{"id":406,"date":"2018-09-13T16:22:05","date_gmt":"2018-09-13T16:22:05","guid":{"rendered":"http:\/\/komiveslab.ucsd.edu\/?page_id=406"},"modified":"2023-02-08T18:23:51","modified_gmt":"2023-02-08T18:23:51","slug":"nfkb-publications","status":"publish","type":"page","link":"https:\/\/komiveslab.ucsd.edu\/?page_id=406","title":{"rendered":"NFkB Publications"},"content":{"rendered":"

Baughman HER, Narang D, Chen W, Villagr\u00e1n\u00a0 Su<\/span>\u00e1rez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA. (2022) An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NF\u03baB p50\/RelA.<\/a> J Biol Chem. 298(9):102349.\u00a0<\/span><\/p>\n

Chen W, Wei L, Wolynes PG, Komives EA. (2021) Single-molecules conformational dynamics of a transcription factor factor reveals a continuum of binding modes controlling association and dissociation.<\/a> Nucleic Acids Res. 49(19):11211-11223<\/p>\n

Stormberg T, Filliaux S, Baughman HER, Komives EA, Lyubchenko YL. (2021) Transcription factor NF-B unravels nucleosomes.<\/a> Biochem Biophys Acta Gen Subj. 1865(9):129934.<\/p>\n

<\/a>Ramsey KM, Chen W, Marion JD, Bergqvist S, Komives EA<\/strong>. (2019) Exclusivity and Compensation in NF\u03baB Dimer Distributions and I\u03baB Inhibition.<\/a> Biochemistry<\/em>. 58(21):2555-2563.<\/p>\n

Narang D, Chen W, Ricci CG, Komives EA. (2018) RelA-Containing NF\u03baB Dimers Have Strikingly Different DNA-Binding Cavities in the Absence of DNA. J Mol Biol.<\/a> 2018;430(10):1510-1520.<\/p>\n

Ramsey KM, Narang D, Komives EA. (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). <\/a> Protein Sci. 2018 Aug 22. doi: 10.1002\/pro.3459.<\/p>\n

Ramsey KM, Dembinski HE, Chen W, Ricci CG, Komives EA. (2017) DNA and I\u03baB\u03b1 Both Induce Long-Range Conformational Changes in NF\u03baB.<\/a> J Mol Biol. 429(7):999-1008. PMC5389416<\/p>\n

Dembinski, HD, Wismer, K, Vargas, JD, Suryawanshi, GW, Kern, N, Kroon, GJA, Dyson, HJ, Hoffmann, A, Komives, EA (2017) Functional importance of stripping in NF\u03baB signaling revealed by a stripping-impaired I\u03baB\u03b1 mutant. <\/a>Proc Natl Acad Sci U S A 114, 1916-1921. PMC5338396<\/p>\n

Potoyan DA, Zheng W, Ferreiro DU, Wolynes PG, Komives EA. (2016) PEST Control of Molecular Stripping of NF\u03baB from DNA Transcription Sites. <\/a>J Phys Chem B. 120(33):8532-8538.<\/p>\n

Trelle MB, Ramsey KM, Lee TC, Zheng W, Lamboy J, Wolynes PG, Deniz A, Komives EA. (2016) Binding of NF\u03baB Appears to Twist the Ankyrin Repeat Domain of I\u03baB\u03b1. Biophys J. 110(4):887-95. PMC4776026<\/p>\n

Potoyan DA, Zheng W, Komives EA, Wolynes PG. (2016) Molecular stripping in the NF-\u03baB\/I\u03baB\/DNA genetic regulatory network. <\/a> Proc Natl Acad Sci U S A. 113(1):110-115. PMC4711861<\/p>\n

Ferreiro DU, Komives EA, Wolynes PG. (2014) Frustration in Biomolecules <\/a>Q Rev Biophys. 2014 Nov;47(4):285-363. PMC4256721<\/p>\n

Alverdi V, Hetrick B, Joseph S, Komives EA. Direct observation of a transient ternary complex during I\u03baB\u03b1-mediated dissociation of NF-\u03baB from DNA. <\/a>Proc Nat Acad Sci 111(1):225-30. PMC3890772<\/p>\n

Dembinski H, Wismer K, Balasubramaniam D, Gonzalez HA, Alverdi V, Iakoucheva LM, Komives EA. (2014)Predicted disorder-to-order transition mutations in I\u03baB\u03b1 disrupt function. <\/a>Phys Chem Chem Phys. 16(14):6480-5. PMC4040282<\/p>\n

Lamboy-Gonzalez, J., Kim, H., Dembinski, H., Ha, T.J., Komives, E. A. (2013) Single molecule FRET reveals the native state dynamics of the I\u03baB\u03b1 ankyrin repeat domain. <\/a>J Mol Biol. 425(14):2578-90. PMC3758917<\/p>\n

Cervantes CF, Handley LD, Sue SC, Dyson HJ, Komives EA. (2013) Long-range effects and functional consequences of stabilizing mutations in the ankyrin repeat domain of I\u03baB\u03b1 <\/a>J Mol Biol. 425(5):902-13. PMC3744861<\/p>\n

Schafer NP, Hoffman RM, Burger A, Craig PO, Komives EA, Wolynes PG. (2012) Discrete kinetic models from funneled energy landscape simulations. <\/a>PLoS One. 2012;7(12):e50635. doi: 10.1371\/journal.pone.0050635. PMC3520928<\/p>\n

Dyson HJ, Komives EA. (2012) Role of disorder in IkB-NFkB interaction. <\/a>IUBMB Life 64(6):499-505. doi: 10.1002\/iub.1044. PMC3575514<\/p>\n

Komives EA. (2012) Consequences of Fuzziness in the NF\u03baB\/I\u03baB\u03b1 Interaction. <\/a>Adv Exp Med Biol. 725:74-85. PMC3603378<\/p>\n

Lamboy, J. A., Kim, H., Lee, K. S., Ha, T. and Komives, E. A. (2011) P Visualization of the nanospring dynamics of the I\u03baB\u03b1 ankyrin repeat domain in real time <\/a>roc. Nat. Acad. Sci. U S A. 108, 10178-83. PMC3121830<\/p>\n

Devries, I., Ferreiro, D. U., S\u00e1nchez, I. E. and Komives, E. A. (2011) Folding Kinetics of the Cooperatively Folded Subdomain of the I\u03baB\u03b1 Ankyrin Repeat Domain. <\/a>J. Mol. Biol. 408, 163-76. PMC3081522<\/p>\n

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.<\/a>Proc Natl Acad Sci U S A. 108, 1367-72. PMC3029698.<\/p>\n

Mathes E, Wang L, Komives E, Ghosh G. (2010) Flexible regions within IkappaBalpha create the ubiquitin-independent degradation signal. <\/a>J Biol Chem. 285, 32927-36. PMCID: PMC2963393.<\/p>\n

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. <\/a>J Mol Biol 405, 754-64. PMC3056351<\/p>\n

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). <\/a>FEBS Lett. 584, 4725-30. PMC3034650.<\/p>\n

Ferreiro, D. U., Komives, E.A. (2010) Molecular Mechanisms of System Control of NF-kappaB Signaling by IkappaBalpha. <\/a>Biochemistry 49, 1560-7. PMC2865148<\/p>\n

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. <\/a>J Am Chem Soc. 132, 1220-1.PMC2812018<\/p>\n

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.<\/a>Biochemistry 48, 8023-31. PMC2728578<\/p>\n

Bergqvist, S., Alverdi, V., Mengel, B., Hoffmann, A., Ghosh, G., Komives, E. A. (2009) Kinetic enhancement of NF-kB-DNA dissociation by IkBa<\/a> Proc. Nat. Acad. Sci. U. S. A., 106, 19328-33.<\/p>\n

Bergqvist, S., Ghosh, G. & Komives, E. A. (2008) The IkappaBalpha\/NF-kappaB complex has two hot spots, one at either end of the interface.<\/a> Prot. Sci. 17, 2051-8.<\/p>\n

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.<\/a> PLoS Comput Biol. 16, 4(5):e1000070.<\/p>\n

Truhlar, S. M. E., Mathes, E., Cervantes, C. F., Ghosh, G., Komives, E. A. (2008) Pre-folding IkBa alters control of NF-kB signaling.<\/a> J. Mol. Biol. 380, 67-82.<\/p>\n

Barrick, D., Ferreiro, D. U., Komives, E. A. (2008) Folding landscapes of ankyrin repeat proteins: experiments meet theory.<\/a> Curr. Opp. Struct. Biol. 18, 27-34.<\/p>\n

Ferreiro, D. U., Hegler, J. A., Komives, E. A. and Wolynes, P. G. (2007) Localizing Frustration in native proteins and protein assemblies.<\/a> Proc. Nat. Acad. Sci. U. S. A. 104, 19819-24.<\/p>\n

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.<\/a> J Mol Biol. 367, 262-74.<\/p>\n

Ferreiro, D. U., Cervantes, C. F., Truhlar, S. M. E., Cho, S. S., Wolynes, P. G., Komives, E. A. (2006) Stabilizing IkappaBalpha by consensus design.<\/a> J. Mol. Biol. 365, 1201-16.<\/p>\n

Truhlar, S. M. E., Torpey, J. W., & Komives, E. A. (2006) Regions of IkappaBalpha that are critical for its inhibition of NF-kappaB-DNA interaction fold upon binding to NF-kappaB.<\/a> Proc. Nat. Acad. Sci. U. S. A. 103, 18951-6.<\/p>\n

Bergqvist, S., Croy, C. H., Kjaergaard, M., Huxford, T., Ghosh, G. & Komives, E. A. (2006) Thermodynamics reveal that helix four in the NLS of NF-kappaB p65 anchors IkappaBalpha, forming a very stable complex.<\/a> J. Mol. Biol. 360, 421-34.<\/p>\n

Ferreiro, D. U., Cho, S. S. Komives, E. A.& Wolynes, P. G. (2005) The energy landscape of modular repeat proteins: Topology determines folding mechanism in the ankyrin family<\/a> J. Mol. Biol. 354, 679-92.<\/p>\n

Croy, C. H, Bergqvist, S. P., Huxford, T., Ghosh, G. & Komives, E. A. (2004) Biophysical characterization of the free IkappaBalpha ankyrin repeat domain in solution.<\/a> Protein Sci. 13, 1767-77.<\/p>\n","protected":false},"excerpt":{"rendered":"

Baughman HER, Narang D, Chen W, Villagr\u00e1n\u00a0 Su\u00e1rez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA. (2022) An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NF\u03baB p50\/RelA. J Biol Chem. 298(9):102349.\u00a0 Chen W, Wei L, Wolynes PG, Komives EA. (2021) Single-molecules conformational dynamics of a transcription factor factor reveals<\/p>\n

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