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Collaborative Publications
2010
Ferreiro, D.U., Komives, E.A. (2010). Molecular mechanisms of system control of Nf-κB signaling by IκBα. Biochemistry 49, 1560–1567. PDF

Markwick, P.R.L., 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, 1220-1221. PDF
2009
Bergqvist, S., Alverdi, V., Mengel, B., Hoffman, A., Ghosh, G., Komives, E.A. (2009) Kinetic enhancement of NF-κB-DNA dissociation by IκBα. Proc. Natl Acad. Sci. USA 106, 19328-19333. PDF

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 IκBα revealed by nuclear magnetic resonance. Biochemistry 48, 8023–8031.PDF
Kearns, J.D., Hoffman, A. (2009) Integrating Computational and Biochemical Studies to Explore Mechanisms in NF-κB Signaling. J. Biol. Chem. 284, 5439–al5443. PDF
O'Dea, E., Hoffman, A. (2009) NF-κB signaling. WIREs Syst Biol Med 1, 107–115. PDF
Savinova, O.V., Hoffman, A., Ghosh, G. (2009). The Nfkb1 and Nfκb2 Proteins p105 and p100 Function as the Core of High-Molecular-Weight
Heterogeneous Complexes. Mol.Cell 34, 591–602. PDF
Shih, V.F.-S., Kearns, J.D., Basak, S., Savinova, O.V., Ghosh, G., Hoffman, A. (2009). Kinetic control of negative feedback regulators of
NF-κB/RelA determines their pathogen- and cytokine-receptor signaling specificity. Proc. Natl. Acad. Sci. USA 106, 9619-9624. PDF

Sue, S.-C., Dyson, H.J. (2009). Interaction of the IκBα C-terminal PEST Sequence with NF-κB: Insights into the Inhibition of NF-κB DNA Binding
by IκBα. Journal of Mol. Biol. 388, 824–838. PDF

Weinkam, P., Romesberg, F.E., Wolynes, P.G., (2009) Chemical Frustration in the Protein Folding Landscape: Grand Canonical Ensemble Simulations of Cytochrome c. Biochemistry. 48, 2394-2402. PDF

2008
Barrick, D., Ferreiro, D.U., Komives, E.K. (2008). Folding landscapes of ankyrin repeat proteins: experiments meet theory. Curr. Opin. Struct. Biol. 18, 27–34. PDF
Basak, S., Shih, V.F., Hoffman, A. (2008). Generation and activation of multiple dimeric transcription factors within the NF-κB signaling system. Mol. Cell. Biol. 28, 3139–3150. PDF

Bergqvist, S., Ghosh, G., Komives, E.A. (2008). The IκBα/NF-κB complex has two hot spots, one at either end of the interface. Protein Sci. 17, 2051–2058. PDF

Ferreiro, D.U., Walczak, A.M., Komives, E.A., Wolynes, P.G. (2008). The energy landscapes of repeat-rontaining proteins: topology, cooperativity, and the folding funnels of fne-dimensional architectures. PLoS Comput. Biol. 4, 1-13. PDF
Lätzer, J., Shen, T., Wolynes, P.G. (2008). Conformational Switching upon Phosphorylation: A Predictive Framework Based on Energy Landscape Principles. Biochemistry. 47, 2110-2122. PDF

Mathes, E., O'Dea, E.L., Hoffman, A., Ghosh, G. (2008). NF-κB dictates the degradation pathway of IκBα. EMBO J. 27, 1357-1367. PDF suppl. PDF

O'Dea, E.L., Kearns, J.D., Hoffman, A. (2008). UV as an amplifier rather than inducer of NF-κB activity. Mol. Cell 30, 632–641. PDF
Sue, S., Cervantes, C.F., Komives, E.A., Dyson, H.J. (2008). Transfer of flexibility between ankyrin repeats in IκBα upon formation of the NF-κB complex. J. Mol. Biol. 380, 917-931. PDF

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

Truhlar, S.M.E., Cervantes, C.F., Torpey, J.W., Kjaergaard, M., Komives, E.A. (2008). Rapid mass spectrometric analysis of 15 N-Leu
incorporation fidelity during preparation of specifically labeled NMR samples. Protein Sci. 17, 1636-1639. PDF
2007
Ferreiro, D.U., Komives, E.A. (2007). The plastic landscape of repeat proteins. Proc. Natl Acad. Sci. USA. 104, 7735–7736. PDF
Ferreiro, D.U., Cervantes, C.F., Truhlar, S.M.E., Cho, S.S., Wolynes, P.G., Komives, E.A. (2007). Stabilizing IκBα by “Consensus” Design. J. Mol. Biol. 365, 1201-1216. PDF
Ferreiro, D.U., Hegler, J.A., Komives, E.A., Wolynes, P.G. (2007) Localizing frustration in native proteins and protein assemblies. Proc. Natl Acad. USA. 104, 19819–19824. PDF
Lätzer, J., Papoian, G.A., Prentiss, M.C., Komives, E.A., Wolynes, P.G. (2007) Induced fit, folding, and recognition of the NF-κB-nuclear localization signals by IκBα and IκBβ. J. Mol. Biol. 367, 262–274. PDF
Sutto, L., Lätzer, J., Hegler, J.A., Ferreiro, D.U., Wolynes, P.G. (2007). Consequences of localized frustration for the folding mechanism of the IM7 protein. Proc. Natl Acad. Sci. USA. 104, 19825–19830. PDF
2006
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-κB p65 Anchors IκBα, Forming a Very Stable Complex. J. Mol. Biol. 360, 421–434. PDF
Lätzer, J., Eastwood, M.P., Wolynes, P.G. (2006). Simulation studies of the fidelity of biomolecular structure ensemble recreation. J. Chem. Phys. 21, 214905. PDF
Truhlar, S.M.E., Torpey, J.W., Komives, E.A. (2006). Regions of IκBa that are critical for its inhibition of NF-κB DNA interaction fold upon binding to NF-κB. Pro. Natl Acad. Sci. USA 103, 18951–18956. PDF
2005
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, 679–692. PDF