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Liebermann DG, Jungwirth J, Riven I, Barak Y, Levy D, Horovitz A, Haran G. From Microstates to Macrostates in the Conformational Dynamics of GroEL: A Single-Molecule Förster Resonance Energy Transfer Study. J Phys Chem Lett 2023:6513-6521. [PMID: 37440608 PMCID: PMC10388350 DOI: 10.1021/acs.jpclett.3c01281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
The chaperonin GroEL is a multisubunit molecular machine that assists in protein folding in the Escherichia coli cytosol. Past studies have shown that GroEL undergoes large allosteric conformational changes during its reaction cycle. Here, we report single-molecule Förster resonance energy transfer measurements that directly probe the conformational transitions of one subunit within GroEL and its single-ring variant under equilibrium conditions. We find that four microstates span the conformational manifold of the protein and interconvert on the submillisecond time scale. A unique set of relative populations of these microstates, termed a macrostate, is obtained by varying solution conditions, e.g., adding different nucleotides or the cochaperone GroES. Strikingly, ATP titration studies demonstrate that the partition between the apo and ATP-ligated conformational macrostates traces a sigmoidal response with a Hill coefficient similar to that obtained in bulk experiments of ATP hydrolysis. These coinciding results from bulk measurements for an entire ring and single-molecule measurements for a single subunit provide new evidence for the concerted allosteric transition of all seven subunits.
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2
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Gruber R, Mondal T, Horovitz A. GroEL Allostery Illuminated by a Relationship between the Hill Coefficient and the MWC Model. Biophys J 2019; 117:1915-1921. [PMID: 31699334 DOI: 10.1016/j.bpj.2019.10.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 10/06/2019] [Accepted: 10/15/2019] [Indexed: 11/30/2022] Open
Abstract
A fundamental problem that has hindered the use of the classic Monod-Wyman-Changuex (MWC) allosteric model since its introduction is that it has been difficult to determine the values of its parameters in a reliable manner because they are correlated with each other and sensitive to the data-fitting method. Consequently, experimental data are often fitted to the Hill equation, which provides a measure of cooperativity but no insights into its origin. In this work, we derived a general relationship between the value of the Hill coefficient and the parameters of the MWC model. It is shown that this relationship can be used to select the best estimate of the true combination of the MWC parameter values from all the possible ones found to fit the data. Here, this approach was applied to fits to the MWC model of curves of the fraction of GroEL molecules in the high-affinity (R) state for ATP as a function of ATP concentration. Such curves were collected at different temperatures, thereby providing insight into the hydrophobic effect associated with the ATP-promoted allosteric switch of GroEL. More generally, the relationship derived here should facilitate future thermodynamic analysis of other MWC-type allosteric systems.
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Affiliation(s)
- Ranit Gruber
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tridib Mondal
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Amnon Horovitz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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Franck JM, Sokolovski M, Kessler N, Matalon E, Gordon-Grossman M, Han SI, Goldfarb D, Horovitz A. Probing water density and dynamics in the chaperonin GroEL cavity. J Am Chem Soc 2014; 136:9396-403. [PMID: 24888581 PMCID: PMC4091268 DOI: 10.1021/ja503501x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
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ATP-dependent binding of the chaperonin
GroEL to its cofactor GroES
forms a cavity in which encapsulated substrate proteins can fold in
isolation from bulk solution. It has been suggested that folding in
the cavity may differ from that in bulk solution owing to steric confinement,
interactions with the cavity walls, and differences between the properties
of cavity-confined and bulk water. However, experimental data regarding
the cavity-confined water are lacking. Here, we report measurements
of water density and diffusion dynamics in the vicinity of a spin
label attached to a cysteine in the Tyr71 → Cys GroES mutant
obtained using two magnetic resonance techniques: electron-spin echo
envelope modulation and Overhauser dynamic nuclear polarization. Residue
71 in GroES is fully exposed to bulk water in free GroES and to confined
water within the cavity of the GroEL–GroES complex. Our data
show that water density and translational dynamics in the vicinity
of the label do not change upon complex formation, thus indicating
that bulk water-exposed and cavity-confined GroES surface water share
similar properties. Interestingly, the diffusion dynamics of water
near the GroES surface are found to be unusually fast relative to
other protein surfaces studied. The implications of these findings
for chaperonin-assisted folding mechanisms are discussed.
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Affiliation(s)
- John M Franck
- Department of Chemistry and Biochemistry, University of California Santa Barbara, California 93106, United States
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Abstract
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and microclusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell organization also organizes signaling and coordinates cellular behavior. We propose a new view of the spatial structure of cell signaling systems. This new view describes cell signaling in terms of dynamic allosteric interactions within and among distinct, spatially organized transient clusters. The clusters vary over time and space and are on length scales from nanometers to micrometers. When considered across these length scales, primary factors in the spatial organization are cell membrane domains and the actin cytoskeleton, both also highly dynamic. A key challenge is to understand the interplay across these multiple scales, link it to the physicochemical basis of the conformational behavior of single molecules and ultimately relate it to cellular function. Overall, our premise is that at these scales, cell signaling should be thought of not primarily as a sequence of diffusion-controlled molecular collisions, but instead transient, allostery-driven cluster re-forming interactions.
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Affiliation(s)
- Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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5
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Abstract
Allosteric propagation results in communication between distinct sites in the protein structure; it also encodes specific effects on cellular pathways, and in this way it shapes cellular response. One example of long-range effects is binding of morphogens to cell surface receptors, which initiates a cascade of protein interactions that leads to genome activation and specific cellular action. Allosteric propagation results from combinations of multiple factors, takes place through dynamic shifts of conformational ensembles, and affects the equilibria of macromolecular interactions. Here, we (a) emphasize the well-known yet still underappreciated role of allostery in conveying explicit signals across large multimolecular assemblies and distances to specify cellular action; (b) stress the need for quantitation of the allosteric effects; and finally, (c) propose that each specific combination of allosteric effectors along the pathway spells a distinct function. The challenges are colossal; the inspiring reward will be predicting function, misfunction, and outcomes of drug regimes.
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Affiliation(s)
- Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, Maryland 21702, USA.
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Bao H, Duong F. Discovery of an auto-regulation mechanism for the maltose ABC transporter MalFGK2. PLoS One 2012; 7:e34836. [PMID: 22529943 PMCID: PMC3328499 DOI: 10.1371/journal.pone.0034836] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2012] [Accepted: 03/06/2012] [Indexed: 01/19/2023] Open
Abstract
The maltose transporter MalFGK2, together with the substrate-binding protein MalE, is one of the best-characterized ABC transporters. In the conventional model, MalE captures maltose in the periplasm and delivers the sugar to the transporter. Here, using nanodiscs and proteoliposomes, we instead find that MalE is bound with high-affinity to MalFGK2 to facilitate the acquisition of the sugar. When the maltose concentration exceeds the transport capacity, MalE captures maltose and dissociates from the transporter. This mechanism explains why the transport rate is high when MalE has low affinity for maltose, and low when MalE has high affinity for maltose. Transporter-bound MalE facilitates the acquisition of the sugar at low concentrations, but also captures and dissociates from the transporter past a threshold maltose concentration. In vivo, this maltose-forced dissociation limits the rate of transport. Given the conservation of the substrate-binding proteins, this mode of allosteric regulation may be universal to ABC importers.
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Affiliation(s)
- Huan Bao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Franck Duong
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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Frank GA, Horovitz A, Haran G. Fluorescence correlation spectroscopy and allostery: the case of GroEL. Methods Mol Biol 2012; 796:205-216. [PMID: 22052492 DOI: 10.1007/978-1-61779-334-9_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) is an experimental technique in which the equilibrium fluctuations of the fluorescent signal of molecules diffusing through a focused laser beam are measured. An autocorrelation analysis of these fluctuations provides information on dynamic processes, such as allosteric transitions, that the molecules undergo provided that they are fast relative to the diffusion time through the beam. In cases when the dynamics are slow relative to the diffusion time through the beam, FCS curves can yield information about the number of conformational states and their relative populations. Hence, FCS can be used to investigate allosteric systems with either slow or fast dynamics but the type of information gained in these two situations is different.Here, the utility of the FCS technique is exemplified in the case of the single-ring version of the Escherichia coli molecular chaperone GroEL that interconverts with relatively slow dynamics between two allosteric states: a T state with low affinity for ATP and an R state with high affinity for ATP. Thermodynamic analysis suggests that the T-state population should become negligible with increasing ATP concentrations, in conflict with the requirement for conformation cycling, which is essential for the operation of molecular machines. Surprisingly, FCS experiments showed that, even at ATP saturation, ~50% of the molecules still populate the T state at any instance of time, indicating constant out-of-equilibrium cycling between T and R.
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Affiliation(s)
- Gabriel A Frank
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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Out-of-equilibrium conformational cycling of GroEL under saturating ATP concentrations. Proc Natl Acad Sci U S A 2010; 107:6270-4. [PMID: 20308583 DOI: 10.1073/pnas.0910246107] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The molecular chaperone GroEL exists in at least two allosteric states, T and R, that interconvert in an ATP-controlled manner. Thermodynamic analysis suggests that the T-state population becomes negligible with increasing ATP concentrations, in conflict with the requirement for conformational cycling, which is essential for the operation of molecular machines. To solve this conundrum, we performed fluorescence correlation spectroscopy on the single-ring version of GroEL, using a fluorescent switch recently built into its structure, which turns "on," i.e., increases its fluorescence dramatically, when ATP is added. A series of correlation functions was measured as a function of ATP concentration and analyzed using singular-value decomposition. The analysis assigned the signal to two states whose dynamics clearly differ. Surprisingly, even at ATP saturation, approximately 50% of the molecules still populate the T state at any instance of time, indicating constant out-of-equilibrium cycling between T and R. Only upon addition of the cochaperonin GroES does the T-state population vanish. Our results suggest a model in which the T/R ratio is controlled by the rate of ADP release after hydrolysis, which can be determined accordingly.
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Hirano T, Akiyama J, Mori S, Kagechika H. Modulation of intramolecular heterodimer-induced fluorescence quenching of tricarbocyanine dye for the development of fluorescent sensor. Org Biomol Chem 2010; 8:5568-75. [DOI: 10.1039/c0ob00207k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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