Large-scale conformational rearrangement of the α5-helix of Gα subunits in complex with the guanine nucleotide exchange factor Ric8A

Srivastava, Dhiraj; Artemyev, Nikolai O.

doi:10.1074/jbc.AC119.011135

Title: Large-scale conformational rearrangement of the α5-helix of Gα subunits in complex with the guanine nucleotide exchange factor Ric8A

Journal Article · Thu Oct 17 00:00:00 EDT 2019 · Journal of Biological Chemistry

DOI:https://doi.org/10.1074/jbc.AC119.011135· OSTI ID:1577142

Srivastava, Dhiraj ^[1];

^[1]

Univ. of Iowa Carver College of Medicine, Iowa City, IA (United States)

Resistance to inhibitors of cholinesterase 8A (Ric8A) protein is an important G protein–coupled receptor (GPCR)-independent regulator of G protein α-subunits (Gα), acting as a guanine nucleotide exchange factor (GEF) and a chaperone. Insights into the complex between Ric8A and Gα hold the key to understanding the mechanisms underlying noncanonical activation of G-protein signaling as well as the folding of nascent Gα proteins. In this work, we examined the structure of the complex of Ric8A with minimized Gαi (miniGα_i) in solution by small-angle X-ray scattering (SAXS) and exploited the scattering profile in modeling of the Ric8A/miniGα_i complex by steered molecular dynamics (SMD) simulations. A small set of models of the complex featured minimal clash scores, excellent agreement with the experimental SAXS data, and a large-scale rearrangement of the signal-transducing α5-helix of Gα away from its β-sheet core. The resulting interface involved the Gα α5-helix bound to the concave surface of Ric8A and the Gα β-sheet that wraps around the C-terminal part of the Ric8A armadillo domain, leading to a severe disruption of the GDP-binding site. Further modeling of the flexible C-terminal tail of Ric8A indicated that it interacts with the effector surface of Gα. This smaller interface may enable the Ric8A-bound Gα to interact with GTP. The two-interface interaction with Gα described here distinguishes Ric8A from GPCRs and non-GPCR regulators of G-protein signaling.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: National Institutes of Health (NIH); National Eye Institute (NEI)

Grant/Contract Number:: RO1 EY-12682

OSTI ID:: 1577142

Journal Information:: Journal of Biological Chemistry, Vol. 294, Issue 47; ISSN 0021-9258

Publisher:: American Society for Biochemistry and Molecular BiologyCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Cited by: 5 works

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References (45)

A Conserved Hydrophobic Core in Gα _i1 Regulates G Protein Activation and Release from Activated Receptor Kaya, Ali I.; Lokits, Alyssa D.; Gilbert, James A. Journal of Biological Chemistry, Vol. 291, Issue 37 https://doi.org/10.1074/jbc.M116.745513	journal	July 2016
RIC-8 (Synembryn) Miller, Kenneth G.; Emerson, Melanie D.; McManus, John R. Neuron, Vol. 27, Issue 2 https://doi.org/10.1016/S0896-6273(00)00037-4	journal	August 2000
Ric-8A, a G protein chaperone with nucleotide exchange activity induces long-range secondary structure changes in Gα Kant, Ravi; Zeng, Baisen; Thomas, Celestine J. eLife, Vol. 5 https://doi.org/10.7554/eLife.19238	journal	December 2016
Ab initio electron density determination directly from solution scattering data Grant, Thomas D. Nature Methods, Vol. 15, Issue 3 https://doi.org/10.1038/nmeth.4581	journal	January 2018
Structural underpinnings of Ric8A function as a G-protein α-subunit chaperone and guanine-nucleotide exchange factor Srivastava, Dhiraj; Gakhar, Lokesh; Artemyev, Nikolai O. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11088-x	journal	July 2019
The GAPs, GEFs, and GDIs of heterotrimeric G-protein alpha subunits Siderovski, David P.; Willard, Francis S. International Journal of Biological Sciences https://doi.org/10.7150/ijbs.1.51	journal	January 2005
Ric-8 regulation of heterotrimeric G proteins Tall, Gregory G. Journal of Receptors and Signal Transduction, Vol. 33, Issue 3 https://doi.org/10.3109/10799893.2013.763828	journal	January 2013
The guanine nucleotide exchange factor Ric-8A induces domain separation and Ras domain plasticity in Gαi1 Van Eps, Ned; Thomas, Celestine J.; Hubbell, Wayne L. Proceedings of the National Academy of Sciences, Vol. 112, Issue 5 https://doi.org/10.1073/pnas.1423878112	journal	January 2015
Molecular chaperoning function of Ric-8 is to fold nascent heterotrimeric G protein subunits Chan, P.; Thomas, C. J.; Sprang, S. R. Proceedings of the National Academy of Sciences, Vol. 110, Issue 10 https://doi.org/10.1073/pnas.1220943110	journal	February 2013
Scalable molecular dynamics with NAMD Phillips, James C.; Braun, Rosemary; Wang, Wei Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802 https://doi.org/10.1002/jcc.20289	journal	January 2005
CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates Svergun, D.; Barberato, C.; Koch, M. H. J. Journal of Applied Crystallography, Vol. 28, Issue 6 https://doi.org/10.1107/S0021889895007047	journal	December 1995
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
The G Protein α Chaperone Ric-8 as a Potential Therapeutic Target Papasergi, Makaía M.; Patel, Bharti R.; Tall, Gregory G. Molecular Pharmacology, Vol. 87, Issue 1 https://doi.org/10.1124/mol.114.094664	journal	October 2014
New Roles for Gα and RGS Proteins: Communication Continues despite Pulling Sisters Apart Wilkie, Thomas M.; Kinch, Lisa Current Biology, Vol. 15, Issue 20 https://doi.org/10.1016/j.cub.2005.10.008	journal	October 2005
Crystal structure of the β2 adrenergic receptor–Gs protein complex Rasmussen, Søren G. F.; DeVree, Brian T.; Zou, Yaozhong Nature, Vol. 477, Issue 7366 https://doi.org/10.1038/nature10361	journal	July 2011
BioXTAS RAW : improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis Hopkins, Jesse Bennett; Gillilan, Richard E.; Skou, Soren Journal of Applied Crystallography, Vol. 50, Issue 5 https://doi.org/10.1107/S1600576717011438	journal	September 2017
Structural basis for GPCR-independent activation of heterotrimeric Gi proteins Kalogriopoulos, Nicholas A.; Rees, Steven D.; Ngo, Tony Proceedings of the National Academy of Sciences, Vol. 116, Issue 33 https://doi.org/10.1073/pnas.1906658116	journal	July 2019
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ ₁ and χ ₂ Dihedral Angles Best, Robert B.; Zhu, Xiao; Shim, Jihyun Journal of Chemical Theory and Computation, Vol. 8, Issue 9 https://doi.org/10.1021/ct300400x	journal	August 2012
ATSAS 2.8 : a comprehensive data analysis suite for small-angle scattering from macromolecular solutions Franke, D.; Petoukhov, M. V.; Konarev, P. V. Journal of Applied Crystallography, Vol. 50, Issue 4 https://doi.org/10.1107/S1600576717007786	journal	June 2017
The Importance of Non-accessible Crosslinks and Solvent Accessible Surface Distance in Modeling Proteins with Restraints From Crosslinking Mass Spectrometry Bullock, Joshua Matthew Allen; Schwab, Jannik; Thalassinos, Konstantinos Molecular & Cellular Proteomics, Vol. 15, Issue 7 https://doi.org/10.1074/mcp.M116.058560	journal	May 2016
Probing the mechanism of rhodopsin-catalyzed transducin activation Natochin, Michael; Moussaif, Mustapha; Artemyev, Nikolai O. Journal of Neurochemistry, Vol. 77, Issue 1 https://doi.org/10.1046/j.1471-4159.2001.t01-1-00221.x	journal	April 2001
Activators of G Protein Signaling Exhibit Broad Functionality and Define a Distinct Core Signaling Triad Blumer, Joe B.; Lanier, Stephen M. Molecular Pharmacology, Vol. 85, Issue 3 https://doi.org/10.1124/mol.113.090068	journal	December 2013
Heterotrimeric G protein activation by G-protein-coupled receptors Oldham, William M.; Hamm, Heidi E. Nature Reviews Molecular Cell Biology, Vol. 9, Issue 1 https://doi.org/10.1038/nrm2299	journal	January 2008
Cryo-EM structure of human rhodopsin bound to an inhibitory G protein Kang, Yanyong; Kuybeda, Oleg; de Waal, Parker W. Nature, Vol. 558, Issue 7711 https://doi.org/10.1038/s41586-018-0215-y	journal	June 2018
Heterotrimeric G protein signaling via GIV/Girdin: Breaking the rules of engagement, space, and time Aznar, Nicolas; Kalogriopoulos, Nicholas; Midde, Krishna K. BioEssays, Vol. 38, Issue 4 https://doi.org/10.1002/bies.201500133	journal	February 2016
QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts Ribeiro, João V.; Bernardi, Rafael C.; Rudack, Till Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep26536	journal	May 2016
Drosophila G-protein signalling: intricate roles for Ric-8? Matsuzaki, Fumio Nature Cell Biology, Vol. 7, Issue 11 https://doi.org/10.1038/ncb1105-1047	journal	November 2005
Conformational changes in the G protein Gs induced by the β2 adrenergic receptor Chung, Ka Young; Rasmussen, Søren G. F.; Liu, Tong Nature, Vol. 477, Issue 7366 https://doi.org/10.1038/nature10488	journal	September 2011
Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine-lysine distances: Evaluating Lysine-Lysine Distances by MD for XL-MS Merkley, Eric D.; Rysavy, Steven; Kahraman, Abdullah Protein Science, Vol. 23, Issue 6 https://doi.org/10.1002/pro.2458	journal	April 2014
Structural basis for nucleotide exchange in heterotrimeric G proteins Dror, R. O.; Mildorf, T. J.; Hilger, D. Science, Vol. 348, Issue 6241 https://doi.org/10.1126/science.aaa5264	journal	June 2015
Liquid-chromatography-coupled SAXS for accurate sizing of aggregating proteins Mathew, Elizabeth; Mirza, Ahmed; Menhart, Nick Journal of Synchrotron Radiation, Vol. 11, Issue 4 https://doi.org/10.1107/S0909049504014086	journal	June 2004
Thermally-induced structural changes in an armadillo repeat protein suggest a novel thermosensor mechanism in a molecular chaperone Bujalowski, Paul J.; Nicholls, Paul; Barral, José M. FEBS Letters, Vol. 589, Issue 1 https://doi.org/10.1016/j.febslet.2014.11.034	journal	November 2014
The Nucleotide Exchange Factor Ric-8A Is a Chaperone for the Conformationally Dynamic Nucleotide-Free State of Gαi1 Thomas, Celestine J.; Briknarová, Klára; Hilmer, Jonathan K. PLoS ONE, Vol. 6, Issue 8 https://doi.org/10.1371/journal.pone.0023197	journal	August 2011
Structure of the adenosine A2A receptor bound to an engineered G protein Carpenter, Byron; Nehmé, Rony; Warne, Tony Nature, Vol. 536, Issue 7614 https://doi.org/10.1038/nature18966	journal	July 2016
Rapid E2-E3 Assembly and Disassembly Enable Processive Ubiquitylation of Cullin-RING Ubiquitin Ligase Substrates Kleiger, Gary; Saha, Anjanabha; Lewis, Steven Cell, Vol. 139, Issue 5 https://doi.org/10.1016/j.cell.2009.10.030	journal	November 2009
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Structure, Function, and Dynamics of the Gα Binding Domain of Ric-8A Zeng, Baisen; Mou, Tung-Chung; Doukov, Tzanko I. Structure, Vol. 27, Issue 7 https://doi.org/10.1016/j.str.2019.04.013	journal	July 2019
VMD: Visual molecular dynamics Humphrey, William; Dalke, Andrew; Schulten, Klaus Journal of Molecular Graphics, Vol. 14, Issue 1 https://doi.org/10.1016/0263-7855(96)00018-5	journal	February 1996
Resistance to inhibitors of cholinesterase 8A catalyzes release of G i-GTP and nuclear mitotic apparatus protein (NuMA) from NuMA/LGN/G i-GDP complexes Tall, G. G.; Gilman, A. G. Proceedings of the National Academy of Sciences, Vol. 102, Issue 46 https://doi.org/10.1073/pnas.0508306102	journal	November 2005
Structural determinants for GoLoco-induced inhibition of nucleotide release by Gα subunits Kimple, Randall J.; Kimple, Michelle E.; Betts, Laurie Nature, Vol. 416, Issue 6883 https://doi.org/10.1038/416878a	journal	April 2002
Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen Zacarias, Sónia; Temporão, Adriana; Carpentier, Philippe JBIC Journal of Biological Inorganic Chemistry, Vol. 25, Issue 6 https://doi.org/10.1007/s00775-020-01814-y	journal	August 2020
AB Initio Electron Density Determination Directly from Solution Scattering Data Grant, Thomas D. Biophysical Journal, Vol. 118, Issue 3 https://doi.org/10.1016/j.bpj.2019.11.2693	journal	February 2020
The GAPs, GEFs, and GDIs of heterotrimeric G-protein alpha subunits S., Willard, Francis; P., Siderovski, David The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/5a9d-2173	text	January 2005
Rapid E2-E3 Assembly and Disassembly Enable Processive Ubiquitylation of Cullin-RING Ubiquitin Ligase Substrates Anjanabha, Saha,; J., Deshaies, Raymond; Steven, Lewis, The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/7baf-c392	text	January 2009
Probing the mechanism of rhodopsin-catalyzed transducin activation: Activation of heterotrimeric G proteins Natochin, Michael; Moussaif, Mustapha; Artemyev, Nikolai O. Journal of Neurochemistry, Vol. 77, Issue 1 https://doi.org/10.1046/j.1471-4159.2001.00221.x	journal	April 2001

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59 BASIC BIOLOGICAL SCIENCES
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
G protein
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chaperone
small-angle X-ray scattering (SAXS)
molecular dynamics
signal transduction
Ric8

Title: Large-scale conformational rearrangement of the α5-helix of Gα subunits in complex with the guanine nucleotide exchange factor Ric8A

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