1
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Iljina M, Mazal H, Dayananda A, Zhang Z, Stan G, Riven I, Haran G. Single-molecule FRET probes allosteric effects on protein-translocating pore loops of a AAA+ machine. Biophys J 2024; 123:374-388. [PMID: 38196191 PMCID: PMC10870172 DOI: 10.1016/j.bpj.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/07/2023] [Accepted: 01/02/2024] [Indexed: 01/11/2024] Open
Abstract
AAA+ proteins (ATPases associated with various cellular activities) comprise a family of powerful ring-shaped ATP-dependent translocases that carry out numerous vital substrate-remodeling functions. ClpB is a AAA+ protein disaggregation machine that forms a two-tiered hexameric ring, with flexible pore loops protruding into its center and binding to substrate proteins. It remains unknown whether these pore loops contribute only passively to substrate-protein threading or have a more active role. Recently, we have applied single-molecule FRET spectroscopy to directly measure the dynamics of substrate-binding pore loops in ClpB. We have reported that the three pore loops of ClpB (PL1-3) undergo large-scale fluctuations on the microsecond timescale that are likely to be mechanistically important for disaggregation. Here, using single-molecule FRET, we study the allosteric coupling between the pore loops and the two nucleotide-binding domains of ClpB (NBD1-2). By mutating the conserved Walker B motifs within the NBDs to abolish ATP hydrolysis, we demonstrate how the nucleotide state of each NBD tunes pore-loop dynamics. This effect is surprisingly long-ranged; in particular, PL2 and PL3 respond differentially to a Walker B mutation in either NBD1 or NBD2, as well as to mutations in both. We characterize the conformational dynamics of pore loops and the allosteric paths connecting NBDs to pore loops by molecular dynamics simulations and find that both principal motions and allosteric paths can be altered by changing the ATPase state of ClpB. Remarkably, PL3, which is highly conserved in AAA+ machines, is found to favor an upward conformation when only NBD1 undergoes ATP hydrolysis but a downward conformation when NBD2 is active. These results explicitly demonstrate a significant long-range allosteric effect of ATP hydrolysis sites on pore-loop dynamics. Pore loops are therefore established as active participants that undergo ATP-dependent conformational changes to translocate substrate proteins through the central pores of AAA+ machines.
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Affiliation(s)
- Marija Iljina
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Ashan Dayananda
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio
| | - Zhaocheng Zhang
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio
| | - George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio.
| | - Inbal Riven
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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2
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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] [What about the content of this article? (0)] [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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3
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Abstract
Internal motions in proteins take place on a broad range of time- and space-scales. The potential roles of these dynamics in the biochemical functions of proteins have intrigued biophysicists for many years, and multiple mechanisms to couple motions to function have been proposed. Some of these mechanisms have relied on equilibrium concepts. For example, the modulation of dynamics was proposed to change the entropy of a protein, hence affecting processes such as binding. This so-called dynamic allostery scenario has been demonstrated in several recent experiments. Perhaps even more intriguing may be models that involve out-of-equilibrium operation, which by necessity require the input of energy. We discuss several recent experimental studies that expose such potential mechanisms for coupling dynamics and function. In Brownian ratchets, for example, directional motion is promoted by switching a protein between two free energy surfaces. An additional example involves the effect of microsecond domain-closure dynamics of an enzyme on its much slower chemical cycle. These observations lead us to propose a novel two-time-scale paradigm for the activity of protein machines: fast equilibrium fluctuations take place on the microsecond-millisecond time scale, while on a slower time scale, free energy is invested in order to push the system out of equilibrium and drive functional transitions. Motions on the two time scales affect each other and are essential for the overall function of these machines.
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Affiliation(s)
- Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Inbal Riven
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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4
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Scheerer D, Adkar BV, Bhattacharyya S, Levy D, Iljina M, Riven I, Dym O, Haran G, Shakhnovich EI. Allosteric communication between ligand binding domains modulates substrate inhibition in adenylate kinase. Proc Natl Acad Sci U S A 2023; 120:e2219855120. [PMID: 37094144 PMCID: PMC10160949 DOI: 10.1073/pnas.2219855120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/22/2023] [Indexed: 04/26/2023] Open
Abstract
Enzymes play a vital role in life processes; they control chemical reactions and allow functional cycles to be synchronized. Many enzymes harness large-scale motions of their domains to achieve tremendous catalytic prowess and high selectivity for specific substrates. One outstanding example is provided by the three-domain enzyme adenylate kinase (AK), which catalyzes phosphotransfer between ATP to AMP. Here we study the phenomenon of substrate inhibition by AMP and its correlation with domain motions. Using single-molecule FRET spectroscopy, we show that AMP does not block access to the ATP binding site, neither by competitive binding to the ATP cognate site nor by directly closing the LID domain. Instead, inhibitory concentrations of AMP lead to a faster and more cooperative domain closure by ATP, leading in turn to an increased population of the closed state. The effect of AMP binding can be modulated through mutations throughout the structure of the enzyme, as shown by the screening of an extensive AK mutant library. The mutation of multiple conserved residues reduces substrate inhibition, suggesting that substrate inhibition is an evolutionary well conserved feature in AK. Combining these insights, we developed a model that explains the complex activity of AK, particularly substrate inhibition, based on the experimentally observed opening and closing rates. Notably, the model indicates that the catalytic power is affected by the microsecond balance between the open and closed states of the enzyme. Our findings highlight the crucial role of protein motions in enzymatic activity.
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Affiliation(s)
- David Scheerer
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Bharat V Adkar
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | | | - Dorit Levy
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Marija Iljina
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Inbal Riven
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Orly Dym
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
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5
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Riven I, Mazal H, Iljina M, Haran G. Fast dynamics shape the function of the
AAA
+ machine
ClpB
: lessons from single‐molecule
FRET
spectroscopy. FEBS J 2022. [DOI: 10.1111/febs.16539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/04/2022] [Accepted: 05/30/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Inbal Riven
- Department of Chemical and Biological Physics Weizmann Institute of Science Rehovot Israel
| | - Hisham Mazal
- Department of Chemical and Biological Physics Weizmann Institute of Science Rehovot Israel
| | - Marija Iljina
- Department of Chemical and Biological Physics Weizmann Institute of Science Rehovot Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics Weizmann Institute of Science Rehovot Israel
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6
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Mazal H, Iljina M, Riven I, Haran G. Ultrafast pore-loop dynamics in a AAA+ machine point to a Brownian-ratchet mechanism for protein translocation. Sci Adv 2021; 7:eabg4674. [PMID: 34516899 PMCID: PMC8442866 DOI: 10.1126/sciadv.abg4674] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 07/14/2021] [Indexed: 05/29/2023]
Abstract
AAA+ ring–shaped machines, such as the disaggregation machines ClpB and Hsp104, mediate ATP-driven substrate translocation through their central channel by a set of pore loops. Recent structural studies have suggested a universal hand-over-hand translocation mechanism with slow and rigid subunit motions. However, functional and biophysical studies are in discord with this model. Here, we directly measure the real-time dynamics of the pore loops of ClpB during substrate threading, using single-molecule FRET spectroscopy. All pore loops undergo large-amplitude fluctuations on the microsecond time scale and change their conformation upon interaction with substrate proteins in an ATP-dependent manner. Conformational dynamics of two of the pore loops strongly correlate with disaggregation activity, suggesting that they are the main contributors to substrate pulling. This set of findings is rationalized in terms of an ultrafast Brownian-ratchet translocation mechanism, which likely acts in parallel to the much slower hand-over-hand process in ClpB and other AAA+ machines.
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7
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Iljina M, Mazal H, Goloubinoff P, Riven I, Haran G. Entropic Inhibition: How the Activity of a AAA+ Machine Is Modulated by Its Substrate-Binding Domain. ACS Chem Biol 2021; 16:775-785. [PMID: 33739813 PMCID: PMC8056383 DOI: 10.1021/acschembio.1c00156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
ClpB is a tightly regulated AAA+ disaggregation machine. Each ClpB molecule is composed of a flexibly attached N-terminal domain (NTD), an essential middle domain (MD) that activates the machine by tilting, and two nucleotide-binding domains. The NTD is not well-characterized structurally and is commonly considered to serve as a dispensable substrate-binding domain. Here, we use single-molecule FRET spectroscopy to directly monitor the real-time dynamics of ClpB's NTD and reveal its unexpected autoinhibitory function. We find that the NTD fluctuates on the microsecond time scale, and these dynamics result in steric hindrance that limits the conformational space of the MD to restrict its tilting. This leads to significantly inhibited ATPase and disaggregation activities of ClpB, an effect that is alleviated upon binding of a substrate protein or the cochaperone DnaK. This entropic inhibition mechanism, which is mediated by ultrafast motions of the NTD and is not dependent on any strong interactions, might be common in related ATP-dependent proteases and other multidomain proteins to ensure their fast and reversible activation.
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Affiliation(s)
- Marija Iljina
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Inbal Riven
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
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8
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Ghosh S, Banerjee-Ghosh K, Levy D, Riven I, Naaman R, Haran G. Substrates Modulate Charge-Reorganization Allosteric Effects in Protein-Protein Association. J Phys Chem Lett 2021; 12:2805-2808. [PMID: 33710900 PMCID: PMC8041378 DOI: 10.1021/acs.jpclett.1c00437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein function may be modulated by an event occurring far away from the functional site, a phenomenon termed allostery. While classically allostery involves conformational changes, we recently observed that charge redistribution within an antibody can also lead to an allosteric effect, modulating the kinetics of binding to target antigen. In the present work, we study the association of a polyhistidine tagged enzyme (phosphoglycerate kinase, PGK) to surface-immobilized anti-His antibodies, finding a significant Charge-Reorganization Allostery (CRA) effect. We further observe that PGK's negatively charged nucleotide substrates modulate CRA substantially, even though they bind far away from the His-tag-antibody interaction interface. In particular, binding of ATP reduces CRA by more than 50%. The results indicate that CRA is affected by the binding of charged molecules to a protein and provide further insight into the significant role that charge redistribution can play in protein function.
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9
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Jungwirth J, Mondal S, Shehade M, Liebermann D, Levy D, Riven I, Haran G. Single-Molecule Insights into Allosteric Regulation of the Nuclear Receptor Protein RXRα. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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10
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Scheerer D, Yuval Aviram H, Mazal H, Riven I, Haran G. Urea as a Protein LID Opener: Overcoming Substrate Inhibition in Adenylate Kinase by Tuning Conformational Dynamics. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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11
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Abstract
![]()
A new
mechanism of allostery in proteins, based on charge rather
than structure, is reported. We demonstrate that dynamic redistribution
of charge within a protein can control its function and affect its
interaction with a binding partner. In particular, the association
of an antibody with its target protein antigen is studied. Dynamic
charge shifting within the antibody during its interaction with the
antigen is enabled by its binding to a metallic surface that serves
as a source for electrons. The kinetics of antibody–antigen
association are enhanced when charge redistribution is allowed, even
though charge injection happens at a position far from the antigen
binding site. This observation points to charge-reorganization
allostery, which should be operative in addition or parallel
to other mechanisms of allostery, and may explain some current observations
on protein interactions.
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Affiliation(s)
- Koyel Banerjee-Ghosh
- Department of Chemical and Biological Physics, Weizmann Institute, Rehovot 76100, Israel
| | - Shirsendu Ghosh
- Department of Chemical and Biological Physics, Weizmann Institute, Rehovot 76100, Israel
| | - Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute, Rehovot 76100, Israel
| | - Inbal Riven
- Department of Chemical and Biological Physics, Weizmann Institute, Rehovot 76100, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute, Rehovot 76100, Israel
| | - Ron Naaman
- Department of Chemical and Biological Physics, Weizmann Institute, Rehovot 76100, Israel
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12
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Kantaev R, Riven I, Goldenzweig A, Barak Y, Dym O, Peleg Y, Albeck S, Fleishman SJ, Haran G. Manipulating the Folding Landscape of a Multidomain Protein. J Phys Chem B 2018; 122:11030-11038. [DOI: 10.1021/acs.jpcb.8b04834] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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13
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Aviram HY, Pirchi M, Barak Y, Riven I, Haran G. Two states or not two states: Single-molecule folding studies of protein L. J Chem Phys 2018; 148:123303. [DOI: 10.1063/1.4997584] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Haim Yuval Aviram
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Menahem Pirchi
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yoav Barak
- Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Inbal Riven
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilad Haran
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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14
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Abstract
Ligand binding to a protein can stabilize it significantly against unfolding. The variation of the folding free energy, ΔΔG0, due to ligand binding can be derived from a simple reaction scheme involving exclusive binding to the native state. One obtains the following expression: , where Kd is the ligand dissociation constant and L is its concentration, R is the universal gas constant and T is the temperature. This expression has been shown to correctly describe experimental results on multiple proteins. In the current work we studied the effect of ligand binding on the stability of the multi-domain protein adenylate kinase from E. coli (AKE). Unfolding experiments were conducted using single-molecule FRET spectroscopy, which allowed us to directly obtain the fraction of unfolded protein in a model-free way from FRET efficiency histograms. Surprisingly, it was found that the effect of two inhibitors (Ap5A and AMPPNP) and a substrate (AMP) on the stability of AKE was much smaller than expected based on Kd values obtained independently using microscale thermophoresis. To shed light on this issue, we measured the Kd for Ap5A over a range of chemical denaturant concentrations where the protein is still folded. It was found that Kd increases dramatically over this range, likely due to the population of folding intermediates, whose binding to the ligand is much weaker than that of the native state. We propose that binding to folding intermediates may dominate the effect of ligands on the stability of multi-domain proteins, and could therefore have a strong impact on protein homeostasis in vivo.
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Affiliation(s)
- Hisham Mazal
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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15
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Ozer E, Chemla Y, Schlesinger O, Aviram HY, Riven I, Haran G, Alfonta L. Cover Image, Volume 114, Number 5, May 2017. Biotechnol Bioeng 2017. [DOI: 10.1002/bit.26127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Eden Ozer
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
| | - Yonatan Chemla
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
| | - Orr Schlesinger
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
| | - Haim Yuval Aviram
- Department of Chemical Physics; Weizmann Institute of Science; Rehovot Israel
| | - Inbal Riven
- Department of Chemical Physics; Weizmann Institute of Science; Rehovot Israel
| | - Gilad Haran
- Department of Chemical Physics; Weizmann Institute of Science; Rehovot Israel
| | - Lital Alfonta
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
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16
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Ozer E, Chemla Y, Schlesinger O, Aviram HY, Riven I, Haran G, Alfonta L. In vitro suppression of two different stop codons. Biotechnol Bioeng 2016; 114:1065-1073. [DOI: 10.1002/bit.26226] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/22/2016] [Accepted: 11/16/2016] [Indexed: 01/12/2023]
Affiliation(s)
- Eden Ozer
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
| | - Yonatan Chemla
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
| | - Orr Schlesinger
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
| | - Haim Yuval Aviram
- Department of Chemical Physics; Weizmann Institute of Science; Rehovot Israel
| | - Inbal Riven
- Department of Chemical Physics; Weizmann Institute of Science; Rehovot Israel
| | - Gilad Haran
- Department of Chemical Physics; Weizmann Institute of Science; Rehovot Israel
| | - Lital Alfonta
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
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17
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Jung Y, Riven I, Feigelson SW, Kartvelishvily E, Tohya K, Miyasaka M, Alon R, Haran G. Three-dimensional localization of T-cell receptors in relation to microvilli using a combination of superresolution microscopies. Proc Natl Acad Sci U S A 2016; 113:E5916-E5924. [PMID: 27647916 PMCID: PMC5056101 DOI: 10.1073/pnas.1605399113] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Leukocyte microvilli are flexible projections enriched with adhesion molecules. The role of these cellular projections in the ability of T cells to probe antigen-presenting cells has been elusive. In this study, we probe the spatial relation of microvilli and T-cell receptors (TCRs), the major molecules responsible for antigen recognition on the T-cell membrane. To this end, an effective and robust methodology for mapping membrane protein distribution in relation to the 3D surface structure of cells is introduced, based on two complementary superresolution microscopies. Strikingly, TCRs are found to be highly localized on microvilli, in both peripheral blood human T cells and differentiated effector T cells, and are barely found on the cell body. This is a decisive demonstration that different types of T cells universally localize their TCRs to microvilli, immediately pointing to these surface projections as effective sensors for antigenic moieties. This finding also suggests how previously reported membrane clusters might form, with microvilli serving as anchors for specific T-cell surface molecules.
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Affiliation(s)
- Yunmin Jung
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Inbal Riven
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sara W Feigelson
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Kazuo Tohya
- Department of Anatomy, Kansai University of Health Sciences, Kumatori, Osaka 590-0482, Japan
| | - Masayuki Miyasaka
- Institute for Academic Initiatives, Osaka University, Suita, Osaka 565-0871, Japan; MediCity Research Laboratory, University of Turku, FI-20521, Turku, Finland
| | - Ronen Alon
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gilad Haran
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel;
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18
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Cohen SS, Riven I, Cortajarena AL, De Rosa L, D’Andrea LD, Regan L, Haran G. Probing the Molecular Origin of Native-State Flexibility in Repeat Proteins. J Am Chem Soc 2015. [DOI: 10.1021/jacs.5b06160] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sharona S. Cohen
- Chemical
Physics Department, Weizmann institute of Science, Rehovot 76100, Israel
| | - Inbal Riven
- Chemical
Physics Department, Weizmann institute of Science, Rehovot 76100, Israel
| | - Aitziber L. Cortajarena
- IMDEA
Nanociencia, CNB-CSIC-IMDEA Nanociencia Associated Unit “Unidad
de Nanobiotecnología”, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain
| | - Lucia De Rosa
- Istituto
di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, via Mezzocannone 16, 80134 Napoli, Italy
| | - Luca D. D’Andrea
- Istituto
di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, via Mezzocannone 16, 80134 Napoli, Italy
| | - Lynne Regan
- Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Gilad Haran
- Chemical
Physics Department, Weizmann institute of Science, Rehovot 76100, Israel
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19
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Nativ R, Riven I, Borer A. O065: Using adenosine tri-phosphate (ATP)-bioluminescence assay to compare outcomes of two strategies to perform environmental cleaning in a hospital setting. Antimicrob Resist Infect Control 2013. [PMCID: PMC3687986 DOI: 10.1186/2047-2994-2-s1-o65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Laviv T, Riven I, Dolev I, Vertkin I, Balana B, Slesinger PA, Slutsky I. Basal GABA regulates GABA(B)R conformation and release probability at single hippocampal synapses. Neuron 2010; 67:253-67. [PMID: 20670833 DOI: 10.1016/j.neuron.2010.06.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2010] [Indexed: 01/27/2023]
Abstract
Presynaptic GABA(B) receptor (GABA(B)R) heterodimers are composed of GB(1a)/GB(2) subunits and critically influence synaptic and cognitive functions. Here, we explored local GABA(B)R activation by integrating optical tools for monitoring receptor conformation and synaptic vesicle release at individual presynaptic boutons of hippocampal neurons. Utilizing fluorescence resonance energy transfer (FRET) spectroscopy, we detected a wide range of FRET values for CFP/YFP-tagged GB(1a)/GB(2) receptors that negatively correlated with release probabilities at single synapses. High FRET of GABA(B)Rs associated with low release probability. Notably, pharmacological manipulations that either reduced or increased basal receptor activation decreased intersynapse variability of GB(1a)/GB(2) receptor conformation. Despite variability along axons, presynaptic GABA(B)R tone was dendrite specific, having a greater impact on synapses at highly innervated proximal branches. Prolonged neuronal inactivity reduced basal receptor activation, leading to homeostatic augmentation of release probability. Our findings suggest that local variations in basal GABA concentration are a major determinant of GB(1a)/GB(2) conformational variability, which contributes to heterogeneity of neurotransmitter release at hippocampal synapses.
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Affiliation(s)
- Tal Laviv
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Laviv T, Riven I, Vertkin I, Dolev I, Slesinger P, Slutsky I. Endogenous GABA Regulates GABABR Conformation and Release Probability at Single Hippocampal Synapses. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Abstract
The traditional view of G protein-coupled receptor (GPCR)-mediated signalling puts the players in this signalling cascade, namely the GPCR, the G protein and its effector, as individual components in space, where the signalling specificity is obtained mainly by the interaction of the GPCR and the Galpha subunits of the G protein. A question is then raised as to how fidelity in receptor signalling is achieved, given that many systems use the same components of the G protein signalling machinery. One possible mechanism for obtaining the specific flow of the downstream signals, from the activated G protein to its specific effector target, in a timely manner, is compartmentalization, a spatial arrangement of the complex in a rather restricted space. Here we review our recent findings related to these issues, using the G protein-coupled potassium channel (GIRK) as a model effector and fluorescence-based approaches to reveal how the signalling complex is arranged and how the G protein exerts its action to activate the GIRK channel in intact cells.
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Affiliation(s)
- Adi Raveh
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
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Raveh A, Riven I, Reuveny E. The use of FRET microscopy to elucidate steady state channel conformational rearrangements and G protein interaction with the GIRK channels. Methods Mol Biol 2008; 491:199-212. [PMID: 18998095 DOI: 10.1007/978-1-59745-526-8_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
while X-ray crystallography provides extremely high-resolution snapshot of protein structure, it lacks the ability to provide dynamic information on the processes involving conformational rearrangements of the protein. Methods to record protein conformational dynamics are present, in particular those that are based on fluorescence measurements, and are now more and more utilized in studying proteins in their natural environment. Here we describe the use of fluorescence resonance energy transfer (FRET) technique to monitor the conformational rearrangements associated with the gating of the G protein-coupled potassium channel (GIRK/Kir3.x), and its relation with the G protein subunits. The FRET technique is combined with total internal fluorescence (TIRF) microscopy, and allows the dissection of the signal originating from channel proteins that reside exclusively in the plasma membrane. Since most of the components associated with GIRK channel gating are intracellular, that involve various biochemical steps, proteins were labeled with genetically encoded variants of the green fluorescence protein and signals were acquired from live cells in culture. Using these methodologies we were able to show that gating conformational rearrangements, i.e. the opening of the channel, involve the rotation and expansion of the channel subunits cytosolic termini, along the channel's central axis. In addition, the G proteins that trigger this process reside very close to the channel, to ensure high signaling specificity and to provide temporal precision of the gating process.
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Affiliation(s)
- Adi Raveh
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
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Riven I, Iwanir S, Reuveny E. GIRK Channel Activation Involves a Local Rearrangement of a Preformed G Protein Channel Complex. Neuron 2006; 51:561-73. [PMID: 16950155 DOI: 10.1016/j.neuron.2006.08.017] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Revised: 06/19/2006] [Accepted: 08/09/2006] [Indexed: 11/15/2022]
Abstract
G protein-coupled signaling is one of the major mechanisms for controlling cellular excitability. One of the main targets for this control at postsynaptic membranes is the G protein-coupled potassium channels (GIRK/Kir3), which generate slow inhibitory postsynaptic potentials following the activation of Pertussis toxin-sensitive G protein-coupled receptors. Using total internal reflection fluorescence (TIRF) microscopy combined with fluorescence resonance energy transfer (FRET), in intact cells, we provide evidence for the existence of a trimeric G protein-channel complex at rest. We show that activation of the channel via the receptor induces a local conformational switch of the G protein to induce channel opening. The presence of such a complex thus provides the means for a precise temporal and highly selective activation of the channel, which is required for fine tuning of neuronal excitability.
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Affiliation(s)
- Inbal Riven
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100
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Riven I, Kalmanzon E, Segev L, Reuveny E. Conformational Rearrangements Associated with the Gating of the G Protein-Coupled Potassium Channel Revealed by FRET Microscopy. Neuron 2003; 38:225-35. [PMID: 12718857 DOI: 10.1016/s0896-6273(03)00193-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
G protein-coupled potassium channels (GIRK/Kir3.x) are key determinants that translate inhibitory chemical neurotransmission into changes in cellular excitability. To understand the mechanism of channel activation by G proteins, it is necessary to define the structural rearrangements in the channel that result from interaction with Gbetagamma subunits. In this study we used a combination of fluorescence spectroscopy and through-the-objective total internal reflection microscopy to monitor the conformational rearrangements associated with the activation of GIRK channels in single intact cells. We detect activation-induced changes in FRET consistent with a rotation and expansion of the termini along the central axis of the channel. We propose that this rotation and expansion of the termini drives the channel to open by bending and possibly rotating the second transmembrane segment.
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Affiliation(s)
- Inbal Riven
- Department of Biological Chemistry, Weizmann Institute of Science, 76100, Rehovot, Israel
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