1
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A conformational switch in clathrin light chain regulates lattice structure and endocytosis at the plasma membrane of mammalian cells. Nat Commun 2023; 14:732. [PMID: 36759616 PMCID: PMC9911608 DOI: 10.1038/s41467-023-36304-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Conformational changes in endocytic proteins are regulators of clathrin-mediated endocytosis. Three clathrin heavy chains associated with clathrin light chains (CLC) assemble into triskelia that link into a geometric lattice that curves to drive endocytosis. Structural changes in CLC have been shown to regulate triskelia assembly in solution, yet the nature of these changes, and their effects on lattice growth, curvature, and endocytosis in cells are unknown. Here, we develop a new correlative fluorescence resonance energy transfer (FRET) and platinum replica electron microscopy method, named FRET-CLEM. With FRET-CLEM, we measure conformational changes in clathrin at thousands of individual morphologically distinct clathrin-coated structures. We discover that the N-terminus of CLC repositions away from the plasma membrane and triskelia vertex as coats curve. Preventing this conformational switch with chemical tools increases lattice sizes and inhibits endocytosis. Thus, a specific conformational switch in the light chain regulates lattice curvature and endocytosis in mammalian cells.
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2
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Münch JL, Paul F, Schmauder R, Benndorf K. Bayesian inference of kinetic schemes for ion channels by Kalman filtering. eLife 2022; 11:e62714. [PMID: 35506659 PMCID: PMC9342998 DOI: 10.7554/elife.62714] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/22/2022] [Indexed: 11/16/2022] Open
Abstract
Inferring adequate kinetic schemes for ion channel gating from ensemble currents is a daunting task due to limited information in the data. We address this problem by using a parallelized Bayesian filter to specify hidden Markov models for current and fluorescence data. We demonstrate the flexibility of this algorithm by including different noise distributions. Our generalized Kalman filter outperforms both a classical Kalman filter and a rate equation approach when applied to patch-clamp data exhibiting realistic open-channel noise. The derived generalization also enables inclusion of orthogonal fluorescence data, making unidentifiable parameters identifiable and increasing the accuracy of the parameter estimates by an order of magnitude. By using Bayesian highest credibility volumes, we found that our approach, in contrast to the rate equation approach, yields a realistic uncertainty quantification. Furthermore, the Bayesian filter delivers negligibly biased estimates for a wider range of data quality. For some data sets, it identifies more parameters than the rate equation approach. These results also demonstrate the power of assessing the validity of algorithms by Bayesian credibility volumes in general. Finally, we show that our Bayesian filter is more robust against errors induced by either analog filtering before analog-to-digital conversion or by limited time resolution of fluorescence data than a rate equation approach.
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Affiliation(s)
- Jan L Münch
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich Schiller University JenaJenaGermany
| | - Fabian Paul
- Department of Biochemistry and Molecular Biology, University of ChicagoChicagoUnited States
| | - Ralf Schmauder
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich Schiller University JenaJenaGermany
| | - Klaus Benndorf
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich Schiller University JenaJenaGermany
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3
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Couch T, Berger K, Kneisley DL, McCullock TW, Kammermeier P, Maclean DM. Topography and motion of acid-sensing ion channel intracellular domains. eLife 2021; 10:68955. [PMID: 34292153 PMCID: PMC8341984 DOI: 10.7554/elife.68955] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/21/2021] [Indexed: 01/12/2023] Open
Abstract
Acid-sensing ion channels (ASICs) are trimeric cation-selective channels activated by decreases in extracellular pH. The intracellular N and C terminal tails of ASIC1 influence channel gating, trafficking, and signaling in ischemic cell death. Despite several X-ray and cryo-EM structures of the extracellular and transmembrane segments of ASIC1, these important intracellular tails remain unresolved. Here, we describe the coarse topography of the chicken ASIC1 intracellular domains determined by fluorescence resonance energy transfer (FRET), measured using either fluorescent lifetime imaging or patch clamp fluorometry. We find the C terminal tail projects into the cytosol by approximately 35 Å and that the N and C tails from the same subunits are closer than adjacent subunits. Using pH-insensitive fluorescent proteins, we fail to detect any relative movement between the N and C tails upon extracellular acidification but do observe axial motions of the membrane proximal segments toward the plasma membrane. Taken together, our study furnishes a coarse topographic map of the ASIC intracellular domains while providing directionality and context to intracellular conformational changes induced by extracellular acidification.
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Affiliation(s)
- Tyler Couch
- Graduate Program in Cellular and Molecular Pharmacology and Physiology, Reno, United States
| | - Kyle Berger
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, United States
| | - Dana L Kneisley
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, United States
| | - Tyler W McCullock
- Graduate Program in Cellular and Molecular Pharmacology and Physiology, Reno, United States
| | - Paul Kammermeier
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, United States
| | - David M Maclean
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, United States
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4
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Cowgill J, Chanda B. The contribution of voltage clamp fluorometry to the understanding of channel and transporter mechanisms. J Gen Physiol 2019; 151:1163-1172. [PMID: 31431491 PMCID: PMC6785729 DOI: 10.1085/jgp.201912372] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Cowgill and Chanda discuss the importance of voltage clamp fluorometry to the functional interpretation of ion channel and transporter structures. Key advances in single particle cryo-EM methods in the past decade have ushered in a resolution revolution in modern biology. The structures of many ion channels and transporters that were previously recalcitrant to crystallography have now been solved. Yet, despite having atomistic models of many complexes, some in multiple conformations, it has been challenging to glean mechanistic insight from these structures. To some extent this reflects our inability to unambiguously assign a given structure to a particular physiological state. One approach that may allow us to bridge this gap between structure and function is voltage clamp fluorometry (VCF). Using this technique, dynamic conformational changes can be measured while simultaneously monitoring the functional state of the channel or transporter. Many of the important papers that have used VCF to probe the gating mechanisms of channels and transporters have been published in the Journal of General Physiology. In this review, we provide an overview of the development of VCF and discuss some of the key problems that have been addressed using this approach. We end with a brief discussion of the outlook for this technique in the era of high-resolution structures.
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Affiliation(s)
- John Cowgill
- Graduate Program in Biophysics, University of Wisconsin, Madison, WI.,Department of Neuroscience, University of Wisconsin, Madison, WI
| | - Baron Chanda
- Department of Neuroscience, University of Wisconsin, Madison, WI .,Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI
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5
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Relative positioning of Kv11.1 (hERG) K + channel cytoplasmic domain-located fluorescent tags toward the plasma membrane. Sci Rep 2018; 8:15494. [PMID: 30341381 PMCID: PMC6195548 DOI: 10.1038/s41598-018-33492-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/01/2018] [Indexed: 12/17/2022] Open
Abstract
Recent cryo-EM data have provided a view of the KCNH potassium channels molecular structures. However, some details about the cytoplasmic domains organization and specially their rearrangements associated to channel functionality are still lacking. Here we used the voltage-dependent dipicrylamine (DPA)-induced quench of fluorescent proteins (FPS) linked to different positions at the cytoplasmic domains of KCNH2 (hERG) to gain some insights about the coarse structure of these channel parts. Fast voltage-clamp fluorometry with HEK293 cells expressing membrane-anchored FPs under conditions in which only the plasma membrane potential is modified, demonstrated DPA voltage-dependent translocation and subsequent FRET-triggered FP quenching. Our data demonstrate for the first time that the distance between an amino-terminal FP tag and the intracellular plasma membrane surface is shorter than that between the membrane and a C-terminally-located tag. The distances varied when the FPs were attached to other positions along the channel cytoplasmic domains. In some cases, we also detected slower fluorometric responses following the fast voltage-dependent dye translocation, indicating subsequent label movements orthogonal to the plasma membrane. This finding suggests the existence of additional conformational rearrangements in the hERG cytoplasmic domains, although their association with specific aspects of channel operation remains to be established.
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6
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Wulf M, Pless SA. High-Sensitivity Fluorometry to Resolve Ion Channel Conformational Dynamics. Cell Rep 2018; 22:1615-1626. [DOI: 10.1016/j.celrep.2018.01.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/01/2017] [Accepted: 01/10/2018] [Indexed: 10/18/2022] Open
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7
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Deng B, Zhu S, Macklin AM, Xu J, Lento C, Sljoka A, Wilson DJ. Suppressing allostery in epitope mapping experiments using millisecond hydrogen / deuterium exchange mass spectrometry. MAbs 2017; 9:1327-1336. [PMID: 28933661 PMCID: PMC5680795 DOI: 10.1080/19420862.2017.1379641] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Localization of the interface between the candidate antibody and its antigen target, commonly known as epitope mapping, is a critical component of the development of therapeutic monoclonal antibodies. With the recent availability of commercial automated systems, hydrogen / deuterium eXchange (HDX) is rapidly becoming the tool for mapping epitopes preferred by researchers in both industry and academia. However, this approach has a significant drawback in that it can be confounded by ‘allosteric’ structural and dynamic changes that result from the interaction, but occur far from the point(s) of contact. Here, we introduce a ‘kinetic’ millisecond HDX workflow that suppresses allosteric effects in epitope mapping experiments. The approach employs a previously introduced microfluidic apparatus that enables millisecond HDX labeling times with on-chip pepsin digestion and electrospray ionization. The ‘kinetic’ workflow also differs from conventional HDX-based epitope mapping in that the antibody is introduced to the antigen at the onset of HDX labeling. Using myoglobin / anti-myoglobin as a model system, we demonstrate that at short ‘kinetic’ workflow labeling times (i.e., 200 ms), the HDX signal is already fully developed at the ‘true’ epitope, but is still largely below the significance threshold at allosteric sites. Identification of the ‘true’ epitope is supported by computational docking predictions and allostery modeling using the rigidity transmission allostery algorithm.
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Affiliation(s)
- Bin Deng
- a Chemistry Department , York University , 4700 Keele Street, Toronto , ON , Canada.,b The Centre for Research in Mass Spectrometry , York University , Toronto , ON , Canada
| | - Shaolong Zhu
- a Chemistry Department , York University , 4700 Keele Street, Toronto , ON , Canada.,b The Centre for Research in Mass Spectrometry , York University , Toronto , ON , Canada
| | - Andrew M Macklin
- a Chemistry Department , York University , 4700 Keele Street, Toronto , ON , Canada.,b The Centre for Research in Mass Spectrometry , York University , Toronto , ON , Canada
| | - Jianrong Xu
- c Department of Pharmacology, Institute of Medical Sciences , Shanghai Jiao Tong University School of Medicine , Shanghai , P.R. China
| | - Cristina Lento
- a Chemistry Department , York University , 4700 Keele Street, Toronto , ON , Canada.,b The Centre for Research in Mass Spectrometry , York University , Toronto , ON , Canada
| | - Adnan Sljoka
- d Department of Informatics , Kwansei Gakuin University , Nishinomiya , Hyogo , Japan
| | - Derek J Wilson
- a Chemistry Department , York University , 4700 Keele Street, Toronto , ON , Canada.,b The Centre for Research in Mass Spectrometry , York University , Toronto , ON , Canada
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8
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Voltage-dependent motion of the catalytic region of voltage-sensing phosphatase monitored by a fluorescent amino acid. Proc Natl Acad Sci U S A 2016; 113:7521-6. [PMID: 27330112 DOI: 10.1073/pnas.1604218113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The cytoplasmic region of voltage-sensing phosphatase (VSP) derives the voltage dependence of its catalytic activity from coupling to a voltage sensor homologous to that of voltage-gated ion channels. To assess the conformational changes in the cytoplasmic region upon activation of the voltage sensor, we genetically incorporated a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), into the catalytic region of Ciona intestinalis VSP (Ci-VSP). Measurements of Anap fluorescence under voltage clamp in Xenopus oocytes revealed that the catalytic region assumes distinct conformations dependent on the degree of voltage-sensor activation. FRET analysis showed that the catalytic region remains situated beneath the plasma membrane, irrespective of the voltage level. Moreover, Anap fluorescence from a membrane-facing loop in the C2 domain showed a pattern reflecting substrate turnover. These results indicate that the voltage sensor regulates Ci-VSP catalytic activity by causing conformational changes in the entire catalytic region, without changing their distance from the plasma membrane.
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9
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Trappl K, Joseph S. Ribosome Induces a Closed to Open Conformational Change in Release Factor 1. J Mol Biol 2016; 428:1333-1344. [PMID: 26827724 DOI: 10.1016/j.jmb.2016.01.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 01/15/2016] [Accepted: 01/22/2016] [Indexed: 11/19/2022]
Abstract
Bacterial translation termination is triggered when a stop codon arrives at the ribosomal A site. Stop codons are recognized by class I release factors (RF1 and RF2 in Escherichia coli), which bind to the ribosome and catalyze the release of the newly synthesized protein. Crystal structures showed that RF1 and RF2 are in an open conformation when bound to the ribosome but are in a closed conformation when not bound to the ribosome. It is not clear whether only the open form of RF1 and RF2 binds to the ribosome. Alternatively, the closed form of RF1 and RF2 may bind to the ribosome and undergo a conformational change to the open state upon binding. We used transition metal ion fluorescence resonance energy transfer experiments to monitor precisely the conformation of RF1 in the absence and presence of the ribosome. Our results indicate that RF1 undergoes a large conformational change from a closed to an open form upon binding to the ribosome. Our results are consistent with the mechanism, in which high termination fidelity is achieved by linking stop codon recognition by RF1 to the change in conformation from closed to open state.
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Affiliation(s)
- Krista Trappl
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0314, USA
| | - Simpson Joseph
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0314, USA.
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10
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Gordon SE, Senning EN, Aman TK, Zagotta WN. Transition metal ion FRET to measure short-range distances at the intracellular surface of the plasma membrane. ACTA ACUST UNITED AC 2016; 147:189-200. [PMID: 26755772 PMCID: PMC4727948 DOI: 10.1085/jgp.201511530] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/21/2015] [Indexed: 11/20/2022]
Abstract
A novel method is presented to measure short distances in cell plasma membranes using transition metal ion FRET with metal ions bound to introduced sites in the membrane. Biological membranes are complex assemblies of lipids and proteins that serve as platforms for cell signaling. We have developed a novel method for measuring the structure and dynamics of the membrane based on fluorescence resonance energy transfer (FRET). The method marries four technologies: (1) unroofing cells to isolate and access the cytoplasmic leaflet of the plasma membrane; (2) patch-clamp fluorometry (PCF) to measure currents and fluorescence simultaneously from a membrane patch; (3) a synthetic lipid with a metal-chelating head group to decorate the membrane with metal-binding sites; and (4) transition metal ion FRET (tmFRET) to measure short distances between a fluorescent probe and a transition metal ion on the membrane. We applied this method to measure the density and affinity of native and introduced metal-binding sites in the membrane. These experiments pave the way for measuring structural rearrangements of membrane proteins relative to the membrane.
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Affiliation(s)
- Sharona E Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Eric N Senning
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Teresa K Aman
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
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11
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Morra G, Genoni A, Colombo G. Mechanisms of Differential Allosteric Modulation in Homologous Proteins: Insights from the Analysis of Internal Dynamics and Energetics of PDZ Domains. J Chem Theory Comput 2015; 10:5677-89. [PMID: 26583250 DOI: 10.1021/ct500326g] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Allostery is a general phenomenon in proteins whereby a perturbation at one site reverberates into a functional change at another one, through modulation of its conformational dynamics. Herein, we address the problem of how the molecular signal encoded by a ligand is differentially transmitted through the structures of two homologous PDZ proteins: PDZ2, which responds to binding with structural and dynamical changes in regions distal from the ligand site, and PDZ3, which is characterized by less-intense dynamical variations. We use novel methods of analysis of MD simulations in the unbound and bound states to investigate the determinants of the differential allosteric behavior of the two proteins. The analysis of the correlations between the redistribution of stabilization energy and local fluctuation patterns highlights the nucleus of residues responsible for the stabilization of the 3D fold, the stability core, as the substructure that defines the difference in the allosteric response: in PDZ2, it undergoes a consistent dynamic and energetic reorganization, whereas in PDZ3, it remains largely unperturbed. Specifically, we observe for PDZ2 a significant anticorrelation between the motions of distal loops and residues of the stability core and differences in the correlation patterns between the bound and unbound states. Such variation is not observed in PDZ3, indicating that its energetics and internal dynamics are less affected by the presence/absence of the ligand. Finally, we propose a model with a direct link between the modulation of the structural, energetic and dynamic properties of a protein, and its allosteric response to a perturbation.
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Affiliation(s)
- Giulia Morra
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche Via Mario Bianco 9, 20131 Milano, Italy
| | - Alessandro Genoni
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche Via Mario Bianco 9, 20131 Milano, Italy.,CNRS, Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France.,Université de Lorraine, Laboratoire SRSMC, UMR 7565, Vandoeuvre-lès-Nancy F-54506, France
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche Via Mario Bianco 9, 20131 Milano, Italy
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12
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DeBerg HA, Bankston JR, Rosenbaum JC, Brzovic PS, Zagotta WN, Stoll S. Structural mechanism for the regulation of HCN ion channels by the accessory protein TRIP8b. Structure 2015; 23:734-44. [PMID: 25800552 DOI: 10.1016/j.str.2015.02.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/13/2015] [Accepted: 02/09/2015] [Indexed: 11/19/2022]
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channels underlie the cationic Ih current present in many neurons. The direct binding of cyclic AMP to HCN channels increases the rate and extent of channel opening and results in a depolarizing shift in the voltage dependence of activation. TRIP8b is an accessory protein that regulates the cell surface expression and dendritic localization of HCN channels and reduces the cyclic nucleotide dependence of these channels. Here, we use electron paramagnetic resonance (EPR) to show that TRIP8b binds to the apo state of the cyclic nucleotide binding domain (CNBD) of HCN2 channels without changing the overall domain structure. With EPR and nuclear magnetic resonance, we locate TRIP8b relative to the HCN channel and identify the binding interface on the CNBD. These data provide a structural framework for understanding how TRIP8b regulates the cyclic nucleotide dependence of HCN channels.
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Affiliation(s)
- Hannah A DeBerg
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - John R Bankston
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Joel C Rosenbaum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Peter S Brzovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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13
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Kesters D, Brams M, Nys M, Wijckmans E, Spurny R, Voets T, Tytgat J, Kusch J, Ulens C. Structure of the SthK carboxy-terminal region reveals a gating mechanism for cyclic nucleotide-modulated ion channels. PLoS One 2015; 10:e0116369. [PMID: 25625648 PMCID: PMC4308110 DOI: 10.1371/journal.pone.0116369] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 12/09/2014] [Indexed: 11/19/2022] Open
Abstract
Cyclic nucleotide-sensitive ion channels are molecular pores that open in response to cAMP or cGMP, which are universal second messengers. Binding of a cyclic nucleotide to the carboxyterminal cyclic nucleotide binding domain (CNBD) of these channels is thought to cause a conformational change that promotes channel opening. The C-linker domain, which connects the channel pore to this CNBD, plays an important role in coupling ligand binding to channel opening. Current structural insight into this mechanism mainly derives from X-ray crystal structures of the C-linker/CNBD from hyperpolarization-activated cyclic nucleotide-modulated (HCN) channels. However, these structures reveal little to no conformational changes upon comparison of the ligand-bound and unbound form. In this study, we take advantage of a recently identified prokaryote ion channel, SthK, which has functional properties that strongly resemble cyclic nucleotide-gated (CNG) channels and is activated by cAMP, but not by cGMP. We determined X-ray crystal structures of the C-linker/CNBD of SthK in the presence of cAMP or cGMP. We observe that the structure in complex with cGMP, which is an antagonist, is similar to previously determined HCN channel structures. In contrast, the structure in complex with cAMP, which is an agonist, is in a more open conformation. We observe that the CNBD makes an outward swinging movement, which is accompanied by an opening of the C-linker. This conformation mirrors the open gate structures of the Kv1.2 channel or MthK channel, which suggests that the cAMP-bound C-linker/CNBD from SthK represents an activated conformation. These results provide a structural framework for better understanding cyclic nucleotide modulation of ion channels, including HCN and CNG channels.
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Affiliation(s)
- Divya Kesters
- Laboratory of Structural Neurobiology, KU Leuven, Herestraat 49, PB601, Leuven, B-3000, Belgium
| | - Marijke Brams
- Laboratory of Structural Neurobiology, KU Leuven, Herestraat 49, PB601, Leuven, B-3000, Belgium
| | - Mieke Nys
- Laboratory of Structural Neurobiology, KU Leuven, Herestraat 49, PB601, Leuven, B-3000, Belgium
| | - Eveline Wijckmans
- Laboratory of Structural Neurobiology, KU Leuven, Herestraat 49, PB601, Leuven, B-3000, Belgium
| | - Radovan Spurny
- Laboratory of Structural Neurobiology, KU Leuven, Herestraat 49, PB601, Leuven, B-3000, Belgium
| | - Thomas Voets
- Laboratory of Ion Channel Research, KU Leuven, Herestraat 49, PB802, Leuven, B-3000, Belgium
| | - Jan Tytgat
- Laboratory of Toxicology and Pharmacology, KU Leuven, Herestraat 49, PB922, Leuven, B-3000, Belgium
| | - Jana Kusch
- University Hospital Jena, Institute of Physiologie II, Kollegiengasse 9, 07743, Jena, Germany
| | - Chris Ulens
- Laboratory of Structural Neurobiology, KU Leuven, Herestraat 49, PB601, Leuven, B-3000, Belgium
- * E-mail:
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14
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Kusch J, Zifarelli G. Patch-clamp fluorometry: electrophysiology meets fluorescence. Biophys J 2014; 106:1250-7. [PMID: 24655500 DOI: 10.1016/j.bpj.2014.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/23/2013] [Accepted: 02/06/2014] [Indexed: 12/26/2022] Open
Abstract
Ion channels and transporters are membrane proteins whose functions are driven by conformational changes. Classical biophysical techniques provide insight into either the structure or the function of these proteins, but a full understanding of their behavior requires a correlation of both these aspects in time. Patch-clamp and voltage-clamp fluorometry combine spectroscopic and electrophysiological techniques to simultaneously detect conformational changes and ionic currents across the membrane. Since its introduction, patch-clamp fluorometry has been responsible for invaluable advances in our knowledge of ion channel biophysics. Over the years, the technique has been applied to many different ion channel families to address several biophysical questions with a variety of spectroscopic approaches and electrophysiological configurations. This review illustrates the strength and the flexibility of patch-clamp fluorometry, demonstrating its potential as a tool for future research.
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Affiliation(s)
- Jana Kusch
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany.
| | - Giovanni Zifarelli
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Genova, Italy.
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15
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Podda MV, Grassi C. New perspectives in cyclic nucleotide-mediated functions in the CNS: the emerging role of cyclic nucleotide-gated (CNG) channels. Pflugers Arch 2013; 466:1241-57. [PMID: 24142069 DOI: 10.1007/s00424-013-1373-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 09/27/2013] [Accepted: 09/28/2013] [Indexed: 01/07/2023]
Abstract
Cyclic nucleotides play fundamental roles in the central nervous system (CNS) under both physiological and pathological conditions. The impact of cAMP and cGMP signaling on neuronal and glial cell functions has been thoroughly characterized. Most of their effects have been related to cyclic nucleotide-dependent protein kinase activity. However, cyclic nucleotide-gated (CNG) channels, first described as key mediators of sensory transduction in retinal and olfactory receptors, have been receiving increasing attention as possible targets of cyclic nucleotides in the CNS. In the last 15 years, consistent evidence has emerged for their expression in neurons and astrocytes of the rodent brain. Far less is known, however, about the functional role of CNG channels in these cells, although several of their features, such as Ca(2+) permeability and prolonged activation in the presence of cyclic nucleotides, make them ideal candidates for mediators of physiological functions in the CNS. Here, we review literature suggesting the involvement of CNG channels in a number of CNS cellular functions (e.g., regulation of membrane potential, neuronal excitability, and neurotransmitter release) as well as in more complex phenomena, like brain plasticity, adult neurogenesis, and pain sensitivity. The emerging picture is that functional and dysfunctional cyclic nucleotide signaling in the CNS has to be reconsidered including CNG channels among possible targets. However, concerted efforts and multidisciplinary approaches are still needed to get more in-depth knowledge in this field.
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Affiliation(s)
- Maria Vittoria Podda
- Institute of Human Physiology, Medical School, Università Cattolica, Largo Francesco Vito 1, 00168, Rome, Italy
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16
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17
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De-la-Rosa V, Rangel-Yescas GE, Ladrón-de-Guevara E, Rosenbaum T, Islas LD. Coarse architecture of the transient receptor potential vanilloid 1 (TRPV1) ion channel determined by fluorescence resonance energy transfer. J Biol Chem 2013; 288:29506-17. [PMID: 23965996 DOI: 10.1074/jbc.m113.479618] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The transient receptor potential vanilloid 1 ion channel is responsible for the perception of high temperatures and low extracellular pH, and it is also involved in the response to some pungent compounds. Importantly, it is also associated with the perception of pain and noxious stimuli. Here, we attempt to discern the molecular organization and location of the N and C termini of the transient receptor potential vanilloid 1 ion channel by measuring FRET between genetically attached enhanced yellow and cyan fluorescent protein to the N or C terminus of the channel protein, expressed in transfected HEK 293 cells or Xenopus laevis oocytes. The static measurements of the domain organization were mapped into an available cryo-electron microscopy density of the channel with good agreement. These measurements also provide novel insights into the organization of terminal domains and their proximity to the plasma membrane.
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18
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Mapping of interactions between the N- and C-termini and the channel core in HERG K+ channels. Biochem J 2013; 451:463-74. [PMID: 23418776 DOI: 10.1042/bj20121717] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The characteristic gating properties of the HERG [human eag (ether-a-go-go)-related gene] potassium channel determine its contribution to cardiac repolarization and in setting the electrical behaviour of a variety of cells. In the present study we analysed, using a site-directed cysteine and disulfide chemistry approach, whether the eag/PAS (Per/Arnt/Sim) and proximal domains at the HERG N-terminus exert a role in controlling the access of the N-terminal flexible tail to its binding site in the channel core for interaction with the gating machinery. Whereas the eag/PAS domain is necessary for disulfide bridging, plus the cysteine residues introduced at positions 3 and 542 of the HERG sequence, the presence of the proximal domain seems to be dispensable. The state-dependent formation of a disulfide bridge between Cys3 and an endogenous cysteine residue at position 723 in the C-terminal C-linker suggests that the N-terminal tail of HERG can also get into close proximity with the C-linker structures located at the bottom of helix S6. Therefore the intrinsic flexibility of the N-tail and its proximity to both the S4-S5 loop and the C-linker may dynamically contribute to the modulation of HERG channel gating.
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19
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State-dependent FRET reports calcium- and voltage-dependent gating-ring motions in BK channels. Proc Natl Acad Sci U S A 2013; 110:5217-22. [PMID: 23479636 DOI: 10.1073/pnas.1219611110] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Large-conductance voltage- and calcium-dependent potassium channels (BK, "Big K+") are important controllers of cell excitability. In the BK channel, a large C-terminal intracellular region containing a "gating-ring" structure has been proposed to transduce Ca(2+) binding into channel opening. Using patch-clamp fluorometry, we have investigated the calcium and voltage dependence of conformational changes of the gating-ring region of BK channels, while simultaneously monitoring channel conductance. Fluorescence resonance energy transfer (FRET) between fluorescent protein inserts indicates that Ca(2+) binding produces structural changes of the gating ring that are much larger than those predicted by current X-ray crystal structures of isolated gating rings.
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20
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Yu X, Wu X, Bermejo GA, Brooks BR, Taraska JW. Accurate high-throughput structure mapping and prediction with transition metal ion FRET. Structure 2012; 21:9-19. [PMID: 23273426 DOI: 10.1016/j.str.2012.11.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/15/2012] [Accepted: 11/17/2012] [Indexed: 11/28/2022]
Abstract
Mapping the landscape of a protein's conformational space is essential to understanding its functions and regulation. The limitations of many structural methods have made this process challenging for most proteins. Here, we report that transition metal ion FRET (tmFRET) can be used in a rapid, highly parallel screen, to determine distances from multiple locations within a protein at extremely low concentrations. The distances generated through this screen for the protein maltose binding protein (MBP) match distances from the crystal structure to within a few angstroms. Furthermore, energy transfer accurately detects structural changes during ligand binding. Finally, fluorescence-derived distances can be used to guide molecular simulations to find low energy states. Our results open the door to rapid, accurate mapping and prediction of protein structures at low concentrations, in large complex systems, and in living cells.
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Affiliation(s)
- Xiaozhen Yu
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiongwu Wu
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Guillermo A Bermejo
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin W Taraska
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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21
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Savalli N, Pantazis A, Yusifov T, Sigg D, Olcese R. The contribution of RCK domains to human BK channel allosteric activation. J Biol Chem 2012; 287:21741-50. [PMID: 22556415 PMCID: PMC3381136 DOI: 10.1074/jbc.m112.346171] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 04/10/2012] [Indexed: 11/06/2022] Open
Abstract
Large conductance voltage- and Ca(2+)-activated K(+) (BK) channels are potent regulators of cellular processes including neuronal firing, synaptic transmission, cochlear hair cell tuning, insulin release, and smooth muscle tone. Their unique activation pathway relies on structurally distinct regulatory domains including one transmembrane voltage-sensing domain (VSD) and two intracellular high affinity Ca(2+)-sensing sites per subunit (located in the RCK1 and RCK2 domains). Four pairs of RCK1 and RCK2 domains form a Ca(2+)-sensing apparatus known as the "gating ring." The allosteric interplay between voltage- and Ca(2+)-sensing apparati is a fundamental mechanism of BK channel function. Using voltage-clamp fluorometry and UV photolysis of intracellular caged Ca(2+), we optically resolved VSD activation prompted by Ca(2+) binding to the gating ring. The sudden increase of intracellular Ca(2+) concentration ([Ca(2+)](i)) induced a hyperpolarizing shift in the voltage dependence of both channel opening and VSD activation, reported by a fluorophore labeling position 202, located in the upper side of the S4 transmembrane segment. The neutralization of the Ca(2+) sensor located in the RCK2 domain abolished the effect of [Ca(2+)](i) increase on the VSD rearrangements. On the other hand, the mutation of RCK1 residues involved in Ca(2+) sensing did not prevent the effect of Ca(2+) release on the VSD, revealing a functionally distinct interaction between RCK1 and RCK2 and the VSD. A statistical-mechanical model quantifies the complex thermodynamics interplay between Ca(2+) association in two distinct sites, voltage sensor activation, and BK channel opening.
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Affiliation(s)
- Nicoletta Savalli
- From the Department of Anesthesiology, Division of Molecular Medicine
| | - Antonios Pantazis
- From the Department of Anesthesiology, Division of Molecular Medicine
| | - Taleh Yusifov
- From the Department of Anesthesiology, Division of Molecular Medicine
| | - Daniel Sigg
- From the Department of Anesthesiology, Division of Molecular Medicine
| | - Riccardo Olcese
- From the Department of Anesthesiology, Division of Molecular Medicine
- the Brain Research Institute, and
- the Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90075
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22
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Barros F, Domínguez P, de la Peña P. Cytoplasmic domains and voltage-dependent potassium channel gating. Front Pharmacol 2012; 3:49. [PMID: 22470342 PMCID: PMC3311039 DOI: 10.3389/fphar.2012.00049] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 03/05/2012] [Indexed: 12/20/2022] Open
Abstract
The basic architecture of the voltage-dependent K+ channels (Kv channels) corresponds to a transmembrane protein core in which the permeation pore, the voltage-sensing components and the gating machinery (cytoplasmic facing gate and sensor–gate coupler) reside. Usually, large protein tails are attached to this core, hanging toward the inside of the cell. These cytoplasmic regions are essential for normal channel function and, due to their accessibility to the cytoplasmic environment, constitute obvious targets for cell-physiological control of channel behavior. Here we review the present knowledge about the molecular organization of these intracellular channel regions and their role in both setting and controlling Kv voltage-dependent gating properties. This includes the influence that they exert on Kv rapid/N-type inactivation and on activation/deactivation gating of Shaker-like and eag-type Kv channels. Some illustrative examples about the relevance of these cytoplasmic domains determining the possibilities for modulation of Kv channel gating by cellular components are also considered.
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Affiliation(s)
- Francisco Barros
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo Oviedo, Asturias, Spain
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23
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Taraska JW. Mapping membrane protein structure with fluorescence. Curr Opin Struct Biol 2012; 22:507-13. [PMID: 22445227 DOI: 10.1016/j.sbi.2012.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 02/22/2012] [Accepted: 02/24/2012] [Indexed: 01/07/2023]
Abstract
Membrane proteins regulate many cellular processes including signaling cascades, ion transport, membrane fusion, and cell-to-cell communications. Understanding the architecture and conformational fluctuations of these proteins is critical to understanding their regulation and functions. Fluorescence methods including intensity mapping, fluorescence resonance energy transfer (FRET), and photo-induced electron transfer, allow for targeted measurements of domains within membrane proteins. These methods can reveal how a protein is structured and how it transitions between different conformational states. Here, I will review recent work done using fluorescence to map the structures of membrane proteins, focusing on how each of these methods can be applied to understanding the dynamic nature of individual membrane proteins and protein complexes.
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Affiliation(s)
- Justin W Taraska
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, United States.
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24
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Bavro VN, De Zorzi R, Schmidt MR, Muniz JRC, Zubcevic L, Sansom MSP, Vénien-Bryan C, Tucker SJ. Structure of a KirBac potassium channel with an open bundle crossing indicates a mechanism of channel gating. Nat Struct Mol Biol 2012; 19:158-63. [PMID: 22231399 PMCID: PMC3272479 DOI: 10.1038/nsmb.2208] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 11/14/2011] [Indexed: 02/04/2023]
Abstract
KirBac channels are prokaryotic homologs of mammalian inwardly rectifying (Kir) potassium channels, and recent crystal structures of both Kir and KirBac channels have provided major insight into their unique structural architecture. However, all of the available structures are closed at the helix bundle crossing, and therefore the structural mechanisms that control opening of their primary activation gate remain unknown. In this study, we engineered the inner pore-lining helix (TM2) of KirBac3.1 to trap the bundle crossing in an apparently open conformation and determined the crystal structure of this mutant channel to 3.05 Å resolution. Contrary to previous speculation, this new structure suggests a mechanistic model in which rotational 'twist' of the cytoplasmic domain is coupled to opening of the bundle-crossing gate through a network of inter- and intrasubunit interactions that involve the TM2 C-linker, slide helix, G-loop and the CD loop.
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Affiliation(s)
- Vassiliy N Bavro
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
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25
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Wang S, Chuang HH. C-terminal dimerization activates the nociceptive transduction channel transient receptor potential vanilloid 1. J Biol Chem 2011; 286:40601-7. [PMID: 21926175 DOI: 10.1074/jbc.m111.256669] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Covalent modification of the specific cysteine residue(s) by oxidative stress robustly potentiates transient receptor potential vanilloid 1 (TRPV1) and sensitizes nociception. Here we provide biochemical evidence of dimerization of TRPV1 subunits upon exposure to phenylarsine oxide and hydrogen peroxide (H(2)O(2)), two chemical surrogates of oxidative stress. A disulfide bond formed between apposing cysteines ligates two C termini, serving as the structural basis of channel sensitization by oxidative covalent C-terminal modification. Systematic cysteine scanning of the C terminus of a cysteineless TRPV1 channel revealed a critical region within which any cysteine introduced phenylarsine oxide activation to mutant TRPV1. Oxidative sensitization persisted even when this region is substituted with a random peptide linker containing a single cysteine. So did insertion of this region to TRPV3, a homolog lacking the corresponding region and resistant to oxidative challenge. These results suggest that the non-conserved linker in the TRPV1 C terminus senses environmental oxidative stress and adjusts channel activity during cumulative oxidative damage by lowering the activation threshold of gating elements shared by TRPV channels.
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Affiliation(s)
- Shu Wang
- Department of Biomedical Sciences, Cornell University, Ithaca, New York 14853, USA
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26
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Crivat G, Taraska JW. Imaging proteins inside cells with fluorescent tags. Trends Biotechnol 2011; 30:8-16. [PMID: 21924508 DOI: 10.1016/j.tibtech.2011.08.002] [Citation(s) in RCA: 189] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/04/2011] [Accepted: 08/04/2011] [Indexed: 11/30/2022]
Abstract
Watching biological molecules provides clues to their function and regulation. Some of the most powerful methods of labeling proteins for imaging use genetically encoded fluorescent fusion tags. There are four standard genetic methods of covalently tagging a protein with a fluorescent probe for cellular imaging. These use (i) autofluorescent proteins, (ii) self-labeling enzymes, (iii) enzymes that catalyze the attachment of a probe to a target sequence, and (iv) biarsenical dyes that target tetracysteine motifs. Each of these techniques has advantages and disadvantages. In this review, we cover new developments in these methods and discuss practical considerations for their use in imaging proteins inside living cells.
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Affiliation(s)
- Georgeta Crivat
- University of Maryland, College Park, Department of Entomology and Program in Cell and Molecular Biology, College Park, MD 20742, USA
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27
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Ma B, Tsai CJ, Haliloğlu T, Nussinov R. Dynamic allostery: linkers are not merely flexible. Structure 2011; 19:907-17. [PMID: 21742258 PMCID: PMC6361528 DOI: 10.1016/j.str.2011.06.002] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 06/05/2011] [Accepted: 06/07/2011] [Indexed: 12/19/2022]
Abstract
Most proteins consist of multiple domains. How do linkers efficiently transfer information between sites that are on different domains to activate the protein? Mere flexibility only implies that the conformations would be sampled. For fast timescales between triggering events and cellular response, which often involves large conformational change, flexibility on its own may not constitute a good solution. We posit that successive conformational states along major allosteric propagation pathways are pre-encoded in linker sequences where each state is encoded by the previous one. The barriers between these states that are hierarchically populated are lower, achieving faster timescales even for large conformational changes. We further propose that evolution has optimized the linker sequences and lengths for efficiency, which explains why mutations in linkers may affect protein function and review the literature in this light.
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Affiliation(s)
- Buyong Ma
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA
| | - Chung-Jung Tsai
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA
| | - Türkan Haliloğlu
- Polymer Research Center and Chemical Engineering Department, Bogazici University, Bebek-Istanbul 34342, Turkey
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA
- Sackler Institute 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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28
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Khushoo A, Yang Z, Johnson AE, Skach WR. Ligand-driven vectorial folding of ribosome-bound human CFTR NBD1. Mol Cell 2011; 41:682-92. [PMID: 21419343 DOI: 10.1016/j.molcel.2011.02.027] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 12/03/2010] [Accepted: 02/23/2011] [Indexed: 11/26/2022]
Abstract
The mechanism by which protein folding is coupled to biosynthesis is a critical, but poorly understood, aspect of protein conformational diseases. Here we use fluorescence resonance energy transfer (FRET) to characterize tertiary structural transitions of nascent polypeptides and show that the first nucleotide-binding domain (NBD1) of human CFTR, whose folding is defective in cystic fibrosis, folds via a cotranslational multistep pathway as it is synthesized on the ribosome. Folding begins abruptly as NBD1 residues 389-500 emerge from the ribosome exit tunnel, initiating compaction of a small, N-terminal α/β-subdomain. Real-time kinetics of synchronized nascent chains revealed that subdomain folding is rapid, occurs coincident with synthesis, and is facilitated by direct ATP binding to the nascent polypeptide. These findings localize the major CF defect late in the NBD1 folding pathway and establish a paradigm wherein a cellular ligand promotes vectorial domain folding by facilitating an energetically favored local peptide conformation.
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Affiliation(s)
- Amardeep Khushoo
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97239, USA
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29
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Abstract
Macromolecules drive the complex behavior of neurons. For example, channels and transporters control the movements of ions across membranes, SNAREs direct the fusion of vesicles at the synapse, and motors move cargo throughout the cell. Understanding the structure, assembly, and conformational movements of these and other neuronal proteins is essential to understanding the brain. Developments in fluorescence have allowed the architecture and dynamics of proteins to be studied in real time and in a cellular context with great accuracy. In this review, we cover classic and recent methods for studying protein structure, assembly, and dynamics with fluorescence. These methods include fluorescence and luminescence resonance energy transfer, single-molecule bleaching analysis, intensity measurements, colocalization microscopy, electron transfer, and bimolecular complementation analysis. We present the principles of these methods, highlight recent work that uses the methods, and discuss a framework for interpreting results as they apply to molecular neurobiology.
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30
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LaFranzo NA, Strulson MK, Yanker DM, Dang LT, Maurer JA. Sequence or structure: using bioinformatics and homology modeling to understand functional relationships in cAMP/cGMP binding domains. MOLECULAR BIOSYSTEMS 2010; 6:894-901. [PMID: 20567776 DOI: 10.1039/b922562e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The relationship between sequence, structure, and function is examined by comparing nineteen cyclic nucleotide monophosphate binding domains of known structure from six different functional families. Comparisons are made by structure and sequence alignment and through the generation of 3610 homology models. This analysis suggests there are only weak relationships between functional families, sequence, and/or structure. However, we have identified that for cyclic nucleotide monophosphate binding domains privileged template structures occur for homology modeling. The existence of privileged template structures, capable of creating accurate modeling for a broad family of proteins, may lead to improved homology modeling protocols.
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Affiliation(s)
- Natalie A LaFranzo
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63110, USA
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31
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Masi A, Cicchi R, Carloni A, Pavone FS, Arcangeli A. Optical methods in the study of protein-protein interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 674:33-42. [PMID: 20549938 DOI: 10.1007/978-1-4419-6066-5_4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Förster (or Fluorescence) resonance energy transfer (FRET) is a physical process in which energy is transferred nonradiatively from an excited fluorophore, serving as a donor, to another chromophore (acceptor). Among the techniques related to fluorescence microscopy, FRET is unique in providing signals sensitive to intra- and intermolecular distances in the 1-10 nm range. Because of its potency, FRET is increasingly used to visualize and quantify the dynamics of protein-protein interaction in living cells, with high spatio-temporal resolution. Here we describe the physical bases of FRET, detailing the principal methods applied: (1) measurement of signal intensity and (2) analysis of fluorescence lifetime (FLIM). Although several technical complications must be carefully considered, both methods can be applied fruitfully to specific fields. For example, FRET based on intensity detection is more suitable to follow biological phenomena at a finely tuned spatial and temporal scale. Furthermore, a specific fluorescence signal occurring close to the plasma membrane (< or = 100 nm) can be obtained using a total internal reflection fluorescence (TIRF) microscopy system. When performing FRET experiments, care must be also taken to the method chosen for labeling interacting proteins. Two principal tools can be applied: (1) fluorophore tagged antibodies; (2) recombinant fluorescent fusion proteins. The latter method essentially takes advantage of the discovery and use of spontaneously fluorescent proteins, like the green fluorescent protein (GFP). Until now, FRET has been widely used to analyze the structural characteristics of several proteins, including integrins and ion channels. More recently, this method has been applied to clarify the interaction dynamics of these classes of membrane proteins with cytosolic signaling proteins. We report two examples in which the interaction dynamics between integrins and ion channels have been studied with FRET methods. Using fluorescent antibodies and applying FRET-FLIM, the direct interaction of beta1 integrin with the receptor for Epidermal Growth Factor (EGF-R) has been proved in living endothelial cells. A different approach, based on TIRFM measurement of the FRET intensity of fluorescently labeled recombinant proteins, suggests that a direct interaction also occurs between integrins and the ether-a-go-go-related-gene 1 (hERG1) K+ channel.
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Affiliation(s)
- Alessio Masi
- Department of Experimental Pathology and Oncology, University of Florence, Italy
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32
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Hirano M, Takeuchi Y, Aoki T, Yanagida T, Ide T. Rearrangements in the KcsA cytoplasmic domain underlie its gating. J Biol Chem 2009; 285:3777-3783. [PMID: 19959477 DOI: 10.1074/jbc.m109.084368] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A change of cytosolic pH 7 to 4 opens the bacterial potassium channel KcsA. However, the overall gating mechanism leading to channel opening, especially the contribution of the cytoplasmic domain, remains unsolved. Here we report that deletion of the cytoplasmic domain resulted in changes in channel conductance and gating behavior at pH 4 without channel opening at pH 7. To probe for rearrangements in the cytoplasmic domain during channel opening, amino acid residues were substituted with cysteines and labeled with a fluorophore (tetramethylrhodamine maleimide) that exhibits increased fluorescence intensity upon transfer from a hydrophilic to hydrophobic environment. In all cases channel open probability (P(o)) was approximately 1 at pH 4 and approximately 0 at pH 7. Major increases in fluorescence intensity were observed for tetramethylrhodamine maleimide-labeled residues in the cytoplasmic domain as pH changed from 7 to 4, which suggests the fluorophores shifted from a hydrophilic to hydrophobic environment. Dipicrylamide, a lipid soluble quencher, reduced the fluorescence intensities of labeled residues in the cytosolic domain at pH 4. These results reveal that a decrease in pH introduces major conformational rearrangements associated with channel opening in the KcsA cytoplasmic domain.
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Affiliation(s)
- Minako Hirano
- From the Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Yuko Takeuchi
- From the Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Takaaki Aoki
- From the Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Toshio Yanagida
- From the Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Toru Ide
- From the Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan.
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33
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Short-distance probes for protein backbone structure based on energy transfer between bimane and transition metal ions. Proc Natl Acad Sci U S A 2009; 106:16227-32. [PMID: 19805285 DOI: 10.1073/pnas.0905207106] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structure and dynamics of proteins underlies the workings of virtually every biological process. Existing biophysical methods are inadequate to measure protein structure at atomic resolution, on a rapid time scale, with limited amounts of protein, and in the context of a cell or membrane. FRET can measure distances between two probes, but depends on the orientation of the probes and typically works only over long distances comparable with the size of many proteins. Also, common probes used for FRET can be large and have long, flexible attachment linkers that position dyes far from the protein backbone. Here, we improve and extend a fluorescence method called transition metal ion FRET that uses energy transfer to transition metal ions as a reporter of short-range distances in proteins with little orientation dependence. This method uses a very small cysteine-reactive dye monobromobimane, with virtually no linker, and various transition metal ions bound close to the peptide backbone as the acceptor. We show that, unlike larger fluorophores and longer linkers, this donor-acceptor pair accurately reports short-range distances and changes in backbone distances. We further extend the method by using cysteine-reactive metal chelators, which allow the technique to be used in protein regions of unknown secondary structure or when native metal ion binding sites are present. This improved method overcomes several of the key limitations of classical FRET for intramolecular distance measurements.
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34
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Biel M, Wahl-Schott C, Michalakis S, Zong X. Hyperpolarization-activated cation channels: from genes to function. Physiol Rev 2009; 89:847-85. [PMID: 19584315 DOI: 10.1152/physrev.00029.2008] [Citation(s) in RCA: 719] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels comprise a small subfamily of proteins within the superfamily of pore-loop cation channels. In mammals, the HCN channel family comprises four members (HCN1-4) that are expressed in heart and nervous system. The current produced by HCN channels has been known as I(h) (or I(f) or I(q)). I(h) has also been designated as pacemaker current, because it plays a key role in controlling rhythmic activity of cardiac pacemaker cells and spontaneously firing neurons. Extensive studies over the last decade have provided convincing evidence that I(h) is also involved in a number of basic physiological processes that are not directly associated with rhythmicity. Examples for these non-pacemaking functions of I(h) are the determination of the resting membrane potential, dendritic integration, synaptic transmission, and learning. In this review we summarize recent insights into the structure, function, and cellular regulation of HCN channels. We also discuss in detail the different aspects of HCN channel physiology in the heart and nervous system. To this end, evidence on the role of individual HCN channel types arising from the analysis of HCN knockout mouse models is discussed. Finally, we provide an overview of the impact of HCN channels on the pathogenesis of several diseases and discuss recent attempts to establish HCN channels as drug targets.
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Affiliation(s)
- Martin Biel
- Center for Integrated Protein Science CIPS-M and Zentrum für Pharmaforschung, Department Pharmazie, Pharmakologie für Naturwissenschaften, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, Munich D-81377, Germany.
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Taraska JW, Puljung MC, Olivier NB, Flynn GE, Zagotta WN. Mapping the structure and conformational movements of proteins with transition metal ion FRET. Nat Methods 2009; 6:532-7. [PMID: 19525958 PMCID: PMC2738593 DOI: 10.1038/nmeth.1341] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 05/06/2009] [Indexed: 11/26/2022]
Abstract
Visualizing conformational dynamics in proteins has been difficult, and the atomic-scale motions responsible for the behavior of most allosteric proteins are unknown. Here, we report that FRET between a small fluorescent dye and a nickel ion bound to a di-histidine motif can be used to monitor small structural rearrangements in proteins. This method provides several key advantages over classical FRET including the ability to measure the dynamics of close range interactions, the use of small probes with short linkers, a low orientation dependence, and the ability to add and remove unique tunable acceptors. We used this ‘transition metal ion FRET’ approach along with x-ray crystallography to determine the structural changes of the gating-ring of the mouse hyperpolarization-activated cyclic nucleotide-regulated ion channel HCN2. Binding of cAMP to the isolated carboxyl-terminal region of HCN2 caused a structural rearrangement involving a movement of the C-helix towards the β-roll of the cAMP-binding domain and a movement of the F′ helix of the C-linker, along with a stabilization of the secondary structure of the helices. Our results suggest a general model for the conformational switch in the cyclic nucleotide-binding site of cyclic nucleotide-regulated ion channels.
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Affiliation(s)
- Justin W Taraska
- Department of Physiology and Biophysics, Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
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Abstract
Cyclic nucleotide-gated (CNG) channels are ion channels which are activated by the binding of cGMP or cAMP. The channels are important cellular switches which transduce changes in intracellular concentrations of cyclic nucleotides into changes of the membrane potential and the Ca2+ concentration. CNG channels play a central role in the signal transduction pathways of vision and olfaction. Structurally, the channels belong to the superfamily of pore-loop cation channels. They share a common domain structure with hyperpolarization-activated cyclic nucleotide-gated (HCN) channels and Eag-like K+ channels. In this chapter, we give an overview on the molecular properties of CNG channels and describe the signal transduction pathways these channels are involved in. We will also summarize recent insights into the physiological and pathophysiological role of CNG channel proteins that have emerged from the analysis of CNG channel-deficient mouse models and human channelopathies.
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Affiliation(s)
- Martin Biel
- Center for Integrated Protein Science CIPS-M and Zentrum für Pharmaforschung-Department Pharmazie, Pharmakologie für Naturwissenschaften, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München, 81377, Germany.
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Craven KB, Olivier NB, Zagotta WN. C-terminal movement during gating in cyclic nucleotide-modulated channels. J Biol Chem 2008; 283:14728-38. [PMID: 18367452 PMCID: PMC2386932 DOI: 10.1074/jbc.m710463200] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2007] [Revised: 02/25/2008] [Indexed: 11/06/2022] Open
Abstract
Activation of cyclic nucleotide-modulated channels such as CNG and HCN channels is promoted by ligand-induced conformational changes in their C-terminal regions. The primary intersubunit interface of these C termini includes two salt bridges per subunit, formed between three residues (one positively charged and two negatively charged amino acids) that we term the SB triad. We previously hypothesized that the SB triad is formed in the closed channel and breaks when the channel opens. Here we tested this hypothesis by dynamically manipulating the SB triad in functioning CNGA1 channels. Reversing the charge at positions Arg-431 and Glu-462, two of the SB triad residues, by either mutation or application of charged reagents increased the favorability of channel opening. To determine how a charge reversal mutation in the SB triad structurally affects the channel, we solved the crystal structure of the HCN2 C-terminal region with the equivalent E462R mutation. The backbone structure of this mutant was very similar to that of wild type, but the SB triad was rearranged such that both salt bridges did not always form simultaneously, suggesting a mechanism for the increased ease of opening of the mutant channels. To prevent movement in the SB triad, we tethered two components of the SB triad region together with cysteine-reactive cross-linkers. Preventing normal movement of the SB triad region with short cross-linkers inhibited channel opening, whereas longer cross-linkers did not. These results support our hypothesis that the SB triad forms in the closed channel and indicate that this region expands as the channel opens.
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Affiliation(s)
- Kimberley B Craven
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
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