51
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Meng Y, Yan X, Wang Y. A simple preparation of Ag@graphene nanocomposites for surface-enhanced Raman spectroscopy of fluorescent anticancer drug. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.03.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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52
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Bai H, Xue R, Bao H, Zhang L, Yethiraj A, Cui Q, Chapman ER. Different states of synaptotagmin regulate evoked versus spontaneous release. Nat Commun 2016; 7:10971. [PMID: 27001899 PMCID: PMC4804166 DOI: 10.1038/ncomms10971] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/05/2016] [Indexed: 12/22/2022] Open
Abstract
The tandem C2-domains of synaptotagmin 1 (syt) function as Ca2+-binding modules that trigger exocytosis; in the absence of Ca2+, syt inhibits spontaneous release. Here, we used proline linkers to constrain and alter the relative orientation of these C2-domains. Short poly-proline helices have a period of three, so large changes in the relative disposition of the C2-domains result from changing the length of the poly-proline linker by a single residue. The length of the linker was varied one residue at a time, revealing a periodicity of three for the ability of the linker mutants to interact with anionic phospholipids and drive evoked synaptic transmission; syt efficiently drove exocytosis when its tandem C2-domains pointed in the same direction. Analysis of spontaneous release revealed a reciprocal relationship between the activation and clamping activities of the linker mutants. Hence, different structural states of syt underlie the control of distinct forms of synaptic transmission. Synaptotagmin contains tandem Ca2+-binding C2-domains that interact with target membranes to trigger exocytosis. Here, Bai et al. manipulate the relative orientation of these two domains using a synthetic polyproline linker and show that a parallel orientation is most effective for membrane interaction and exocytosis.
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Affiliation(s)
- Hua Bai
- Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Renhao Xue
- Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Huan Bao
- Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Leili Zhang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Arun Yethiraj
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Edwin R Chapman
- Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin 53705, USA
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53
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Handing KB, Shabalin IG, Szlachta K, Majorek KA, Minor W. Crystal structure of equine serum albumin in complex with cetirizine reveals a novel drug binding site. Mol Immunol 2016; 71:143-151. [PMID: 26896718 DOI: 10.1016/j.molimm.2016.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/02/2016] [Accepted: 02/08/2016] [Indexed: 01/08/2023]
Abstract
Serum albumin (SA) is the main transporter of drugs in mammalian blood plasma. Here, we report the first crystal structure of equine serum albumin (ESA) in complex with antihistamine drug cetirizine at a resolution of 2.1Å. Cetirizine is bound in two sites--a novel drug binding site (CBS1) and the fatty acid binding site 6 (CBS2). Both sites differ from those that have been proposed in multiple reports based on equilibrium dialysis and fluorescence studies for mammalian albumins as cetirizine binding sites. We show that the residues forming the binding pockets in ESA are highly conserved in human serum albumin (HSA), and suggest that binding of cetirizine to HSA will be similar. In support of that hypothesis, we show that the dissociation constants for cetirizine binding to CBS2 in ESA and HSA are identical using tryptophan fluorescence quenching. Presence of lysine and arginine residues that have been previously reported to undergo nonenzymatic glycosylation in CBS1 and CBS2 suggests that cetirizine transport in patients with diabetes could be altered. A review of all available SA structures from the PDB shows that in addition to the novel drug binding site we present here (CBS1), there are two pockets on SA capable of binding drugs that do not overlap with fatty acid binding sites and have not been discussed in published reviews.
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Affiliation(s)
- Katarzyna B Handing
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA; New York Structural Genomics Research Consortium (NYSGRC), USA
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA; New York Structural Genomics Research Consortium (NYSGRC), USA
| | - Karol Szlachta
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA; Faculty of Physics, Warsaw University of Technology, 00-662 Warszawa, Poland
| | - Karolina A Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA; New York Structural Genomics Research Consortium (NYSGRC), USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA; New York Structural Genomics Research Consortium (NYSGRC), USA.
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54
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Zhu W, Varga Z, Silva JR. Molecular motions that shape the cardiac action potential: Insights from voltage clamp fluorometry. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 120:3-17. [PMID: 26724572 DOI: 10.1016/j.pbiomolbio.2015.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/11/2015] [Accepted: 12/16/2015] [Indexed: 01/04/2023]
Abstract
Very recently, voltage-clamp fluorometry (VCF) protocols have been developed to observe the membrane proteins responsible for carrying the ventricular ionic currents that form the action potential (AP), including those carried by the cardiac Na(+) channel, NaV1.5, the L-type Ca(2+) channel, CaV1.2, the Na(+)/K(+) ATPase, and the rapid and slow components of the delayed rectifier, KV11.1 and KV7.1. This development is significant, because VCF enables simultaneous observation of ionic current kinetics with conformational changes occurring within specific channel domains. The ability gained from VCF, to connect nanoscale molecular movement to ion channel function has revealed how the voltage-sensing domains (VSDs) control ion flux through channel pores, mechanisms of post-translational regulation and the molecular pathology of inherited mutations. In the future, we expect that this data will be of great use for the creation of multi-scale computational AP models that explicitly represent ion channel conformations, connecting molecular, cell and tissue electrophysiology. Here, we review the VCF protocol, recent results, and discuss potential future developments, including potential use of these experimental findings to create novel computational models.
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Affiliation(s)
- Wandi Zhu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Zoltan Varga
- MTA-DE-NAP B Ion Channel Structure-Function Research Group, RCMM, University of Debrecen, Debrecen, Hungary
| | - Jonathan R Silva
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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55
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Skjold-Jørgensen J, Vind J, Svendsen A, Bjerrum MJ. Lipases That Activate at High Solvent Polarities. Biochemistry 2015; 55:146-56. [PMID: 26645098 DOI: 10.1021/acs.biochem.5b01114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thermomyces lanuginosus lipase (TlL) and related lipases become activated in low-polarity environments that exist at the water-lipid interface where a structural change of the "lid" region occurs. In this work, we have investigated the activation of TlL (Lipase_W89) and certain lid mutants, containing either a single positive charge mutation, E87K (Lipase_K87_W89), within the lid region or a lid residue composition of both lipase and esterase character (Hybrid_W89) as a function of solvent polarity. Activation differences between the variants and TlL were studied by a combination of biophysical and theoretical methods. To investigate the structural changes taking place in the lid region upon lipase activation, we used a fluorescence-based method measuring the efficiency of Trp89 in the lid to quench the fluorescence of a bimane molecule attached in front (C255) and behind (C61) the lid. These structural changes were compared to the enzymatic activity of each variant at the water-substrate interface and to theoretical calculations of the energies associated with lid opening as a function of the dielectric constant (ε) of the environment. Our results show that the lid in Lipase_K87_W89 undergoes a pronounced structural transition toward an open conformation around ε = 50, whereas only small changes are detected for Lipase_W89 ascribed to the stabilizing effect of the positive charge mutation on the open lid conformation. Interestingly, Hybrid_W89, with the same charge as Lipase_W89, shows a stabilization of the open lid even more pronounced at high solvent polarities than that of Lipase_K87_W89, allowing activation at ε < 80. This is further indicated by measurement of the lipase activity for each variant showing that Hybrid_W89 is more quickly activated at the water-lipid interface of a true, natural substrate. Combined, we show that a correlation exists between structural changes and enzymatic activities detected on one hand and theoretical calculations on lid opening energies on the other. These results highlight the key role that the lid plays in determining the polarity-dependent activation of lipases.
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Affiliation(s)
- Jakob Skjold-Jørgensen
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen, Denmark.,Novozymes A/S , Brudelysvej 35, DK-2880 Bagværd, Denmark
| | - Jesper Vind
- Novozymes A/S , Brudelysvej 35, DK-2880 Bagværd, Denmark
| | - Allan Svendsen
- Novozymes A/S , Brudelysvej 35, DK-2880 Bagværd, Denmark
| | - Morten J Bjerrum
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen, Denmark
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56
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Jarzab M, Wenta T, Zurawa-Janicka D, Polit A, Gieldon AJ, Wysocka M, Glaza P, Skorko-Glonek J, Ciarkowski J, Lesner A, Lipinska B. Intra- and intersubunit changes accompanying thermal activation of the HtrA2(Omi) protease homotrimer. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:283-296. [PMID: 26702898 DOI: 10.1016/j.bbapap.2015.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/26/2015] [Accepted: 12/14/2015] [Indexed: 01/16/2023]
Abstract
HtrA2(Omi) protease is involved in the maintenance of mitochondrial homeostasis and stimulation of apoptosis as well as in development of cancer and neurodegenerative disorders. The protein is a homotrimer whose subunits comprise serine protease domain (PD) and PDZ regulatory domain. In the basal, inactive state, a tight interdomain interface limits access both to the PDZ peptide (carboxylate) binding site and to the PD catalytic center. The molecular mechanism of activation is not well understood. To further the knowledge of HtrA2 thermal activation we monitored the dynamics of the PDZ-PD interactions during temperature increase using tryptophan-induced quenching (TrIQ) method. The TrIQ results suggested that during activation the PDZ domain changed its position versus PD inside a subunit, including a prominent change affecting the L3 regulatory loop of PD, and also changed its interactions with the PD of the adjacent subunit (PD*), specifically with its L1* regulatory loop containing the active site serine. The α5 helix of PDZ was involved in both, the intra- and intersubunit changes of interactions and thus seems to play an important role in HtrA2 activation. The amino acid substitutions designed to decrease the PDZ interactions with the PD or PD* promoted protease activity at a wide range of temperatures, which supports the conclusions based on the TrIQ analysis. The model presented in this work describes PDZ movement in relation to PD and PD*, resulting in an increased access to the peptide binding and active sites, and conformational changes of the L3 and L1* loops.
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Affiliation(s)
- Miroslaw Jarzab
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Tomasz Wenta
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Dorota Zurawa-Janicka
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Agnieszka Polit
- Department of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Artur J Gieldon
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
| | - Magdalena Wysocka
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
| | - Przemyslaw Glaza
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Joanna Skorko-Glonek
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Jerzy Ciarkowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
| | - Barbara Lipinska
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.
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57
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Abstract
The lactose permease of Escherichia coli (LacY), a highly dynamic membrane protein, catalyzes symport of a galactopyranoside and an H(+) by using an alternating access mechanism, and the transport cycle involves multiple conformational states. Single-domain camelid nanobodies (Nbs) developed against a LacY mutant immobilized in an outward (periplasmic)-open conformation bind to the flexible WT protein and stabilize the open-outward conformation(s). Here, we use site-directed, distance-dependent Trp quenching/unquenching of fluorescent probes inserted on opposite surfaces of LacY to assess the conformational states of the protein complexed with each of eight unique Nbs that bind exclusively to the periplasmic side and block transport, but increase the accessibility of the sugar-binding site. Nb binding involves conformational selection of LacY molecules with exposed binding epitopes. Each of eight Nbs induces quenching with three pairs of cytoplasmic Trp/fluorophore probes, indicating closing of cytoplasmic cavity. In reciprocal fashion, the same Nbs induce unquenching of fluorescence in three pairs of periplasmic probes due to opening of the periplasmic cavity. Because the extent of fluorescence change with various Nbs differs and the differences correlate with changes in the rate of sugar binding, it is also concluded that the Nbs stabilize several different outward-open conformations of LacY.
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58
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Skjold-Jørgensen J, Bhatia VK, Vind J, Svendsen A, Bjerrum MJ, Farrens D. The Enzymatic Activity of Lipases Correlates with Polarity-Induced Conformational Changes: A Trp-Induced Quenching Fluorescence Study. Biochemistry 2015; 54:4186-96. [PMID: 26087334 DOI: 10.1021/acs.biochem.5b00328] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Triacylglycerol hydrolases (EC 3.1.1.3) are thought to become activated when they encounter the water-lipid interface causing a "lid" region to move and expose the catalytic site. Here, we tested this idea by looking for lid movements in Thermomyces lanuginosus lipase (TL lipase), and in variants with a mutated lid region of esterase (Esterase) and esterase/lipase (Hybrid) character. To measure lid movements, we employed the tryptophan-induced quenching (TrIQ) fluorescence method to measure how effectively a Trp residue on the lid of these mutants (at position 87 or 89) could quench a fluorescent probe (bimane) placed at nearby site 255 on the protein. To test if lid movement is induced when the enzyme detects a lower-polarity environment (such as at the water-lipid interface), we performed these studies in solvents with different dielectric constants (ε). The results show that lid movement is highly dependent on the particular lid residue composition and solvent polarity. The data suggest that in aqueous solution (ε = 80), the Esterase lid is in an "open" conformation, whereas for the TL lipase and Hybrid, the lid remains "closed". At lower solvent polarities (ε < 46), the lid region for all of the mutants is more "open". Interestingly, these behaviors mirror the structural changes thought to take place upon activation of the enzyme at the water-lipid interface. Together, these results support the idea that lipases are more active in low-polarity solvents because the lid adopts an "open" conformation and indicate that relatively small conformational changes in the lid region play a key role in the activation mechanism of these enzymes.
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Affiliation(s)
- Jakob Skjold-Jørgensen
- †Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK 2100 Copenhagen, Denmark.,‡Novozymes A/S, Brudelysvej 35, DK 2880 Bagværd, Denmark
| | | | - Jesper Vind
- ‡Novozymes A/S, Brudelysvej 35, DK 2880 Bagværd, Denmark
| | - Allan Svendsen
- ‡Novozymes A/S, Brudelysvej 35, DK 2880 Bagværd, Denmark
| | - Morten J Bjerrum
- †Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK 2100 Copenhagen, Denmark
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59
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Mattila JP, Shnyrova AV, Sundborger AC, Hortelano ER, Fuhrmans M, Neumann S, Müller M, Hinshaw JE, Schmid SL, Frolov VA. A hemi-fission intermediate links two mechanistically distinct stages of membrane fission. Nature 2015; 524:109-113. [PMID: 26123023 PMCID: PMC4529379 DOI: 10.1038/nature14509] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 05/05/2015] [Indexed: 12/22/2022]
Abstract
Fusion and fission drive all vesicular transport. Although topologically opposite, these reactions pass through the same hemi-fusion/fission intermediate1,2, characterized by a ‘stalk’ in which only the inner monolayers of the two compartments have merged to form a localized non-bilayer connection1-3. Formation of the hemi-fission intermediate requires energy input from proteins catalyzing membrane remodeling; however the relationship between protein conformational rearrangements and hemi-fusion/fission remains obscure. Here we analyzed how the GTPase cycle of dynamin, the prototypical membrane fission catalyst4-6, is directly coupled to membrane remodeling. We used intra-molecular chemical cross-linking to stabilize dynamin in its GDP•AlF4--bound transition-state. In the absence of GTP this conformer produced stable hemi-fission, but failed to progress to complete fission, even in the presence of GTP. Further analysis revealed that the pleckstrin homology domain (PHD) locked in its membrane-inserted state facilitated hemi-fission. A second mode of dynamin activity, fueled by GTP hydrolysis, couples dynamin disassembly with cooperative diminishing of the PHD wedging, thus destabilizing the hemi-fission intermediate to complete fission. Molecular simulations corroborate the bimodal character of dynamin action and indicate radial and axial forces as dominant, although not independent drivers of hemi-fission and fission transformations, respectively. Mirrored in the fusion reaction7-8, the force bimodality might constitute a general paradigm for leakage-free membrane remodeling.
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Affiliation(s)
- Juha-Pekka Mattila
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75201
| | - Anna V Shnyrova
- Biophysics Unit (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of The Basque Country, Leioa, Spain
| | - Anna C Sundborger
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892
| | - Eva Rodriguez Hortelano
- Biophysics Unit (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of The Basque Country, Leioa, Spain
| | - Marc Fuhrmans
- Institute for Theoretical Physics, Georg-August University, 37077 Göttingen, Germany
| | - Sylvia Neumann
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Marcus Müller
- Institute for Theoretical Physics, Georg-August University, 37077 Göttingen, Germany
| | - Jenny E Hinshaw
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892
| | - Sandra L Schmid
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75201
| | - Vadim A Frolov
- Biophysics Unit (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of The Basque Country, Leioa, Spain.,IKERBASQUE, Basque Foundation of Science, Bilbao, Spain
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60
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A signal-on fluorosensor based on quench-release principle for sensitive detection of antibiotic rapamycin. BIOSENSORS-BASEL 2015; 5:131-40. [PMID: 25822756 PMCID: PMC4493541 DOI: 10.3390/bios5020131] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/13/2015] [Accepted: 03/20/2015] [Indexed: 11/17/2022]
Abstract
An antibiotic rapamycin is one of the most commonly used immunosuppressive drugs, and also implicated for its anti-cancer activity. Hence, the determination of its blood level after organ transplantation or tumor treatment is of great concern in medicine. Although there are several rapamycin detection methods, many of them have limited sensitivity, and/or need complicated procedures and long assay time. As a novel fluorescent biosensor for rapamycin, here we propose "Q'-body", which works on the fluorescence quench-release principle inspired by the antibody-based quenchbody (Q-body) technology. We constructed rapamycin Q'-bodies by linking the two interacting domains FKBP12 and FRB, whose association is triggered by rapamycin. The fusion proteins were each incorporated position-specifically with one of fluorescence dyes ATTO520, tetramethylrhodamine, or ATTO590 using a cell-free translation system. As a result, rapid rapamycin dose-dependent fluorescence increase derived of Q'-bodies was observed, especially for those with ATTO520 with a lowest detection limit of 0.65 nM, which indicates its utility as a novel fluorescent biosensor for rapamycin.
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61
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A specialized molecular motion opens the Hv1 voltage-gated proton channel. Nat Struct Mol Biol 2015; 22:283-290. [PMID: 25730777 PMCID: PMC4385474 DOI: 10.1038/nsmb.2978] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 01/30/2015] [Indexed: 12/22/2022]
Abstract
The Hv1 proton channel is unique among voltage-gated channels for containing the pore and gate within its voltage-sensing domain. Pore opening has been proposed to include assembly of the selectivity filter between an arginine (R3) of segment S4 and an aspartate (D1) of segment S1. We determined whether gating involves motion of S1, using Ciona intestinalis Hv1. We found that channel opening is concomitant with solution access to the pore-lining face of S1, from the cytoplasm to deep inside the pore. Voltage- and patch-clamp fluorometry showed that this involves a motion of S1 relative to its surroundings. S1 motion and the S4 motion that precedes it are each influenced by residues on the other helix, thus suggesting a dynamic interaction between S1 and S4. Our findings suggest that the S1 of Hv1 has specialized to function as part of the channel's gate.
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62
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Structure-Based Biophysical Analysis of the Interaction of Rhodopsin with G Protein and Arrestin. Methods Enzymol 2015; 556:563-608. [DOI: 10.1016/bs.mie.2014.12.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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63
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Abstract
The lactose permease of Escherichia coli (LacY), a highly dynamic polytopic membrane protein, catalyzes stoichiometric galactoside/H(+) symport by an alternating access mechanism and exhibits multiple conformations, the distribution of which is altered by sugar binding. We have developed single-domain camelid nanobodies (Nbs) against a LacY mutant in an outward (periplasmic)-open conformation to stabilize this state of the WT protein. Twelve purified Nbs inhibit lactose transport in right-side-out membrane vesicles, indicating that the Nbs recognize epitopes on the periplasmic side of LacY. Stopped-flow kinetics of sugar binding by WT LacY in detergent micelles or reconstituted into proteoliposomes reveals dramatic increases in galactoside-binding rates induced by interaction with the Nbs. Thus, WT LacY in complex with the great majority of the Nbs exhibits varied increases in access of sugar to the binding site with an increase in association rate constants (kon) of up to ∼ 50-fold (reaching 10(7) M(-1) ⋅ s(-1)). In contrast, with the double-Trp mutant, which is already open on the periplasmic side, the Nbs have little effect. The findings are clearly consistent with stabilization of WT conformers with an open periplasmic cavity. Remarkably, some Nbs drastically decrease the rate of dissociation of bound sugar leading to increased affinity (greater than 200-fold for lactose).
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64
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Turriani E, Höbartner C, Jovin TM. Mg2+-dependent conformational changes and product release during DNA-catalyzed RNA ligation monitored by Bimane fluorescence. Nucleic Acids Res 2014; 43:40-50. [PMID: 25505142 PMCID: PMC4288166 DOI: 10.1093/nar/gku1268] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Among the deoxyribozymes catalyzing the ligation of two RNA substrates, 7S11 generates a branched RNA containing a 2',5'-linkage. We have attached the small fluorogenic probe Bimane to the triphosphate terminated RNA substrate and utilized emission intensity and anisotropy to follow structural rearrangements leading to a catalytically active complex upon addition of Mg(2+). Bimane coupled to synthetic oligonucleotides is quenched by nearby guanines via photoinduced electron transfer. The degree of quenching is sensitive to changes in the base pairing of the residues involved and in their distances to the probe. These phenomena permit the characterization of various sequential processes in the assembly and function of 7S11: binding of Mg(2+) to the triphosphate moiety, release of quenching of the probe by the 5'-terminal G residues of R-RNA as they engage in secondary base-pair interactions, local rearrangement into a distinct active conformation, and continuous release of the Bimane-labeled pyrophosphate during the course of reaction at 37°C. It was possible to assign equilibrium and rate constants and structural interpretations to the sequence of conformational transitions and catalysis, information useful for optimizing the design of next generation deoxyribozymes. The fluorescent signatures, thermodynamic equilibria and catalytic function of numerous mutated (base/substituted) molecules were examined.
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Affiliation(s)
- Elisa Turriani
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy Laboratory for Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Claudia Höbartner
- Max Planck Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany and Institute for Organic and Biomolecular Chemistry, Georg August University Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
| | - Thomas M Jovin
- Laboratory for Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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65
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Jones Brunette AM, Farrens DL. Distance mapping in proteins using fluorescence spectroscopy: tyrosine, like tryptophan, quenches bimane fluorescence in a distance-dependent manner. Biochemistry 2014; 53:6290-301. [PMID: 25144569 PMCID: PMC4196733 DOI: 10.1021/bi500493r] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Tryptophan-induced quenching of fluorophores
(TrIQ) uses intramolecular
fluorescence quenching to assess distances in proteins too small (<15
Å) to be easily probed by traditional Forster resonance energy
transfer methods. A powerful aspect of TrIQ is its ability to obtain
an ultrafast snapshot of a protein conformation, by identifying “static
quenching” (contact between the Trp and probe at the moment
of light excitation). Here we report new advances in this site-directed
fluorescence labeling (SDFL) approach, gleaned from recent studies
of T4 lysozyme (T4L). First, we show that like TrIQ, tyrosine-induced
quenching (TyrIQ) occurs for the fluorophore bimane in a distance-dependent
fashion, although with some key differences. The Tyr “sphere
of quenching” for bimane (≤10 Å) is smaller than
for Trp (≤15 Å, Cα–Cα distance), and
the size difference between the quenching residue (Tyr) and control
(Phe) differs by only a hydroxyl group. Second, we show how TrIQ and
TyrIQ can be used together to assess the magnitude and energetics
of a protein movement. In these studies, we placed a bimane (probe)
and Trp or Tyr (quencher) on opposite ends of a “hinge”
in T4L and conducted TrIQ and TyrIQ measurements. Our results are
consistent with an ∼5 Å change in Cα–Cα
distances between these sites upon substrate binding, in agreement
with the crystal structures. Subsequent Arrhenius analysis suggests
the activation energy barrier (Ea) to
this movement is relatively low (∼1.5–2.5 kcal/mol).
Together, these results demonstrate that TyrIQ, used together with
TrIQ, significantly expands the power of quenching-based distance
mapping SDFL studies.
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Affiliation(s)
- Amber M Jones Brunette
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239-3098, United States
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66
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Zhu J, Tan M, Zhang L, Yin Q. Elongation flow-triggered morphology transitions of dendritic polyethylene amphiphilic assemblies: host-guest implications. SOFT MATTER 2014; 10:6506-6513. [PMID: 25046698 DOI: 10.1039/c4sm01012d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The assemblies and transformations of dendritic polyethylene (DPE)-poly(oligo(ethyleneglycol) methacrylate) (POEGMA) amphiphilic micelles have been demonstrated by cryo-TEM and DLS techniques under elongation flow stimuli. The flow rate-dependence of the dissymmetry ratio suggests the possibility that a combination of shear and elongation could also be responsible for the transitions of DPE-POEGMAs, but it is obvious that the exposure of elongation flow is essential and plays a key role in the assembly and fusion of the DPE-POEGMA micelles. Fluorescence resonance energy transfer (FRET) is used to provide insight into the assembly and fusion of DPE-POEGMA under elongation flow. The FRET results show that a shorter separation distance of DiO-DiI with higher elongation rate can result in higher FRET efficiency. Furthermore, DPE-POEGMAs can display the responsive switching ability of the elongation flow-triggered FRET.
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Affiliation(s)
- Jieqing Zhu
- DSAPM Lab, PCFM Lab, OFCM Institute, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, China.
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67
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Abstract
Galactoside/H(+) symport across the cytoplasmic membrane of Escherichia coli is catalyzed by lactose permease (LacY), which uses an alternating access mechanism with opening and closing of deep cavities on the periplasmic and cytoplasmic sides. In this study, conformational changes in LacY initiated by galactoside binding were monitored in real time by Trp quenching/unquenching of bimane, a small fluorophore covalently attached to the protein. Rates of change in bimane fluorescence on either side of LacY were measured by stopped flow with LacY in detergent or in proteoliposomes and were compared with rates of galactoside binding. With LacY in proteoliposomes, the periplasmic cavity is tightly sealed and the substrate-binding rate is limited by the rate of opening of this cavity. Rates of opening, measured as unquenching of bimane fluorescence, are 20-30 s(-1), independent of sugar concentration and essentially the same in detergent or in proteoliposomes. On the cytoplasmic side of LacY in proteoliposomes, slow bimane quenching (i.e., closing of the cavity) is observed at a rate that is also independent of sugar concentration and similar to the rate of sugar binding from the periplasmic side. Therefore, opening of the periplasmic cavity not only limits access of sugar to the binding site of LacY but also controls the rate of closing of the cytoplasmic cavity.
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68
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Sinha A, Jones Brunette AM, Fay JF, Schafer CT, Farrens DL. Rhodopsin TM6 can interact with two separate and distinct sites on arrestin: evidence for structural plasticity and multiple docking modes in arrestin-rhodopsin binding. Biochemistry 2014; 53:3294-307. [PMID: 24724832 PMCID: PMC4039336 DOI: 10.1021/bi401534y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
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Various studies have implicated the
concave surface of arrestin
in the binding of the cytosolic surface of rhodopsin. However, specific
sites of contact between the two proteins have not previously been
defined in detail. Here, we report that arrestin shares part of the
same binding site on rhodopsin as does the transducin Gα subunit C-terminal tail, suggesting binding of both proteins to
rhodopsin may share some similar underlying mechanisms. We also identify
two areas of contact between the proteins near this region. Both sites
lie in the arrestin N-domain, one in the so-called “finger”
loop (residues 67–79) and the other in the 160 loop (residues
155–165). We mapped these sites using a novel tryptophan-induced
quenching method, in which we introduced Trp residues into arrestin
and measured their ability to quench the fluorescence of bimane probes
attached to cysteine residues on TM6 of rhodopsin (T242C and T243C).
The involvement of finger loop binding to rhodopsin was expected,
but the evidence of the arrestin 160 loop contacting rhodopsin was
not. Remarkably, our data indicate one site on rhodopsin can interact
with multiple structurally separate sites on arrestin that are almost
30 Å apart. Although this observation at first seems paradoxical,
in fact, it provides strong support for recent hypotheses that structural
plasticity and conformational changes are involved in the arrestin–rhodopsin
binding interface and that the two proteins may be able to interact
through multiple docking modes, with arrestin binding to both monomeric
and dimeric rhodopsin.
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Affiliation(s)
- Abhinav Sinha
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239-3098, United States
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69
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Lee H, Kim J, Kim H, Kim Y, Choi Y. A folate receptor-specific activatable probe for near-infrared fluorescence imaging of ovarian cancer. Chem Commun (Camb) 2014; 50:7507-7510. [DOI: 10.1039/c4cc02301c] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
A folate receptor-specific activatable probe for in vivo near-infrared fluorescence imaging with a high target-to-background ratio was synthesized.
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Affiliation(s)
- Hawon Lee
- Molecular Imaging & Therapy Branch
- National Cancer Center
- Goyang-si, Korea
| | - Jisu Kim
- Molecular Imaging & Therapy Branch
- National Cancer Center
- Goyang-si, Korea
| | - Hyunjin Kim
- Molecular Imaging & Therapy Branch
- National Cancer Center
- Goyang-si, Korea
| | - Youngmi Kim
- Department of Chemistry
- Institute of Nanosensor and Biotechnology
- Dankook University
- Yongin-si, Korea
| | - Yongdoo Choi
- Molecular Imaging & Therapy Branch
- National Cancer Center
- Goyang-si, Korea
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70
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Alexiev U, Farrens DL. Fluorescence spectroscopy of rhodopsins: insights and approaches. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:694-709. [PMID: 24183695 DOI: 10.1016/j.bbabio.2013.10.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/11/2013] [Accepted: 10/16/2013] [Indexed: 01/30/2023]
Abstract
Fluorescence spectroscopy has become an established tool at the interface of biology, chemistry and physics because of its exquisite sensitivity and recent technical advancements. However, rhodopsin proteins present the fluorescence spectroscopist with a unique set of challenges and opportunities due to the presence of the light-sensitive retinal chromophore. This review briefly summarizes some approaches that have successfully met these challenges and the novel insights they have yielded about rhodopsin structure and function. We start with a brief overview of fluorescence fundamentals and experimental methodologies, followed by more specific discussions of technical challenges rhodopsin proteins present to fluorescence studies. Finally, we end by discussing some of the unique insights that have been gained specifically about visual rhodopsin and its interactions with affiliate proteins through the use of fluorescence spectroscopy. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- Ulrike Alexiev
- Physics Department, Freie Universität Berlin, Berlin, Germany.
| | - David L Farrens
- Departments of Biochemistry and Molecular Biology, Oregon Health Sciences University, USA
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71
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Tsukamoto H, Farrens DL. A constitutively activating mutation alters the dynamics and energetics of a key conformational change in a ligand-free G protein-coupled receptor. J Biol Chem 2013; 288:28207-16. [PMID: 23940032 DOI: 10.1074/jbc.m113.472464] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
G protein-coupled receptors (GPCRs) undergo dynamic transitions between active and inactive conformations. Usually, these conversions are triggered when the receptor detects an external signal, but some so-called constitutively activating mutations, or CAMs, induce a GPCR to bind and activate G proteins in the absence of external stimulation, in ways still not fully understood. Here, we investigated how a CAM alters the structure of a GPCR and the dynamics involved as the receptor transitions between different conformations. Our approach used site-directed fluorescence labeling (SDFL) spectroscopy to compare opsin, the ligand-free form of the GPCR rhodopsin, with opsin containing the CAM M257Y, focusing specifically on key movements that occur in the sixth transmembrane helix (TM6) during GPCR activation. The site-directed fluorescence labeling data indicate opsin is constrained to an inactive conformation both in detergent micelles and lipid membranes, but when it contains the M257Y CAM, opsin is more dynamic and can interact with a G protein mimetic. Further study of these receptors using tryptophan-induced quenching (TrIQ) methods indicates that in detergent, the CAM significantly increases the population of receptors in the active state, but not in lipids. Subsequent Arrhenius analysis of the TrIQ data suggests that, both in detergent and lipids, the CAM lowers the energy barrier for TM6 movement, a key transition required for conversion between the inactive and active conformations. Together, these data suggest that the lowered energy barrier is a primary effect of the CAM on the receptor dynamics and energetics.
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Affiliation(s)
- Hisao Tsukamoto
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239-3098
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72
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Leelaram MN, Bhat AG, Godbole AA, Bhat RS, Manjunath R, Nagaraja V. Type IA topoisomerase inhibition by clamp closure. FASEB J 2013; 27:3030-8. [PMID: 23612788 DOI: 10.1096/fj.12-226118] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bacterial DNA topoisomerase I (topoI) catalyzes relaxation of negatively supercoiled DNA. The enzyme alters DNA topology through protein-operated DNA gate, switching between open and closed conformations during its reaction. We describe the mechanism of inhibition of Mycobacterium smegmatis and Mycobacterium tuberculosis topoI by monoclonal antibodies (mAbs) that bind with high affinity and inhibit at 10-50 nM concentration. Unlike other inhibitors of topoisomerases, the mAbs inhibited several steps of relaxation reaction, namely DNA binding, cleavage, strand passage, and enzyme-DNA dissociation. The enhanced religation of the cleaved DNA in presence of the mAb indicated closing of the enzyme DNA gate. The formation of enzyme-DNA heterocatenane in the presence of the mAbs as a result of closing the gate could be inferred by the salt resistance of the complex, visualized by atomic force microscopy and confirmed by fluorescence measurements. Locking the enzyme-DNA complex as a closed clamp restricted the movements of the DNA gate, affecting all of the major steps of the relaxation reaction. Enzyme trapped on DNA in closed clamp conformation formed roadblock for the elongating DNA polymerase. The unusual multistep inhibition of mycobacterial topoisomerases may facilitate lead molecule development, and the mAbs would also serve as valuable tools to probe the enzyme mechanism.
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Affiliation(s)
- Majety Naga Leelaram
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
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73
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Kim YJ, Hofmann KP, Ernst OP, Scheerer P, Choe HW, Sommer ME. Crystal structure of pre-activated arrestin p44. Nature 2013; 497:142-6. [PMID: 23604253 DOI: 10.1038/nature12133] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 04/02/2013] [Indexed: 12/21/2022]
Abstract
Arrestins interact with G-protein-coupled receptors (GPCRs) to block interaction with G proteins and initiate G-protein-independent signalling. Arrestins have a bi-lobed structure that is stabilized by a long carboxy-terminal tail (C-tail), and displacement of the C-tail by receptor-attached phosphates activates arrestins for binding active GPCRs. Structures of the inactive state of arrestin are available, but it is not known how C-tail displacement activates arrestin for receptor coupling. Here we present a 3.0 Å crystal structure of the bovine arrestin-1 splice variant p44, in which the activation step is mimicked by C-tail truncation. The structure of this pre-activated arrestin is profoundly different from the basal state and gives insight into the activation mechanism. p44 displays breakage of the central polar core and other interlobe hydrogen-bond networks, leading to a ∼21° rotation of the two lobes as compared to basal arrestin-1. Rearrangements in key receptor-binding loops in the central crest region include the finger loop, loop 139 (refs 8, 10, 11) and the sequence Asp 296-Asn 305 (or gate loop), here identified as controlling the polar core. We verified the role of these conformational alterations in arrestin activation and receptor binding by site-directed fluorescence spectroscopy. The data indicate a mechanism for arrestin activation in which C-tail displacement releases critical central-crest loops from restricted to extended receptor-interacting conformations. In parallel, increased flexibility between the two lobes facilitates a proper fitting of arrestin to the active receptor surface. Our results provide a snapshot of an arrestin ready to bind the active receptor, and give an insight into the role of naturally occurring truncated arrestins in the visual system.
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Affiliation(s)
- Yong Ju Kim
- Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany
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74
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Hong Y, Muenzner J, Grimm SK, Pletneva EV. Origin of the conformational heterogeneity of cardiolipin-bound cytochrome C. J Am Chem Soc 2012; 134:18713-23. [PMID: 23066867 DOI: 10.1021/ja307426k] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Interactions of cytochrome c (cyt c) with cardiolipin (CL) partially unfold the protein, activating its peroxidase function, a critical event in the execution of apoptosis. However, structural features of the altered protein species in the heterogeneous ensemble are difficult to probe with ensemble averaging. Analyses of the dye-to-heme distance distributions P(r) from time-resolved FRET (TR-FRET) have uncovered two distinct types of CL-bound cyt c conformations, extended and compact. We have combined TR-FRET, fluorescence correlation spectroscopy (FCS), and biolayer interferometry to develop a systematic understanding of the functional partitioning between the two conformations. The two subpopulations are in equilibrium with each other, with a submillisecond rate of conformational exchange reflecting the protein folding into a compact non-native state, as well as protein interactions with the lipid surface. Electrostatic interactions with the negatively charged lipid surface that correlate with physiologically relevant changes in CL concentrations strongly affect the kinetics of cyt c binding and conformational exchange. A predominantly peripheral binding mechanism, rather than deep protein insertion into the membrane, provides a rationale for the general denaturing effect of the CL surface and the large-scale protein unfolding. These findings closely relate to cyt c folding dynamics and suggest a general strategy for extending the time window in monitoring the kinetics of folding.
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Affiliation(s)
- Yuning Hong
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
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75
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Lindhoud S, Westphal AH, Borst JW, van Mierlo CPM. Illuminating the off-pathway nature of the molten globule folding intermediate of an α-β parallel protein. PLoS One 2012; 7:e45746. [PMID: 23029219 PMCID: PMC3448718 DOI: 10.1371/journal.pone.0045746] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 08/22/2012] [Indexed: 11/19/2022] Open
Abstract
Partially folded protein species transiently form during folding of most proteins. Often, these species are molten globules, which may be on- or off-pathway to the native state. Molten globules are ensembles of interconverting protein conformers that have a substantial amount of secondary structure, but lack virtually all tertiary side-chain packing characteristics of natively folded proteins. Due to solvent-exposed hydrophobic groups, molten globules are prone to aggregation, which can have detrimental effects on organisms. The molten globule observed during folding of the 179-residue apoflavodoxin from Azotobacter vinelandii is off-pathway, as it has to unfold before native protein can form. Here, we study folding of apoflavodoxin and characterize its molten globule using fluorescence spectroscopy and Förster Resonance Energy Transfer (FRET). Apoflavodoxin is site-specifically labeled with fluorescent donor and acceptor dyes, utilizing dye-inaccessibility of Cys69 in cofactor-bound protein. Donor (i.e., Alexa Fluor 488) is covalently attached to Cys69 in all apoflavodoxin variants used. Acceptor (i.e., Alexa Fluor 568) is coupled to Cys1, Cys131 and Cys178, respectively. Our FRET data show that apoflavodoxin's molten globule forms in a non-cooperative manner and that its N-terminal 69 residues fold last. In addition, striking conformational differences between molten globule and native protein are revealed, because the inter-label distances sampled in the 111-residue C-terminal segment of the molten globule are shorter than observed for native apoflavodoxin. Thus, FRET sheds light on the off-pathway nature of the molten globule during folding of an α-β parallel protein.
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Affiliation(s)
- Simon Lindhoud
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Adrie H. Westphal
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Microspectroscopy Centre, Wageningen University, Wageningen, The Netherlands
| | - Jan Willem Borst
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Microspectroscopy Centre, Wageningen University, Wageningen, The Netherlands
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76
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Pantazis A, Olcese R. Relative transmembrane segment rearrangements during BK channel activation resolved by structurally assigned fluorophore-quencher pairing. ACTA ACUST UNITED AC 2012; 140:207-18. [PMID: 22802360 PMCID: PMC3409098 DOI: 10.1085/jgp.201210807] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Voltage-activated proteins can sense, and respond to, changes in the electric field pervading the cell membrane by virtue of a transmembrane helix bundle, the voltage-sensing domain (VSD). Canonical VSDs consist of four transmembrane helices (S1-S4) of which S4 is considered a principal component because it possesses charged residues immersed in the electric field. Membrane depolarization compels the charges, and by extension S4, to rearrange with respect to the field. The VSD of large-conductance voltage- and Ca-activated K(+) (BK) channels exhibits two salient inconsistencies from the canonical VSD model: (1) the BK channel VSD possesses an additional nonconserved transmembrane helix (S0); and (2) it exhibits a "decentralized" distribution of voltage-sensing charges, in helices S2 and S3, in addition to S4. Considering these unique features, the voltage-dependent rearrangements of the BK VSD could differ significantly from the standard model of VSD operation. To understand the mode of operation of this unique VSD, we have optically tracked the relative motions of the BK VSD transmembrane helices during activation, by manipulating the quenching environment of site-directed fluorescent labels with native and introduced Trp residues. Having previously reported that S0 and S4 diverge during activation, in this work we demonstrate that S4 also diverges from S1 and S2, whereas S2, compelled by its voltage-sensing charged residues, moves closer to S1. This information contributes spatial constraints for understanding the BK channel voltage-sensing process, revealing the structural rearrangements in a non-canonical VSD.
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Affiliation(s)
- Antonios Pantazis
- Department of Anesthesiology, Division of Molecular Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90075, USA
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77
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Goldberg JM, Speight LC, Fegley MW, Petersson EJ. Minimalist probes for studying protein dynamics: thioamide quenching of selectively excitable fluorescent amino acids. J Am Chem Soc 2012; 134:6088-91. [PMID: 22471784 PMCID: PMC3360930 DOI: 10.1021/ja3005094] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Fluorescent probe pairs that can be selectively excited in the presence of Trp and Tyr are of great utility in studying conformational changes in proteins. However, the size of these probe pairs can restrict their incorporation to small portions of a protein sequence where their effects on secondary and tertiary structure can be tolerated. Our findings show that a thioamide bond-a single atom substitution of the peptide backbone-can quench fluorophores that are red-shifted from intrinsic protein fluorescence, such as acridone. Using steady-state and fluorescence lifetime measurements, we further demonstrate that this quenching occurs through a dynamic electron-transfer mechanism. In a proof-of-principle experiment, we apply this technique to monitor unfolding in a model peptide system, the villin headpiece HP35 fragment. Thioamide analogues of the natural amino acids can be placed in a variety of locations in a protein sequence, allowing one to make a large number of measurements to model protein folding.
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Affiliation(s)
- Jacob M. Goldberg
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Lee C. Speight
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
| | | | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
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78
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Chen Y, Milam SL, Erickson HP. SulA inhibits assembly of FtsZ by a simple sequestration mechanism. Biochemistry 2012; 51:3100-9. [PMID: 22432817 DOI: 10.1021/bi201669d] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We have investigated the inhibition by SulA of the assembly of Escherichia coli FtsZ. Using quantitative GTPase and fluorescence assays, we found that SulA inhibition resulted in an increase in the apparent critical concentration for FtsZ assembly. The increase in apparent critical concentration was always less than the total amount of SulA added, suggesting that the association of SulA and FtsZ was of modest affinity. Isothermal titration calorimetry gave a value of 0.78 μM for the dissociation constant of the FtsZ-SulA complex, similar in magnitude to the 0.72 μM critical concentration of FtsZ protofilament assembly at steady state. We modeled the reaction as an equilibrium competition between (a) FtsZ subunits assembling onto protofilaments or (b) binding SulA. When FtsZ was assembled in GMPCPP or in EDTA, the inhibition by SulA was reduced. The reduced inhibition could be explained by a 3- and 10-fold weaker binding of SulA to FtsZ. The mutant D212G, which has no GTPase activity and therefore minimal subunit cycling, was shown here to assemble one-stranded protofilaments, and the assembly was blocked by SulA. We also assayed the SulA and FtsZ proteins from Pseudomonas. The SulA inhibition was stronger than with the E. coli proteins, and the model indicated a 5-fold higher affinity of Pseudomonas SulA for FtsZ.
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Affiliation(s)
- Yaodong Chen
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710-3709, USA.
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79
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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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80
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Kim S, Choi J, Majima T. Self-assembly of polydeoxyadenylic acid studied at the single-molecule level. J Phys Chem B 2011; 115:15399-405. [PMID: 22085264 DOI: 10.1021/jp208911t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The investigation on the self-assembly of polydeoxyadenylic acid (poly(dA)) is highly important to fully understand its biological function and for its application in the field of nanotechnology. Using the fluorescence resonance energy transfer (FRET) technique, we report investigations for the self-assembly of adenine oligomers induced by pH and coralyne binding at the single-molecule level and in the bulk phase. Results presented here show that A-motif 1 (Alexa488-5'-(dA)(20)-3'-Cy5-5'-(dA)(20)-3'-Alexa488) forms the wire-type duplex at acidic pH, whereas the same conformation of A-motif 2 (Alexa488-5'-(dA)(20)-3'-Cy5-3'-(dA)(20)-5'-Alexa488) is induced by coralyne binding at neutral pH. These results indicate that poly(dA) at acidic pH forms a right-handed helical duplex with parallel-mannered chains, whereas the coralyne-poly(dA) binding induces a stable antiparallel duplex. Furthermore, we found that the antiparallel duplex of poly(dA) formed by coralyne binding has a rather extended and less twisted structure as compared to the parallel duplex of poly(dA) formed at acidic pH. On the other hand, from dilution experiments, we found that the parallel duplex formed at acidic pH is converted to "S-form", which has the single-stranded structure with short intramolecular double-stranded regions formed by intramolecular A:A base pairing, while the A-motif-coralyne assembly is dissociated into single strands below a certain concentration. The formation of S-form with a short intramolecular double-stranded region formed at acidic pH and very low concentration is confirmed by the quantitative analysis of FCS curve to measure the hydrodynamic radius of a molecule.
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Affiliation(s)
- Sooyeon Kim
- The Institute of Scientific and Industrial (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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81
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Site-specific in vitro and in vivo incorporation of molecular probes to study G-protein-coupled receptors. Curr Opin Chem Biol 2011; 15:392-8. [DOI: 10.1016/j.cbpa.2011.03.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 03/15/2011] [Accepted: 03/17/2011] [Indexed: 12/20/2022]
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82
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Chen Y, Erickson HP. Conformational changes of FtsZ reported by tryptophan mutants. Biochemistry 2011; 50:4675-84. [PMID: 21510681 DOI: 10.1021/bi200106d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
E. coli FtsZ has no native tryptophan. We showed previously that the mutant FtsZ L68W gave a 2.5-fold increase in trp fluorescence when assembly was induced by GTP. L68 is probably buried in the protofilament interface upon assembly, causing the fluorescence increase. In the present study we introduced trp residues at several other locations and examined them for assembly-induced fluorescence changes. L189W, located on helix H7 and buried between the N- and C-terminal subdomains, showed a large fluorescence increase, comparable to L68W. This may reflect a shift or rotation of the two subdomains relative to each other. L160W showed a smaller increase in fluorescence, and Y222W a decrease in fluorescence, upon assembly. These two are located on the surface of the N and C subdomains, near the domain boundary. The changes in fluorescence may reflect movements of the domains or of nearby side chains. We prepared a double mutant Y222W/S151C and coupled ATTO-655 to the cys. The Cα of trp in the C-terminal subdomain was 10 Å away from that of the cys in the N-terminal subdomain, permitting the ATTO to make van der Waals contact with the trp. The ATTO fluorescence showed strong tryptophan-induced quenching. The quenching was reduced following assembly, consistent with a movement apart of the two subdomains. Movements of one to several angstroms are probably sufficient to account for the changes in trp fluorescence and trp-induced quenching of ATTO. Assembly in GDP plus DEAE dextran produces tubular polymers that are related to the highly curved, mini-ring conformation. No change in trp fluorescence was observed upon assembly of these tubes, suggesting that the mini-ring conformation is the same as that of a relaxed, monomeric FtsZ.
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Affiliation(s)
- Yaodong Chen
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710-3709, USA
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Farrens DL. What site-directed labeling studies tell us about the mechanism of rhodopsin activation and G-protein binding. Photochem Photobiol Sci 2010; 9:1466-74. [PMID: 20967340 DOI: 10.1039/c0pp00283f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rhodopsin is the photoreceptor protein responsible for dim-light vision in mammals. Due to extensive biophysical, structural and computational analysis of this membrane protein, it is presently the best understood G-protein coupled receptor (GPCR). Here I briefly review one approach that has been extensively used to identify dynamic and structural changes in rhodopsin--the use of site-directed labeling methods (SDL) coupled with electron paramagnetic resonance (EPR) and fluorescence spectroscopy. These SDL studies involve introducing individual cysteine residues into the receptor, then labeling them with cysteine-reactive probes for subsequent analysis by the appropriate spectroscopy. I will give a brief overview of how SDL methods are carried out and how the data is analyzed. Then, I will discuss how SDL studies were carried out on rhodopsin, and how they were used to identify a key structural change that occurs in rhodopsin upon activation--movement of transmembrane helix 6 (TM6). I will also briefly discuss how the SDL studies of rhodopsin compare with SDL studies of other GPCRs, and compare the SDL data with early and recent crystal structures of rhodopsin. Finally, I will discuss why the TM6 movement is required for rhodopsin to couple with the G-protein transducin, and speculate how this mechanism might be a universal method used by all GPCRs to bind G-proteins and perhaps other proteins involved in visual signal transduction, such as arrestin and rhodopsin kinase.
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Affiliation(s)
- David L Farrens
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, Oregon 97239, USA
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