Specializing in Biophysics Research

Baughman HER, Narang D, Chen W, Villagrán  Suárez 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 NFκB p50/RelA. J Biol Chem. 298(9):102349. 

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. Nucleic Acids Res. 49(19):11211-11223

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

Ramsey KM, Chen W, Marion JD, Bergqvist S, Komives EA. (2019) Exclusivity and Compensation in NFκB Dimer Distributions and IκB Inhibition. Biochemistry. 58(21):2555-2563.

Narang D, Chen W, Ricci CG, Komives EA. (2018) RelA-Containing NFκB Dimers Have Strikingly Different DNA-Binding Cavities in the Absence of DNA. J Mol Biol. 2018;430(10):1510-1520.

Ramsey KM, Narang D, Komives EA. (2018) Prediction of the Presence of a Seventh Ankyrin Repeat in IκBε from Homology Modeling Combined with Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS). Protein Sci. 2018 Aug 22. doi: 10.1002/pro.3459.

Ramsey KM, Dembinski HE, Chen W, Ricci CG, Komives EA. (2017) DNA and IκBα Both Induce Long-Range Conformational Changes in NFκB. J Mol Biol. 429(7):999-1008. PMC5389416

Dembinski, HD, Wismer, K, Vargas, JD, Suryawanshi, GW, Kern, N, Kroon, GJA, Dyson, HJ, Hoffmann, A, Komives, EA (2017) Functional importance of stripping in NFκB signaling revealed by a stripping-impaired IκBα mutant. Proc Natl Acad Sci U S A 114, 1916-1921. PMC5338396

Potoyan DA, Zheng W, Ferreiro DU, Wolynes PG, Komives EA. (2016) PEST Control of Molecular Stripping of NFκB from DNA Transcription Sites. J Phys Chem B. 120(33):8532-8538.

Trelle MB, Ramsey KM, Lee TC, Zheng W, Lamboy J, Wolynes PG, Deniz A, Komives EA. (2016) Binding of NFκB Appears to Twist the Ankyrin Repeat Domain of IκBα. Biophys J. 110(4):887-95. PMC4776026

Potoyan DA, Zheng W, Komives EA, Wolynes PG. (2016) Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network. Proc Natl Acad Sci U S A. 113(1):110-115. PMC4711861

Ferreiro DU, Komives EA, Wolynes PG. (2014) Frustration in Biomolecules Q Rev Biophys. 2014 Nov;47(4):285-363. PMC4256721

Alverdi V, Hetrick B, Joseph S, Komives EA. Direct observation of a transient ternary complex during IκBα-mediated dissociation of NF-κB from DNA. Proc Nat Acad Sci 111(1):225-30. PMC3890772

Dembinski H, Wismer K, Balasubramaniam D, Gonzalez HA, Alverdi V, Iakoucheva LM, Komives EA. (2014)Predicted disorder-to-order transition mutations in IκBα disrupt function. Phys Chem Chem Phys. 16(14):6480-5. PMC4040282

Lamboy-Gonzalez, J., Kim, H., Dembinski, H., Ha, T.J., Komives, E. A. (2013) Single molecule FRET reveals the native state dynamics of the IκBα ankyrin repeat domain. J Mol Biol. 425(14):2578-90. PMC3758917

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 IκBα J Mol Biol. 425(5):902-13. PMC3744861

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

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

Komives EA. (2012) Consequences of Fuzziness in the NFκB/IκBα Interaction. Adv Exp Med Biol. 725:74-85. PMC3603378

Lamboy, J. A., Kim, H., Lee, K. S., Ha, T. and Komives, E. A. (2011) P Visualization of the nanospring dynamics of the IκBα ankyrin repeat domain in real time roc. Nat. Acad. Sci. U S A. 108, 10178-83. PMC3121830

Devries, I., Ferreiro, D. U., Sánchez, I. E. and Komives, E. A. (2011) Folding Kinetics of the Cooperatively Folded Subdomain of the IκBα Ankyrin Repeat Domain. J. Mol. Biol. 408, 163-76. PMC3081522

Sue SC, Alverdi V, Komives EA, Dyson HJ. (2011) Detection of a ternary complex of NF-kappaB and IkappaBalpha with DNA provides insights into how IkappaBalpha removes NF-kappaB from transcription sites.Proc Natl Acad Sci U S A. 108, 1367-72. PMC3029698.

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

Cervantes, C. F., Bergqvist, S., Kjaergaard, M., Kroon, G., Sue, S-C., Dyson, H. J., and Komives, E. A. (2010)The RelA nuclear localization signal folds upon binding to IkBa. J Mol Biol 405, 754-64. PMC3056351

Devries, I., Hampton-Smith, R. J., Mulvihill, M., Alverdi, V., Peet, D. J., and Komives, E. A., (2010)Consequences of IkappaB alpha hydroxylation by the factor inhibiting HIF (FIH). FEBS Lett. 584, 4725-30. PMC3034650.

Ferreiro, D. U., Komives, E.A. (2010) Molecular Mechanisms of System Control of NF-kappaB Signaling by IkappaBalpha. Biochemistry 49, 1560-7. PMC2865148

Markwick, P. R., Cervantes, C. F., Abel, B. L., Komives, E. A., Blackledge, M. , McCammon, J. A. (2010)Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. J Am Chem Soc. 132, 1220-1.PMC2812018

Cervantes, C. F., Markwick, P. R. L., Sue, S. C., McCammon, J. A., Dyson, H. J., Komives, E. A. (2009)Functional dynamics of the folded ankyrin repeats of IkappaB alpha revealed by nuclear magnetic resonance.Biochemistry 48, 8023-31. PMC2728578

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

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

Ferreiro, D.U., Walczak, A. M., Komives, E. A. and Wolynes, P. G. (2008) The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures. PLoS Comput Biol. 16, 4(5):e1000070.

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

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

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

Latzer, J., Papoian, G. A., Prentiss, M. C., Komives, E. A., Wolynes, P. G. (2007) Induced fit, folding, and recognition of the NF-kappaB-nuclear localization signals by IkappaBalpha and IkappaBbeta. J Mol Biol. 367, 262-74.

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. J. Mol. Biol. 365, 1201-16.

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. Proc. Nat. Acad. Sci. U. S. A. 103, 18951-6.

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. J. Mol. Biol. 360, 421-34.

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 J. Mol. Biol. 354, 679-92.

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. Protein Sci. 13, 1767-77.