. Sci Adv.  Nov 7;4(11):eaau1447     PMC6221542
  160. Markwick PRL, Peacock RB, Komives EA. (2019) Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery. Biophys J. 116(1):49-56. PMC6342732
  161. Ramsey KM, Chen W, Marion JD, Bergqvist S, Komives EA. (2019) Exclusivity and Compensation in NFκB Dimer Distributions and IκB Inhibition. Biochemistry. 58(21):2555-2563. PMC6642826
  162. Maity K, Heumann JM, McGrath AP, Kopcho NJ, Hsu PK, Lee CW, Mapes JH, Garza D, Krishnan S, Morgan GP, Hendargo KJ, Klose T, Rees SD, Medrano-Soto A, Saier MH Jr, Piñeros M, Komives EA, Schroeder JI, Chang G, Stowell MHB. (2019) Cryo-EM structure of OSCA1.2 from Oryza sativa elucidates the mechanical basis of potential membrane hyperosmolality gating. Proc Natl Acad Sci U S A. 116(28):14309-14318.161.
  163. Kalogriopoulos NA, Rees SD, Ngo T, Kopcho NJ, Ilatovskiy AV, Sun N, Komives EA, Chang G, Ghosh P, Kufareva I. (2019) Structural basis for GPCR-independent activation of heterotrimeric Gi proteins. Proc Natl Acad Sci U S A. 116(33):16394-16403.
  164. Kopcho N, Chang G, Komives EA. (2019) Dynamics of ABC Transporter P-glycoprotein in Three Conformational States. Sci Repts 9, 1. 15092.
  165. Galaz-Davison P, Molina JA, Silletti S, Komives EA, Knauer SH, Artsimovitch I, Ramírez-Sarmiento CA. (2019) Differential Local Stability Governs the Metamorphic Fold Switch of Bacterial Virulence Factor RfaH. Biophys J. pii: S0006-3495(19)30937-3.
  166. Lumpkin RJ, Komives EA. (2019) DECA, A Comprehensive, Automatic Post-processing Program for HDX-MS Data. Mol Cell Proteomics. 18, 2516-2523.