{"id":88,"date":"2016-08-04T16:13:45","date_gmt":"2016-08-04T16:13:45","guid":{"rendered":"http:\/\/localhost:8888\/wordpress\/?page_id=88"},"modified":"2021-07-07T00:51:53","modified_gmt":"2021-07-07T00:51:53","slug":"elizabeth-a-komives","status":"publish","type":"page","link":"https:\/\/komiveslab.ucsd.edu\/?page_id=88","title":{"rendered":"Elizabeth A. Komives"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\"> Dr. Elizabeth A. Komives <\/h2>\n\n\n\n<div style=\"height:32px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<div class=\"wp-block-media-text alignwide is-stacked-on-mobile is-vertically-aligned-top\" style=\"grid-template-columns:19% auto\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"350\" height=\"350\" src=\"https:\/\/i2.wp.com\/komiveslab.ucsd.edu\/wordpress\/wp-content\/uploads\/2016\/09\/ElizabethKomives.jpg?resize=350%2C350\" alt=\"\" class=\"wp-image-295 size-full\" srcset=\"https:\/\/i0.wp.com\/komiveslab.ucsd.edu\/wp-content\/uploads\/2016\/09\/ElizabethKomives.jpg?w=350&amp;ssl=1 350w, https:\/\/i0.wp.com\/komiveslab.ucsd.edu\/wp-content\/uploads\/2016\/09\/ElizabethKomives.jpg?resize=150%2C150&amp;ssl=1 150w, https:\/\/i0.wp.com\/komiveslab.ucsd.edu\/wp-content\/uploads\/2016\/09\/ElizabethKomives.jpg?resize=300%2C300&amp;ssl=1 300w\" sizes=\"auto, (max-width: 350px) 100vw, 350px\" data-recalc-dims=\"1\" \/><\/figure><div class=\"wp-block-media-text__content\">\n<p>Distinguished Professor of Chemistry and Biochemistry <\/p>\n\n\n\n<p>Department of Chemistry &amp; Biochemistry<\/p>\n\n\n\n<p> U.C. San Diego<br> La Jolla, CA 92093-0378<br> Telephone: (858) 534-3058<br> email: ekomives@ucsd.edu<\/p>\n<\/div><\/div>\n\n\n\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading\">Education<\/h2>\n\n\n\n<p>MASSACHUSETTS INSTITUTE OF TECHNOLOGY<br>M.S. in Toxicology, B.S. in Chemistry, 1982<\/p>\n\n\n\n<p>UNIVERSITY OF CALIFORNIA SAN FRANCISCO<br>Ph.D. in Pharmaceutical Chemistry with Paul R. Ortiz de Montellano 1982 &#8211; 1987<br>Research Topic: The Mechanism of p-Bond Oxidation by Cytochrome P-450<\/p>\n\n\n\n<p>HARVARD UNIVERSITY<br>NIH Postdoctoral Fellow with Jeremy R. Knowles 1987 &#8211; 1990<br>Research Topics: Analysis of Triosephosphate Isomerase Mutants using FTIR and X-ray crystallography<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Academic Honors<\/h2>\n\n\n\n<ul class=\"wp-block-list\"><li>Regents Fellowship (1982 &#8211; 1983)<\/li><li>Graduate Opportunity Fellowship (1983 &#8211; 1984)<\/li><li>NIH Graduate Traineeship (1984 &#8211; 1986)<\/li><li>NIH Postdoctoral Traineeship (1987 &#8211; 1989)<\/li><li>Long Award for Excellence in Teaching (1983)<\/li><li>Rita Allen Scholar (1991 &#8211; 1996)<\/li><li>Searle Scholar (1992 &#8211; 1995)<\/li><li>Kaiser Award for Excellence in Teaching, First Year Medical Students (1999)<\/li><li>Brown and Williamson Scholar, University of Louisville (2000)<\/li><li>Barany Award for Outstanding Contributions to Biophysics, Biophysical Society (2000)<\/li><li>Bruno Zimm Scholar (first awardee, 2010)<\/li><li>Distinguished Professor (2019-present)<\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Professional Activities<\/h2>\n\n\n\n<ul class=\"wp-block-list\"><li>Advisory Committee, UCSF Mass Spectrometry Resource (1999 &#8211; 2017)<\/li><li>Nominating Committee, Protein Society, (2001 &#8211; 2004)<\/li><li>Session Chair, Biophysics of Protein Binding Events, ACS National Meeting (2002)<\/li><li>Council, Biophysical Society (2002 &#8211; 2006)<\/li><li>Minority Affairs Committee, Biophysical Society (2006-9)<\/li><li>Session Chair, Protein Binding and Conformation, ASMS Meeting Montreal (2003)<\/li><li>Editorial Board, Molecular and Cellular Proteomics (2002 &#8211; 2008)<\/li><li>Associate Editor, Molecular and Cellular Proteomics (2008-2019)<\/li><li>Editorial Advisory Board, Biochemistry (2007-present)<\/li><li>Chair, Molecular Biophysics Subgroup, Biophysical Society (2008)<\/li><li>Awards Committee, Biophysical Society (2015-present, Chair, 2016-2017)<\/li><li>Chair, Intrinsically Disordered Proteins Subgroup, Biophysical Society (2014)<\/li><li>Executive Council, Protein Society (2017-2019)<\/li><li>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<\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">University Service<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"http:\/\/bpmsf.ucsd.edu\/\" target=\"_blank\" rel=\"noreferrer noopener\">Mass Spectrometry Facility (Faculty Oversight)<\/a><\/li><li><a href=\"http:\/\/mbtg.ucsd.edu\/\" target=\"_blank\" rel=\"noreferrer noopener\">Molecular Biophysics Training Program (Program Director)<\/a><\/li><li><a href=\"http:\/\/cancer.ucsd.edu\/\" target=\"_blank\" rel=\"noreferrer noopener\">Cancer Center Member<\/a><\/li><li><a href=\"http:\/\/biomedsci.ucsd.edu\/\" target=\"_blank\" rel=\"noreferrer noopener\">Biomedical Sciences Graduate Program Member<\/a><\/li><li><a href=\"http:\/\/interfaces.ucsd.edu\/\" target=\"_blank\" rel=\"noreferrer noopener\">Interfaces Training Program Steering Committee Member<\/a><\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Publications<\/h2>\n\n\n\n<p>Visit the <a href=\"http:\/\/localhost:8888\/wordpresspublications\/\">publications<\/a> section for PDF files of recent publications.<\/p>\n\n\n\n<ol class=\"wp-block-list\"><li>Penman, B. W.; Crespi, C. L.; Liber, H. L.; <strong>Komives, E. A<\/strong>. and Thilly, W. G. (1983) &#8220;Mutation of Human Lymphoblasts Exposed to Low Concentrations of Chemical Mutagens for Long Periods of Time&#8221;.\u00a0 <em>Mutat. Res.<\/em>\u00a0 <em>108<\/em>: 417 &#8211; 436.<\/li><li>DeLuca, J. G.; Kaden, D. A.; <strong>Komives, E. A<\/strong>. and Thilly, W.G. (1984) &#8220;Mutation of Xeroderma Pigmentosum Lymphoblasts by Far-ultraviolet Light&#8221;. <em>Mutat. Res.<\/em> <em>128<\/em>: 47 &#8211; 57.<\/li><li>Kaden, D. A.; Call, K. M.; Leong, P. M.; <strong>Komives, E. A<\/strong>. and Thilly, W.G. (1987) &#8220;Killing and Mutation of Human Lymphoblast Cells by Aflatoxin B1: Evidence for an Inducible Repair Response&#8221;.\u00a0 <em>Can. Res.<\/em>\u00a0 <em>47<\/em>: 1993 &#8211; 2001.<\/li><li>Ortiz de Montellano, P. R. and <strong>Komives, E. A.<\/strong> (1985) &#8220;Branchpoint for Heme Alkylation and Metabolite Formation in the Oxidation of Arylacetylenes by Cytochrome P-450&#8221;. <em>J. Biol. Chem.<\/em> <em>260<\/em>: 3330 &#8211; 3336.<\/li><li><strong>Komives, E. A<\/strong>. and Ortiz de Montellano, P. R. (1987) &#8220;Mechanism of Oxidation of \u03c0-Bonds by Cytochrome P-450: Electronic Requirements of the Transition State in the Turnover of Phenylacetylenes&#8221;. <em>J. Biol. Chem.<\/em> <em>262<\/em>: 9793 &#8211; 9802.<\/li><li><strong>Komives, E. A.<\/strong>, Tew, D., Olmstead, M. M. and Ortiz de Montellano, P. R. (1988) &#8220;Models for Cytochrome P-450 Prosthetic Heme Alkylation. Reaction of Diazoacetophenone with (Tetraphenylporphyrinato)iron(II) Chloride&#8221;\u00a0 <em>Inorganic Chem.<\/em> <em>27<\/em>: 3112 &#8211; 3117.<\/li><li><strong>Komives, E. A.<\/strong>, Chang. L. C., Lolis, E., Tilton, R. F., Petsko, G. and Knowles, J. R. (1991) &#8220;Electrophilic Catalysis in Triosephosphate Isomerase: The Role of Histidine-95&#8221; <em>Biochemistry 30<\/em>, \u00a0\u00a0\u00a0 3011 &#8211; 3019.<\/li><li>Warn-Cramer, B. J., Broze, G. J. and <strong>Komives, E. A<\/strong>. (1992) &#8220;cDNA Sequence of Rabbit Tissue Factor Pathway Inhibitor&#8221; <em>Nucleic Acids Research<\/em> 20: 3548.\u00a0 Corrigendum.<\/li><li>Lodi, P. J., Chang. L. C., Knowles, J. R. and <strong>Komives, E. A<\/strong>. (1994) &#8220;Triosephosphtae Isomerase Requires a Positively Charged Active Site: The Role of Lysine-12&#8221; <em>Biochemistry<\/em>\u00a0 <em>33<\/em>: 2809 &#8211; 2814.<\/li><li>Joseph-McCarthy, D., Rost, L. E., <strong>Komives, E. A.<\/strong> and Petsko, G. A. (1994) &#8220;Crystal Structure of the Mutant Yeast Triosephosphate Isomerase in which the Catalytic Base Glu-165 is Changed to Asp&#8221; <em>Biochemistry<\/em>\u00a0 <em>33<\/em>: 2824 &#8211; 2830.<\/li><li>Joseph-McCarthy, D., Lolis, E., <strong>Komives, E. A<\/strong>. and Petsko, G. A. (1994) &#8220;Crystal Structure of the K12M\/G15A Triosephosphate Isomerase Double Mutant and Electrostatic Analysis of the Active Site&#8221; <em>Biochemistry<\/em>\u00a0 <em>33<\/em>: 2815 &#8211; 2823.<\/li><li>Zhang, Z., Sugio, S., <strong>Komives, E. A.<\/strong>, Liu, K. D., Knowles, J. R., Petsko, G. A. and Ringe, D. (1994) &#8220;Crystal Structure of Recombinant Chicken Triosephosphate Isomerase-Phosphoglycolohydroxamate Complex at 1.8-\u00c5 Resolution&#8221; <em>Biochemistry<\/em>\u00a0 <em>33<\/em>: 2830 &#8211; 2837.<\/li><li>Fanuel, L., Granier, B., Wilkin, JM., Bellefroid-Bourguignon, C., Joris, B., Knowles, J., <strong>Komives, E<\/strong>., Van Beeumen, J., Ghuysen, JM., Frere, J. M. (1994) &#8220;The precursor of the Streptomyces R61 DD-peptidase containing a C-terminal extension is inactive&#8221; <em>Febs Letters<\/em> <em>351<\/em>: 49-52.<\/li><li>White, C. E., Kempi, N. M. and <strong>Komives, E. A<\/strong>. (1994) &#8220;Expression of Highly Disulfide-Bonded Proteins in <em>Pichia Pastoris<\/em>&#8221;\u00a0 <em>Structure<\/em> <em>\u00a02<\/em>: 1003 &#8211; 1005.<\/li><li>Srinivasan, J., Hu, S., Hrabal, R., Zhu, Y., <strong>Komives, E. A<\/strong>. and Ni, F. (1994) &#8220;Thrombin-Bound Structure of an EGF Subdomain from Thrombomodulin Determined by Transferred Nuclear Overhauser Effects&#8221; <em>Biochemistry<\/em> <em>\u00a033<\/em>: 13553 &#8211; 13560.<\/li><li>Lougheed, J. L., Bowman, C. A. Meininger, D. P.and <strong>Komives, E. A<\/strong>. (1995) &#8220;Thrombin Inhibition by Cyclic Peptides from Thrombomodulin&#8221; <em>Protein Science. 4<\/em>:773-780.<\/li><li>Hunter, M. J. and <strong>Komives, E. A<\/strong>. (1995) &#8220;Deprotection of S-Acetamidomethyl Cysteine Containing Peptides by Silver Trifluoromethanesulfonate Avoids the Oxidation of Methionines&#8221; <em>Anal. Biochem<\/em>. <em>228<\/em>:173 &#8211; 177.<\/li><li>Meininger, D. P., Hunter, M. J. and <strong>Komives, E. A<\/strong>. (1995) &#8220;Synthesis and Preliminary Structure of the Fourth EGF-like Domain of Thrombomodulin&#8221; <em>Protein Science<\/em>\u00a0 4, 1683 &#8211; 1695 .<\/li><li>Hunter, M. J. and <strong>Komives, E. A<\/strong>. (1995) &#8220;Thrombin-Binding Affinities of Different Disulfide Bonding Isomers of the Fifth EGF-like Domain of Thrombomodulin&#8221; <em>Protein Science<\/em> <em>4<\/em>: 2129 &#8211; 2137.<\/li><li><strong>Komives, E. A.<\/strong>, Lougheed, J. C., Liu, K., Zhang, Z., Petsko, G. A. and Ringe, D. (1995) &#8220;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&#8221; <em>Biochemistry<\/em> <em>34<\/em>: 13612-21.<\/li><li>White, C. E., Hunter, M. J., Meininger, D. P., White, L. R. and <strong>Komives, E. A<\/strong>. (1995) &#8220;Large Scale Expression, Purification and Characterization of the Smallest Active Fragment of Thrombomodulin: The Roles of the Sixth Domain and of Methionine-388&#8221;\u00a0 <em>Protein Engineering<\/em> 8, 1177 &#8211; 1187.<\/li><li>Blackmar, C., Healy, V. L., Narendra, U., Hrabal, R., Ni, F. and <strong>Komives, E. A.<\/strong> (1995) &#8220;Structure\/Activity of the Region of Thrombomodulin that binds to Thrombin&#8221; <em>Bioorganic Chemistry<\/em> <em>23<\/em>, 519 &#8211; 527.<\/li><li><strong>Komives, E. A.<\/strong>, Hunter, M. J., Meininger, D. P., White, L. R. and White, C. E. (1995) &#8220;Structure\/Function of the Fourth and Fifth EGF Domains of Thrombomodulin&#8221;\u00a0 <em>Techniques in Protein Chemistry VII<\/em> 391 &#8211; 400.<\/li><li>Hrabal, R., <strong>Komives, E. A.<\/strong> and Ni, F. (1996) &#8220;Structural Resiliency of an EGF-like Subdomain Bound to its Target Protein, Thrombin&#8221; <em>Protein Science <\/em>\u00a0<em>5<\/em>, 195 &#8211; 203.<\/li><li>Chen, Y. L., Cino, J.,White, C. E. and <strong>Komives, E. A<\/strong>. (1996) &#8220;Continuous Production of Thrombomodulin from a <em>Pichia pastoris<\/em> in Fermentation&#8221; <em>J. Chem. Tech. and Biotech. <\/em>\u00a0<em>67<\/em>, 143 &#8211; 148.<\/li><li>Chen, Y. L., Cino, J., Hart, G., Freedman, D., White, C. E. and <strong>Komives, E. A.<\/strong> (1997) &#8220;High Protein Expression in Fermentation of Recombinant <em>Pichia Pastoris<\/em> by Fed Batch Process&#8221; <em>Process Biochemistry<\/em> <em>32<\/em>, 107 &#8211; 111.<\/li><li>White, C. E., Hunter, M. J., Meininger, D. P., Garrod, S. and <strong>Komives, E. A.<\/strong> (1996) &#8220;The Fifth EGF-like domain of Thrombomodulin Does Not Have An EGF-like Disulfide Bonding Pattern&#8221; <em>Proc. Nat. Acad. Sci. U. S. A.<\/em>\u00a0 <em>93<\/em>, 10177 &#8211; 82.<\/li><li><strong>Komives, E. A<\/strong>., Lougheed, J. C., Zhang, Z., Sugio, S., Narayana, N., Xuong, N. H., Petsko, G. and Ringe, D. (1996)&#8221;The Structural Basis for Pseudoreversion of the H95N Lesion by the Secondary S96P Mutation in Triosephosphate Isomerase&#8221; <em>Biochemistry 35<\/em>, 15474-484.<\/li><li>Vindigni, A., White, C. E., <strong>Komives, E. A.<\/strong> and Di Cera, E. (1997) &#8220;Energetics of Thrombin-Thrombomodulin Interaction&#8221; <em>Biochemistry<\/em>\u00a0 <em>36<\/em>, 6674 &#8211; 6681.<\/li><li>Gleeson, M.A. G., White. C. E., Meininger, D. P. and <strong>Komives, E. A<\/strong>. (1997) &#8220;Generation of Protease Deficient Strains of <em>Pichia pastoris<\/em> and Their Use in Heterologous Protein Expression&#8221; <em>Methods in Molecular Biology<\/em> <em>103<\/em>, 81 \u2013 94.<\/li><li>Sampoli Benitez B., Hunter, M. J., Meininger D. P. and <strong>Komives, E. A<\/strong>. (1997) &#8220;Structure of the Fifth EGF-like Domain of Thrombomodulin: An EGF-like Domain with a Novel Disulfide Bonding Pattern&#8221;\u00a0 (1997) <em>J. Mol. Biol.<\/em> <em>273<\/em>, 913 &#8211; 926.<\/li><li>Mandell, J. G., Falick, A. M. and <strong>Komives, E. A.<\/strong> (1998) &#8220;Measurement of Amide Hydrogen Exchange by MALDI-TOF Mass Spectrometry&#8221; <em>Anal. Chem.<\/em> <em>70<\/em>, 3987 &#8211; 3995.<\/li><li>Mandell, J. G., Falick, A. M. and <strong>Komives, E. A.<\/strong> (1998) &#8220;Identification of Protein-Protein Interfaces by Decreased Amide Proton Solvent Accessibility&#8221; <em>Proc. Nat. Acad. Sci. U. S. A.<\/em> <em>95<\/em>, 14705 &#8211; 14710.<\/li><li>Struppe, J., <strong>Komives, E. A.<\/strong>, Taylor, S. S. and Vold, R. R. (1998) &#8220;2H NMR Studies of a Myristoylated Peptide in Neutral and Acidic Phospholipid Bicelles.&#8221; <em>Biochemistry<\/em> 37, 15523 &#8211; 15527.<\/li><li>Greenwald, J., Le, V., Corrigan, A., Fischer, W., <strong>Komives, E.<\/strong>, Vale, W., Choe, S. (1998) Characterization of the extracellular ligand-binding domain of the type II activin receptor.\u00a0\u00a0 <em>Biochemistry<\/em> 37, 16711 &#8211; 16718.<\/li><li>Mentz, S., DeLacalle, S. Baerga-Ortiz, A. J., Knauer, M. F., Knauer, D. J. and <strong>Komives, E. A<\/strong>. (1999) &#8220;Binding and Internalization of Thrombin by Human Astrocyte Cells&#8221; <em>J. Neurochemistry<\/em> <em>72<\/em>, 980 \u2013 987.<\/li><li>Wood, M. J. and <strong>Komives, E. A.<\/strong> (1999) &#8220;Production of Large Quantities of Isotopically-Labeled Protein in <em>Pichia pastoris<\/em> by Fermentation&#8221; <em>J. Biomolecular NMR<\/em> <em>13<\/em>, 149 &#8211; 159.<\/li><li>Zhang, Z., <strong>Komives, E. A.<\/strong> Sugio, S., Blacklow, S. C., Narayana, N., Xuong, N. H., Stock, A. M., Petsko, G. and Ringe, D. (1999) &#8220;The role of water in the catalytic efficiency of triosephosphate isomerase&#8221;.\u00a0 <em>Biochemistry 38<\/em>, 4389 \u2013 4397.<\/li><li>Mandell, J. G., Falick, A. M. and <strong>Komives, E. A.<\/strong> (1999) &#8220;Identification of Protein-Protein Interfaces by Amide Proton Exchange Coupled to MALDI-TOF Mass Spectrometry&#8221; in Mass Spectrometry in Biology and Medicine, A. L. Burlingame, ed.\u00a0 Humana Press pgs 91 &#8211; 109.<\/li><li>Glover, K. J., Martini, P. M., Vold. R. R. and <strong>Komives, E. A.<\/strong> (1999) &#8220;Preparation of insoluble transmembrane peptides: <em>Glycophorin-A, Prion (110-137), FGFR (368-397).<\/em>\u00a0 <em>Anal. Biochem<\/em>. <em>272<\/em>, 270 &#8211; 4.<\/li><li>Baerga-Ortiz, A. J., Rezaie, A. R. and <strong>Komives, E. A<\/strong>. (2000) &#8220;Electrostatic Dependence of the Thrombin-Thrombomodulin interaction&#8221; <em>J. Mol. Biol.<\/em> 296: 651 &#8211; 658.<\/li><li>Wood, M. J., Sampoli Benitez, B., <strong>Komives, E. A.<\/strong> (2000) &#8220;Solution structure of the smallest cofactor-active fragment of thrombomodulin&#8221; <em>Nature Struct. Biol.<\/em> 7: 200 &#8211; 204.<\/li><li>Sampoli Benitez, B.and <strong>Komives, E. A. <\/strong>(2000) Disulfide bond plasticity in EGF&#8221; <em>Proteins, Structure, Function and Genetics<\/em> <em>40<\/em>, 168 &#8211; 174.<\/li><li>Whiles, J. A., Brasseur, R., Glover, K. J., Melacini, G., <strong>Komives, E. A.<\/strong> and Vold, R. R. (2001) &#8220;Orientation and the Effects of Mastoparan X on Phospholipid Bicelles.&#8221; <em>Biophys. J.<\/em> <em>80<\/em>, 280 &#8211; 293.<\/li><li>Mandell, J. G. Baerga-Ortiz, A., Akashi, S., Takio, K. and <strong>Komives, E. A<\/strong>. (2001) &#8220;Solvent Accessibility of the Thrombin-Thrombomodulin Interface&#8221; <em>J. Mol. Biol. 306<\/em>, 575-589.<\/li><li>Hughes, C. A., Mandell, J. G., Anand, G. S., Stock, A. M. and <strong>Komives, E. A<\/strong>. (2001) &#8220;Phosphorylation Causes Subtle Changes in Solvent Accessibility at the Interdomain Interface of Methylesterase CheB&#8221; <em>J. Mol. Biol.<\/em> <em>\u00a0307<\/em>, 967-976.<\/li><li>Glover, K. J., Whiles, J. A., Wu, G., Yu, N., Deems, R., Struppe, J. O., Stark, R. E., <strong>Komives, E. A.<\/strong> and Vold, R. R. (2001) &#8220;Structural Evaluation of Phospholipid Bicelles for Solution-State Studies of Membrane Associated Biomolecules&#8221; <em>Biophys. J<\/em>. 81, 2163 &#8211; 2171.<\/li><li>Glover, K. J., Whiles, J. A., Wood, M. J., Melacini, G., <strong>Komives, E. A.<\/strong> and Vold, R. R. (2001) \u201cConformational dimorphism and transmembrane orientation of Prion protein residues 110-136 in bicelles\u201d <em>Biochemistry 40<\/em>, 13137-13142.<\/li><li>Baerga-Ortiz, A., Hughes, C. A., Mandell, J. G. and <strong>Komives, E. A.<\/strong> (2002) \u201cEpitope 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\u201d <em>Protein Science<\/em> <em>11<\/em>, 1300-1308.<\/li><li>Anand, G. S., Hughes, C. A., Jones, J. M., Taylor, S. S. and <strong>Komives, E. A.<\/strong> (2002) \u201cAmide H\/<sup>2<\/sup>H exchange reveals communication between the cAMP- and catalytic subunit-binding sites in the regulatory subunit of protein kinase A\u201d <em>J. Mol. Biol.<\/em> <em>\u00a0323<\/em>, 377-386.<\/li><li>Whiles, J. A. Glover, K. J., Vold, R. R. and <strong>Komives, E. A.<\/strong> (2002) \u201cMethods for studying transmembrane peptides in bicelles: Consequences of hydrophobic mismatch and peptide sequence.\u201d <em>J. Mag. Res.<\/em> <em>158<\/em>, 149-156.<\/li><li>Huxford, T. Mischler, D., Reeves, R. Sengchanthalangsy, L. L. Huang, D.-B., Phelps, C. B., Hughes, C. A., <strong>Komives, E. A<\/strong>. and Ghosh, G. (2002) \u201cSolvent exposed non-contacting amino acids play a critical role in the NF-kB\/IkBa complex formation\u201d <em>J. Mol. Biol.<\/em> <em>324, 587-597<\/em>.<\/li><li>Wood, M. J., Becvar, L. A., Prieto, J. H., Melacini, G., and <strong>Komives, E. A.<\/strong> (2003) \u201cNMR Structures Reveal How Oxidation Inactivates Thrombomodulin<sup>\u201d<\/sup> <em>Biochemistry<\/em> 42, 11932-42.<\/li><li>Jennings, L. L., Malecki, M., <strong>Komives, E. A.<\/strong> and Taylor, P. (2003) \u201cDirect Analysis of the Kinetic Profiles of Organophosphate-Acetycholinesterase Adducts by MALDI-TOF Mass Spectrometry\u201d <em>Biochemistry<\/em> <em>42<\/em>, 11083-91.<\/li><li>Croy, J. E., Shin, W. D., Knauer, M. F., Knauer, D. J., and <strong>Komives, E. A.<\/strong> (2003) \u201cAll three LDL receptor homology regions of the LDL receptor-related protein (LRP) bind multiple ligands\u201d <em>Biochemistry<\/em> <em>42<\/em>, 13049-57.<\/li><li>Anand, G. S., Law, D., Mandell, J. G., Snead, A. N., Tsigelny, I., Taylor, S. S., Ten Eyck, L., and <strong>Komives, E. A.<\/strong> (2003) \u201cIdentification of the Protein Kinase A Regulatory RIa-Catalytic Subunit Interface by Amide H\/<sup>2<\/sup>H Exchange and Protein Docking\u201d <em>Proc. Nat. Acad. Sci. U. S. A.<\/em> <em>100<\/em>, 13264-13269.<\/li><li>Baerga-Ortiz, A., Bergqvist, S. P., Mandell, J. G. and <strong>Komives, E. A.<\/strong> (2004) \u201cTwo different proteins that compete for binding to thrombin have opposite kinetic and thermodynamic profiles\u201d. <em>Protein Science 13<\/em>, 166-176.<\/li><li>Croy, C. H., Koeppe, J. R., Bergqvist, S. P.and <strong>Komives, E. A.<\/strong> (2004) \u201cAllosteric Changes in Solvent Accessibility Observed in Thrombin upon Active Site Occupation\u201d <em>Biochemistry<\/em> <em>43<\/em>, 5346-55.<\/li><li>Croy, J. E., Brandon, T. and <strong>Komives, E. A.<\/strong> (2004) \u201cTwo apolipoprotein E mimetic peptides, apoE(130-149) and apoE(141-155)<sup>2<\/sup>, bind to LRP1\u201d <em>Biochemistry<\/em> <em>43<\/em>, 7328-35.<\/li><li>Croy, C. H, Bergqvist, S. P., Huxford, T., Ghosh, G. and <strong>Komives, E. A.<\/strong> (2004) \u201cBiophysical Characterization of Free IkBa in Solution\u201d <em>Protein Scienc<\/em>e <em>13<\/em>, 1767-77.<\/li><li>Prieto, J. H., Sampoli Benitez, B. A., Melacini, G., Johnson, D. A., Wood<sup>, <\/sup>M. A. and <strong>Komives, E. A.<\/strong> (2005) \u201cDynamics of the Fragment of Thrombomodulin containing the fourth and fifth EGF-like domains correlate with function\u201d <em>Biochemistry<\/em> <em>44<\/em>, 1225-1233.<\/li><li><strong>Komives, E. A.<\/strong> (2005) \u201cProtein-protein interaction dynamics by amide H\/<sup>2<\/sup>H exchange mass spectrometry\u201d, <em>Int. J. Mass Spectrom. 240<\/em>, 285-290.<\/li><li>Wood, M. J., Prieto, J. H. and <strong>Komives, E. A.<\/strong> (2005) \u201cStructural and functional consequences of methionine oxidation in thrombomodulin\u201d <em>Biochim. Biophys. Acta 1703<\/em>, 141-147.<\/li><li>Koeppe, J. R., Seitova, A., Mather, T. and <strong>Komives, E. A.<\/strong> (2005) \u201cThrombomodulin tightens the thrombin active site loops to promote protein C activation\u201d <em>Biochemistry <\/em>44, 14784-91<\/li><li>Ferreiro, D. U., Cho, S. S. <strong>Komives, E. A.<\/strong> and Wolynes, P. G. (2005) \u201cThe energy landscape of modular repeat proteins: Topology determines folding mechanism in the ankyrin family\u201d <em>J. Mol. Biol.<\/em> 354, 679-92.<\/li><li>Hotchko, M., Anand, G., <strong>Komives, E. A.<\/strong>, and Ten Eyck, L. (2006) &#8220;Automated extraction of backbone deuteration levels from amide H\/<sup>2<\/sup>H exchange mass spectrometry experiments&#8221; <em>Protein Science<\/em> 15, 583 &#8211; 601. PMC2249778<\/li><li>Shi, J., Koeppe, J. R., <strong>Komives, E. A.<\/strong> and Taylor, P. (2006) Ligand-induced conformational changes in the acetylcholine binding protein analyzed by hydrogen-deuterium exchange mass spectrometry. <em>J Biol Chem.<\/em> 281, 12170-7.<\/li><li>Chen, A., <strong>Komives, E. A.<\/strong> and Schroeder, J. I. (2006) An improved grafting technique for mature Arabidopsis plants demonstrates long-distance shoot-to-root transport of phytochelatins in Arabidopsis. <em>Plant Physiol.<\/em> 141, 108-20.<\/li><li>Koeppe, J. R. and <strong>Komives, E. A<\/strong>. (2006) Amide H\/<sup>2<\/sup>H Exchange Reveals a Mechanism of Thrombin Activation. <em>Biochemistry<\/em> 45, 7724-32. PMC2535819<\/li><li>Bergqvist, S., Croy, C. H., Kjaergaard, M., Huxford, T., Ghosh, G. and <strong>Komives, E. A<\/strong>. (2006) Thermodynamics reveal that helix four in the NLS of NF-kappaB p65 anchors IkappaBalpha, forming a very stable complex. <em>J. Mol. Biol. <\/em>360, 421-34.<\/li><li>Truhlar, S. M. E., Croy, C. H., Torpey, J. W., Koeppe, J. R. and <strong>Komives, E. A.<\/strong> (2006) Solvent Accessibility of Protein Surfaces by Amide H\/<sup>2<\/sup>H Exchange MALDI-TOF Mass Spectrometry. <em>J. Am. Soc. Mass Spectrom. 17<\/em>, 1490 &#8211; 97.<\/li><li>Truhlar, S. M. E., Torpey, J. W., and <strong>Komives, E. A.<\/strong> (2006) Regions of IkBa that are critical for its inhibition of NF\u2011kB\u2022DNA interaction fold upon binding to NF-kB. <em>Proc. Nat. Acad. Sci. U. S. A. <\/em>103, 18951-6.\u00a0 PMC1748158<\/li><li>Ferreiro, D. U., Cervantes, C. F., Truhlar, S. M. E., Cho, S. S., Wolynes, P. G., and <strong>Komives, E. A.<\/strong>\u00a0 (2007) Stabilizing IkBalpha by \u2018consensus\u2019 design.\u00a0 <em>J. Mol. Biol.<\/em> 365, 1201-16. PMC1866275<\/li><li>Latzer, J., Papoian, G. A., Prentiss, M. C., <strong>Komives, E. A.<\/strong>, Wolynes, P. G. (2007) Induced fit, folding, and recognition of the NF-kappaB-nuclear localization signals by IkappaBalpha and IkappaBbeta. <em>J Mol Biol. 367<\/em>, 262-74.<\/li><li>Wu, X., Li, Z. F., Brooks, R., <strong>Komives, E. A.<\/strong>, 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. <em>J. Immunol.<\/em> <em>179<\/em>, 4939-44.<\/li><li>Sung, D. Y., Lee, D., Harris, H., Raab, A., Feldmann, J., Meharg, A., Kumabe, B., <strong>Komives, E. A<\/strong>. and Schroeder, J. I. (2007)\u00a0 Identification of an arsenic tolerant double mutant with a thiol-mediated component and increased arsenic tolerance in phyA mutants. <em>Plant J. 49<\/em>, 1064-75.<\/li><li>Anand, G. S., Hotchko, M., Brown, S. H., Ten Eyck, L. F., <strong>Komives, E. A.<\/strong> 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. <em>J Mol Biol. 374<\/em>, 487-99.<\/li><li>Ferreiro, D. U., Hegler, J. A., Komives, E. A. and Wolynes, P. G. (2007) Localizing Frustration in native proteins and protein assemblies. <em>Proc. Nat. Acad. Sci. U. S. A.<\/em> <em>104<\/em>, 19819-24. PMC2148382<\/li><li>Barrick, D., Ferreiro, D. U., <strong>Komives, E. A.<\/strong> (2008) Folding landscapes of ankyrin repeat proteins: experiments meet theory. <em>Curr. Opp. Struct. Biol.<\/em> 18, 27-34.PMC2680087<\/li><li>Truhlar, S. M. E., Cervantes, Torpey, J., Kjaergaard, M., <strong>Komives, E. A<\/strong>. (2008) Rapid mass spectrometric analysis of <sup>15<\/sup>N-Leu incorporation fidelity during preparation of specifically labeled NMR samples. <em>Protein Sci 17<\/em>, 1636\u20131639. PMC2525515<\/li><li>Huang CM, Torpey JW, Liu YT, Chen YR, Williams KE, <strong>Komives EA<\/strong>, Gallo RL. (2008) A Peptide with ProGln C-terminus in the Human Saliva Peptidome Exerts Bactericidal Activity Against Propionibacterium acnes. <em>Antimicrob Agents Chemother.<\/em> <em>52<\/em>, 1834-6. PMC2346631<\/li><li>Betts, G. N, van der Geer, P., and <strong>Komives, E. A.<\/strong> (2008) Structural and Functional Consequences of Tyrosine Phosphorylation in the LRP1 Cytoplasmic Domain. <em>J Biol Chem. 283<\/em>, 15656-64. PMC2414285<\/li><li>Mendoza-C\u00f3zatl DG, Butko E, Springer F, Torpey JW, <strong>Komives EA<\/strong>, 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. <em>Plant J. 54<\/em>, 249-59.<\/li><li>Ferreiro, D.U., Walczak, A. M., <strong>Komives, E. A.<\/strong> 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<\/li><li>Sue, S.C., Cervantes, C., <strong>Komives, E.A.<\/strong>, Dyson, H.J. (2008) Transfer of flexibility between ankyrin repeats in IkappaBalpha upon formation of the NF-kappaB complex. <em>J Mol Biol.<\/em> 380, 917-931.PMC2603615<\/li><li>Koeppe, J. R., Beach, M. A., Baerga-Ortiz, A., Kerns, S. J. and <strong>Komives, E. A<\/strong>. (2008) Mutations in the fourth EGF-like domain affect thrombomodulin-induced changes in the active site of thrombin. <em>Biochemistry<\/em> 47, 10933-9. PMC2630536<\/li><li>Gertsman, I., Gan, L., Guttman, M., Lee, K., Duda, R. L., Hendrix, R. W., <strong>Komives, E. A.<\/strong>, Johnson, J. E. (2009) \u201cTertiary transitions about quaternary staples guides viral capsid maturation in Bacteriophage HK97\u201d <em>Nature<\/em> <em>458<\/em>, 646-50.PMC2765791<\/li><li>Bergqvist, S., Ghosh, G. and <strong>Komives, E. A<\/strong>. (2008) The IkBa \/NF-kB complex has two hot-spots, one at either end of the interface. <em>Prot. Sci.<\/em> <em>17<\/em>, 2051-8.PMCID: PMC2590914<\/li><li>Truhlar, S. M. E., Mathes, E., Cervantes, C. F., Ghosh, G., <strong>Komives, E. A<\/strong>. (2008) Pre-folding IkBa alters control of NF-kB signaling. <em>J. Mol. Biol.<\/em> <em>380<\/em>, 67-82.PMC2519148<\/li><li>Sung DY, Kim TH, <strong>Komives EA<\/strong>, Mendoza-C\u00f3zatl DG, Schroeder JI. (2009) ARS5 is a component of the 26S proteasome complex, and negatively regulates thiol biosynthesis and arsenic tolerance in Arabidopsis. <em>Plant J<\/em>. 59(5), 802-13. PMC2830867<\/li><li>Guttman<sup>, <\/sup>M., Betts, G. N., Ghassemian, M., Barnes, H., van der Geer, P. and <strong>Komives, E. A.<\/strong> (2009) Interactions of the NPXY microdomains of the LDL Receptor-Related Protein 1. <em>Proteomics<\/em> <em>9<\/em>, 5016-28. PMC2862490<\/li><li>Bergqvist, S., Alverdi, V., Mengel, B., Hoffmann, A., Ghosh, G., and <strong>Komives, E. A.<\/strong> (2009) Kinetic enhancement of NF-kB\u2022DNA dissociation by IkBa. <em>Proc. Nat. Acad. Sci. U. S. A. 106,<\/em> 19328-33. PMC2780789<\/li><li>Cervantes, C. F., Markwick, P. R. L., Sue, S. C., McCammon, J. A., Dyson, H. J., <strong>Komives, E. A.<\/strong> (2009) Functional dynamics of the folded ankyrin repeats of IkappaB alpha revealed by nuclear magnetic resonance. <em>Biochemistry 48<\/em>, 8023-31. PMC2728578<\/li><li>Markwick, P. R., Cervantes, C. F., Abel, B. L., <strong>Komives, E. A.<\/strong>, Blackledge, M. McCammon, J. A. (2010) Enhanced conformational space sampling improves the prediction of chemical shifts in proteins.\u00a0 <em>J Am Chem Soc. 132<\/em>, 1220-1.PMC2812018<\/li><li>Guttman, M., Prieto, J. H., Croy, J. E., <strong>Komives, E. A.<\/strong> (2010) Decoding of Lipoprotein-Receptor Interactions: Properties of Ligand Binding Modules Governing Interactions with Apolipoprotein E. <em>Biochemistry 49<\/em>, 1207-16.PMC2821871<\/li><li>Gertsman, I., <strong>Komives, E. A.<\/strong>, Johnson, J. E. (2010) HK97 Maturation Studied by Crystallography and H\/(2)H Exchange Reveals the Structural Basis for Exothermic Particle Transitions. <em>J Mol Biol.<\/em> 397, 560-574. PMC2938056.<\/li><li>Guttman, M., Prieto, J. H., Handel. T., Domaille, P., <strong>Komives, E. A.<\/strong> (2010) Structure of the Minimal Interface Between ApoE and LRP. <em>J. Mol. 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F., Bergqvist, S., Kjaergaard, M., Kroon, G., Sue, S-C., Dyson, H. J., and <strong>Komives, E. A.<\/strong> (2010) The RelA nuclear localization signal folds upon binding to IkBa. <em>J Mol Biol<\/em> 405, 754-64. PMC3056351<\/li><li>Sue SC, Alverdi V, <strong>Komives EA<\/strong>, 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. <em>Proc Natl Acad Sci U S A. <\/em>108, 1367-72. PMC3029698.<\/li><li>Devries, I., Ferreiro, D. U., S\u00e1nchez, I. E. and <strong>Komives, E. A.<\/strong> (2011) Folding Kinetics of the Cooperatively Folded Subdomain of the I\u03baB\u03b1 Ankyrin Repeat Domain. <em>J. Mol. Biol.<\/em> 408, 163-76. PMC3081522<\/li><li>Lamboy, J. A., Kim, H., Lee, K. S., Ha, T. and <strong>Komives, E. A.<\/strong> (2011) Visualization of the nanospring dynamics of the IkBa ankyrin repeat domain in real time <em>Proc. Nat. Acad. Sci. U S A.<\/em> 108, 10178-83. PMC3121830<\/li><li>Treuheit, NA, Beach, MA. and <strong>Komives, EA<\/strong>. (2011) Thermodynamic compensation upon binding to exosite 1 and the active site of thrombin <em>Biochemistry<\/em> 50, 4590-6. PMC3107735<\/li><li>Mulvihill, M, Guttman, M. and <strong>Komives EA <\/strong>(2011) Protein Interactions among Fe65, the Low-Density Lipoprotein Receptor-Related Protein, and the Amyloid Precursor Protein <em>Biochemistry<\/em> 50(28):6208-16. PMC3139566<\/li><li>Ferreiro DU, Hegler JA, <strong>Komives EA<\/strong>, Wolynes PG. (2011) On the role of frustration in the energy landscapes of allosteric proteins. <em>Proc Natl Acad Sci U S A.<\/em> 108, 3499-503. PMC3048099.<\/li><li>Guttman, M. and <strong>Komives, EA<\/strong> (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. <em>Biochemistry<\/em> 50(51):11001-8. PMC3263374<\/li><li>Craig PO, L\u00e4tzer J, Weinkam P, Hoffman RM, Ferreiro DU, <strong>Komives EA<\/strong>, Wolynes PG. (2011) Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes. <em>J Am Chem Soc<\/em>. 133(43):17463-72. doi: 10.1021\/ja207506zPMC3203634<\/li><li>Jobe TO, Sung DY, Akmakjian G, Pham A, <strong>Komives EA<\/strong>, Mendoza-C\u00f3zatl DG, Schroeder JI. (2012) Feedback inhibition by thiols outranks glutathione depletion: a luciferase-based screen reveals glutathione-deficient \u03b3-ECS and glutathione synthetase mutants impaired in cadmium-induced sulfate assimilation. <em>Plant J<\/em>. 70(5):783-795 doi: 10.1111\/j.1365-313X.2012.04924.x<\/li><li><strong>Komives EA<\/strong>. (2012) Consequences of Fuzziness in the NF\u03baB\/I\u03baB\u03b1 Interaction. <em>Adv Exp Med Biol<\/em>. 725:74-85. PMC3603378<\/li><li>Dyson HJ, <strong>Komives EA<\/strong>. (2012) Role of disorder in IkB-NFkB interaction. <em>IUBMB Life<\/em> 64(6):499-505. doi: 10.1002\/iub.1044. PMC3575514<\/li><li>Meyer JG, <strong>Komives EA<\/strong>. (2012) Charge state coalescence during electrospray ionization improves peptide identification by tandem mass spectrometry. <em>J Am Soc Mass Spec<\/em> 23, 1390-1399. doi: 10.1007\/s13361-012-0404-0.<\/li><li>Guo L, Ghassemian M, <strong>Komives EA<\/strong>, Russell P. (2012) Cadmium-Induced Proteome Remodeling Regulated by Spc1\/Sty1 and Zip1 in Fission Yeast. <em>Toxicol Sci<\/em>. <em>129(1)<\/em>:200-212. doi: 10.1093\/toxsci\/kfs179 PMC3713068<\/li><li>Fuglestad B, Gasper PM, Tonelli M, McCammon JA, Markwick PR, <strong>Komives EA<\/strong>. (2012) The dynamic structure of thrombin in solution. <em>Biophys J<\/em>. 103(1):79-88. PMC3388214<\/li><li>Gasper, PM, Fuglestad, B., <strong>Komives, EA<\/strong>, Markwick, PRL, McCammon, JA. 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PMC4258113<\/li><li>Li N, Stein RS, He W, <strong>Komives E<\/strong>, Wang W. (2013) Identification of methyllysine peptides binding to CBX6 chromodomain in the human proteome. <em>Mol Cell Proteomics<\/em>. 12(10):2750-60. PMC3790288<\/li><li>Alverdi V, Hetrick B, Joseph S, <strong>Komives EA<\/strong> (2014) Direct observation of a transient ternary complex during I\u03baB\u03b1-mediated dissociation of NF\u03baB from DNA. <em>Proc Nat Acad Sci USA<\/em> 111(1):225-30. doi: 10.1073\/pnas.1318115111 PMC3890772<\/li><li>Meyer JG, Kim S, Maltby DA, Ghassemian M, Bandeira N, <strong>Komives EA<\/strong> (2014) Expanding proteome coverage with orthogonal-specificity alpha-lytic proteases. <em>Mol Cell Proteomics<\/em> 13, 823-35. doi: 10.1074\/mcp.M113.034710 PMC3945911<\/li><li>Dembinski H, Wismer K, Balasubramaniam D, Gonzalez HA, Alverdi V, Iakoucheva L, and <strong>Komives EA<\/strong> (2014) Predicted disorder-to-order transition mutations in I\u03baB\u03b1 disrupt function. Phys. Chem. Chem. Phys., 2014, 16 (14), 6480 \u2013 6485 doi: 10.1039\/c3cp54427c PMC4040282<\/li><li>Perera VR, Newton GL, Parnell JM, <strong>Komives EA<\/strong>, 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<\/li><li>Boechi L, Pierce L, <strong>Komives EA<\/strong>, McCammon JA. (2014) Trypsinogen activation as observed in accelerated molecular dynamics simulations. <em>Protein Sci. 23<\/em>(11):1550-8. doi: 10.1002\/pro.2532 PMC4241106<\/li><li>Balasubramaniam D, Schiffer J, Parnell J, Mir SP, Amaro RE, <strong>Komives EA<\/strong>. (2015) How the Ankyrin and SOCS Box Protein, ASB9, Binds to Creatine Kinase. <em>Biochemistry<\/em> 108(9):2350-61. doi: 10.1021\/bi501420n. PMC4348336<\/li><li>Mangas I, Taylor P, Vilanova E, Est\u00e9vez J, Fran\u00e7a TC, <strong>Komives EA<\/strong>, Radi\u0107 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<\/li><li>Ram\u00edrez-Sarmiento CA, Baez M, Zamora RA, Balasubramaniam D, Babul J, <strong>Komives EA<\/strong>, Guix\u00e9 V. (2015) The folding unit of phosphofructokinase-2 as defined by the biophysical properties of a monomeric mutant. <em>Biophys J. 108(9)<\/em>:2350-61. doi: 10.1016\/j.bpj.2015.04.001.<\/li><li>Handley LD, Treuheit NA, Venkatesh VJ, <strong>Komives EA<\/strong>. (2015) Thrombomodulin binding selects the catalytically active form of thrombin. <em>Biochemistry<\/em>. 2015 54(43):6650-8. doi: 10.1021\/acs.biochem.5b00825. PMC4697735<\/li><li>Potoyan DA, Zheng W, <strong>Komives EA<\/strong>, Wolynes PG. (2016) Molecular stripping in the NF-\u03baB\/I\u03baB\/DNA genetic regulatory network. Proc Natl Acad Sci U S A. 113(1):110-115. PMC4711861<\/li><li>Trelle MB, Ramsey KM, Lee TC, Zheng W, Lamboy J, Wolynes PG, Deniz A, <strong>Komives EA<\/strong>. (2016) Binding of NF\u03baB Appears to Twist the Ankyrin Repeat Domain of I\u03baB\u03b1. <em>Biophys J. 110<\/em>(4):887-95. PMC4776026<\/li><li>Potoyan DA, Zheng W, Ferreiro DU, Wolynes PG, <strong>Komives EA<\/strong>. (2016) PEST Control of Molecular Stripping of NF\u03baB from DNA Transcription Sites. <em>J Phys Chem B<\/em>. 120(33):8532-8538. PMC5389414<\/li><li>Mukherjee SP, Quintas PO, McNulty R, <strong>Komives EA<\/strong>, Dyson HJ. (2016) Structural characterization of the ternary complex that mediates termination of NF-\u03baB signaling by I\u03baB\u03b1. <em>Proc Natl Acad Sci U S A<\/em> <em>113<\/em>(22):6212-7. PMC4896678<\/li><li>Medina E, C\u00f3rdova C, Villalobos P, Reyes J, <strong>Komives EA<\/strong>, Ram\u00edrez-Sarmiento CA, Babul J. (2016) Three-Dimensional Domain Swapping Changes the Folding Mechanism of the Forkhead Domain of FoxP1. <em>Biophys J. 110<\/em>(11):2349-60.<\/li><li>Schiffer JM, Malmstrom RD, Parnell J, Ramirez-Sarmiento C, Reyes J, Amaro RE, <strong>Komives EA<\/strong> (2016) Model of the Ankyrin and SOCS Box Protein, ASB9, E3 Ligase Reveals a Mechanism for Dynamic Ubiquitin Transfer. <em>Structure<\/em> 24(8):1248-56. PMC4972691<\/li><li>14 Handley, LD, Fuglestad, B, Stearns, K, Tonelli, M, Fenwick, RB, Markwick, PRL, and <strong>Komives, EA<\/strong> (2017) NMR reveals a dynamic allosteric pathway in thrombin. <em>Scientific Reports<\/em> 7:39575. PMC5216386<\/li><li>Dembinski, HE, Wismer, K, Vargas, JD, Suryawanshi, GW, Kern, N, Kroon, GJA, Dyson, HJ, Hoffmann, A, <strong>Komives, EA<\/strong> (2017) Functional importance of stripping in NF\u03baB signaling revealed by a stripping-impaired I\u03baB\u03b1 mutant. <em>Proc Natl Acad Sci U S A<\/em> <em>114<\/em>, 1916-1921. PMC5338396<\/li><li>Ramsey KM, Dembinski HE, Chen W, Ricci CG, <strong>Komives EA<\/strong>. (2017) DNA and I\u03baB\u03b1 Both Induce Long-Range Conformational Changes in NF\u03baB. <em>J Mol Biol.<\/em> 429(7):999-1008. PMC5389416<\/li><li>Carvajal AI, Vallejos G, <strong>Komives EA<\/strong>, Castro-Fern\u00e1ndez V, Leonardo DA, Garratt RC, Ram\u00edrez-Sarmiento CA, Babul J. (2017) Unusual dimerization of a BcCsp mutant leads to reduced conformational dynamics. <em>FEBS J<\/em>. 284(12):1882-1896.<\/li><li>144 Kromann-Hansen T, Lange EL, S\u00f8rensen HP, Hassanzadeh-Ghassabeh G, Huang M, Jensen JK, Muyldermans S, Declerck PJ, <strong>Komives EA<\/strong>, Andreasen PA. (2017) Discovery of a novel conformational equilibrium in urokinase-type plasminogen activator. <em>Sci Rep<\/em>. 7(1):3385 PMC5469797<\/li><li>Wong J, Young T, Zhang J, Liu S, Leser G, <strong>Komives EA<\/strong>, 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. <em>Nat Comm<\/em> 8, 781, 1-11. PMC5626764<\/li><li>Lumpkin, RJ, Gu, H, Zhu, Y, Leonard, M, Ahmad, AS, Clauser, KR, Meyer, JR, Bennett, EJ, <strong>Komives, EA<\/strong> (2017) Site-specific identification and quantitation of endogenous SUMO modifications under native conditions <em>Nat Comm<\/em> 8(1):1171. PMC5660086<\/li><li>Ferreiro DU, <strong>Komives EA<\/strong>, Wolynes PG. (2017) Frustration, function and folding. <em>Curr Opin Struct Biol.<\/em> 48:68-73. <\/li><li>Potoyan DA, Bueno C, Zheng W, <strong>Komives EA<\/strong>, Wolynes PG. (2017) Resolving the NF\u03baB Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors. <em>J Am Chem Soc. <\/em>139(51):18558-18566. \u00a0PMC5803749<\/li><li>Kim JK, Liu J, Hu X, Yu C, Roskamp K, Sankaran B, Huang L, <strong>Komives EA<\/strong>, Qiao F. (2017) Structural Basis for Shelterin Bridge Assembly. <em>Mol Cell<\/em>. 68(4):698-714. e5. PMC5698806<\/li><li>West AMV, <strong>Komives EA<\/strong>, Corbett KD. (2018) Conformational dynamics of the Hop1 HORMA domain reveal a common mechanism with the spindle checkpoint protein Mad2. <em>Nucleic Acids Res<\/em>. 46(1):279-292. PMC5758881<\/li><li>Kromann-Hansen T, Lange EL, Lund IK, H\u00f8yer-Hansen G, Andreasen PA, <strong>Komives EA<\/strong>. (2018) Ligand binding modulates the structural dynamics and activity of urokinase-type plasminogen activator: A possible mechanism of plasminogen activation. <em>PLoS One<\/em>. 13(2):e0192661.\u00a0 PMC5805342 <\/li><li>Narang D, Chen W, Ricci CG, <strong>Komives EA<\/strong>. (2018) RelA-containing NF\u03baB dimers have strikingly different DNA-binding cavities in the absence of DNA. <em>J Mol Biol<\/em>. 430(10):1510-1520. PMC5951767<\/li><li>Ramirez-Sarmiento C, and <strong>Komives EA<\/strong>. (2018) Hydrogen-deuterium exchange mass spectrometry reveals folding and allostery in protein-protein interactions, <em>Methods<\/em> S1046-2023(17)30457-7. PMC6051914<\/li><li>Peacock R, Davis J, Markwick PRL, <strong>Komives EA<\/strong>. (2018) Dynamic Consequences of Mutation of Tryptophan 215 in Thrombin. <em>Biochemistry<\/em> 57(18):2694-2703. PMC5940494<\/li><li>Rahnamoun H, Lee J, Sun X, Lu H, Ramsey KH, <strong>Komives EA<\/strong>, Lauberth SM (2018) RNAs Interact with BRD4 to Promote Enhanced Chromatin Engagement and Transcription Activation. <em>Nat Struct Mol Biol<\/em> 25(8):687-697.<\/li><li>Ramsey KM, Narang D, <strong>Komives EA<\/strong> (2018) Prediction of the Presence of a Seventh Ankyrin Repeat in I\u03baB\u03b5 from Homology Modeling Combined with Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS). <em>Protein Sci<\/em> 27(9):1624-1635. PMC6194264.<\/li><li>Gudlur A, Zeraik AE, Hirve N, Rajanikanth V, Bobkov AA, Ma G, Zheng S, Wang Y, Zhou Y, <strong>Komives EA<\/strong>, Hogan PG. (2018) Calcium sensing by the STIM1 ER-luminal domain. <em>Nat Commun.<\/em> 9(1):4536. PMC6208404<\/li><li>Hard R, Li N, He W, Ross B, Mo GCH, Peng Q, Stein RSL, <strong>Komives E<\/strong>, Wang Y, Zhang J, Wang W. (2018) Deciphering and engineering chromodomain-methyllysine peptide recognition. <em>Sci Adv.<\/em>\u00a0 Nov 7;4(11):eaau1447 \u00a0\u00a0\u00a0\u00a0PMC6221542 <\/li><li>Markwick PRL, Peacock RB, <strong>Komives EA<\/strong>. (2019) Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery. <em>Biophys J<\/em>. 116(1):49-56. PMC6342732<\/li><li>Ramsey KM, Chen W, Marion JD, Bergqvist S, <strong>Komives EA<\/strong>. (2019) Exclusivity and Compensation in NF\u03baB Dimer Distributions and I\u03baB Inhibition. <em>Biochemistry<\/em>. 58(21):2555-2563. PMC6642826<\/li><li>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, Pi\u00f1eros M, <strong>Komives EA<\/strong>, 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. <em>Proc Natl Acad Sci U S A. 116<\/em>(28):14309-14318.161.<\/li><li>Kalogriopoulos NA, Rees SD, Ngo T, Kopcho NJ, Ilatovskiy AV, Sun N, <strong>Komives EA<\/strong>, Chang G, Ghosh P, Kufareva I. (2019) Structural basis for GPCR-independent activation of heterotrimeric Gi proteins. <em>Proc Natl Acad Sci U S A. 116<\/em>(33):16394-16403.<\/li><li>Kopcho N, Chang G, Komives EA. (2019) Dynamics of ABC Transporter P-glycoprotein in Three Conformational States. <em>Sci Repts<\/em> 9, 1. 15092.<\/li><li>Galaz-Davison P, Molina JA, Silletti S, Komives EA, Knauer SH, Artsimovitch I, Ram\u00edrez-Sarmiento CA. (2019) Differential Local Stability Governs the Metamorphic Fold Switch of Bacterial Virulence Factor RfaH. <em>Biophys J.<\/em> pii: S0006-3495(19)30937-3.<\/li><li>Lumpkin RJ, Komives EA. (2019) DECA, A Comprehensive, Automatic Post-processing Program for HDX-MS Data. <em>Mol Cell Proteomics<\/em>. 18, 2516-2523.<\/li><li>Kopcho N, Chang G, <strong>Komives EA<\/strong>. (2019) Dynamics of ABC Transporter P-glycoprotein in Three Conformational States. <em>Sci Rep<\/em>. 9(1):15092.<\/li><li>Perez-Riba A, <strong>Komives E<\/strong>, Main ERG, Itzhaki LS. (2019) Decoupling a tandem-repeat protein: Impact of multiple loop insertions on a modular scaffold. <em>Sci Rep<\/em>. 9(1):15439.<\/li><li>Galaz-Davison P, Molina JA, Silletti S, <strong>Komives EA<\/strong>, Knauer SH, Artsimovitch I, Ram\u00edrez-Sarmiento CA. (2020) Differential Local Stability Governs the Metamorphic Fold Switch of Bacterial Virulence Factor RfaH. <em>Biophys J<\/em>. 118(1):96-104. <em>Paper of the year in BJ!<\/em><\/li><li>Engen JR and <strong>Komives EA<\/strong>, (2020) Complementarity of Hydrogen\/Deuterium Exchange Mass Spectrometry and Cryo-Electron Microscopy. <em>Trends Biochem Sci<\/em>. S0968-0004(20)30125-0.<\/li><li>Lumpkin RJ, Baker RW, Leschziner AE, <strong>Komives EA<\/strong>. (2020) Structure and dynamics of the ASB9 CUL-RING E3 Ligase. <em>Nat Commun<\/em>. 11(1):2866.<\/li><li>Medina E, Villalobos P, Hamilton GL, Komives EA, Sanabria H, Ram\u00edrez-Sarmiento CA, Babul J. (2020) Intrinsically Disordered Regions of the DNA-Binding Domain of Human FoxP1 Facilitate Domain Swapping. <em>J Mol Biol<\/em>. \u00a0432(19):5411-5429.<\/li><li>Chen M, Chen X, Schafer NP, Clementi C, <strong>Komives EA<\/strong>, Ferreiro DU, Wolynes PG. (2020) Surveying biomolecular frustration at atomic resolution. <em>Nat Commun.<\/em> 11(1):5944.<\/li><li>Lumpkin RJ, Ahmad, AS, Blake, R, Condon, CJ, <strong>Komives EA<\/strong>. (2020) The Mechanism of NEDD8 Activation of CUL5 Ubiquitin E3 Ligases. (2021) <em>Mol Cell Proteomics 20<\/em>:100019.<\/li><li>Hoffmeister H, Fuchs A, <strong>Komives EA<\/strong>, Groebner-Ferreira R, Strobl L, Heizinger JL, Merkl R, Dove S, L\u00e4ngst G. (2021) Sequence and functional differences in the ATPase domains of CHD3 &amp; SNF2H promise potential for selective regulability and drugability. <em>FEBS J <\/em>doi: 10.1111\/febs.15699.<\/li><li>Peacock RJ, McGrann T, Tonelli M, <strong>Komives EA<\/strong>. (2021) Serine protease dynamics revealed by NMR analysis of the thrombin-thrombomodulin complex. <em>Sci Reports<\/em>11(1):9354. doi: 10.1038\/s41598-021-88432-z<\/li><li>Stormberg T, Filliaux S, Baughman HER, <strong>Komives EA<\/strong>, Lyubchenko YL. (2021) Transcription Factor NF-\u03baB Unravels Nucleosomes. <em>Biochem Biophys Acta<\/em>. Gen Subj. 1865(9):129934.<\/li><li>Schmidt SH, Weng JH, Aoto PC, Boassa D, Mathea S, Silletti S, Hu J, Wallbott M, <strong>Komives EA<\/strong>, Knapp S, Herberg FW, Taylor SS.Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2.(2021) <em>Proc Natl Acad Sci U S A.<\/em> 118(23):e2100844118.<\/li><\/ol>\n\n\n\n<p><\/p>\n\n\n\n<p><\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Dr. Elizabeth A. Komives Distinguished Professor of Chemistry and Biochemistry Department of Chemistry &amp; Biochemistry U.C. San Diego La Jolla, CA 92093-0378 Telephone: (858) 534-3058 email: ekomives@ucsd.edu Education MASSACHUSETTS INSTITUTE OF TECHNOLOGYM.S. in Toxicology, B.S. in Chemistry, 1982 UNIVERSITY OF CALIFORNIA SAN FRANCISCOPh.D. in Pharmaceutical Chemistry with Paul R. Ortiz de Montellano 1982 &#8211; 1987Research Topic: The Mechanism of p-Bond<\/p>\n<div class=\"clearfix\"><\/div>\n<div class=\"pull-left padding-top-25\"><a href=\"https:\/\/komiveslab.ucsd.edu\/?page_id=88\" class=\"btn btn-theme\">Continue reading<span class=\"screen-reader-text\"> &#8220;Elizabeth A. Komives&#8221;<\/span> <i class=\"fa fa-fw fa-long-arrow-right\"><\/i> <\/a>  <\/div>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"spay_email":"","footnotes":""},"class_list":["post-88","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/komiveslab.ucsd.edu\/index.php?rest_route=\/wp\/v2\/pages\/88","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/komiveslab.ucsd.edu\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/komiveslab.ucsd.edu\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/komiveslab.ucsd.edu\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/komiveslab.ucsd.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=88"}],"version-history":[{"count":20,"href":"https:\/\/komiveslab.ucsd.edu\/index.php?rest_route=\/wp\/v2\/pages\/88\/revisions"}],"predecessor-version":[{"id":748,"href":"https:\/\/komiveslab.ucsd.edu\/index.php?rest_route=\/wp\/v2\/pages\/88\/revisions\/748"}],"wp:attachment":[{"href":"https:\/\/komiveslab.ucsd.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=88"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}