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Elizabeth A. Komives - Publications

University of California, San Diego, La Jolla, CA 
Structure, function, dynamics and thermodynamics of protein-protein interactions: NMR, mass spectrometry and kinetics

137 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Ramsey KM, Chen W, Marion JD, Bergqvist S, Komives EA. Exclusivity and Compensation in NFκB Dimer distributions and IκB inhibition. Biochemistry. PMID 31033276 DOI: 10.1021/Acs.Biochem.9B00008  0.4
2018 Ramsey KM, Narang D, Komives EA. Prediction of the Presence of a Seventh Ankyrin Repeat in IκBε from Homology Modeling Combined with Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS). Protein Science : a Publication of the Protein Society. PMID 30133030 DOI: 10.1002/Pro.3459  0.4
2018 Rahnamoun H, Lee J, Sun Z, Lu H, Ramsey KM, Komives EA, Lauberth SM. RNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation. Nature Structural & Molecular Biology. 25: 687-697. PMID 30076409 DOI: 10.1038/S41594-018-0102-0  0.4
2018 Narang D, Chen W, Ricci CG, Komives EA. RelA-containing NFκB dimers have strikingly different DNA-binding cavities in the absence of DNA. Journal of Molecular Biology. PMID 29625198 DOI: 10.1016/J.Jmb.2018.03.020  0.4
2017 Ramsey KM, Dembinski HE, Chen W, Ricci CG, Komives EA. DNA and IκBα both induce long range conformational changes in NFκB. Journal of Molecular Biology. PMID 28249778 DOI: 10.1016/J.Jmb.2017.02.017  0.4
2017 Dembinski HE, Wismer K, Vargas JD, Suryawanshi GW, Kern N, Kroon G, Dyson HJ, Hoffmann A, Komives EA. Functional importance of stripping in NFκB signaling revealed by a stripping-impaired IκBα mutant. Proceedings of the National Academy of Sciences of the United States of America. PMID 28167786 DOI: 10.1073/Pnas.1610192114  0.4
2017 Handley LD, Fuglestad B, Stearns K, Tonelli M, Fenwick RB, Markwick PR, Komives EA. NMR reveals a dynamic allosteric pathway in thrombin. Scientific Reports. 7: 39575. PMID 28059082 DOI: 10.1038/Srep39575  1
2016 Schiffer JM, Malmstrom RD, Parnell J, Ramirez-Sarmiento C, Reyes J, Amaro RE, Komives EA. Model of the Ankyrin and SOCS Box Protein, ASB9, E3 Ligase Reveals a Mechanism for Dynamic Ubiquitin Transfer. Structure (London, England : 1993). PMID 27396830 DOI: 10.1016/J.Str.2016.05.016  1
2016 Trelle MB, Ramsey KM, Lee TC, Zheng W, Lamboy J, Wolynes PG, Deniz A, Komives EA. Binding of NFκB Appears to Twist the Ankyrin Repeat Domain of IκBα. Biophysical Journal. 110: 887-95. PMID 26910425 DOI: 10.1016/J.Bpj.2016.01.001  1
2015 Handley LD, Treuheit NA, Venkatesh VJ, Komives EA. Thrombomodulin Binding Selects the Catalytically Active Form of Thrombin. Biochemistry. 54: 6650-8. PMID 26468766 DOI: 10.1021/Acs.Biochem.5B00825  1
2015 Ramírez-Sarmiento CA, Baez M, Zamora RA, Balasubramaniam D, Babul J, Komives EA, Guixé V. The folding unit of phosphofructokinase-2 as defined by the biophysical properties of a monomeric mutant. Biophysical Journal. 108: 2350-61. PMID 25954892 DOI: 10.1016/J.Bpj.2015.04.001  1
2015 Mangas I, Taylor P, Vilanova E, Estévez J, França TC, Komives E, Radi? Z. Resolving pathways of interaction of mipafox and a sarin analog with human acetylcholinesterase by kinetics, mass spectrometry and molecular modeling approaches. Archives of Toxicology. PMID 25743373 DOI: 10.1007/S00204-015-1481-1  1
2015 Balasubramaniam D, Schiffer J, Parnell J, Mir SP, Amaro RE, Komives EA. How the ankyrin and SOCS box protein, ASB9, binds to creatine kinase. Biochemistry. 54: 1673-80. PMID 25654263 DOI: 10.1021/Bi501420N  1
2014 Ferreiro DU, Komives EA, Wolynes PG. Frustration in biomolecules. Quarterly Reviews of Biophysics. 47: 285-363. PMID 25225856 DOI: 10.1017/S0033583514000092  1
2014 Perera VR, Newton GL, Parnell JM, Komives EA, Pogliano K. Purification and characterization of the Staphylococcus aureus bacillithiol transferase BstA. Biochimica Et Biophysica Acta. 1840: 2851-61. PMID 24821014 DOI: 10.1016/J.Bbagen.2014.05.001  1
2014 Balasubramaniam D, Komives EA. The phylogenetics of dynamics in DNA clamp proteins. Structure (London, England : 1993). 22: 511-2. PMID 24717558 DOI: 10.1016/J.Str.2014.03.006  1
2014 Dembinski H, Wismer K, Balasubramaniam D, Gonzalez HA, Alverdi V, Iakoucheva LM, Komives EA. Predicted disorder-to-order transition mutations in IκBα disrupt function. Physical Chemistry Chemical Physics : Pccp. 16: 6480-5. PMID 24605363 DOI: 10.1039/C3Cp54427C  1
2014 Meyer JG, Kim S, Maltby DA, Ghassemian M, Bandeira N, Komives EA. Expanding proteome coverage with orthogonal-specificity α-lytic proteases. Molecular & Cellular Proteomics : McP. 13: 823-35. PMID 24425750 DOI: 10.1074/Mcp.M113.034710  1
2014 Alverdi V, Hetrick B, Joseph S, Komives EA. Direct observation of a transient ternary complex during IκBα-mediated dissociation of NF-κB from DNA. Proceedings of the National Academy of Sciences of the United States of America. 111: 225-30. PMID 24367071 DOI: 10.1073/Pnas.1318115111  1
2013 Li N, Stein RS, He W, Komives E, Wang W. Identification of methyllysine peptides binding to chromobox protein homolog 6 chromodomain in the human proteome. Molecular & Cellular Proteomics : McP. 12: 2750-60. PMID 23842000 DOI: 10.1074/Mcp.O112.025015  1
2013 Ramírez-Sarmiento CA, Baez M, Wilson CA, Babul J, Komives EA, Guixé V. Observation of solvent penetration during cold denaturation of E. coli phosphofructokinase-2. Biophysical Journal. 104: 2254-63. PMID 23708365 DOI: 10.1016/J.Bpj.2013.04.024  1
2013 Lamboy JA, Kim H, Dembinski H, Ha T, Komives EA. Single-molecule FRET reveals the native-state dynamics of the IκBα ankyrin repeat domain. Journal of Molecular Biology. 425: 2578-90. PMID 23619335 DOI: 10.1016/J.Jmb.2013.04.015  1
2013 Stein RS, Li N, He W, Komives E, Wang W. Recognition of methylated peptides by Drosophila melanogaster polycomb chromodomain. Journal of Proteome Research. 12: 1467-77. PMID 23320494 DOI: 10.1021/Pr3011205  1
2013 Cervantes CF, Handley LD, Sue SC, Dyson HJ, Komives EA. Long-range effects and functional consequences of stabilizing mutations in the ankyrin repeat domain of IκBα. Journal of Molecular Biology. 425: 902-13. PMID 23274114 DOI: 10.1016/J.Jmb.2012.12.012  1
2013 Balasubramaniam D, Komives EA. Hydrogen-exchange mass spectrometry for the study of intrinsic disorder in proteins. Biochimica Et Biophysica Acta. 1834: 1202-9. PMID 23099262 DOI: 10.1016/J.Bbapap.2012.10.009  1
2013 Schafer NP, Hoffman RMB, Burger A, Craig PO, Komives EA, Wolynes PG. Correction: Discrete kinetic models from funneled energy landscape simulations (PLoS ONE) Plos One. 8. DOI: 10.1371/Annotation/16C11A12-4245-403C-80Ab-E6662Baf16Cd  1
2012 Schafer NP, Hoffman RM, Burger A, Craig PO, Komives EA, Wolynes PG. Discrete kinetic models from funneled energy landscape simulations. Plos One. 7: e50635. PMID 23251375 DOI: 10.1371/Journal.Pone.0050635  1
2012 Meyer JG, Komives EA. Charge state coalescence during electrospray ionization improves peptide identification by tandem mass spectrometry Journal of the American Society For Mass Spectrometry. 23: 1390-1399. PMID 22610994 DOI: 10.1007/S13361-012-0404-0  1
2012 Guo L, Ghassemian M, Komives EA, Russell P. Cadmium-induced proteome remodeling regulated by Spc1/Sty1 and Zip1 in fission yeast. Toxicological Sciences : An Official Journal of the Society of Toxicology. 129: 200-12. PMID 22610605 DOI: 10.1093/Toxsci/Kfs179  1
2012 Dyson HJ, Komives EA. Role of disorder in IκB-NFκB interaction. Iubmb Life. 64: 499-505. PMID 22573609 DOI: 10.1002/Iub.1044  1
2012 Komives EA. Consequences of fuzziness in the NFκB/IκBα interaction. Advances in Experimental Medicine and Biology. 725: 74-85. PMID 22399319 DOI: 10.1007/978-1-4614-0659-4_5  1
2012 Jobe TO, Sung DY, Akmakjian G, Pham A, Komives EA, Mendoza-Cózatl DG, Schroeder JI. Feedback inhibition by thiols outranks glutathione depletion: a luciferase-based screen reveals glutathione-deficient γ-ECS and glutathione synthetase mutants impaired in cadmium-induced sulfate assimilation. The Plant Journal : For Cell and Molecular Biology. 70: 783-95. PMID 22283708 DOI: 10.1111/J.1365-313X.2012.04924.X  1
2011 Guttman M, Komives EA. The structure, dynamics, and binding of the LA45 module pair of the low-density lipoprotein receptor suggest an important role for LA4 in ligand release. Biochemistry. 50: 11001-8. PMID 22091758 DOI: 10.1021/Bi2014486  1
2011 Craig PO, Lätzer J, Weinkam P, Hoffman RM, Ferreiro DU, Komives EA, Wolynes PG. Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes. Journal of the American Chemical Society. 133: 17463-72. PMID 21913704 DOI: 10.1021/Ja207506Z  1
2011 Mulvihill MM, Guttman M, Komives EA. Protein interactions among Fe65, the low-density lipoprotein receptor-related protein, and the amyloid precursor protein. Biochemistry. 50: 6208-16. PMID 21650223 DOI: 10.1021/Bi200508F  1
2011 Lamboy JA, Kim H, Lee KS, Ha T, Komives EA. Visualization of the nanospring dynamics of the IkappaBalpha ankyrin repeat domain in real time. Proceedings of the National Academy of Sciences of the United States of America. 108: 10178-83. PMID 21628581 DOI: 10.1073/Pnas.1102226108  1
2011 Treuheit NA, Beach MA, Komives EA. Thermodynamic compensation upon binding to exosite 1 and the active site of thrombin. Biochemistry. 50: 4590-6. PMID 21526769 DOI: 10.1021/Bi2004069  1
2011 DeVries I, Ferreiro DU, Sánchez IE, Komives EA. Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain. Journal of Molecular Biology. 408: 163-76. PMID 21329696 DOI: 10.1016/J.Jmb.2011.02.021  1
2011 Ferreiro DU, Hegler JA, Komives EA, Wolynes PG. On the role of frustration in the energy landscapes of allosteric proteins. Proceedings of the National Academy of Sciences of the United States of America. 108: 3499-503. PMID 21273505 DOI: 10.1073/Pnas.1018980108  1
2011 Sue SC, Alverdi V, Komives EA, Dyson HJ. Detection of a ternary complex of NF-kappaB and IkappaBalpha with DNA provides insights into how IkappaBalpha removes NF-kappaB from transcription sites. Proceedings of the National Academy of Sciences of the United States of America. 108: 1367-72. PMID 21220295 DOI: 10.1073/Pnas.1014323108  1
2011 Cervantes CF, Bergqvist S, Kjaergaard M, Kroon G, Sue SC, Dyson HJ, Komives EA. The RelA nuclear localization signal folds upon binding to IκBα. Journal of Molecular Biology. 405: 754-64. PMID 21094161 DOI: 10.1016/J.Jmb.2010.10.055  1
2010 Devries IL, Hampton-Smith RJ, Mulvihill MM, Alverdi V, Peet DJ, Komives EA. Consequences of IkappaB alpha hydroxylation by the factor inhibiting HIF (FIH). Febs Letters. 584: 4725-30. PMID 21056038 DOI: 10.1016/J.Febslet.2010.10.060  1
2010 Mathes E, Wang L, Komives E, Ghosh G. Flexible regions within I{kappa}B{alpha} create the ubiquitin-independent degradation signal. The Journal of Biological Chemistry. 285: 32927-36. PMID 20682784 DOI: 10.1074/Jbc.M110.107326  1
2010 Gertsman I, Fu CY, Huang R, Komives EA, Johnson JE. Critical salt bridges guide capsid assembly, stability, and maturation behavior in bacteriophage HK97. Molecular & Cellular Proteomics : McP. 9: 1752-63. PMID 20332083 DOI: 10.1074/Mcp.M000039-Mcp201  1
2010 Guttman M, Prieto JH, Handel TM, Domaille PJ, Komives EA. Structure of the minimal interface between ApoE and LRP. Journal of Molecular Biology. 398: 306-19. PMID 20303980 DOI: 10.1016/J.Jmb.2010.03.022  1
2010 Gertsman I, Komives EA, Johnson JE. HK97 maturation studied by crystallography and H/2H exchange reveals the structural basis for exothermic particle transitions. Journal of Molecular Biology. 397: 560-74. PMID 20093122 DOI: 10.1016/J.Jmb.2010.01.016  1
2010 Markwick PR, Cervantes CF, Abel BL, Komives EA, Blackledge M, McCammon JA. Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. Journal of the American Chemical Society. 132: 1220-1. PMID 20063881 DOI: 10.1021/Ja9093692  1
2010 Ferreiro DU, Komives EA. Molecular mechanisms of system control of NF-kappaB signaling by IkappaBalpha. Biochemistry. 49: 1560-7. PMID 20055496 DOI: 10.1021/Bi901948J  1
2010 Guttman M, Prieto JH, Croy JE, Komives EA. Decoding of lipoprotein-receptor interactions: properties of ligand binding modules governing interactions with apolipoprotein E. Biochemistry. 49: 1207-16. PMID 20030366 DOI: 10.1021/Bi9017208  1
2009 Bergqvist S, Alverdi V, Mengel B, Hoffmann A, Ghosh G, Komives EA. Kinetic enhancement of NF-kappaBxDNA dissociation by IkappaBalpha. Proceedings of the National Academy of Sciences of the United States of America. 106: 19328-33. PMID 19887633 DOI: 10.1073/Pnas.0908797106  1
2009 Guttman M, Betts GN, Barnes H, Ghassemian M, van der Geer P, Komives EA. Interactions of the NPXY microdomains of the low density lipoprotein receptor-related protein 1. Proteomics. 9: 5016-28. PMID 19771558 DOI: 10.1002/Pmic.200900457  1
2009 Cervantes CF, Markwick PR, Sue SC, McCammon JA, Dyson HJ, Komives EA. Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance. Biochemistry. 48: 8023-31. PMID 19591507 DOI: 10.1021/Bi900712R  1
2009 Sung DY, Kim TH, Komives EA, Mendoza-Cózatl DG, Schroeder JI. ARS5 is a component of the 26S proteasome complex, and negatively regulates thiol biosynthesis and arsenic tolerance in Arabidopsis. The Plant Journal : For Cell and Molecular Biology. 59: 802-13. PMID 19453443 DOI: 10.1111/J.1365-313X.2009.03914.X  1
2009 Gertsman I, Gan L, Guttman M, Lee K, Speir JA, Duda RL, Hendrix RW, Komives EA, Johnson JE. An unexpected twist in viral capsid maturation. Nature. 458: 646-50. PMID 19204733 DOI: 10.1038/Nature07686  1
2008 Bergqvist S, Ghosh G, Komives EA. The IkappaBalpha/NF-kappaB complex has two hot spots, one at either end of the interface. Protein Science : a Publication of the Protein Society. 17: 2051-8. PMID 18824506 DOI: 10.1110/Ps.037481.108  1
2008 Koeppe JR, Beach MA, Baerga-Ortiz A, Kerns SJ, Komives EA. Mutations in the fourth EGF-like domain affect thrombomodulin-induced changes in the active site of thrombin. Biochemistry. 47: 10933-9. PMID 18803401 DOI: 10.1021/Bi8008278  1
2008 Truhlar SM, Cervantes CF, Torpey JW, Kjaergaard M, Komives EA. Rapid mass spectrometric analysis of 15N-Leu incorporation fidelity during preparation of specifically labeled NMR samples. Protein Science : a Publication of the Protein Society. 17: 1636-9. PMID 18567787 DOI: 10.1110/Ps.036418.108  1
2008 Sue SC, Cervantes C, Komives EA, Dyson HJ. Transfer of flexibility between ankyrin repeats in IkappaB* upon formation of the NF-kappaB complex. Journal of Molecular Biology. 380: 917-31. PMID 18565540 DOI: 10.1016/J.Jmb.2008.05.048  1
2008 Truhlar SM, Mathes E, Cervantes CF, Ghosh G, Komives EA. Pre-folding IkappaBalpha alters control of NF-kappaB signaling. Journal of Molecular Biology. 380: 67-82. PMID 18511071 DOI: 10.1016/J.Jmb.2008.02.053  1
2008 Ferreiro DU, Walczak AM, Komives EA, Wolynes PG. The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures. Plos Computational Biology. 4: e1000070. PMID 18483553 DOI: 10.1371/Journal.Pcbi.1000070  1
2008 Truhlar SM, Komives EA. LRR domain folding: just put a cap on it! Structure (London, England : 1993). 16: 655-7. PMID 18462667 DOI: 10.1016/J.Str.2008.04.002  1
2008 Betts GN, van der Geer P, Komives EA. Structural and functional consequences of tyrosine phosphorylation in the LRP1 cytoplasmic domain. The Journal of Biological Chemistry. 283: 15656-64. PMID 18381291 DOI: 10.1074/Jbc.M709514200  1
2008 Huang CM, Torpey JW, Liu YT, Chen YR, Williams KE, Komives EA, Gallo RL. A peptide with a ProGln C terminus in the human saliva peptidome exerts bactericidal activity against Propionibacterium acnes. Antimicrobial Agents and Chemotherapy. 52: 1834-6. PMID 18285475 DOI: 10.1128/Aac.01347-07  1
2008 Barrick D, Ferreiro DU, Komives EA. Folding landscapes of ankyrin repeat proteins: experiments meet theory. Current Opinion in Structural Biology. 18: 27-34. PMID 18243686 DOI: 10.1016/J.Sbi.2007.12.004  1
2008 Mendoza-Cózatl DG, Butko E, Springer F, Torpey JW, Komives EA, Kehr J, Schroeder JI. Identification of high levels of phytochelatins, glutathione and cadmium in the phloem sap of Brassica napus. A role for thiol-peptides in the long-distance transport of cadmium and the effect of cadmium on iron translocation. The Plant Journal : For Cell and Molecular Biology. 54: 249-59. PMID 18208526 DOI: 10.1111/J.1365-313X.2008.03410.X  1
2007 Ferreiro DU, Hegler JA, Komives EA, Wolynes PG. Localizing frustration in native proteins and protein assemblies. Proceedings of the National Academy of Sciences of the United States of America. 104: 19819-24. PMID 18077414 DOI: 10.1073/Pnas.0709915104  1
2007 Anand GS, Hotchko M, Brown SH, Ten Eyck LF, Komives EA, Taylor SS. R-subunit isoform specificity in protein kinase A: distinct features of protein interfaces in PKA types I and II by amide H/2H exchange mass spectrometry. Journal of Molecular Biology. 374: 487-99. PMID 17942118 DOI: 10.1016/J.Jmb.2007.09.035  1
2007 Wu X, Li ZF, Brooks R, Komives EA, Torpey JW, Engvall E, Gonias SL, Shelton GD. Autoantibodies in canine masticatory muscle myositis recognize a novel myosin binding protein-C family member. Journal of Immunology (Baltimore, Md. : 1950). 179: 4939-44. PMID 17878394 DOI: 10.4049/Jimmunol.179.7.4939  1
2007 Ferreiro DU, Komives EA. The plastic landscape of repeat proteins. Proceedings of the National Academy of Sciences of the United States of America. 104: 7735-6. PMID 17483477 DOI: 10.1073/Pnas.0702682104  1
2007 Sung DY, Lee D, Harris H, Raab A, Feldmann J, Meharg A, Kumabe B, Komives EA, Schroeder JI. Identification of an arsenic tolerant double mutant with a thiol-mediated component and increased arsenic tolerance in phyA mutants. The Plant Journal : For Cell and Molecular Biology. 49: 1064-75. PMID 17335514 DOI: 10.1111/J.1365-313X.2006.03018.X  1
2007 Lätzer J, Papoian GA, Prentiss MC, Komives EA, Wolynes PG. Induced fit, folding, and recognition of the NF-kappaB-nuclear localization signals by IkappaBalpha and IkappaBbeta. Journal of Molecular Biology. 367: 262-74. PMID 17257619 DOI: 10.1016/J.Jmb.2006.12.006  1
2007 Ferreiro DU, Cervantes CF, Truhlar SM, Cho SS, Wolynes PG, Komives EA. Stabilizing IkappaBalpha by "consensus" design. Journal of Molecular Biology. 365: 1201-16. PMID 17174335 DOI: 10.1016/J.Jmb.2006.11.044  1
2006 Truhlar SM, Torpey JW, Komives EA. Regions of IkappaBalpha that are critical for its inhibition of NF-kappaB.DNA interaction fold upon binding to NF-kappaB. Proceedings of the National Academy of Sciences of the United States of America. 103: 18951-6. PMID 17148610 DOI: 10.1073/Pnas.0605794103  1
2006 Truhlar SM, Croy CH, Torpey JW, Koeppe JR, Komives EA. Solvent accessibility of protein surfaces by amide H/2H exchange MALDI-TOF mass spectrometry. Journal of the American Society For Mass Spectrometry. 17: 1490-7. PMID 16934999 DOI: 10.1016/J.Jasms.2006.07.023  1
2006 Koeppe JR, Komives EA. Amide H/2H exchange reveals a mechanism of thrombin activation. Biochemistry. 45: 7724-32. PMID 16784223 DOI: 10.1021/Bi060405H  1
2006 Bergqvist S, Croy CH, Kjaergaard M, Huxford T, Ghosh G, Komives EA. Thermodynamics reveal that helix four in the NLS of NF-kappaB p65 anchors IkappaBalpha, forming a very stable complex. Journal of Molecular Biology. 360: 421-34. PMID 16756995 DOI: 10.1016/J.Jmb.2006.05.014  1
2006 Chen A, Komives EA, Schroeder JI. An improved grafting technique for mature Arabidopsis plants demonstrates long-distance shoot-to-root transport of phytochelatins in Arabidopsis. Plant Physiology. 141: 108-20. PMID 16531489 DOI: 10.1104/Pp.105.072637  1
2006 Hotchko M, Anand GS, Komives EA, Ten Eyck LF. Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments. Protein Science : a Publication of the Protein Society. 15: 583-601. PMID 16501228 DOI: 10.1110/Ps.051774906  1
2006 Shi J, Koeppe JR, Komives EA, Taylor P. Ligand-induced conformational changes in the acetylcholine-binding protein analyzed by hydrogen-deuterium exchange mass spectrometry. The Journal of Biological Chemistry. 281: 12170-7. PMID 16484218 DOI: 10.1074/Jbc.M600154200  1
2005 Mandell JG, Baerga-Ortiz A, Croy CH, Falick AM, Komives EA. Application of amide proton exchange mass spectrometry for the study of protein-protein interactions. Current Protocols in Protein Science / Editorial Board, John E. Coligan ... [Et Al.]. Unit20.9. PMID 18429282 DOI: 10.1002/0471140864.Ps2009S40  1
2005 Koeppe JR, Seitova A, Mather T, Komives EA. Thrombomodulin tightens the thrombin active site loops to promote protein C activation. Biochemistry. 44: 14784-91. PMID 16274226 DOI: 10.1021/Bi0510577  1
2005 Ferreiro DU, Cho SS, Komives EA, Wolynes PG. The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family. Journal of Molecular Biology. 354: 679-92. PMID 16257414 DOI: 10.1016/J.Jmb.2005.09.078  1
2005 Mandell JG, Baerga-Ortiz A, Falick AM, Komives EA. Measurement of solvent accessibility at protein-protein interfaces. Methods in Molecular Biology (Clifton, N.J.). 305: 65-80. PMID 15939994 DOI: 10.1385/1-59259-912-5:065  1
2005 Wood MJ, Helena Prieto J, Komives EA. Structural and functional consequences of methionine oxidation in thrombomodulin. Biochimica Et Biophysica Acta. 1703: 141-7. PMID 15680222 DOI: 10.1016/J.Bbapap.2004.09.007  1
2005 Prieto JH, Sampoli Benitez BA, Melacini G, Johnson DA, Wood MJ, Komives EA. Dynamics of the fragment of thrombomodulin containing the fourth and fifth epidermal growth factor-like domains correlate with function. Biochemistry. 44: 1225-33. PMID 15667216 DOI: 10.1021/Bi0478852  1
2005 Komives EA. Protein-protein interaction dynamics by amide H/ 2H exchange mass spectrometry International Journal of Mass Spectrometry. 240: 285-290. DOI: 10.1016/J.Ijms.2004.09.016  1
2004 Croy CH, Bergqvist S, Huxford T, Ghosh G, Komives EA. Biophysical characterization of the free IkappaBalpha ankyrin repeat domain in solution. Protein Science : a Publication of the Protein Society. 13: 1767-77. PMID 15215520 DOI: 10.1110/Ps.04731004  1
2004 Croy JE, Brandon T, Komives EA. Two apolipoprotein E mimetic peptides, ApoE(130-149) and ApoE(141-155)2, bind to LRP1. Biochemistry. 43: 7328-35. PMID 15182176 DOI: 10.1021/Bi036208P  1
2004 Croy CH, Koeppe JR, Bergqvist S, Komives EA. Allosteric changes in solvent accessibility observed in thrombin upon active site occupation. Biochemistry. 43: 5246-55. PMID 15122890 DOI: 10.1021/Bi0499718  1
2004 Baerga-Ortiz A, Bergqvist S, Mandell JG, Komives EA. Two different proteins that compete for binding to thrombin have opposite kinetic and thermodynamic profiles. Protein Science : a Publication of the Protein Society. 13: 166-76. PMID 14691232 DOI: 10.1110/Ps.03120604  1
2003 Croy JE, Shin WD, Knauer MF, Knauer DJ, Komives EA. All three LDL receptor homology regions of the LDL receptor-related protein bind multiple ligands. Biochemistry. 42: 13049-57. PMID 14596620 DOI: 10.1021/Bi034752S  1
2003 Anand GS, Law D, Mandell JG, Snead AN, Tsigelny I, Taylor SS, Ten Eyck LF, Komives EA. Identification of the protein kinase A regulatory RIalpha-catalytic subunit interface by amide H/2H exchange and protein docking. Proceedings of the National Academy of Sciences of the United States of America. 100: 13264-9. PMID 14583592 DOI: 10.1073/Pnas.2232255100  1
2003 Wood MJ, Becvar LA, Prieto JH, Melacini G, Komives EA. NMR structures reveal how oxidation inactivates thrombomodulin. Biochemistry. 42: 11932-42. PMID 14556624 DOI: 10.1021/Bi034646Q  1
2003 Jennings LL, Malecki M, Komives EA, Taylor P. Direct analysis of the kinetic profiles of organophosphate-acetylcholinesterase adducts by MALDI-TOF mass spectrometry. Biochemistry. 42: 11083-91. PMID 12974645 DOI: 10.1021/Bi034756X  1
2002 Huxford T, Mishler D, Phelps CB, Huang DB, Sengchanthalangsy LL, Reeves R, Hughes CA, Komives EA, Ghosh G. Solvent exposed non-contacting amino acids play a critical role in NF-kappaB/IkappaBalpha complex formation. Journal of Molecular Biology. 324: 587-97. PMID 12460563 DOI: 10.2210/Pdb1My5/Pdb  1
2002 Whiles JA, Glover KJ, Vold RR, Komives EA. Methods for studying transmembrane peptides in bicelles: consequences of hydrophobic mismatch and peptide sequence. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 158: 149-56. PMID 12419680 DOI: 10.1016/S1090-7807(02)00068-X  1
2002 Anand GS, Hughes CA, Jones JM, Taylor SS, Komives EA. Amide H/2H exchange reveals communication between the cAMP and catalytic subunit-binding sites in the R(I)alpha subunit of protein kinase A. Journal of Molecular Biology. 323: 377-86. PMID 12381327 DOI: 10.1016/S0022-2836(02)00919-1  1
2002 Baerga-Ortiz A, Hughes CA, Mandell JG, Komives EA. Epitope mapping of a monoclonal antibody against human thrombin by H/D-exchange mass spectrometry reveals selection of a diverse sequence in a highly conserved protein. Protein Science : a Publication of the Protein Society. 11: 1300-8. PMID 12021429 DOI: 10.1110/Ps.4670102  1
2002 Komives EA, Baerga-Ortiz A, Mandell JG, Hughes CA. Biophysics of protein-protein interfaces using biacore, NMR and amide exchange Proceedings 50th Asms Conference On Mass Spectrometry and Allied Topics. 119-120.  1
2001 Glover KJ, Whiles JA, Wood MJ, Melacini G, Komives EA, Vold RR. Conformational dimorphism and transmembrane orientation of prion protein residues 110-136 in bicelles. Biochemistry. 40: 13137-42. PMID 11683621 DOI: 10.1021/Bi011485M  1
2001 Glover KJ, Whiles JA, Wu G, Yu N, Deems R, Struppe JO, Stark RE, Komives EA, Vold RR. Structural evaluation of phospholipid bicelles for solution-state studies of membrane-associated biomolecules. Biophysical Journal. 81: 2163-71. PMID 11566787 DOI: 10.1016/S0006-3495(01)75864-X  1
2001 Hughes CA, Mandell JG, Anand GS, Stock AM, Komives EA. Phosphorylation causes subtle changes in solvent accessibility at the interdomain interface of methylesterase CheB. Journal of Molecular Biology. 307: 967-76. PMID 11286548 DOI: 10.1006/Jmbi.2001.4523  1
2001 Mandell JG, Baerga-Ortiz A, Akashi S, Takio K, Komives EA. Solvent accessibility of the thrombin-thrombomodulin interface. Journal of Molecular Biology. 306: 575-89. PMID 11178915 DOI: 10.1006/Jmbi.2000.4416  1
2001 Whiles JA, Brasseur R, Glover KJ, Melacini G, Komives EA, Vold RR. Orientation and effects of mastoparan X on phospholipid bicelles. Biophysical Journal. 80: 280-93. PMID 11159401 DOI: 10.1016/S0006-3495(01)76013-4  1
2000 Sampoli Benitez BA, Komives EA. Disulfide bond plasticity in epidermal growth factor. Proteins. 40: 168-74. PMID 10813841 DOI: 10.1002/(Sici)1097-0134(20000701)40:1<168::Aid-Prot180>3.0.Co;2-N  1
2000 Wood MJ, Sampoli Benitez BA, Komives EA. Solution structure of the smallest cofactor-active fragment of thrombomodulin. Nature Structural Biology. 7: 200-4. PMID 10700277 DOI: 10.1038/73302  1
2000 Baerga-Ortiz A, Rezaie AR, Komives EA. Electrostatic dependence of the thrombin-thrombomodulin interaction. Journal of Molecular Biology. 296: 651-8. PMID 10669614 DOI: 10.1006/Jmbi.1999.3447  1
1999 Glover KJ, Martini PM, Vold RR, Komives EA. Preparation of insoluble transmembrane peptides: glycophorin-A, prion (110-137), and FGFR (368-397). Analytical Biochemistry. 272: 270-4. PMID 10415099 DOI: 10.1006/Abio.1999.4182  1
1999 Zhang Z, Komives EA, Sugio S, Blacklow SC, Narayana N, Xuong NH, Stock AM, Petsko GA, Ringe D. The role of water in the catalytic efficiency of triosephosphate isomerase. Biochemistry. 38: 4389-97. PMID 10194358 DOI: 10.1021/Bi9826759  1
1999 Wood MJ, Komives EA. Production of large quantities of isotopically labeled protein in Pichia pastoris by fermentation. Journal of Biomolecular Nmr. 13: 149-59. PMID 10070756 DOI: 10.1023/A:1008398313350  1
1999 Mentz S, de Lacalle S, Baerga-Ortiz A, Knauer MF, Knauer DJ, Komives EA. Mechanism of thrombin clearance by human astrocytoma cells. Journal of Neurochemistry. 72: 980-7. PMID 10037469 DOI: 10.1046/J.1471-4159.1999.0720980.X  1
1998 Mandell JG, Falick AM, Komives EA. Identification of protein-protein interfaces by decreased amide proton solvent accessibility. Proceedings of the National Academy of Sciences of the United States of America. 95: 14705-10. PMID 9843953 DOI: 10.1073/Pnas.95.25.14705  1
1998 Struppe J, Komives EA, Taylor SS, Vold RR. 2H NMR studies of a myristoylated peptide in neutral and acidic phospholipid bicelles. Biochemistry. 37: 15523-7. PMID 9799515 DOI: 10.1021/Bi981326B  1
1998 Mandell JG, Falick AM, Komives EA. Measurement of amide hydrogen exchange by MALDI-TOF mass spectrometry. Analytical Chemistry. 70: 3987-95. PMID 9784743 DOI: 10.1021/Ac980553G  1
1998 Gleeson MA, White CE, Meininger DP, Komives EA. Generation of protease-deficient strains and their use in heterologous protein expression. Methods in Molecular Biology (Clifton, N.J.). 103: 81-94. PMID 9680635 DOI: 10.1385/0-89603-421-6:81  1
1997 Sampoli Benitez BA, Hunter MJ, Meininger DP, Komives EA. Structure of the fifth EGF-like domain of thrombomodulin: An EGF-like domain with a novel disulfide-bonding pattern. Journal of Molecular Biology. 273: 913-26. PMID 9367781 DOI: 10.1006/Jmbi.1997.1356  1
1997 Vindigni A, White CE, Komives EA, Di Cera E. Energetics of thrombin-thrombomodulin interaction. Biochemistry. 36: 6674-81. PMID 9184147 DOI: 10.1021/Bi962766A  1
1997 Chen Y, Cino J, Hart G, Freedman D, White C, Komives EA. High protein expression in fermentation of recombinant Pichia pastoris by a fed-batch process Process Biochemistry. 32: 107-111. DOI: 10.1016/S0032-9592(96)00052-0  1
1996 Komives EA, Lougheed JC, Zhang Z, Sugio S, Narayana N, Xuong NH, Petsko GA, Ringe D. The structural basis for pseudoreversion of the H95N lesion by the secondary S96P mutation in triosephosphate isomerase. Biochemistry. 35: 15474-84. PMID 8952501 DOI: 10.1021/Bi961556V  1
1996 White CE, Hunter MJ, Meininger DP, Garrod S, Komives EA. The fifth epidermal growth factor-like domain of thrombomodulin does not have an epidermal growth factor-like disulfide bonding pattern Proceedings of the National Academy of Sciences of the United States of America. 93: 10177-10182. PMID 8816772 DOI: 10.1073/Pnas.93.19.10177  1
1996 Hrabal R, Komives EA, Ni F. Structural resiliency of an EGF-like subdomain bound to its target protein, thrombin. Protein Science : a Publication of the Protein Society. 5: 195-203. PMID 8745396 DOI: 10.1002/Pro.5560050202  1
1996 Komives EA, Hunter MJ, Meininger DP, White LR, White CE. Structure/function of the fourth and fifth EGF domains of thrombomodulin Techniques in Protein Chemistry. 7: 391-400. DOI: 10.1016/S1080-8914(96)80043-3  1
1995 White CE, Hunter MJ, Meininger DP, White LR, Komives EA. Large-scale expression, purification and characterization of small fragments of thrombomodulin: the roles of the sixth domain and of methionine 388. Protein Engineering. 8: 1177-87. PMID 8819984 DOI: 10.1093/Protein/8.11.1177  1
1995 Hunter MJ, Komives EA. Deprotection of S-acetamidomethyl cysteine-containing peptides by silver trifluoromethanesulfonate avoids the oxidation of methionines. Analytical Biochemistry. 228: 173-7. PMID 8572278 DOI: 10.1006/abio.1995.1333  1
1995 Hunter MJ, Komives EA. Thrombin-binding affinities of different disulfide-bonded isomers of the fifth EGF-like domain of thrombomodulin. Protein Science : a Publication of the Protein Society. 4: 2129-37. PMID 8535250 DOI: 10.1002/Pro.5560041019  1
1995 Meininger DP, Hunter MJ, Komives EA. Synthesis, activity, and preliminary structure of the fourth EGF-like domain of thrombomodulin. Protein Science : a Publication of the Protein Society. 4: 1683-95. PMID 8528067 DOI: 10.1002/Pro.5560040904  1
1995 Lougheed JC, Bowman CL, Meininger DP, Komives EA. Thrombin inhibition by cyclic peptides from thrombomodulin. Protein Science : a Publication of the Protein Society. 4: 773-80. PMID 7613475 DOI: 10.1002/Pro.5560040417  1
1995 Komives EA, Lougheed JC, Liu K, Sugio S, Zhang Z, Petsko GA, Ringe D. The structural basis for pseudoreversion of the E165D lesion by the secondary S96P mutation in triosephosphate isomerase depends on the positions of active site water molecules. Biochemistry. 34: 13612-21. PMID 7577950 DOI: 10.1021/Bi00041A041  1
1995 Blackmar C, Healy VL, Narendra U, Hrabal R, Feng NI, Komives EA. Structure/activity of the region of thrombomodulin that binds thrombin Bioorganic Chemistry. 23: 519-527. DOI: 10.1006/Bioo.1995.1037  1
1994 Lodi PJ, Chang LC, Knowles JR, Komives EA. Triosephosphate isomerase requires a positively charged active site: the role of lysine-12. Biochemistry. 33: 2809-14. PMID 8130193 DOI: 10.1021/Bi00176A009  1
1994 Fanuel L, Granier B, Wilkin JM, Bellefroid-Bourguignon C, Joris B, Knowles J, Komives E, Van Beeumen J, Ghuysen JM, Frère JM. The precursor of the Streptomyces R61 DD-peptidase containing a C-terminal extension is inactive. Febs Letters. 351: 49-52. PMID 8076692 DOI: 10.1016/0014-5793(94)00822-1  1
1994 Srinivasan J, Hu S, Hrabal R, Zhu Y, Komives EA, Ni F. Thrombin-bound structure of an EGF subdomain from human thrombomodulin determined by transferred nuclear Overhauser effects. Biochemistry. 33: 13553-60. PMID 7947766 DOI: 10.1021/Bi00250A007  1
1992 Warn-Cramer BJ, Broze GJ, Komives EA. Corrigendum: cDNA sequence of rabbit tissue factor pathway inhibitor (Nucleic Acids Research (1990) 18 (6440)) Nucleic Acids Research. 20: 3548.  1
1991 Komives EA, Chang LC, Lolis E, Tilton RF, Petsko GA, Knowles JR. Electrophilic catalysis in triosephosphate isomerase: the role of histidine-95. Biochemistry. 30: 3011-9. PMID 2007138 DOI: 10.1021/Bi00226A005  1
1988 Komives EA, Tew D, Olmstead MM, Ortiz De Montellano PR. Models for cytochrome P450 prosthetic heme alkylation. Reaction of diazoacetophenone with (tetraphenylporphyrinato)iron(II) chloride Inorganic Chemistry. 27: 3112-3117. DOI: 10.1021/Ic00291A014  1
1987 Komives EA, Ortiz de Montellano PR. Mechanism of oxidation of pi bonds by cytochrome P-450. Electronic requirements of the transition state in the turnover of phenylacetylenes. The Journal of Biological Chemistry. 262: 9793-802. PMID 3597438  1
1985 Ortiz de Montellano PR, Komives EA. Branchpoint for heme alkylation and metabolite formation in the oxidation of arylacetylenes by cytochrome P-450. The Journal of Biological Chemistry. 260: 3330-6. PMID 3972828  1
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