Long-range Coupling Between Separate Docking Sites in Interleukin-1β

Heidary, David K.; Roy, M.; Daumy, Gaston O.; Yao, Cong; Jennings, Patricia A.

doi:10.1016/j.jmb.2005.08.072

Cited by 19 publications

(30 citation statements)

References 37 publications

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“…1C). The protein folding transitions were monitored by the changes in fluorescence intensity as a function of denaturant concentration (17). A comparative plot of the apparent fraction of unfolded protein, F app , as function of final denaturant concentration is given in Fig.…”

Section: Resultsmentioning

confidence: 99%

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β-Bulge triggers route-switching on the functional landscape of interleukin-1β

Capraro

Roy

Onuchic

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Proteins fold into three-dimensional structures in a funneled energy landscape. This landscape is also used for functional activity. Frustration in this landscape can arise from the competing evolutionary pressures of biological function and reliable folding. Thus, the ensemble of partially folded states can populate multiple routes on this journey to the native state. Although protein folding kinetics experiments have shown the presence of such routes for several proteins, there has been sparse information about the structural diversity of these routes. In addition, why a given protein populates a particular route more often than another protein of similar structure and sequence is not clear. Whereas multiple routes are observed in theoretical studies on the folding of interleukin-1β (IL-1β), experimental results indicate one dominant route where the central portion of the protein folds first, and is then followed by closure of the barrel in this β-trefoil fold. Here we show, using a combination of computation and experiment, that the presence of functionally important regions like the β-bulge in the signaling protein IL-1β strongly influences the choice of folding routes. By deleting the β-bulge, we directly observe the presence of routeswitching. This route-switching provides a direct link between route selection and the folding and functional landscapes of a protein.pulse-labeling | geometric frustration T he energy landscape theory and the funnel concept provide a solution to the protein folding search problem (1). The presence of multiple routes to the native state within this funnel is evident in both simulation and experimental studies (2) and is thought to add to the robustness of the landscape. The question remains, what factors control the route selection for folding? There is speculation that functional residues are a hindrance to folding and may add heterogeneity and roughness to the landscape (2-8). These residues need to be conserved for the protein to function correctly and therefore cannot be optimized for folding. However, the rest of the protein can evolve to make folding more efficient by making the energy landscape more funneled. Thus, it is possible that the most frustrated parts of the protein are the functional sites within the native structure. We hypothesize that functional regions within a protein that are geometrically frustrated drive route selection.The 12 β-stranded inflammatory cytokine, interleukin-1β (IL-1β), is an excellent system to probe the modulation of the folding landscape by perturbing functional regions. Structure-based models (where native interactions dominate the energy function) have identified the functionally important β-bulge (located between β-strands 4 and 5) as a region that is geometrically frustrated and suggest that contacts with this region direct folding route selection (9, 10). Deletion of the β-bulge maintains high affinity receptor binding but abrogates signaling activity, effectively converting the agonist into an antagonist molecule (11). To experime...

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Section: Resultsmentioning

confidence: 99%

“…Equilibrium unfolding titrations were measured using average fluorescence wavelength as previously described (17). The data were fit to a two-state model as described (27) using in-house software.…”

Section: Methodsmentioning

confidence: 99%

β-Bulge triggers route-switching on the functional landscape of interleukin-1β

Capraro

Roy

Onuchic

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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“…Transdomain "cross-talk" between a catalytic center and a distal loop is an emerging theme by which single domains can transmit cellular signals (7,(53)(54)(55). In the single-domain protein interleukin-1β, point mutations that are distal to the receptor binding interface have no effect on stability, yet they have significant effects on the binding properties (55). In multidomain proteins, there are also examples of transdomain communication across individual domains, including in cAMP-dependent protein kinase (56) and in COOH-terminal Src kinase (Csk) (7).…”

Section: Discussionmentioning

confidence: 99%

Allostery in the ferredoxin protein motif does not involve a conformational switch

Nechushtai

Lammert²,

Michaeli³

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Regulation of protein function via cracking, or local unfolding and refolding of substructures, is becoming a widely recognized mechanism of functional control. Oftentimes, cracking events are localized to secondary and tertiary structure interactions between domains that control the optimal position for catalysis and/or the formation of protein complexes. Small changes in free energy associated with ligand binding, phosphorylation, etc., can tip the balance and provide a regulatory functional switch. However, understanding the factors controlling function in single-domain proteins is still a significant challenge to structural biologists. We investigated the functional landscape of a single-domain planttype ferredoxin protein and the effect of a distal loop on the electron-transfer center. We find the global stability and structure are minimally perturbed with mutation, whereas the functional properties are altered. Specifically, truncating the L1,2 loop does not lead to large-scale changes in the structure, determined via X-ray crystallography. Further, the overall thermal stability of the protein is only marginally perturbed by the mutation. However, even though the mutation is distal to the iron-sulfur cluster (∼20 Å), it leads to a significant change in the redox potential of the ironsulfur cluster (57 mV). Structure-based all-atom simulations indicate correlated dynamical changes between the surface-exposed loop and the iron-sulfur cluster-binding region. Our results suggest intrinsic communication channels within the ferredoxin fold, composed of many short-range interactions, lead to the propagation of long-range signals. Accordingly, protein interface interactions that involve L1,2 could potentially signal functional changes in distal regions, similar to what is observed in other allosteric systems.electron transfer | functional energy landscape | iron-sulfur proteins | protein folding O ver the last several decades, our understanding of protein function has evolved from a rather static perspective, where signaling and function have been understood through surface complementarity arguments, such as the "lock and key" paradigm (1, 2), to a more dynamic view where protein conformational fluctuations are inextricably linked to function (3). As our understanding of protein dynamics expands, we are revealing many mechanisms by which proteins exploit conformational fluctuations to perform cellular function. In multidomain proteins, relative repositioning of domains is often linked to their levels of activity. For example, large-scale domain rearrangements in the four-domain Src kinase (4) and C-terminal Src kinase (5, 6) lead to these proteins being in so-called "on" or "off" states, and functional regulation may be obtained by adjusting the balance between these conformations (7). In proteins such as adenylate kinase, domain rearrangements can be rate limiting during each round of catalysis (8), where the enzyme cycles between ligandcompetent and ligand-release conformations. Because the kinetics of these tra...

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“…␤-Strands 6 -10 in IL-1␤ (trefoil 2 and the leading edge of trefoil 3) were protected first during protein refolding as detected by pulse labeling NMR (22). These strands comprise an on-route folding intermediate of IL-1␤ (23,50). Interestingly, the areas adjacent to the sequence corresponding to one of the two main functional loops, the ␤-bulge, are also highly protected in pro-IL-1␤.…”

Section: The C-terminal Region Of Pro-il-1␤ (Residues 117-269) Displamentioning

confidence: 99%

Pro-interleukin (IL)-1β Shares a Core Region of Stability as Compared with Mature IL-1β While Maintaining a Distinctly Different Configurational Landscape

Hailey¹,

Andersen³

et al. 2009

Journal of Biological Chemistry

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Interleukin-1␤ (IL-1␤) is a master cytokine involved in initiating the innate immune response in vertebrates (Dinarello, C. A. (1994) FASEB J. 8, 1314 -1325). It is first synthesized as an inactive 269-residue precursor (pro-interleukin-1␤ or pro-IL-1␤). Pro-IL-1␤ requires processing by caspase-1 to generate the active, mature 153-residue cytokine. In this study, we combined hydrogen/deuterium exchange mass spectrometry, circular dichroism spectroscopy, and enzymatic digestion comparative studies to investigate the configurational landscape of pro-IL-1␤ and the role the N terminus plays in modulating the landscape. We find that the N terminus keeps pro-IL-1␤ in a protease-labile state while maintaining a core region of stability in the C-terminal region, the eventual mature protein. In mature IL-1␤, this highly protected region maps back to the area protected earliest in the NMR studies characterizing an on-route kinetic refolding intermediate. This protected region also encompasses two important functional loops that participate in the IL-1␤/receptor binding interface required for biological activity. We propose that the purpose of the N-terminal precursor region in pro-IL-1␤ is to suppress the function of the eventual mature region while keeping a structurally and also functionally important core region primed for the final folding into the native, active state of the mature protein. The presence of the self-inhibiting precursor region provides yet another layer of regulation in the life cycle of this important cytokine.Nearly all cell types respond to interleukin (IL)-1␤, 4 in a very sensitive manner, via binding to the interleukin-1 receptor type 1 (IL-1RI) (2). Although essential in the immune response, overproduction of IL-1␤ can lead to both acute (sepsis) as well as chronic (rheumatoid arthritis, atherosclerosis, obesity, and diabetes) disease states (3). Thus, the expression, activation, and secretion of this cytokine are tightly controlled (4). Although many cell types express IL-1␤, it is predominately produced and secreted by monocytes and macrophages (1). The protein is synthesized as a biologically inactive 269-residue precursor molecule, pro-interleukin-1␤ (pro-IL-1␤), and the 153-residue active mature IL-1␤ is generated from the C-terminal domain. Processing of the proprotein involves the recently discovered NALP-1 and NALP-3 inflammasomes, which are responsible for activating procaspase-1 (5). The inflammasome function is integral in wound repair as well as for combating infection (6 -9).In vivo, the 31-kDa pro-IL-1␤ precursor is processed to the active C-terminal 17-kDa form by the interleukin-1 converting enzyme, caspase-1 (10, 11). Caspase-1 is a cysteine protease that recognizes two cleavage sites in pro-IL-1␤, the Asp 27 2Gly 28 and Asp 116 2Ala 117 peptide bonds (Fig. 1A). These cleavage sites are conserved across mammals (12-14). The activation pathway is believed to proceed with cleavage first at Asp 27 2Gly 28 (site 1) followed by Asp 116 2Ala 117 (site 2). These processing events lead ...

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Long-range Coupling Between Separate Docking Sites in Interleukin-1β

Cited by 19 publications

References 37 publications

β-Bulge triggers route-switching on the functional landscape of interleukin-1β

β-Bulge triggers route-switching on the functional landscape of interleukin-1β

Allostery in the ferredoxin protein motif does not involve a conformational switch

Pro-interleukin (IL)-1β Shares a Core Region of Stability as Compared with Mature IL-1β While Maintaining a Distinctly Different Configurational Landscape

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