1
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Gurevich VV. Arrestins: A Small Family of Multi-Functional Proteins. Int J Mol Sci 2024; 25:6284. [PMID: 38892473 PMCID: PMC11173308 DOI: 10.3390/ijms25116284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/24/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
The first member of the arrestin family, visual arrestin-1, was discovered in the late 1970s. Later, the other three mammalian subtypes were identified and cloned. The first described function was regulation of G protein-coupled receptor (GPCR) signaling: arrestins bind active phosphorylated GPCRs, blocking their coupling to G proteins. It was later discovered that receptor-bound and free arrestins interact with numerous proteins, regulating GPCR trafficking and various signaling pathways, including those that determine cell fate. Arrestins have no enzymatic activity; they function by organizing multi-protein complexes and localizing their interaction partners to particular cellular compartments. Today we understand the molecular mechanism of arrestin interactions with GPCRs better than the mechanisms underlying other functions. However, even limited knowledge enabled the construction of signaling-biased arrestin mutants and extraction of biologically active monofunctional peptides from these multifunctional proteins. Manipulation of cellular signaling with arrestin-based tools has research and likely therapeutic potential: re-engineered proteins and their parts can produce effects that conventional small-molecule drugs cannot.
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2
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Hasanbasri Z, Tessmer MH, Stoll S, Saxena S. Modeling of Cu(II)-based protein spin labels using rotamer libraries. Phys Chem Chem Phys 2024; 26:6806-6816. [PMID: 38324256 PMCID: PMC10883468 DOI: 10.1039/d3cp05951k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
The bifunctional spin label double-histidine copper-(II) capped with nitrilotriacetate [dHis-Cu(II)-NTA], used in conjunction with electron paramagnetic resonance (EPR) methods can provide high-resolution distance data for investigating protein structure and backbone conformational diversity. Quantitative utilization of this data is limited due to a lack of rapid and accurate dHis-Cu(II)-NTA modeling methods that can be used to translate experimental data into modeling restraints. Here, we develop two dHis-Cu(II)-NTA rotamer libraries using a set of recently published molecular dynamics simulations and a semi-empirical meta-dynamics-based conformational ensemble sampling tool for use with the recently developed chiLife bifunctional spin label modeling method. The accuracy of both the libraries and the modeling method are tested by comparing model predictions to experimentally determined distance distributions. We show that this method is accurate with absolute deviation between the predicted and experimental modes between 0.0-1.2 Å with an average of 0.6 Å over the test data used. In doing so, we also validate the generality of the chiLife bifunctional label modeling method. Taken together, the increased structural resolution and modeling accuracy of dHis-Cu(II)-NTA over other spin labels promise improvements in the accuracy and resolution of protein models by EPR.
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Affiliation(s)
- Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, PA, 15260, USA.
| | - Maxx H Tessmer
- Department of Chemistry, University of Washington, WA, 98195, USA.
| | - Stefan Stoll
- Department of Chemistry, University of Washington, WA, 98195, USA.
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, PA, 15260, USA.
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3
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Gurevich VV. Do arrestin oligomers have specific functions? CELL SIGNALING 2023; 1:42-46. [PMID: 37664541 PMCID: PMC10473880 DOI: 10.46439/signaling.1.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Arrestins are a small family of versatile regulators of cell signaling. Arrestins regulate signaling and trafficking of G protein-coupled receptors, regulate and direct to particular subcellular compartments numerous protein kinases, ubiquitin ligases, etc. Three out of four arrestin subtypes expressed in vertebrates self-associate, each forming oligomers of a distinct size and shape. While the structures of the solution oligomers of arrestin-1, -2, and -3 have been elucidated, no function specific for the oligomeric form of either of these three subtypes has been identified thus far. Considering how multi-functional average-sized (~45 kDa) arrestin proteins were found to be, it appears likely that certain functions are predominantly or exclusively fulfilled by monomeric and oligomeric forms of each subtype.
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4
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Gurevich VV, Gurevich EV. Solo vs. Chorus: Monomers and Oligomers of Arrestin Proteins. Int J Mol Sci 2022; 23:ijms23137253. [PMID: 35806256 PMCID: PMC9266314 DOI: 10.3390/ijms23137253] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 02/05/2023] Open
Abstract
Three out of four subtypes of arrestin proteins expressed in mammals self-associate, each forming oligomers of a distinct kind. Monomers and oligomers have different subcellular localization and distinct biological functions. Here we summarize existing evidence regarding arrestin oligomerization and discuss specific functions of monomeric and oligomeric forms, although too few of the latter are known. The data on arrestins highlight biological importance of oligomerization of signaling proteins. Distinct modes of oligomerization might be an important contributing factor to the functional differences among highly homologous members of the arrestin protein family.
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5
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Sander CL, Luu J, Kim K, Furkert D, Jang K, Reichenwallner J, Kang M, Lee HJ, Eger BT, Choe HW, Fiedler D, Ernst OP, Kim YJ, Palczewski K, Kiser PD. Structural evidence for visual arrestin priming via complexation of phosphoinositols. Structure 2022; 30:263-277.e5. [PMID: 34678158 PMCID: PMC8818024 DOI: 10.1016/j.str.2021.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/06/2021] [Accepted: 09/29/2021] [Indexed: 02/05/2023]
Abstract
Visual arrestin (Arr1) terminates rhodopsin signaling by blocking its interaction with transducin. To do this, Arr1 translocates from the inner to the outer segment of photoreceptors upon light stimulation. Mounting evidence indicates that inositol phosphates (InsPs) affect Arr1 activity, but the Arr1-InsP molecular interaction remains poorly defined. We report the structure of bovine Arr1 in a ligand-free state featuring a near-complete model of the previously unresolved C-tail, which plays a crucial role in regulating Arr1 activity. InsPs bind to the N-domain basic patch thus displacing the C-tail, suggesting that they prime Arr1 for interaction with rhodopsin and help direct Arr1 translocation. These structures exhibit intact polar cores, suggesting that C-tail removal by InsP binding is insufficient to activate Arr1. These results show how Arr1 activity can be controlled by endogenous InsPs in molecular detail.
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Affiliation(s)
- Christopher L. Sander
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA,Department of Ophthalmology and the Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA
| | - Jennings Luu
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA,Department of Ophthalmology and the Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA
| | - Kyumhyuk Kim
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - David Furkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Kiyoung Jang
- Department of Lifestyle Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | | | - MinSoung Kang
- Department of Lifestyle Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea,Thin Film Materials Research Center, Korea Research Institute of Chemical Technology (KRICT), 141 Gajeong-ro, Daejeon 34114, Republic of Korea
| | - Ho-Jun Lee
- Department of Ophthalmology and the Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA,Research Service, VA Long Beach Healthcare System, Long Beach, CA 90822, USA
| | - Bryan T. Eger
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hui-Woog Choe
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Oliver P. Ernst
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Yong Ju Kim
- Department of Lifestyle Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea,Department of Oriental Medicine Resources, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - Krzysztof Palczewski
- Department of Ophthalmology and the Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA,Department of Chemistry and Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA,Department of Physiology & Biophysics, University of California, Irvine, CA 92697, USA
| | - Philip D. Kiser
- Department of Ophthalmology and the Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA,Department of Physiology & Biophysics, University of California, Irvine, CA 92697, USA,Research Service, VA Long Beach Healthcare System, Long Beach, CA 90822, USA,Lead contact
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6
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Functional compartmentalization of photoreceptor neurons. Pflugers Arch 2021; 473:1493-1516. [PMID: 33880652 DOI: 10.1007/s00424-021-02558-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 12/16/2022]
Abstract
Retinal photoreceptors are neurons that convert dynamically changing patterns of light into electrical signals that are processed by retinal interneurons and ultimately transmitted to vision centers in the brain. They represent the essential first step in seeing without which the remainder of the visual system is rendered moot. To support this role, the major functions of photoreceptors are segregated into three main specialized compartments-the outer segment, the inner segment, and the pre-synaptic terminal. This compartmentalization is crucial for photoreceptor function-disruption leads to devastating blinding diseases for which therapies remain elusive. In this review, we examine the current understanding of the molecular and physical mechanisms underlying photoreceptor functional compartmentalization and highlight areas where significant knowledge gaps remain.
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7
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Barnes CL, Malhotra H, Calvert PD. Compartmentalization of Photoreceptor Sensory Cilia. Front Cell Dev Biol 2021; 9:636737. [PMID: 33614665 PMCID: PMC7889997 DOI: 10.3389/fcell.2021.636737] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Functional compartmentalization of cells is a universal strategy for segregating processes that require specific components, undergo regulation by modulating concentrations of those components, or that would be detrimental to other processes. Primary cilia are hair-like organelles that project from the apical plasma membranes of epithelial cells where they serve as exclusive compartments for sensing physical and chemical signals in the environment. As such, molecules involved in signal transduction are enriched within cilia and regulating their ciliary concentrations allows adaptation to the environmental stimuli. The highly efficient organization of primary cilia has been co-opted by major sensory neurons, olfactory cells and the photoreceptor neurons that underlie vision. The mechanisms underlying compartmentalization of cilia are an area of intense current research. Recent findings have revealed similarities and differences in molecular mechanisms of ciliary protein enrichment and its regulation among primary cilia and sensory cilia. Here we discuss the physiological demands on photoreceptors that have driven their evolution into neurons that rely on a highly specialized cilium for signaling changes in light intensity. We explore what is known and what is not known about how that specialization appears to have driven unique mechanisms for photoreceptor protein and membrane compartmentalization.
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Affiliation(s)
| | | | - Peter D. Calvert
- Department of Ophthalmology and Visual Sciences, Center for Vision Research, SUNY Upstate Medical University, Syracuse, NY, United States
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8
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Chen Q, Zhuo Y, Sharma P, Perez I, Francis DJ, Chakravarthy S, Vishnivetskiy SA, Berndt S, Hanson SM, Zhan X, Brooks EK, Altenbach C, Hubbell WL, Klug CS, Iverson TM, Gurevich VV. An Eight Amino Acid Segment Controls Oligomerization and Preferred Conformation of the two Non-visual Arrestins. J Mol Biol 2020; 433:166790. [PMID: 33387531 DOI: 10.1016/j.jmb.2020.166790] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 12/16/2022]
Abstract
G protein coupled receptors signal through G proteins or arrestins. A long-standing mystery in the field is why vertebrates have two non-visual arrestins, arrestin-2 and arrestin-3. These isoforms are ~75% identical and 85% similar; each binds numerous receptors, and appear to have many redundant functions, as demonstrated by studies of knockout mice. We previously showed that arrestin-3 can be activated by inositol-hexakisphosphate (IP6). IP6 interacts with the receptor-binding surface of arrestin-3, induces arrestin-3 oligomerization, and this oligomer stabilizes the active conformation of arrestin-3. Here, we compared the impact of IP6 on oligomerization and conformational equilibrium of the highly homologous arrestin-2 and arrestin-3 and found that these two isoforms are regulated differently. In the presence of IP6, arrestin-2 forms "infinite" chains, where each promoter remains in the basal conformation. In contrast, full length and truncated arrestin-3 form trimers and higher-order oligomers in the presence of IP6; we showed previously that trimeric state induces arrestin-3 activation (Chen et al., 2017). Thus, in response to IP6, the two non-visual arrestins oligomerize in different ways in distinct conformations. We identified an insertion of eight residues that is conserved across arrestin-2 homologs, but absent in arrestin-3 that likely accounts for the differences in the IP6 effect. Because IP6 is ubiquitously present in cells, this suggests physiological consequences, including differences in arrestin-2/3 trafficking and JNK3 activation. The functional differences between two non-visual arrestins are in part determined by distinct modes of their oligomerization. The mode of oligomerization might regulate the function of other signaling proteins.
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Affiliation(s)
- Qiuyan Chen
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; The Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Ya Zhuo
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; The Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Ivette Perez
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Derek J Francis
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | | | - Sandra Berndt
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Susan M Hanson
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Xuanzhi Zhan
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Evan K Brooks
- University of California Los Angeles, Los Angeles, CA 90095, USA
| | | | - Wayne L Hubbell
- University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Candice S Klug
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; The Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry and the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA.
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9
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Gamble Jarvi A, Casto J, Saxena S. Buffer effects on site directed Cu 2+-labeling using the double histidine motif. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 320:106848. [PMID: 33164758 DOI: 10.1016/j.jmr.2020.106848] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/25/2020] [Accepted: 10/07/2020] [Indexed: 05/09/2023]
Abstract
The double histidine, or dHis, motif has emerged as a powerful spin labeling tool to determine the conformations and dynamics, subunit orientation, native metal binding site location, and other physical characteristics of proteins by Cu2+-based electron paramagnetic resonance. Here, we investigate the efficacy of this technique in five common buffer systems, and show that buffer choice can impact the loading of Cu2+-NTA into dHis sites, and more generally, the sensitivity of the overall technique. We also present a standardized and optimized examination of labeling of the dHis motif with Cu2+-NTA for EPR based distance measurements. We provide optimal loading procedures, using representative EPR and UV/Vis data for each step in the process. From this data, we find that maximal dHis loading can be achieved in under 30 min with low temperature sample incubation. Using only these optimal procedures, we see up to a 28% increase in fully labeled proteins compared to previously published results in N-ethylmorpholine. Using both this optimized procedure as well as a more optimal buffer, we can achieve up to 80% fully loaded proteins, which corresponds to a 64% increase compared to the prior data. These results provide insight and deeper understanding of the dHis Cu2+-NTA system, the variables that impact its efficacy, and present a method by which these issues may be mitigated for the most efficient labeling.
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Affiliation(s)
- Austin Gamble Jarvi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Joshua Casto
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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10
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Biological Role of Arrestin-1 Oligomerization. J Neurosci 2020; 40:8055-8069. [PMID: 32948676 DOI: 10.1523/jneurosci.0749-20.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 11/21/2022] Open
Abstract
Members of the arrestin superfamily have great propensity of self-association, but the physiological significance of this phenomenon is unclear. To determine the biological role of visual arrestin-1 oligomerization in rod photoreceptors, we expressed mutant arrestin-1 with severely impaired self-association in mouse rods and analyzed mice of both sexes. We show that the oligomerization-deficient mutant is capable of quenching rhodopsin signaling normally, as judged by electroretinography and single-cell recording. Like wild type, mutant arrestin-1 is largely excluded from the outer segments in the dark, proving that the normal intracellular localization is not due the size exclusion of arrestin-1 oligomers. In contrast to wild type, supraphysiological expression of the mutant causes shortening of the outer segments and photoreceptor death. Thus, oligomerization reduces the cytotoxicity of arrestin-1 monomer, ensuring long-term photoreceptor survival.SIGNIFICANCE STATEMENT Visual arrestin-1 forms dimers and tetramers. The biological role of its oligomerization is unclear. To test the role of arrestin-1 self-association, we expressed oligomerization-deficient mutant in arrestin-1 knock-out mice. The mutant quenches light-induced rhodopsin signaling like wild type, demonstrating that in vivo monomeric arrestin-1 is necessary and sufficient for this function. In rods, arrestin-1 moves from the inner segments and cell bodies in the dark to the outer segments in the light. Nonoligomerizing mutant undergoes the same translocation, demonstrating that the size of the oligomers is not the reason for arrestin-1 exclusion from the outer segments in the dark. High expression of oligomerization-deficient arrestin-1 resulted in rod death. Thus, oligomerization reduces the cytotoxicity of high levels of arrestin-1 monomer.
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11
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Singewald K, Bogetti X, Sinha K, Rule GS, Saxena S. Double Histidine Based EPR Measurements at Physiological Temperatures Permit Site‐Specific Elucidation of Hidden Dynamics in Enzymes. Angew Chem Int Ed Engl 2020; 59:23040-23044. [DOI: 10.1002/anie.202009982] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/31/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Kevin Singewald
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Xiaowei Bogetti
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Kaustubh Sinha
- Department of Biological Sciences Carnegie Mellon University Pittsburgh PA 15213 USA
| | - Gordon S Rule
- Department of Biological Sciences Carnegie Mellon University Pittsburgh PA 15213 USA
| | - Sunil Saxena
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
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12
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Singewald K, Bogetti X, Sinha K, Rule GS, Saxena S. Double Histidine Based EPR Measurements at Physiological Temperatures Permit Site‐Specific Elucidation of Hidden Dynamics in Enzymes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Kevin Singewald
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Xiaowei Bogetti
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Kaustubh Sinha
- Department of Biological Sciences Carnegie Mellon University Pittsburgh PA 15213 USA
| | - Gordon S Rule
- Department of Biological Sciences Carnegie Mellon University Pittsburgh PA 15213 USA
| | - Sunil Saxena
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
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13
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Gurevich VV, Gurevich EV. Targeting arrestin interactions with its partners for therapeutic purposes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 121:169-197. [PMID: 32312421 DOI: 10.1016/bs.apcsb.2019.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Most vertebrates express four arrestin subtypes: two visual ones in photoreceptor cells and two non-visuals expressed ubiquitously. The latter two interact with hundreds of G protein-coupled receptors, certain receptors of other types, and numerous non-receptor partners. Arrestins have no enzymatic activity and work by interacting with other proteins, often assembling multi-protein signaling complexes. Arrestin binding to every partner affects cell signaling, including pathways regulating cell survival, proliferation, and death. Thus, targeting individual arrestin interactions has therapeutic potential. This requires precise identification of protein-protein interaction sites of both participants and the choice of the side of each interaction which would be most advantageous to target. The interfaces involved in each interaction can be disrupted by small molecule therapeutics, as well as by carefully selected peptides of the other partner that do not participate in the interactions that should not be targeted.
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Affiliation(s)
- Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
| | - Eugenia V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
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14
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Mayer D, Damberger FF, Samarasimhareddy M, Feldmueller M, Vuckovic Z, Flock T, Bauer B, Mutt E, Zosel F, Allain FHT, Standfuss J, Schertler GFX, Deupi X, Sommer ME, Hurevich M, Friedler A, Veprintsev DB. Distinct G protein-coupled receptor phosphorylation motifs modulate arrestin affinity and activation and global conformation. Nat Commun 2019; 10:1261. [PMID: 30890705 PMCID: PMC6424980 DOI: 10.1038/s41467-019-09204-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 02/22/2019] [Indexed: 12/15/2022] Open
Abstract
Cellular functions of arrestins are determined in part by the pattern of phosphorylation on the G protein-coupled receptors (GPCRs) to which arrestins bind. Despite high-resolution structural data of arrestins bound to phosphorylated receptor C-termini, the functional role of each phosphorylation site remains obscure. Here, we employ a library of synthetic phosphopeptide analogues of the GPCR rhodopsin C-terminus and determine the ability of these peptides to bind and activate arrestins using a variety of biochemical and biophysical methods. We further characterize how these peptides modulate the conformation of arrestin-1 by nuclear magnetic resonance (NMR). Our results indicate different functional classes of phosphorylation sites: 'key sites' required for arrestin binding and activation, an 'inhibitory site' that abrogates arrestin binding, and 'modulator sites' that influence the global conformation of arrestin. These functional motifs allow a better understanding of how different GPCR phosphorylation patterns might control how arrestin functions in the cell.
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Affiliation(s)
- Daniel Mayer
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232, Villigen, Switzerland.
- Department of Biology, ETH Zürich, 8093, Zürich, Switzerland.
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, 92093-0636, California, USA.
| | | | | | - Miki Feldmueller
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232, Villigen, Switzerland
- Department of Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Ziva Vuckovic
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232, Villigen, Switzerland
- Department of Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Tilman Flock
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232, Villigen, Switzerland
- Department of Biology, ETH Zürich, 8093, Zürich, Switzerland
- Fitzwilliam College, Cambridge, CB3 0DG, UK
| | - Brian Bauer
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Berlin, 10117, Germany
| | - Eshita Mutt
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232, Villigen, Switzerland
| | | | | | - Jörg Standfuss
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Gebhard F X Schertler
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232, Villigen, Switzerland
- Department of Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Xavier Deupi
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232, Villigen, Switzerland
- Condensed Matter Theory, Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Martha E Sommer
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Berlin, 10117, Germany
| | - Mattan Hurevich
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232, Villigen, Switzerland.
- Department of Biology, ETH Zürich, 8093, Zürich, Switzerland.
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, NG7 2RD, UK.
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK.
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15
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Gamble Jarvi A, Cunningham TF, Saxena S. Efficient localization of a native metal ion within a protein by Cu2+-based EPR distance measurements. Phys Chem Chem Phys 2019; 21:10238-10243. [DOI: 10.1039/c8cp07143h] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A native paramagnetic metal binding site in a protein is located with less than 2 Å resolution by a combination of double histidine (dHis) based Cu2+ labeling and long range distance measurements by EPR.
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Affiliation(s)
| | | | - Sunil Saxena
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
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16
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Vishnivetskiy SA, Sullivan LS, Bowne SJ, Daiger SP, Gurevich EV, Gurevich VV. Molecular Defects of the Disease-Causing Human Arrestin-1 C147F Mutant. Invest Ophthalmol Vis Sci 2018; 59:13-20. [PMID: 29305604 PMCID: PMC5756042 DOI: 10.1167/iovs.17-22180] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Purpose The purpose of this study was to identify the molecular defect in the disease-causing human arrestin-1 C147F mutant. Methods The binding of wild-type (WT) human arrestin-1 and several mutants with substitutions in position 147 (including C147F, which causes dominant retinitis pigmentosa in humans) to phosphorylated and unphosphorylated light-activated rhodopsin was determined. Thermal stability of WT and mutant human arrestin-1, as well as unfolded protein response in 661W cells, were also evaluated. Results WT human arrestin-1 was selective for phosphorylated light-activated rhodopsin. Substitutions of Cys-147 with smaller side chain residues, Ala or Val, did not substantially affect binding selectivity, whereas residues with bulky side chains in the position 147 (Ile, Leu, and disease-causing Phe) greatly increased the binding to unphosphorylated rhodopsin. Functional survival of mutant proteins with bulky substitutions at physiological and elevated temperature was also compromised. C147F mutant induced unfolded protein response in cultured cells. Conclusions Bulky Phe substitution of Cys-147 in human arrestin-1 likely causes rod degeneration due to reduced stability of the protein, which induces unfolded protein response in expressing cells.
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Affiliation(s)
| | - Lori S Sullivan
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas, United States
| | - Sara J Bowne
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas, United States
| | - Stephen P Daiger
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas, United States
| | - Eugenia V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, United States
| | - Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, United States
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17
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Samaranayake S, Song X, Vishnivetskiy SA, Chen J, Gurevich EV, Gurevich VV. Enhanced Mutant Compensates for Defects in Rhodopsin Phosphorylation in the Presence of Endogenous Arrestin-1. Front Mol Neurosci 2018; 11:203. [PMID: 29973866 PMCID: PMC6020793 DOI: 10.3389/fnmol.2018.00203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/22/2018] [Indexed: 01/16/2023] Open
Abstract
We determined the effects of different expression levels of arrestin-1-3A mutant with enhanced binding to light-activated rhodopsin that is independent of phosphorylation. To this end, transgenic mice that express mutant rhodopsin with zero, one, or two phosphorylation sites, instead of six in the WT mouse rhodopsin, and normal complement of WT arrestin-1, were bred with mice expressing enhanced phosphorylation-independent arrestin-1-3A mutant. The resulting lines were characterized by retinal histology (thickness of the outer nuclear layer, reflecting the number of rod photoreceptors, and the length of the outer segments, which reflects rod health), as well as single- and double-flash ERG to determine the functionality of rods and the rate of photoresponse recovery. The effect of co-expression of enhanced arrestin-1-3A mutant with WT arrestin-1 in these lines depended on its level: higher (240% of WT) expression reduced the thickness of ONL and the length of OS, whereas lower (50% of WT) expression was harmless in the retinas expressing rhodopsin with zero or one phosphorylation site, and improved photoreceptor morphology in animals expressing rhodopsin with two phosphorylation sites. Neither expression level increased the amplitude of the a- and b-wave of the photoresponse in any of the lines. However, high expression of enhanced arrestin-1-3A mutant facilitated photoresponse recovery 2-3-fold, whereas lower level was ineffective. Thus, in the presence of normal complement of WT arrestin-1 only supra-physiological expression of enhanced mutant is sufficient to compensate for the defects of rhodopsin phosphorylation.
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Affiliation(s)
- Srimal Samaranayake
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
| | - Xiufeng Song
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
| | | | - Jeannie Chen
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Eugenia V. Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
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18
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Latorraca NR, Wang JK, Bauer B, Townshend RJL, Hollingsworth SA, Olivieri JE, Xu HE, Sommer ME, Dror RO. Molecular mechanism of GPCR-mediated arrestin activation. Nature 2018; 557:452-456. [PMID: 29720655 PMCID: PMC6294333 DOI: 10.1038/s41586-018-0077-3] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 03/06/2018] [Indexed: 12/26/2022]
Abstract
Despite intense interest in discovering drugs that cause G-protein-coupled receptors (GPCRs) to selectively stimulate or block arrestin signalling, the structural mechanism of receptor-mediated arrestin activation remains unclear1,2. Here we reveal this mechanism through extensive atomic-level simulations of arrestin. We find that the receptor's transmembrane core and cytoplasmic tail-which bind distinct surfaces on arrestin-can each independently stimulate arrestin activation. We confirm this unanticipated role of the receptor core, and the allosteric coupling between these distant surfaces of arrestin, using site-directed fluorescence spectroscopy. The effect of the receptor core on arrestin conformation is mediated primarily by interactions of the intracellular loops of the receptor with the arrestin body, rather than the marked finger-loop rearrangement that is observed upon receptor binding. In the absence of a receptor, arrestin frequently adopts active conformations when its own C-terminal tail is disengaged, which may explain why certain arrestins remain active long after receptor dissociation. Our results, which suggest that diverse receptor binding modes can activate arrestin, provide a structural foundation for the design of functionally selective ('biased') GPCR-targeted ligands with desired effects on arrestin signalling.
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Affiliation(s)
- Naomi R Latorraca
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Jason K Wang
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Brian Bauer
- Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Scott A Hollingsworth
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia E Olivieri
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - H Eric Xu
- VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Martha E Sommer
- Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Ron O Dror
- Biophysics Program, Stanford University, Stanford, CA, USA.
- Department of Computer Science, Stanford University, Stanford, CA, USA.
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
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19
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Indrischek H, Prohaska SJ, Gurevich VV, Gurevich EV, Stadler PF. Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes. BMC Evol Biol 2017; 17:163. [PMID: 28683816 PMCID: PMC5501109 DOI: 10.1186/s12862-017-1001-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 06/19/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The cytosolic arrestin proteins mediate desensitization of activated G protein-coupled receptors (GPCRs) via competition with G proteins for the active phosphorylated receptors. Arrestins in active, including receptor-bound, conformation are also transducers of signaling. Therefore, this protein family is an attractive therapeutic target. The signaling outcome is believed to be a result of structural and sequence-dependent interactions of arrestins with GPCRs and other protein partners. Here we elucidated the detailed evolution of arrestins in deuterostomes. RESULTS Identity and number of arrestin paralogs were determined searching deuterostome genomes and gene expression data. In contrast to standard gene prediction methods, our strategy first detects exons situated on different scaffolds and then solves the problem of assigning them to the correct gene. This increases both the completeness and the accuracy of the annotation in comparison to conventional database search strategies applied by the community. The employed strategy enabled us to map in detail the duplication- and deletion history of arrestin paralogs including tandem duplications, pseudogenizations and the formation of retrogenes. The two rounds of whole genome duplications in the vertebrate stem lineage gave rise to four arrestin paralogs. Surprisingly, visual arrestin ARR3 was lost in the mammalian clades Afrotheria and Xenarthra. Duplications in specific clades, on the other hand, must have given rise to new paralogs that show signatures of diversification in functional elements important for receptor binding and phosphate sensing. CONCLUSION The current study traces the functional evolution of deuterostome arrestins in unprecedented detail. Based on a precise re-annotation of the exon-intron structure at nucleotide resolution, we infer the gain and loss of paralogs and patterns of conservation, co-variation and selection.
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Affiliation(s)
- Henrike Indrischek
- Computational EvoDevo Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany.
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany.
- Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany.
| | - Sonja J Prohaska
- Computational EvoDevo Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
- Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
| | - Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University, 2200 Pierce Ave, Nashville, TN 37232, USA
| | - Eugenia V Gurevich
- Department of Pharmacology, Vanderbilt University, 2200 Pierce Ave, Nashville, TN 37232, USA
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
- Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, D-04103, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, Leipzig, D-04103, Germany
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna, A-1090, Austria
- Center for non-coding RNA in Technology and Health, Grønegårdsvej 3, Frederiksberg C, DK-1870, Denmark
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
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20
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Vishnivetskiy SA, Lee RJ, Zhou XE, Franz A, Xu Q, Xu HE, Gurevich VV. Functional role of the three conserved cysteines in the N domain of visual arrestin-1. J Biol Chem 2017; 292:12496-12502. [PMID: 28536260 DOI: 10.1074/jbc.m117.790386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/22/2017] [Indexed: 11/06/2022] Open
Abstract
Arrestins specifically bind active and phosphorylated forms of their cognate G protein-coupled receptors, blocking G protein coupling and often redirecting the signaling to alternative pathways. High-affinity receptor binding is accompanied by two major structural changes in arrestin: release of the C-tail and rotation of the two domains relative to each other. The first requires detachment of the arrestin C-tail from the body of the molecule, whereas the second requires disruption of the network of charge-charge interactions at the interdomain interface, termed the polar core. These events can be facilitated by mutations destabilizing the polar core or the anchoring of the C-tail that yield "preactivated" arrestins that bind phosphorylated and unphosphorylated receptors with high affinity. Here we explored the functional role in arrestin activation of the three native cysteines in the N domain, which are conserved in all arrestin subtypes. Using visual arrestin-1 and rhodopsin as a model, we found that substitution of these cysteines with serine, alanine, or valine virtually eliminates the effects of the activating polar core mutations on the binding to unphosphorylated rhodopsin while only slightly reducing the effects of the C-tail mutations. Thus, these three conserved cysteines play a role in the domain rotation but not in the C-tail release.
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Affiliation(s)
| | - Regina J Lee
- Vanderbilt University, Nashville, Tennessee 37232
| | - X Edward Zhou
- VARI-SIMM Center, Center for Structure and Function of Drug Targets, Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | | | - Qiuyi Xu
- Vanderbilt University, Nashville, Tennessee 37232
| | - H Eric Xu
- VARI-SIMM Center, Center for Structure and Function of Drug Targets, Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503
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21
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Leelananda SP, Lindert S. Computational methods in drug discovery. Beilstein J Org Chem 2016; 12:2694-2718. [PMID: 28144341 PMCID: PMC5238551 DOI: 10.3762/bjoc.12.267] [Citation(s) in RCA: 285] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/22/2016] [Indexed: 12/11/2022] Open
Abstract
The process for drug discovery and development is challenging, time consuming and expensive. Computer-aided drug discovery (CADD) tools can act as a virtual shortcut, assisting in the expedition of this long process and potentially reducing the cost of research and development. Today CADD has become an effective and indispensable tool in therapeutic development. The human genome project has made available a substantial amount of sequence data that can be used in various drug discovery projects. Additionally, increasing knowledge of biological structures, as well as increasing computer power have made it possible to use computational methods effectively in various phases of the drug discovery and development pipeline. The importance of in silico tools is greater than ever before and has advanced pharmaceutical research. Here we present an overview of computational methods used in different facets of drug discovery and highlight some of the recent successes. In this review, both structure-based and ligand-based drug discovery methods are discussed. Advances in virtual high-throughput screening, protein structure prediction methods, protein-ligand docking, pharmacophore modeling and QSAR techniques are reviewed.
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Affiliation(s)
- Sumudu P Leelananda
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
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22
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Lindert S, McCammon JA. Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction. J Chem Theory Comput 2016; 11:1337-46. [PMID: 25883538 PMCID: PMC4393324 DOI: 10.1021/ct500995d] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Indexed: 12/13/2022]
Abstract
![]()
Many excellent methods exist that
incorporate cryo-electron microscopy
(cryoEM) data to constrain computational protein structure prediction
and refinement. Previously, it was shown that iteration of two such
orthogonal sampling and scoring methods – Rosetta and molecular
dynamics (MD) simulations – facilitated exploration of conformational
space in principle. Here, we go beyond a proof-of-concept study and
address significant remaining limitations of the iterative MD–Rosetta
protein structure refinement protocol. Specifically, all parts of
the iterative refinement protocol are now guided by medium-resolution
cryoEM density maps, and previous knowledge about the native structure
of the protein is no longer necessary. Models are identified solely
based on score or simulation time. All four benchmark proteins showed
substantial improvement through three rounds of the iterative refinement
protocol. The best-scoring final models of two proteins had sub-Ångstrom
RMSD to the native structure over residues in secondary structure
elements. Molecular dynamics was most efficient in refining secondary
structure elements and was thus highly complementary to the Rosetta
refinement which is most powerful in refining side chains and loop
regions.
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23
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Gurevich EV, Gurevich VV. Beyond traditional pharmacology: new tools and approaches. Br J Pharmacol 2015; 172:3229-41. [PMID: 25572005 DOI: 10.1111/bph.13066] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 11/24/2014] [Accepted: 01/02/2015] [Indexed: 12/14/2022] Open
Abstract
Traditional pharmacology is defined as the science that deals with drugs and their actions. While small molecule drugs have clear advantages, there are many cases where they have proved to be ineffective, prone to unacceptable side effects, or where due to a particular disease aetiology they cannot possibly be effective. A dominant feature of the small molecule drugs is their single mindedness: they provide either continuous inhibition or continuous activation of the target. Because of that, these drugs tend to engage compensatory mechanisms leading to drug tolerance, drug resistance or, in some cases, sensitization and consequent loss of therapeutic efficacy over time and/or unwanted side effects. Here we discuss new and emerging therapeutic tools and approaches that have potential for treating the majority of disorders for which small molecules are either failing or cannot be developed. These new tools include biologics, such as recombinant hormones and antibodies, as well as approaches involving gene transfer (gene therapy and genome editing) and the introduction of specially designed self-replicating cells. It is clear that no single method is going to be a 'silver bullet', but collectively, these novel approaches hold promise for curing practically every disorder.
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Affiliation(s)
- E V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - V V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
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24
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Ostermaier MK, Schertler GFX, Standfuss J. Molecular mechanism of phosphorylation-dependent arrestin activation. Curr Opin Struct Biol 2014; 29:143-51. [PMID: 25484000 DOI: 10.1016/j.sbi.2014.07.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/16/2014] [Accepted: 07/18/2014] [Indexed: 12/31/2022]
Abstract
The past years have seen tremendous progress towards understanding how arrestins recognize phosphorylated G protein-coupled receptors (GPCRs). Two arrestin crystal structures, one of a pre-activated splice variant and one bound to a GPCR phosphopeptide, provided insights into the conformational changes upon phosphate recognition. Scanning mutagenesis and spectroscopic studies complete the picture of arrestin activation and receptor binding. Most perspicuous is the C-tail exchange mechanism, by which the C-tail of arrestin is released from its basal conformation and replaced by the phosphorylated GPCR C-terminus. Three positively charged clusters could act as conserved arrestin phosphosensors. Variations in the pattern of phosphorylation in a GPCR and variations within the C-terminus of different GPCRs may encode specificity to arrestin subtypes and particular physiological responses.
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Affiliation(s)
- Martin K Ostermaier
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Gebhard F X Schertler
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen, Switzerland; Deparment of Biology, ETH Zurich, Wolfgang-Pauli-Str. 27, 8093 Zürich, Switzerland
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen, Switzerland.
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25
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Abstract
Virtually all currently used therapeutic agents are small molecules, largely because the development and delivery of small molecule drugs is relatively straightforward. Small molecules have serious limitations: drugs of this type can be fairly good enzyme inhibitors, receptor ligands, or allosteric modulators. However, most cellular functions are mediated by protein interactions with other proteins, and targeting protein-protein interactions by small molecules presents challenges that are unlikely to be overcome with these compounds as the only tools. Recent advances in gene delivery techniques and characterization of cell type-specific promoters open the prospect of using reengineered signaling-biased proteins as next-generation therapeutics. The first steps in targeted engineering of proteins with desired functional characteristics look very promising. As quintessential scaffolds that act strictly via interactions with other proteins in the cell, arrestins represent a perfect model for the development of these novel therapeutic agents with enormous potential: custom-designed signaling proteins will allow us to tell the cell what to do and when to do it in a way it cannot disobey.
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26
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Ostermaier MK, Peterhans C, Jaussi R, Deupi X, Standfuss J. Functional map of arrestin-1 at single amino acid resolution. Proc Natl Acad Sci U S A 2014; 111:1825-30. [PMID: 24449856 PMCID: PMC3918777 DOI: 10.1073/pnas.1319402111] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arrestins function as adapter proteins that mediate G protein-coupled receptor (GPCR) desensitization, internalization, and additional rounds of signaling. Here we have compared binding of the GPCR rhodopsin to 403 mutants of arrestin-1 covering its complete sequence. This comprehensive and unbiased mutagenesis approach provides a functional dimension to the crystal structures of inactive, preactivated p44 and phosphopeptide-bound arrestins and will guide our understanding of arrestin-GPCR complexes. The presented functional map quantitatively connects critical interactions in the polar core and along the C tail of arrestin. A series of amino acids (Phe375, Phe377, Phe380, and Arg382) anchor the C tail in a position that blocks binding of the receptor. Interaction of phosphates in the rhodopsin C terminus with Arg29 controls a C-tail exchange mechanism in which the C tail of arrestin is released and exposes several charged amino acids (Lys14, Lys15, Arg18, Lys20, Lys110, and Lys300) for binding of the phosphorylated receptor C terminus. In addition to this arrestin phosphosensor, our data reveal several patches of amino acids in the finger (Gln69 and Asp73-Met75) and the lariat loops (L249-S252 and Y254) that can act as direct binding interfaces. A stretch of amino acids at the edge of the C domain (Trp194-Ser199, Gly337-Gly340, Thr343, and Thr345) could act as membrane anchor, binding interface for a second rhodopsin, or rearrange closer to the central loops upon complex formation. We discuss these interfaces in the context of experimentally guided docking between the crystal structures of arrestin and light-activated rhodopsin.
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Affiliation(s)
| | | | | | - Xavier Deupi
- Laboratory of Biomolecular Research and
- Condensed Matter Theory Group, Paul Scherrer Institute, 5232 Villigen, Switzerland
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27
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Gurevich VV, Song X, Vishnivetskiy SA, Gurevich EV. Enhanced phosphorylation-independent arrestins and gene therapy. Handb Exp Pharmacol 2014; 219:133-152. [PMID: 24292828 PMCID: PMC4516159 DOI: 10.1007/978-3-642-41199-1_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A variety of heritable and acquired disorders is associated with excessive signaling by mutant or overstimulated GPCRs. Since any conceivable treatment of diseases caused by gain-of-function mutations requires gene transfer, one possible approach is functional compensation. Several structurally distinct forms of enhanced arrestins that bind phosphorylated and even non-phosphorylated active GPCRs with much higher affinity than parental wild-type proteins have the ability to dampen the signaling by hyperactive GPCR, pushing the balance closer to normal. In vivo this approach was so far tested only in rod photoreceptors deficient in rhodopsin phosphorylation, where enhanced arrestin improved the morphology and light sensitivity of rods, prolonged their survival, and accelerated photoresponse recovery. Considering that rods harbor the fastest, as well as the most demanding and sensitive GPCR-driven signaling cascade, even partial success of functional compensation of defect in rhodopsin phosphorylation by enhanced arrestin demonstrates the feasibility of this strategy and its therapeutic potential.
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Affiliation(s)
- Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University, 2200 Pierce Avenue, Nashville, TN, 37232, USA,
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28
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Abstract
Programmed cell death (apoptosis) is a coordinated set of events eventually leading to the massive activation of specialized proteases (caspases) that cleave numerous substrates, orchestrating fairly uniform biochemical changes than culminate in cellular suicide. Apoptosis can be triggered by a variety of stimuli, from external signals or growth factor withdrawal to intracellular conditions, such as DNA damage or ER stress. Arrestins regulate many signaling cascades involved in life-or-death decisions in the cell, so it is hardly surprising that numerous reports document the effects of ubiquitous nonvisual arrestins on apoptosis under various conditions. Although these findings hardly constitute a coherent picture, with the same arrestin subtypes, sometimes via the same signaling pathways, reported to promote or inhibit cell death, this might reflect real differences in pro- and antiapoptotic signaling in different cells under a variety of conditions. Recent finding suggests that one of the nonvisual subtypes, arrestin-2, is specifically cleaved by caspases. Generated fragment actively participates in the core mechanism of apoptosis: it assists another product of caspase activity, tBID, in releasing cytochrome C from mitochondria. This is the point of no return in committing vertebrate cells to death, and the aspartate where caspases cleave arrestin-2 is evolutionary conserved in vertebrate, but not in invertebrate arrestins. In contrast to wild-type arrestin-2, its caspase-resistant mutant does not facilitate cell death.
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Affiliation(s)
- Seunghyi Kook
- Department of Pharmacology, Vanderbilt University, 2200 Pierce Ave, Nashville, TN, 37232, USA
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29
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Chen Q, Zhuo Y, Kim M, Hanson SM, Francis DJ, Vishnivetskiy SA, Altenbach C, Klug CS, Hubbell WL, Gurevich VV. Self-association of arrestin family members. Handb Exp Pharmacol 2014; 219:205-23. [PMID: 24292832 DOI: 10.1007/978-3-642-41199-1_11] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mammals express four arrestin subtypes, three of which have been shown to self-associate. Cone photoreceptor-specific arrestin-4 is the only one that is a constitutive monomer. Visual arrestin-1 forms tetramers both in crystal and in solution, but the shape of its physiologically relevant solution tetramer is very different from that in the crystal. The biological role of the self-association of arrestin-1, expressed at very high levels in rod and cone photoreceptors, appears to be protective, reducing the concentration of cytotoxic monomers. The two nonvisual arrestin subtypes are highly homologous, and self-association of both is facilitated by IP6, yet they form dramatically different oligomers. Arrestin-2 apparently self-associates into "infinite" chains, very similar to those observed in IP6-soaked crystals, where IP6 connects the concave sides of the N- and C-domains of adjacent protomers. In contrast, arrestin-3 only forms dimers, in which IP6 likely connects the C-domains of two arrestin-3 molecules. Thus, each of the three self-associating arrestins does it in its own way, forming three different types of oligomers. The physiological role of the oligomerization of arrestin-1 and both nonvisual arrestins might be quite different, and in each case it remains to be definitively elucidated.
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Affiliation(s)
- Qiuyan Chen
- Department of Pharmacology, Vanderbilt University, 2200 Pierce Avenue, Nashville, TN, 37232, USA
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30
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Vishnivetskiy SA, Ostermaier MK, Singhal A, Panneels V, Homan KT, Glukhova A, Sligar SG, Tesmer JJG, Schertler GF, Standfuss J, Gurevich VV. Constitutively active rhodopsin mutants causing night blindness are effectively phosphorylated by GRKs but differ in arrestin-1 binding. Cell Signal 2013; 25:2155-62. [PMID: 23872075 PMCID: PMC3774132 DOI: 10.1016/j.cellsig.2013.07.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 07/11/2013] [Indexed: 11/24/2022]
Abstract
The effects of activating mutations associated with night blindness on the stoichiometry of rhodopsin interactions with G protein-coupled receptor kinase 1 (GRK1) and arrestin-1 have not been reported. Here we show that the monomeric form of WT rhodopsin and its constitutively active mutants M257Y, G90D, and T94I, reconstituted into HDL particles are effectively phosphorylated by GRK1, as well as two more ubiquitously expressed subtypes, GRK2 and GRK5. All versions of arrestin-1 tested (WT, pre-activated, and constitutively monomeric mutants) bind to monomeric rhodopsin and show the same selectivity for different functional forms of rhodopsin as in native disc membranes. Rhodopsin phosphorylation by GRK1 and GRK2 promotes arrestin-1 binding to a comparable extent, whereas similar phosphorylation by GRK5 is less effective, suggesting that not all phosphorylation sites on rhodopsin are equivalent in promoting arrestin-1 binding. The binding of WT arrestin-1 to phospho-opsin is comparable to the binding to its preferred target, P-Rh*, suggesting that in photoreceptors arrestin-1 only dissociates after opsin regeneration with 11-cis-retinal, which converts phospho-opsin into inactive phospho-rhodopsin that has lower affinity for arrestin-1. Reduced binding of arrestin-1 to the phospho-opsin form of G90D mutant likely contributes to night blindness caused by this mutation in humans.
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Affiliation(s)
| | - Martin K. Ostermaier
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen 5232, Switzerland
| | - Ankita Singhal
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen 5232, Switzerland
| | - Valerie Panneels
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen 5232, Switzerland
| | - Kristoff T. Homan
- Life Sciences Institute, Departments of Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-2216, USA
| | - Alisa Glukhova
- Life Sciences Institute, Departments of Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-2216, USA
| | - Stephen G. Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
| | - John J. G. Tesmer
- Life Sciences Institute, Departments of Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-2216, USA
| | - Gebhard F.X. Schertler
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen 5232, Switzerland
- Department of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen 5232, Switzerland
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31
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Song X, Seo J, Baameur F, Vishnivetskiy SA, Chen Q, Kook S, Kim M, Brooks EK, Altenbach C, Hong Y, Hanson SM, Palazzo MC, Chen J, Hubbell WL, Gurevich EV, Gurevich VV. Rapid degeneration of rod photoreceptors expressing self-association-deficient arrestin-1 mutant. Cell Signal 2013; 25:2613-24. [PMID: 24012956 DOI: 10.1016/j.cellsig.2013.08.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 08/23/2013] [Indexed: 10/26/2022]
Abstract
Arrestin-1 binds light-activated phosphorhodopsin and ensures timely signal shutoff. We show that high transgenic expression of an arrestin-1 mutant with enhanced rhodopsin binding and impaired oligomerization causes apoptotic rod death in mice. Dark rearing does not prevent mutant-induced cell death, ruling out the role of arrestin complexes with light-activated rhodopsin. Similar expression of WT arrestin-1 that robustly oligomerizes, which leads to only modest increase in the monomer concentration, does not affect rod survival. Moreover, WT arrestin-1 co-expressed with the mutant delays retinal degeneration. Thus, arrestin-1 mutant directly affects cell survival via binding partner(s) other than light-activated rhodopsin. Due to impaired self-association of the mutant its high expression dramatically increases the concentration of the monomer. The data suggest that monomeric arrestin-1 is cytotoxic and WT arrestin-1 protects rods by forming mixed oligomers with the mutant and/or competing with it for the binding to non-receptor partners. Thus, arrestin-1 self-association likely serves to keep low concentration of the toxic monomer. The reduction of the concentration of harmful monomer is an earlier unappreciated biological function of protein oligomerization.
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Affiliation(s)
- Xiufeng Song
- Vanderbilt University, Nashville, TN 37232, United States
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32
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Lindert S, Meiler J, McCammon JA. Iterative Molecular Dynamics-Rosetta Protein Structure Refinement Protocol to Improve Model Quality. J Chem Theory Comput 2013; 9:3843-3847. [PMID: 23956701 PMCID: PMC3744128 DOI: 10.1021/ct400260c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Indexed: 02/02/2023]
Abstract
Rosetta is one of the prime tools for high resolution protein structure refinement. While its scoring function can distinguish native-like from non-native-like conformations in many cases, the method is limited by conformational sampling for larger proteins, that is, leaving a local energy minimum in which the search algorithm may get stuck. Here, we test the hypothesis that iteration of Rosetta with an orthogonal sampling and scoring strategy might facilitate exploration of conformational space. Specifically, we run short molecular dynamics (MD) simulations on models created by de novo folding of large proteins into cryoEM density maps to enable sampling of conformational space not directly accessible to Rosetta and thus provide an escape route from the conformational traps. We present a combined MD-Rosetta protein structure refinement protocol that can overcome some of these sampling limitations. Two of four benchmark proteins showed incremental improvement through all three rounds of the iterative refinement protocol. Molecular dynamics is most efficient in applying subtle but important rearrangements within secondary structure elements and is thus highly complementary to the Rosetta refinement, which focuses on side chains and loop regions.
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Affiliation(s)
- Steffen Lindert
- Department of Pharmacology, University of California
San Diego, La Jolla, California
92093, United States
- Center for Theoretical
Biological Physics, La Jolla, California 92093, United
States
| | - Jens Meiler
- Department of Chemistry
and Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37212,
United States
| | - J. Andrew McCammon
- Department of Pharmacology, University of California
San Diego, La Jolla, California
92093, United States
- Center for Theoretical
Biological Physics, La Jolla, California 92093, United
States
- Howard Hughes
Medical Institute, University of California San Diego, La Jolla, California
92093, United States
- Department
of Chemistry and
Biochemistry, NSF Center for Theoretical Biological Physics, National
Biomedical Computation Resource, University of California
San Diego, La Jolla, California
92093, United States
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33
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Vishnivetskiy SA, Baameur F, Findley KR, Gurevich VV. Critical role of the central 139-loop in stability and binding selectivity of arrestin-1. J Biol Chem 2013; 288:11741-50. [PMID: 23476014 DOI: 10.1074/jbc.m113.450031] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Arrestin-1 selectively binds active phosphorylated rhodopsin (P-Rh*), demonstrating much lower affinity for inactive phosphorylated (P-Rh) and unphosphorylated active (Rh*) forms. Receptor interaction induces significant conformational changes in arrestin-1, which include large movement of the previously neglected 139-loop in the center of the receptor binding surface, away from the incoming receptor. To elucidate the functional role of this loop, in mouse arrestin-1 we introduced deletions of variable lengths and made several substitutions of Lys-142 in it and Asp-72 in the adjacent loop. Several mutants with perturbations in the 139-loop demonstrate increased binding to P-Rh*, dark P-Rh, Rh*, and phospho-opsin. Enhanced binding of arrestin-1 mutants to non-preferred forms of rhodopsin correlates with decreased thermal stability. The 139-loop perturbations increase P-Rh* binding of arrestin-1 at low temperatures and further change its binding profile on the background of 3A mutant, where the C-tail is detached from the body of the molecule by triple alanine substitution. Thus, the 139-loop stabilizes basal conformation of arrestin-1 and acts as a brake, preventing its binding to non-preferred forms of rhodopsin. Conservation of this loop in other subtypes suggests that it has the same function in all members of the arrestin family.
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34
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Gurevich VV, Gurevich EV. Structural determinants of arrestin functions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 118:57-92. [PMID: 23764050 PMCID: PMC4514030 DOI: 10.1016/b978-0-12-394440-5.00003-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Arrestins are a small protein family with only four members in mammals. Arrestins demonstrate an amazing versatility, interacting with hundreds of different G protein-coupled receptor (GPCR) subtypes, numerous nonreceptor signaling proteins, and components of the internalization machinery, as well as cytoskeletal elements, including regular microtubules and centrosomes. Here, we focus on the structural determinants that mediate various arrestin functions. The receptor-binding elements in arrestins were mapped fairly comprehensively, which set the stage for the construction of mutants targeting particular GPCRs. The elements engaged by other binding partners are only now being elucidated and in most cases we have more questions than answers. Interestingly, even very limited and imprecise identification of structural requirements for the interaction with very few other proteins has enabled the development of signaling-biased arrestin mutants. More comprehensive understanding of the structural underpinning of different arrestin functions will pave the way for the construction of arrestins that can link the receptor we want to the signaling pathway of our choosing.
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Affiliation(s)
- Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
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35
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Involvement of distinct arrestin-1 elements in binding to different functional forms of rhodopsin. Proc Natl Acad Sci U S A 2012; 110:942-7. [PMID: 23277586 DOI: 10.1073/pnas.1215176110] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Solution NMR spectroscopy of labeled arrestin-1 was used to explore its interactions with dark-state phosphorylated rhodopsin (P-Rh), phosphorylated opsin (P-opsin), unphosphorylated light-activated rhodopsin (Rh*), and phosphorylated light-activated rhodopsin (P-Rh*). Distinct sets of arrestin-1 elements were seen to be engaged by Rh* and inactive P-Rh, which induced conformational changes that differed from those triggered by binding of P-Rh*. Although arrestin-1 affinity for Rh* was seen to be low (K(D) > 150 μM), its affinity for P-Rh (K(D) ~80 μM) was comparable to the concentration of active monomeric arrestin-1 in the outer segment, suggesting that P-Rh generated by high-gain phosphorylation is occupied by arrestin-1 under physiological conditions and will not signal upon photo-activation. Arrestin-1 was seen to bind P-Rh* and P-opsin with fairly high affinity (K(D) of~50 and 800 nM, respectively), implying that arrestin-1 dissociation is triggered only upon P-opsin regeneration with 11-cis-retinal, precluding noise generated by opsin activity. Based on their observed affinity for arrestin-1, P-opsin and inactive P-Rh very likely affect the physiological monomer-dimer-tetramer equilibrium of arrestin-1, and should therefore be taken into account when modeling photoreceptor function. The data also suggested that complex formation with either P-Rh* or P-opsin results in a global transition in the conformation of arrestin-1, possibly to a dynamic molten globule-like structure. We hypothesize that this transition contributes to the mechanism that triggers preferential interactions of several signaling proteins with receptor-activated arrestins.
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36
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Vishnivetskiy SA, Chen Q, Palazzo MC, Brooks EK, Altenbach C, Iverson TM, Hubbell WL, Gurevich VV. Engineering visual arrestin-1 with special functional characteristics. J Biol Chem 2012; 288:3394-405. [PMID: 23250748 DOI: 10.1074/jbc.m112.445437] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Arrestin-1 preferentially binds active phosphorylated rhodopsin. Previously, a mutant with enhanced binding to unphosphorylated active rhodopsin (Rh*) was shown to partially compensate for lack of rhodopsin phosphorylation in vivo. Here we showed that reengineering of the receptor binding surface of arrestin-1 further improves the binding to Rh* while preserving protein stability. In mammals, arrestin-1 readily self-associates at physiological concentrations. The biological role of this phenomenon can only be elucidated by replacing wild type arrestin-1 in living animals with a non-oligomerizing mutant retaining all other functions. We demonstrate that constitutively monomeric forms of arrestin-1 are sufficiently stable for in vivo expression. We also tested the idea that individual functions of arrestin-1 can be independently manipulated to generate mutants with the desired combinations of functional characteristics. Here we showed that this approach is feasible; stable forms of arrestin-1 with high Rh* binding can be generated with or without the ability to self-associate. These novel molecular tools open the possibility of testing of the biological role of arrestin-1 self-association and pave the way to elucidation of full potential of compensational approach to gene therapy of gain-of-function receptor mutations.
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37
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Abstract
Arrestin-1 (visual arrestin) binds to light-activated phosphorylated rhodopsin (P-Rh*) to terminate G-protein signaling. To map conformational changes upon binding to the receptor, pairs of spin labels were introduced in arrestin-1 and double electron-electron resonance was used to monitor interspin distance changes upon P-Rh* binding. The results indicate that the relative position of the N and C domains remains largely unchanged, contrary to expectations of a "clam-shell" model. A loop implicated in P-Rh* binding that connects β-strands V and VI (the "finger loop," residues 67-79) moves toward the expected location of P-Rh* in the complex, but does not assume a fully extended conformation. A striking and unexpected movement of a loop containing residue 139 away from the adjacent finger loop is observed, which appears to facilitate P-Rh* binding. This change is accompanied by smaller movements of distal loops containing residues 157 and 344 at the tips of the N and C domains, which correspond to "plastic" regions of arrestin-1 that have distinct conformations in monomers of the crystal tetramer. Remarkably, the loops containing residues 139, 157, and 344 appear to have high flexibility in both free arrestin-1 and the P-Rh*complex.
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38
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Francis DJ, Hubbell WL, Klug CS. Probing Protein Secondary Structure using EPR: Investigating a Dynamic Region of Visual Arrestin. APPLIED MAGNETIC RESONANCE 2012; 43:405-419. [PMID: 25419051 PMCID: PMC4240029 DOI: 10.1007/s00723-012-0369-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
One key application of site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy is the determination of sequence-specific secondary structure in proteins. Regular secondary structure leads to a periodic variation in both side chain motion and solvent accessibility, two properties easily monitored by EPR techniques. Specifically, saturation recovery (SR) EPR spectroscopy has proven to be useful for making accessibility measurements for multiple protein structure populations by determining individual accessibilities and is therefore well suited to study the structure of proteins exhibiting multiple conformations in equilibrium. Here we employ both continuous wave and SR EPR spectroscopy in combination to examine the secondary structure of a short sequence showing conformational heterogeneity in visual rod arrestin. The EPR data presented here clearly distinguish between the unstructured loop and the helical structure formed in the crystallographic tetramer of visual arrestin and show that this region is unstructured in solution.
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Affiliation(s)
- Derek J. Francis
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Wayne L. Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Candice S. Klug
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
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39
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Najafi M, Calvert PD. Transport and localization of signaling proteins in ciliated cells. Vision Res 2012; 75:11-8. [PMID: 22922002 DOI: 10.1016/j.visres.2012.08.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/05/2012] [Accepted: 08/08/2012] [Indexed: 11/16/2022]
Abstract
Most cells in the human body elaborate cilia which serve a wide variety of functions, including cell and tissue differentiation during development, sensing physical and chemical properties of the extracellular milieu and mechanical force generation. Common among cilia is the transduction of external stimuli into signals that regulate the activities of the cilia and the cells that possess them. These functions require the transport and localization of specialized proteins to the cilium, a process that many recent studies have shown to be vital for normal cell function and, ultimately, the health of the organism. Here we discuss several mechanisms proposed for the transport and localization of soluble and peripheral membrane proteins to, or their exclusion from the ciliary compartment with a focus on how the structure of the cytoplasm and the size and shape of proteins influence these processes. Additionally, we examine the impact of cell and protein structure on our ability to accurately measure the relative concentrations of fluorescently tagged proteins amongst various cellular domains, which is integral to our understanding of the molecular mechanisms underlying protein localization and transport.
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Affiliation(s)
- Mehdi Najafi
- Department of Ophthalmology and the Center for Vision Research, SUNY Upstate Medical University, United States
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40
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Lindert S, Alexander N, Wötzel N, Karakaş M, Stewart PL, Meiler J. EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps. Structure 2012; 20:464-78. [PMID: 22405005 DOI: 10.1016/j.str.2012.01.023] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 01/23/2012] [Accepted: 01/26/2012] [Indexed: 11/17/2022]
Abstract
Electron density maps of membrane proteins or large macromolecular complexes are frequently only determined at medium resolution between 4 Å and 10 Å, either by cryo-electron microscopy or X-ray crystallography. In these density maps, the general arrangement of secondary structure elements (SSEs) is revealed, whereas their directionality and connectivity remain elusive. We demonstrate that the topology of proteins with up to 250 amino acids can be determined from such density maps when combined with a computational protein folding protocol. Furthermore, we accurately reconstruct atomic detail in loop regions and amino acid side chains not visible in the experimental data. The EM-Fold algorithm assembles the SSEs de novo before atomic detail is added using Rosetta. In a benchmark of 27 proteins, the protocol consistently and reproducibly achieves models with root mean square deviation values <3 Å.
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Affiliation(s)
- Steffen Lindert
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37212, USA
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41
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Yanamala N, Gardner E, Riciutti A, Klein-Seetharaman J. The cytoplasmic rhodopsin-protein interface: potential for drug discovery. Curr Drug Targets 2012; 13:3-14. [PMID: 21777183 PMCID: PMC3275648 DOI: 10.2174/138945012798868461] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2010] [Revised: 02/08/2011] [Accepted: 02/10/2011] [Indexed: 01/20/2023]
Abstract
The mammalian dim-light photoreceptor rhodopsin is a prototypic G protein coupled receptor (GPCR), interacting with the G protein, transducin, rhodopsin kinase, and arrestin. All of these proteins interact with rhodopsin at its cytoplasmic surface. Structural and modeling studies have provided in-depth descriptions of the respective interfaces. Overlap and thus competition for binding surfaces is a major regulatory mechanism for signal processing. Recently, it was found that the same surface is also targeted by small molecules. These ligands can directly interfere with the binding and activation of the proteins of the signal transduction cascade, but they can also allosterically modulate the retinal ligand binding pocket. Because the pocket that is targeted contains residues that are highly conserved across Class A GPCRs, these findings imply that it may be possible to target multiple GPCRs with the same ligand(s). This is desirable for example in complex diseases such as cancer where multiple GPCRs participate in the disease networks.
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Affiliation(s)
- Naveena Yanamala
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Eric Gardner
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Alec Riciutti
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Judith Klein-Seetharaman
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
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42
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Hatmal MM, Li Y, Hegde BG, Hegde PB, Jao CC, Langen R, Haworth IS. Computer modeling of nitroxide spin labels on proteins. Biopolymers 2012; 97:35-44. [PMID: 21792846 PMCID: PMC3422567 DOI: 10.1002/bip.21699] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 06/24/2011] [Accepted: 06/25/2011] [Indexed: 01/26/2023]
Abstract
Electron paramagnetic resonance using site-directed spin labeling can be used as an approach for determination of protein structures that are difficult to solve by other methods. One important aspect of this approach is the measurement of interlabel distances using the double electron-electron resonance (DEER) method. Interpretation of experimental data could be facilitated by a computational approach to calculation of interlabel distances. We describe an algorithm, PRONOX, for rapid computation of interlabel distances based on calculation of spin label conformer distributions at any site of a protein. The program incorporates features of the label distribution established experimentally, including weighting of favorable conformers of the label. Distances calculated by PRONOX were compared with new DEER distances for amphiphysin and annexin B12 and with published data for FCHo2 (F-BAR), endophilin, and α-synuclein, a total of 44 interlabel distances. The program reproduced these distances accurately (r(2) = 0.94, slope = 0.98). For 9 of the 11 distances for amphiphysin, PRONOX reproduced the experimental data to within 2.5 Å. The speed and accuracy of PRONOX suggest that the algorithm can be used for fitting to DEER data for determination of protein tertiary structure.
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Affiliation(s)
- Ma’mon M. Hatmal
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern CA, Los Angeles, CA 90089, USA
- Department of Biochemistry, University of Southern California, Los Angeles, CA, 90033-9151, USA
| | - Yiyu Li
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern CA, Los Angeles, CA 90089, USA
| | - Balachandra G. Hegde
- Zilkha Neurogenetic Institute, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033, USA
| | - Prabhavati B. Hegde
- Zilkha Neurogenetic Institute, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033, USA
| | - Christine C. Jao
- Zilkha Neurogenetic Institute, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033, USA
| | - Ralf Langen
- Department of Biochemistry, University of Southern California, Los Angeles, CA, 90033-9151, USA
- Zilkha Neurogenetic Institute, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033, USA
| | - Ian S. Haworth
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern CA, Los Angeles, CA 90089, USA
- Department of Biochemistry, University of Southern California, Los Angeles, CA, 90033-9151, USA
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43
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Steric volume exclusion sets soluble protein concentrations in photoreceptor sensory cilia. Proc Natl Acad Sci U S A 2011; 109:203-8. [PMID: 22184246 DOI: 10.1073/pnas.1115109109] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Proteins segregate into discrete subcellular compartments via a variety of mechanisms, including motor protein transport, local binding, and diffusion barriers. This physical separation of cell functions serves, in part, as a mechanism for controlling compartment activity by allowing regulation of local protein concentrations. In this study we explored how soluble protein size impacts access to the confined space within the retinal photoreceptor outer segment signaling compartment and discovered a strikingly steep relationship. We find that GFP monomers, dimers, and trimers expressed transgenically in frog rods are present in the outer segment at 1.8-, 2.9-, and 6.8-fold lower abundances, relative to the cell body, than the small soluble fluorescent marker, calcein. Theoretical analysis, based on statistical-mechanical models of molecular access to polymer meshes, shows that these observations can be explained by the steric hindrance of molecules occupying the highly constrained spaces between outer segment disc membranes. This mechanism may answer a long-standing question of how the soluble regulatory protein, arrestin, is effectively excluded from the outer segments of dark-adapted rods and cones. Generally, our results suggest an alternate mode for the control of protein access to cell domains based on dynamic, size-dependent compartmental partitioning that does not require diffusion barriers, active transport, or large numbers of immobile binding sites.
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44
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One-step purification of a functional, constitutively activated form of visual arrestin. Protein Expr Purif 2011; 82:55-60. [PMID: 22133714 DOI: 10.1016/j.pep.2011.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 11/06/2011] [Accepted: 11/07/2011] [Indexed: 01/24/2023]
Abstract
Desensitization of agonist-activated G protein-coupled receptors (GPCRs) requires phosphorylation followed by the binding of arrestin, a ~48 kDa soluble protein. While crystal structures for the inactive, 'basal' state of various arrestins are available, the conformation of 'activated' arrestin adopted upon interaction with activated GPCRs remains unknown. As a first step towards applying high-resolution structural methods to study arrestin conformation and dynamics, we have utilized the subtilisin prodomain/Profinity eXact™ fusion-tag system for the high-level bacterial expression and one-step purification of wild-type visual arrestin (arrestin 1) as well as a mutant form (R175E) of the protein that binds to non-phosphorylated, light-activated rhodopsin (Rho∗). The results show that both prodomain/Profinity eXact™ fusion-tagged wild-type and R175E arrestins can be expressed to levels approaching 2-3 mg/l in Luria-Bertani media, and that the processed, tag-free mature forms can be purified to near homogeneity using a Bio-Scale™ Mini Profinity eXact™ cartridge on the Profinia™ purification system. Functional analysis of R175E arrestin generated using this approach shows that it binds to non-phosphorylated rhodopsin in a light-dependent manner. These findings should facilitate the structure determination of this 'constitutively activated' state of arrestin 1 as well as the monitoring of conformational changes upon interaction with Rho∗.
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Zhan X, Kaoud TS, Dalby KN, Gurevich VV. Nonvisual arrestins function as simple scaffolds assembling the MKK4-JNK3α2 signaling complex. Biochemistry 2011; 50:10520-9. [PMID: 22047447 DOI: 10.1021/bi201506g] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Arrestins make up a small family of proteins with four mammalian members that play key roles in the regulation of multiple G protein-coupled receptor-dependent and -independent signaling pathways. Although arrestins were reported to serve as scaffolds for MAP kinase cascades, promoting the activation of JNK3, ERK1/2, and p38, the molecular mechanisms involved were not elucidated, and even the direct binding of arrestins with MAP kinases was never demonstrated. Here, using purified proteins, we show that both nonvisual arrestins directly bind JNK3α2 and its upstream activator MKK4, and that the affinity of arrestin-3 for these kinases is higher than that of arrestin-2. Reconstitution of the MKK4-JNK3α2 signaling module from pure proteins in the presence of different arrestin-3 concentrations showed that arrestin-3 acts as a "true" scaffold, facilitating JNK3α2 phosphorylation by bringing the two kinases together. Both the level of JNK3α2 phosphorylation by MKK4 and JNK3α2 activity toward its substrate ATF2 increase at low and then decrease at high arrestin-3 levels, yielding a bell-shaped concentration dependence expected with true scaffolds that do not activate the upstream kinase or its substrate. Thus, direct binding of both kinases and true scaffolding is the molecular mechanism of action of arrestin-3 on the MKK4-JNK3α2 signaling module.
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Affiliation(s)
- Xuanzhi Zhan
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
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Gurevich VV, Hanson SM, Song X, Vishnivetskiy SA, Gurevich EV. The functional cycle of visual arrestins in photoreceptor cells. Prog Retin Eye Res 2011; 30:405-30. [PMID: 21824527 DOI: 10.1016/j.preteyeres.2011.07.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 07/20/2011] [Accepted: 07/21/2011] [Indexed: 01/14/2023]
Abstract
Visual arrestin-1 plays a key role in the rapid and reproducible shutoff of rhodopsin signaling. Its highly selective binding to light-activated phosphorylated rhodopsin is an integral part of the functional perfection of rod photoreceptors. Structure-function studies revealed key elements of the sophisticated molecular mechanism ensuring arrestin-1 selectivity and paved the way to the targeted manipulation of the arrestin-1 molecule to design mutants that can compensate for congenital defects in rhodopsin phosphorylation. Arrestin-1 self-association and light-dependent translocation in photoreceptor cells work together to keep a constant supply of active rhodopsin-binding arrestin-1 monomer in the outer segment. Recent discoveries of arrestin-1 interaction with other signaling proteins suggest that it is a much more versatile signaling regulator than previously thought, affecting the function of the synaptic terminals and rod survival. Elucidation of the fine molecular mechanisms of arrestin-1 interactions with rhodopsin and other binding partners is necessary for the comprehensive understanding of rod function and for devising novel molecular tools and therapeutic approaches to the treatment of visual disorders.
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Affiliation(s)
- Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University, 2200 Pierce Ave, PRB, Rm 417D, Nashville, TN 37232, USA.
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Cleghorn WM, Tsakem EL, Song X, Vishnivetskiy SA, Seo J, Chen J, Gurevich EV, Gurevich VV. Progressive reduction of its expression in rods reveals two pools of arrestin-1 in the outer segment with different roles in photoresponse recovery. PLoS One 2011; 6:e22797. [PMID: 21818392 PMCID: PMC3144249 DOI: 10.1371/journal.pone.0022797] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 07/02/2011] [Indexed: 01/10/2023] Open
Abstract
Light-induced rhodopsin signaling is turned off with sub-second kinetics by rhodopsin phosphorylation followed by arrestin-1 binding. To test the availability of the arrestin-1 pool in dark-adapted outer segment (OS) for rhodopsin shutoff, we measured photoresponse recovery rates of mice with arrestin-1 content in the OS of 2.5%, 5%, 60%, and 100% of wild type (WT) level by two-flash ERG with the first (desensitizing) flash at 160, 400, 1000, and 2500 photons/rod. The time of half recovery (thalf) in WT retinas increases with the intensity of the initial flash, becoming ∼2.5-fold longer upon activation of 2500 than after 160 rhodopsins/rod. Mice with 60% and even 5% of WT arrestin-1 level recovered at WT rates. In contrast, the mice with 2.5% of WT arrestin-1 had a dramatically slower recovery than the other three lines, with the thalf increasing ∼28 fold between 160 and 2500 rhodopsins/rod. Even after the dimmest flash, the rate of recovery of rods with 2.5% of normal arrestin-1 was two times slower than in other lines, indicating that arrestin-1 level in the OS between 100% and 5% of WT is sufficient for rapid recovery, whereas with lower arrestin-1 the rate of recovery dramatically decreases with increased light intensity. Thus, the OS has two distinct pools of arrestin-1: cytoplasmic and a separate pool comprising ∼2.5% that is not immediately available for rhodopsin quenching. The observed delay suggests that this pool is localized at the periphery, so that its diffusion across the OS rate-limits the recovery. The line with very low arrestin-1 expression is the first where rhodopsin inactivation was made rate-limiting by arrestin manipulation.
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Affiliation(s)
- Whitney M. Cleghorn
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Elviche L. Tsakem
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Xiufeng Song
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Sergey A. Vishnivetskiy
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jungwon Seo
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jeannie Chen
- Department of Cell and Neurobiology, University of Southern California, Los Angeles, California, United States of America
| | - Eugenia V. Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Vsevolod V. Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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Maurice P, Kamal M, Jockers R. Asymmetry of GPCR oligomers supports their functional relevance. Trends Pharmacol Sci 2011; 32:514-20. [PMID: 21715028 DOI: 10.1016/j.tips.2011.05.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 05/19/2011] [Accepted: 05/20/2011] [Indexed: 01/29/2023]
Abstract
G protein-coupled receptors (GPCRs) can exist as dimers or as larger oligomeric clusters that enable intercommunication between different receptor protomers within the same complex. This phenomenon is observed at three distinct levels: (i) at the level of ligand binding where the activation of one protomer can allosterically inhibit or facilitate ligand binding to the second protomer; (ii) at the level of ligand-induced conformational switches, which occur between transmembrane domains of the two protomers; and (iii) within GPCR-associated protein complexes, either directly at the level of GPCR-interacting proteins or at further downstream levels of the complex. Intercommunication at these different levels introduces asymmetry within GPCR dimers wherein each protomer fulfills its specific task. In this review, we discuss how the asymmetric behavior of GPCRs highlights the advantage of oligomeric receptor organization and supports the functional relevance of GPCR dimerization.
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Affiliation(s)
- Pascal Maurice
- Inserm, U1016, Institut Cochin, 22 rue Méchain, 75014 Paris, France
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Ahmed MR, Zhan X, Song X, Kook S, Gurevich VV, Gurevich EV. Ubiquitin ligase parkin promotes Mdm2-arrestin interaction but inhibits arrestin ubiquitination. Biochemistry 2011; 50:3749-63. [PMID: 21466165 DOI: 10.1021/bi200175q] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Numerous mutations in E3 ubiquitin ligase parkin were shown to associate with familial Parkinson's disease. Here we show that parkin binds arrestins, versatile regulators of cell signaling. Arrestin-parkin interaction was demonstrated by coimmunoprecipitation of endogenous proteins from brain tissue and shown to be direct using purified proteins. Parkin binding enhances arrestin interactions with another E3 ubiquitin ligase, Mdm2, apparently by shifting arrestin conformational equilibrium to the basal state preferred by Mdm2. Although Mdm2 was reported to ubiquitinate arrestins, parkin-dependent increase in Mdm2 binding dramatically reduces the ubiquitination of both nonvisual arrestins, basal and stimulated by receptor activation, without affecting receptor internalization. Several disease-associated parkin mutations differentially affect the stimulation of Mdm2 binding. All parkin mutants tested effectively suppress arrestin ubiquitination, suggesting that bound parkin shields arrestin lysines targeted by Mdm2. Parkin binding to arrestins along with its effects on arrestin interaction with Mdm2 and ubiquitination is a novel function of this protein with implications for Parkinson's disease pathology.
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Affiliation(s)
- M Rafiuddin Ahmed
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, USA
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Vishnivetskiy SA, Gimenez LE, Francis DJ, Hanson SM, Hubbell WL, Klug CS, Gurevich VV. Few residues within an extensive binding interface drive receptor interaction and determine the specificity of arrestin proteins. J Biol Chem 2011; 286:24288-99. [PMID: 21471193 DOI: 10.1074/jbc.m110.213835] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Arrestins bind active phosphorylated forms of G protein-coupled receptors, terminating G protein activation, orchestrating receptor trafficking, and redirecting signaling to alternative pathways. Visual arrestin-1 preferentially binds rhodopsin, whereas the two non-visual arrestins interact with hundreds of G protein-coupled receptor subtypes. Here we show that an extensive surface on the concave side of both arrestin-2 domains is involved in receptor binding. We also identified a small number of residues on the receptor binding surface of the N- and C-domains that largely determine the receptor specificity of arrestins. We show that alanine substitution of these residues blocks the binding of arrestin-1 to rhodopsin in vitro and of arrestin-2 and -3 to β2-adrenergic, M2 muscarinic cholinergic, and D2 dopamine receptors in intact cells, suggesting that these elements critically contribute to the energy of the interaction. Thus, in contrast to arrestin-1, where direct phosphate binding is crucial, the interaction of non-visual arrestins with their cognate receptors depends to a lesser extent on phosphate binding and more on the binding to non-phosphorylated receptor elements.
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