101
|
Sun R, Sode O, Dama JF, Voth GA. Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics. J Chem Theory Comput 2017; 13:2332-2341. [PMID: 28345907 PMCID: PMC5425946 DOI: 10.1021/acs.jctc.7b00077] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The protein mediated hydrolysis of nucleoside triphosphates such as ATP or GTP is one of the most important and challenging biochemical reactions in nature. The chemical environment (water structure, catalytic metal, and amino acid residues) adjacent to the hydrolysis site contains hundreds of atoms, usually greatly limiting the amount of the free energy sampling that one can achieve from computationally demanding electronic structure calculations such as QM/MM simulations. Therefore, the combination of QM/MM molecular dynamics with the recently developed transition-tempered metadynamics (TTMetaD), an enhanced sampling method that can provide a high-quality free energy estimate at an early stage in a simulation, is an ideal approach to address the biomolecular nucleoside triphosphate hydrolysis problem. In this work the ATP hydrolysis process in monomeric and filamentous actin is studied as an example application of the combined methodology. The performance of TTMetaD in these demanding QM/MM simulations is compared with that of the more conventional well-tempered metadynamics (WTMetaD). Our results show that TTMetaD exhibits much better exploration of the hydrolysis reaction free energy surface in two key collective variables (CVs) during the early stages of the QM/MM simulation than does WTMetaD. The TTMetaD simulations also reveal that a key third degree of freedom, the O-H bond-breaking and proton transfer from the lytic water, must be biased for TTMetaD to converge fully. To perturb the NTP hydrolysis dynamics to the least extent and to properly focus the MetaD free energy sampling, we also adopt here the recently developed metabasin metadynamics (MBMetaD) to construct a self-limiting bias potential that only applies to the lytic water after its nucleophilic attack of the phosphate of ATP. With these new, state-of-the-art enhanced sampling metadynamics techniques, we present an effective and accurate computational strategy for combining QM/MM molecular dynamics simulation with free energy sampling methodology, including a means to analyze the convergence of the calculations through robust numerical criteria.
Collapse
Affiliation(s)
- Rui Sun
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Olaseni Sode
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - James F Dama
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| |
Collapse
|
102
|
Knott EP, Assi M, Rao SNR, Ghosh M, Pearse DD. Phosphodiesterase Inhibitors as a Therapeutic Approach to Neuroprotection and Repair. Int J Mol Sci 2017; 18:E696. [PMID: 28338622 PMCID: PMC5412282 DOI: 10.3390/ijms18040696] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/10/2017] [Accepted: 03/15/2017] [Indexed: 12/21/2022] Open
Abstract
A wide diversity of perturbations of the central nervous system (CNS) result in structural damage to the neuroarchitecture and cellular defects, which in turn are accompanied by neurological dysfunction and abortive endogenous neurorepair. Altering intracellular signaling pathways involved in inflammation and immune regulation, neural cell death, axon plasticity and remyelination has shown therapeutic benefit in experimental models of neurological disease and trauma. The second messengers, cyclic adenosine monophosphate (cyclic AMP) and cyclic guanosine monophosphate (cyclic GMP), are two such intracellular signaling targets, the elevation of which has produced beneficial cellular effects within a range of CNS pathologies. The only known negative regulators of cyclic nucleotides are a family of enzymes called phosphodiesterases (PDEs) that hydrolyze cyclic nucleotides into adenosine monophosphate (AMP) or guanylate monophosphate (GMP). Herein, we discuss the structure and physiological function as well as the roles PDEs play in pathological processes of the diseased or injured CNS. Further we review the approaches that have been employed therapeutically in experimental paradigms to block PDE expression or activity and in turn elevate cyclic nucleotide levels to mediate neuroprotection or neurorepair as well as discuss both the translational pathway and current limitations in moving new PDE-targeted therapies to the clinic.
Collapse
Affiliation(s)
- Eric P Knott
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA.
| | - Mazen Assi
- The Miami Project to Cure Paralysis, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
| | - Sudheendra N R Rao
- The Miami Project to Cure Paralysis, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
| | - Mousumi Ghosh
- The Miami Project to Cure Paralysis, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
- The Department of Neurological Surgery, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
| | - Damien D Pearse
- The Miami Project to Cure Paralysis, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
- The Department of Neurological Surgery, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
- The Neuroscience Program, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
- The Interdisciplinary Stem Cell Institute, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
- Bruce Wayne Carter Department of Veterans Affairs Medical Center, Miami, FL 33136, USA.
| |
Collapse
|
103
|
Tunc-Ozdemir M, Jones AM. Ligand-induced dynamics of heterotrimeric G protein-coupled receptor-like kinase complexes. PLoS One 2017; 12:e0171854. [PMID: 28187200 PMCID: PMC5302818 DOI: 10.1371/journal.pone.0171854] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/26/2017] [Indexed: 02/08/2023] Open
Abstract
Background Arabidopsis, 7-transmembrane Regulator of G signaling protein 1 (AtRGS1) modulates canonical G protein signaling by promoting the inactive state of heterotrimeric G protein complex on the plasma membrane. It is known that plant leucine-rich repeat receptor–like kinases (LRR RLKs) phosphorylate AtRGS1 in vitro but little is known about the in vivo interaction, molecular dynamics, or the cellular consequences of this interaction. Methods Therefore, a subset of the known RLKs that phosphorylate AtRGS1 were selected for elucidation, namely, BAK1, BIR1, FLS2. Several microscopies for both static and dynamic protein-protein interactions were used to follow in vivo interactions between the RLKs and AtRGS1 after the presentation of the Pathogen-associated Molecular Pattern, Flagellin 22 (Flg22). These microscopies included Förster Resonance Energy Transfer, Bimolecular Fluoresence Complementation, and Cross Number and Brightness Fluorescence Correlation Spectroscopy. In addition, reactive oxygen species and calcium changes in living cells were quantitated using luminometry and R-GECO1 microscopy. Results The LRR RLKs BAK1 and BIR1, interact with AtRGS1 at the plasma membrane. The RLK ligand flg22 sets BAK1 in motion toward AtRGS1 and BIR1 away, both returning to the baseline orientations by 10 minutes. The C-terminal tail of AtRGS1 is important for the interaction with BAK1 and for the tempo of the AtRGS1/BIR1 dynamics. This window of time corresponds to the flg22-induced transient production of reactive oxygen species and calcium release which are both attenuated in the rgs1 and the bak1 null mutants. Conclusions A temporal model of these interactions is proposed. flg22 binding induces nearly instantaneous dimerization between FLS2 and BAK1. Phosphorylated BAK1 interacts with and enables AtRGS1 to move away from BIR1 and AtRGS1 becomes phosphorylated leading to its endocytosis thus leading to de-repression by permitting AtGPA1 to exchange GDP for GTP. Finally, the G protein complex becomes dissociated thus AGB1 interacts with its effector proteins leading to changes in reactive oxygen species and calcium.
Collapse
Affiliation(s)
- Meral Tunc-Ozdemir
- Department of Biology University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Alan M. Jones
- Department of Biology University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
104
|
Zhang T, Xu P, Wang W, Wang S, Caruana JC, Yang HQ, Lian H. Arabidopsis G-Protein β Subunit AGB1 Interacts with BES1 to Regulate Brassinosteroid Signaling and Cell Elongation. FRONTIERS IN PLANT SCIENCE 2017; 8:2225. [PMID: 29375601 PMCID: PMC5767185 DOI: 10.3389/fpls.2017.02225] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/18/2017] [Indexed: 05/07/2023]
Abstract
In Arabidopsis, brassinosteroids (BR) are major growth-promoting hormones, which integrate with the heterotrimeric guanine nucleotide-binding protein (G-protein) signals and cooperatively modulate cell division and elongation. However, the mechanisms of interaction between BR and G-protein are not well understood. Here, we show that the G-protein β subunit AGB1 directly interacts with the BR transcription factor BES1 in vitro and in vivo. An AGB1-null mutant, agb1-2, displays BR hyposensitivity and brassinazole (BRZ, BR biosynthesis inhibitor) hypersensitivity, which suggests that AGB1 positively mediates the BR signaling pathway. Moreover, we demonstrate that AGB1 synergistically regulates expression of BES1 target genes, including the BR biosynthesis genes CPD and DWF4 and the SAUR family genes required for promoting cell elongation. Further, Western blot analysis of BES1 phosphorylation states indicates that the interaction between AGB1 and BES1 alters the phosphorylation status of BES1 and increases the ratio of dephosphorylated to phosphorylated BES1, which leads to accumulation of dephosphorylated BES1 in the nucleus. Finally, AGB1 promotes BES1 binding to BR target genes and stimulates the transcriptional activity of BES1. Taken together, our results demonstrate that AGB1 positively regulates cell elongation by affecting the phosphorylation status and transcriptional activity of BES1.
Collapse
Affiliation(s)
- Ting Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Pengbo Xu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenxiu Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Sheng Wang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Julie C. Caruana
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
| | - Hong-Quan Yang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hongli Lian
- Key Laboratory of Urban Agriculture (South), School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Hongli Lian,
| |
Collapse
|
105
|
Vithani N, Batra S, Prakash B, Nair NN. Elucidating the GTP Hydrolysis Mechanism in FeoB: A Hydrophobic Amino-Acid Substituted GTPase. ACS Catal 2016. [DOI: 10.1021/acscatal.6b03365] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Neha Vithani
- Department
of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Sahil Batra
- Department
of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Balaji Prakash
- Department
of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysore, 570020, India
| | - Nisanth N. Nair
- Department
of Chemistry, Indian Institute of Technology, Kanpur 208016, India
| |
Collapse
|
106
|
Kant R, Zeng B, Thomas CJ, Bothner B, Sprang SR. Ric-8A, a G protein chaperone with nucleotide exchange activity induces long-range secondary structure changes in Gα. eLife 2016; 5. [PMID: 28008853 PMCID: PMC5182059 DOI: 10.7554/elife.19238] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/22/2016] [Indexed: 11/24/2022] Open
Abstract
Cytosolic Ric-8A has guanine nucleotide exchange factor (GEF) activity and is a chaperone for several classes of heterotrimeric G protein α subunits in vertebrates. Using Hydrogen-Deuterium Exchange-Mass Spectrometry (HDX-MS) we show that Ric-8A disrupts the secondary structure of the Gα Ras-like domain that girds the guanine nucleotide-binding site, and destabilizes the interface between the Gαi1 Ras and helical domains, allowing domain separation and nucleotide release. These changes are largely reversed upon binding GTP and dissociation of Ric-8A. HDX-MS identifies a potential Gα interaction site in Ric-8A. Alanine scanning reveals residues crucial for GEF activity within that sequence. HDX confirms that, like G protein-coupled receptors (GPCRs), Ric-8A binds the C-terminus of Gα. In contrast to GPCRs, Ric-8A interacts with Switches I and II of Gα and possibly at the Gα domain interface. These extensive interactions provide both allosteric and direct catalysis of GDP unbinding and release and GTP binding. DOI:http://dx.doi.org/10.7554/eLife.19238.001
Collapse
Affiliation(s)
- Ravi Kant
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, United States
| | - Baisen Zeng
- Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, United States
| | - Celestine J Thomas
- Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, United States
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, United States
| | - Stephen R Sprang
- Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, United States
| |
Collapse
|
107
|
Gupta S, Chakraborty S, Vij R, Auerbach A. A mechanism for acetylcholine receptor gating based on structure, coupling, phi, and flip. J Gen Physiol 2016; 149:85-103. [PMID: 27932572 PMCID: PMC5217088 DOI: 10.1085/jgp.201611673] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/20/2016] [Accepted: 11/10/2016] [Indexed: 01/29/2023] Open
Abstract
Gupta et al. use single-channel electrophysiology to investigate the gating mechanism of acetylcholine receptor ion channels. They propose that channel opening starts at the M2–M3 linker and ligand-binding sites and proceeds through four brief intermediate conformations before ending with the collapse of a gate bubble. Nicotinic acetylcholine receptors are allosteric proteins that generate membrane currents by isomerizing (“gating”) between resting and active conformations under the influence of neurotransmitters. Here, to explore the mechanisms that link the transmitter-binding sites (TBSs) with the distant gate, we use mutant cycle analyses to measure coupling between residue pairs, phi value analyses to sequence domain rearrangements, and current simulations to reproduce a microsecond shut component (“flip”) apparent in single-channel recordings. Significant interactions between amino acids separated by >15 Å are rare; an exception is between the αM2–M3 linkers and the TBSs that are ∼30 Å apart. Linker residues also make significant, local interactions within and between subunits. Phi value analyses indicate that without agonists, the linker is the first region in the protein to reach the gating transition state. Together, the phi pattern and flip component suggest that a complete, resting↔active allosteric transition involves passage through four brief intermediate states, with brief shut events arising from sojourns in all or a subset. We derive energy landscapes for gating with and without agonists, and propose a structure-based model in which resting→active starts with spontaneous rearrangements of the M2–M3 linkers and TBSs. These conformational changes stabilize a twisted extracellular domain to promote transmembrane helix tilting, gate dilation, and the formation of a “bubble” that collapses to initiate ion conduction. The energy landscapes suggest that twisting is the most energetically unfavorable step in the resting→active conformational change and that the rate-limiting step in the reverse process is bubble formation.
Collapse
Affiliation(s)
- Shaweta Gupta
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| | - Srirupa Chakraborty
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| | - Ridhima Vij
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| | - Anthony Auerbach
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| |
Collapse
|
108
|
Electric-field-stimulated protein mechanics. Nature 2016; 540:400-405. [PMID: 27926732 DOI: 10.1038/nature20571] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 10/24/2016] [Indexed: 12/17/2022]
Abstract
The internal mechanics of proteins-the coordinated motions of amino acids and the pattern of forces constraining these motions-connects protein structure to function. Here we describe a new method combining the application of strong electric field pulses to protein crystals with time-resolved X-ray crystallography to observe conformational changes in spatial and temporal detail. Using a human PDZ domain (LNX2PDZ2) as a model system, we show that protein crystals tolerate electric field pulses strong enough to drive concerted motions on the sub-microsecond timescale. The induced motions are subtle, involve diverse physical mechanisms, and occur throughout the protein structure. The global pattern of electric-field-induced motions is consistent with both local and allosteric conformational changes naturally induced by ligand binding, including at conserved functional sites in the PDZ domain family. This work lays the foundation for comprehensive experimental study of the mechanical basis of protein function.
Collapse
|
109
|
Mechanism of the intrinsic arginine finger in heterotrimeric G proteins. Proc Natl Acad Sci U S A 2016; 113:E8041-E8050. [PMID: 27911799 DOI: 10.1073/pnas.1612394113] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterotrimeric G proteins are crucial molecular switches that maintain a large number of physiological processes in cells. The signal is encoded into surface alterations of the Gα subunit that carries GTP in its active state and GDP in its inactive state. The ability of the Gα subunit to hydrolyze GTP is essential for signal termination. Regulator of G protein signaling (RGS) proteins accelerates this process. A key player in this catalyzed reaction is an arginine residue, Arg178 in Gαi1, which is already an intrinsic part of the catalytic center in Gα in contrast to small GTPases, at which the corresponding GTPase-activating protein (GAP) provides the arginine "finger." We applied time-resolved FTIR spectroscopy in combination with isotopic labeling and site-directed mutagenesis to reveal the molecular mechanism, especially of the role of Arg178 in the intrinsic Gαi1 mechanism and the RGS4-catalyzed mechanism. Complementary biomolecular simulations (molecular mechanics with molecular dynamics and coupled quantum mechanics/molecular mechanics) were performed. Our findings show that Arg178 is bound to γ-GTP for the intrinsic Gαi1 mechanism and pushed toward a bidentate α-γ-GTP coordination for the Gαi1·RGS4 mechanism. This movement induces a charge shift toward β-GTP, increases the planarity of γ-GTP, and thereby catalyzes the hydrolysis.
Collapse
|
110
|
Mahoney JP, Sunahara RK. Mechanistic insights into GPCR-G protein interactions. Curr Opin Struct Biol 2016; 41:247-254. [PMID: 27871057 DOI: 10.1016/j.sbi.2016.11.005] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/24/2016] [Accepted: 11/04/2016] [Indexed: 01/24/2023]
Abstract
G protein-coupled receptors (GPCRs) respond to extracellular stimuli and interact with several intracellular binding partners to elicit cellular responses, including heterotrimeric G proteins. Recent structural and biophysical studies have highlighted the dynamic nature of GPCRs and G proteins and have identified specific conformational changes important for receptor-mediated nucleotide exchange on Gα. While domain separation within Gα is necessary for GDP release, opening the inter-domain interface is insufficient to stimulate nucleotide exchange. Rather, an activated receptor promotes GDP release by allosterically disrupting the nucleotide-binding site via interactions with the Gα N-termini and C-termini. Highlighting the allosteric nature of GPCRs, recent studies suggest that agonist binding alone poorly stabilizes an active conformation of several receptors. Rather, full stabilization of the receptor in an active state requires formation of the agonist-receptor-G protein ternary complex. In turn, nucleotide-free Gα is able to stabilize conformational changes around the receptor's agonist-binding site to enhance agonist affinity.
Collapse
Affiliation(s)
- Jacob P Mahoney
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Roger K Sunahara
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, United States.
| |
Collapse
|
111
|
Cetin M, Evenson WE, Gross GG, Jalali-Yazdi F, Krieger D, Arnold D, Takahashi TT, Roberts RW. RasIns: Genetically Encoded Intrabodies of Activated Ras Proteins. J Mol Biol 2016; 429:562-573. [PMID: 27865780 DOI: 10.1016/j.jmb.2016.11.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 11/11/2016] [Accepted: 11/12/2016] [Indexed: 01/11/2023]
Abstract
K- and H-Ras are the most commonly mutated genes in human tumors and are critical for conferring and maintaining the oncogenic phenotype in tumors with poor prognoses. Here, we design genetically encoded antibody-like ligands (intrabodies) that recognize active, GTP-bound K- and H-Ras. These ligands, which use the 10th domain of human fibronectin as their scaffold, are stable inside the cells and when fused with a fluorescent protein label, the constitutively active G12V mutant H-Ras. Primary selection of ligands against Ras with mRNA display resulted in an intrabody (termed RasIn1) that binds with a KD of 2.1μM to H-Ras(G12V) (GTP), excellent state selectivity, and remarkable specificity for K- and H-Ras. RasIn1 recognizes residues in the Switch I region of Ras, similar to Raf-RBD, and competes with Raf-RBD for binding. An affinity maturation selection based on RasIn1 resulted in RasIn2, which binds with a KD of 120nM and also retains excellent state selectivity. Both of these intrabodies colocalize with H-Ras, K-Ras, and G12V mutants inside the cells, providing new potential tools to monitor and modulate Ras-mediated signaling. Finally, RasIn1 and Rasin2 both display selectivity for the G12V mutants as compared with wild-type Ras providing a potential route for mutant selective recognition of Ras.
Collapse
Affiliation(s)
- Mehmet Cetin
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - William E Evenson
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Garrett G Gross
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Farzad Jalali-Yazdi
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Daniel Krieger
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Don Arnold
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Terry T Takahashi
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Richard W Roberts
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA.
| |
Collapse
|
112
|
Charpentier TH, Waldo GL, Lowery-Gionta EG, Krajewski K, Strahl BD, Kash TL, Harden TK, Sondek J. Potent and Selective Peptide-based Inhibition of the G Protein Gαq. J Biol Chem 2016; 291:25608-25616. [PMID: 27742837 DOI: 10.1074/jbc.m116.740407] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 10/13/2016] [Indexed: 11/06/2022] Open
Abstract
In contrast to G protein-coupled receptors, for which chemical and peptidic inhibitors have been extensively explored, few compounds are available that directly modulate heterotrimeric G proteins. Active Gαq binds its two major classes of effectors, the phospholipase C (PLC)-β isozymes and Rho guanine nucleotide exchange factors (RhoGEFs) related to Trio, in a strikingly similar fashion: a continuous helix-turn-helix of the effectors engages Gαq within its canonical binding site consisting of a groove formed between switch II and helix α3. This information was exploited to synthesize peptides that bound active Gαq in vitro with affinities similar to full-length effectors and directly competed with effectors for engagement of Gαq A representative peptide was specific for active Gαq because it did not bind inactive Gαq or other classes of active Gα subunits and did not inhibit the activation of PLC-β3 by Gβ1γ2 In contrast, the peptide robustly prevented activation of PLC-β3 or p63RhoGEF by Gαq; it also prevented G protein-coupled receptor-promoted neuronal depolarization downstream of Gαq in the mouse prefrontal cortex. Moreover, a genetically encoded form of this peptide flanked by fluorescent proteins inhibited Gαq-dependent activation of PLC-β3 at least as effectively as a dominant-negative form of full-length PLC-β3. These attributes suggest that related, cell-penetrating peptides should effectively inhibit active Gαq in cells and that these and genetically encoded sequences may find application as molecular probes, drug leads, and biosensors to monitor the spatiotemporal activation of Gαq in cells.
Collapse
Affiliation(s)
- Thomas H Charpentier
- From the Departments of Pharmacology and.,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | | | | | - Krzysztof Krajewski
- Biochemistry and Biophysics.,High-Throughput Peptide Synthesis and Array Facility, and
| | - Brian D Strahl
- Biochemistry and Biophysics.,High-Throughput Peptide Synthesis and Array Facility, and
| | | | | | - John Sondek
- From the Departments of Pharmacology and .,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599.,Biochemistry and Biophysics
| |
Collapse
|
113
|
Carpenter B, Tate CG. Engineering a minimal G protein to facilitate crystallisation of G protein-coupled receptors in their active conformation. Protein Eng Des Sel 2016; 29:583-594. [PMID: 27672048 PMCID: PMC5181381 DOI: 10.1093/protein/gzw049] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/01/2016] [Accepted: 08/23/2016] [Indexed: 11/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) modulate cytoplasmic signalling in response to extracellular stimuli, and are important therapeutic targets in a wide range of diseases. Structure determination of GPCRs in all activation states is important to elucidate the precise mechanism of signal transduction and to facilitate optimal drug design. However, due to their inherent instability, crystallisation of GPCRs in complex with cytoplasmic signalling proteins, such as heterotrimeric G proteins and β-arrestins, has proved challenging. Here, we describe the design of a minimal G protein, mini-Gs, which is composed solely of the GTPase domain from the adenylate cyclase stimulating G protein Gs. Mini-Gs is a small, soluble protein, which efficiently couples GPCRs in the absence of Gβγ subunits. We engineered mini-Gs, using rational design mutagenesis, to form a stable complex with detergent-solubilised β1-adrenergic receptor (β1AR). Mini G proteins induce similar pharmacological and structural changes in GPCRs as heterotrimeric G proteins, but eliminate many of the problems associated with crystallisation of these complexes, specifically their large size, conformational dynamics and instability in detergent. They are therefore novel tools, which will facilitate the biochemical and structural characterisation of GPCRs in their active conformation.
Collapse
Affiliation(s)
- Byron Carpenter
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus , Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus , Francis Crick Avenue, Cambridge CB2 0QH, UK
| |
Collapse
|
114
|
Urano D, Maruta N, Trusov Y, Stoian R, Wu Q, Liang Y, Jaiswal DK, Thung L, Jackson D, Botella JR, Jones AM. Saltational evolution of the heterotrimeric G protein signaling mechanisms in the plant kingdom. Sci Signal 2016; 9:ra93. [DOI: 10.1126/scisignal.aaf9558] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
115
|
Chang DD, Colecraft HM. Rad and Rem are non-canonical G-proteins with respect to the regulatory role of guanine nucleotide binding in Ca(V)1.2 channel regulation. J Physiol 2016; 593:5075-90. [PMID: 26426338 DOI: 10.1113/jp270889] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/27/2015] [Indexed: 12/15/2022] Open
Abstract
Rad and Rem are Ras-like G-proteins linked to diverse cardiovascular functions and pathophysiology. Understanding how Rad and Rem are regulated is important for deepened insights into their pathophysiological roles. As in other Ras-like G-proteins, Rad and Rem contain a conserved guanine-nucleotide binding domain (G-domain). Canonically, G-domains are key control modules, functioning as nucleotide-regulated switches of G-protein activity. Whether Rad and Rem G-domains conform to this canonical paradigm is ambiguous. Here, we used multiple functional measurements in HEK293 cells and cardiomyocytes (Ca(V)1.2 currents, Ca(2+) transients, Ca(V)β binding) as biosensors to probe the role of the G-domain in regulation of Rad and Rem function. We utilized Rad(S105N) and Rem(T94N), which are the cognate mutants to Ras(S17N), a dominant-negative variant of Ras that displays decreased nucleotide binding affinity. In HEK293 cells, over-expression of either Rad(S105N) or Rem(T94N) strongly inhibited reconstituted Ca(V)1.2 currents to the same extent as their wild-type (wt) counterparts, contrasting with reports that Rad(S105N) is functionally inert in HEK293 cells. Adenovirus-mediated expression of either wt Rad or Rad(S105N) in cardiomyocytes dramatically blocked L-type calcium current (I(Ca,L)) and inhibited Ca(2+)-induced Ca(2+) release, contradicting reports that Rad(S105N) acts as a dominant negative in heart. By contrast, Rem(T94N) was significantly less effective than wt Rem at inhibiting I(Ca,L) and Ca(2+) transients in cardiomyocytes. FRET analyses in cardiomyocytes revealed that both Rad(S105N) and Rem(T94N) had moderately reduced binding affinity for Ca(V)βs relative to their wt counterparts. The results indicate Rad and Rem are non-canonical G-proteins with respect to the regulatory role of their G-domain in Ca(V)1.2 regulation.
Collapse
Affiliation(s)
- Donald D Chang
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Henry M Colecraft
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
| |
Collapse
|
116
|
Young A, Dandekar U, Pan C, Sader A, Zheng JJ, Lewis RA, Farber DB. GNAI3: Another Candidate Gene to Screen in Persons with Ocular Albinism. PLoS One 2016; 11:e0162273. [PMID: 27607449 PMCID: PMC5015898 DOI: 10.1371/journal.pone.0162273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 08/21/2016] [Indexed: 11/18/2022] Open
Abstract
Ocular albinism type 1 (OA), caused by mutations in the OA1 gene, encodes a G-protein coupled receptor, OA1, localized in melanosomal membranes of the retinal pigment epithelium (RPE). This disorder is characterized by both RPE macro-melanosomes and abnormal decussation of ganglion cell axons at the brain's optic chiasm. We demonstrated previously that Oa1 specifically activates Gαi3, which also signals in the Oa1 transduction pathway that regulates melanosomal biogenesis. In this study, we screened the human Gαi3 gene, GNAI3, in DNA samples from 26 patients who had all clinical characteristics of OA but in whom a specific mutation in the OA1 gene had not been found, and in 6 normal control individuals. Using the Agilent HaloPlex Target Enrichment System and next-generation sequencing (NGS) on the Illumina MiSeq platform, we identified 518 variants after rigorous filtering. Many of these variants were corroborated by Sanger sequencing. Overall, 98.8% coverage of the GNAI3 gene was obtained by the HaloPlex amplicons. Of all variants, 6 non-synonymous and 3 synonymous were in exons, 41 in a non-coding exon embedded in the 3' untranslated region (UTR), 6 in the 5' UTR, and 462 in introns. These variants included novel SNVs, insertions, deletions, and a frameshift mutation. All were found in at least one patient but none in control samples. Using computational methods, we modeled the GNAI3 protein and its non-synonymous exonic mutations and determined that several of these may be the cause of disease in the patients studied. Thus, we have identified GNAI3 as a second gene possibly responsible for X-linked ocular albinism.
Collapse
Affiliation(s)
- Alejandra Young
- Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States of America
- Molecular Biology Institute, UCLA, Los Angeles, CA, United States of America
| | - Uma Dandekar
- UCLA-GenoSeq Core, UCLA, Los Angeles, CA, United States of America
| | - Calvin Pan
- UCLA-GenoSeq Core, UCLA, Los Angeles, CA, United States of America
| | - Avery Sader
- Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States of America
| | - Jie J. Zheng
- Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States of America
| | - Richard A. Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Debora B. Farber
- Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States of America
- Molecular Biology Institute, UCLA, Los Angeles, CA, United States of America
- Brain Research Institute, UCLA, Los Angeles, CA, United States of America
- * E-mail:
| |
Collapse
|
117
|
Heterologous Expression of Der Homologs in an Escherichia coli der Mutant and Their Functional Complementation. J Bacteriol 2016; 198:2284-96. [PMID: 27297882 DOI: 10.1128/jb.00384-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/03/2016] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED The unique Escherichia coli GTPase Der (double Era-like GTPase), which contains tandemly repeated GTP-binding domains, has been shown to play an essential role in 50S ribosomal subunit biogenesis. The depletion of Der results in the accumulation of precursors of 50S ribosomal subunits that are structurally unstable at low Mg(2+) concentrations. Der homologs are ubiquitously found in eubacteria. Conversely, very few are conserved in eukaryotes, and none is conserved in archaea. In the present study, to verify their conserved role in bacterial 50S ribosomal subunit biogenesis, we cloned Der homologs from two gammaproteobacteria, Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium; two pathogenic bacteria, Staphylococcus aureus and Neisseria gonorrhoeae; and the extremophile Deinococcus radiodurans and then evaluated whether they could functionally complement the E. coli der-null phenotype. Only K. pneumoniae and S Typhimurium Der proteins enabled the E. coli der-null strain to grow under nonpermissive conditions. Sucrose density gradient experiments revealed that the expression of K. pneumoniae and S Typhimurium Der proteins rescued the structural instability of 50S ribosomal subunits, which was caused by E. coli Der depletion. To determine what allows their complementation, we constructed Der chimeras. We found that only Der chimeras harboring both the linker and long C-terminal regions could reverse the growth defects of the der-null strain. Our findings suggest that ubiquitously conserved essential GTPase Der is involved in 50S ribosomal subunit biosynthesis in various bacteria and that the linker and C-terminal regions may participate in species-specific recognition or interaction with the 50S ribosomal subunit. IMPORTANCE In Escherichia coli, Der (double Era-like GTPase) is an essential GTPase that is important for the production of mature 50S ribosomal subunits. However, to date, its precise role in ribosome biogenesis has not been clarified. In this study, we used five Der homologs from gammaproteobacteria, pathogenic bacteria, and an extremophile to elucidate their conserved function in 50S ribosomal subunit biogenesis. Among them, Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium Der homologs implicated the participation of Der in ribosome assembly in E. coli Our results show that the linker and C-terminal regions of Der homologs are correlated with its functional complementation in E. coli der mutants, suggesting that they are involved in species-specific recognition or interaction with 50S ribosomal subunits.
Collapse
|
118
|
Syrovatkina V, Alegre KO, Dey R, Huang XY. Regulation, Signaling, and Physiological Functions of G-Proteins. J Mol Biol 2016; 428:3850-68. [PMID: 27515397 DOI: 10.1016/j.jmb.2016.08.002] [Citation(s) in RCA: 265] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 07/31/2016] [Accepted: 08/03/2016] [Indexed: 12/31/2022]
Abstract
Heterotrimeric guanine-nucleotide-binding regulatory proteins (G-proteins) mainly relay the information from G-protein-coupled receptors (GPCRs) on the plasma membrane to the inside of cells to regulate various biochemical functions. Depending on the targeted cell types, tissues, and organs, these signals modulate diverse physiological functions. The basic schemes of heterotrimeric G-proteins have been outlined. In this review, we briefly summarize what is known about the regulation, signaling, and physiological functions of G-proteins. We then focus on a few less explored areas such as the regulation of G-proteins by non-GPCRs and the physiological functions of G-proteins that cannot be easily explained by the known G-protein signaling pathways. There are new signaling pathways and physiological functions for G-proteins to be discovered and further interrogated. With the advancements in structural and computational biological techniques, we are closer to having a better understanding of how G-proteins are regulated and of the specificity of G-protein interactions with their regulators.
Collapse
Affiliation(s)
- Viktoriya Syrovatkina
- Department of Physiology and Biophysics, Weill Cornell Medical College, of Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Kamela O Alegre
- Department of Physiology and Biophysics, Weill Cornell Medical College, of Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Raja Dey
- Department of Physiology and Biophysics, Weill Cornell Medical College, of Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Xin-Yun Huang
- Department of Physiology and Biophysics, Weill Cornell Medical College, of Cornell University, 1300 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
119
|
Lemmon MA, Freed DM, Schlessinger J, Kiyatkin A. The Dark Side of Cell Signaling: Positive Roles for Negative Regulators. Cell 2016; 164:1172-1184. [PMID: 26967284 DOI: 10.1016/j.cell.2016.02.047] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Indexed: 12/12/2022]
Abstract
Cell signaling is dominated by analyzing positive responses to stimuli. Signal activation is balanced by negative regulators that are generally considered to terminate signaling. Rather than exerting only negative effects, however, many such regulators play important roles in enhancing cell-signaling control. Considering responses downstream of selected cell-surface receptors, we discuss how receptor internalization affects signaling specificity and how rapid kinase/phosphatase and GTP/GDP cycles increase responsiveness and allow kinetic proofreading in receptor signaling. We highlight the blurring of distinctions between positive and negative signals, recasting signal termination as the response to a switch-like transition into a new cellular state.
Collapse
Affiliation(s)
- Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, West Haven, CT 06516, USA.
| | - Daniel M Freed
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, West Haven, CT 06516, USA
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, West Haven, CT 06516, USA
| | - Anatoly Kiyatkin
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, West Haven, CT 06516, USA
| |
Collapse
|
120
|
Sprang SR. Invited review: Activation of G proteins by GTP and the mechanism of Gα-catalyzed GTP hydrolysis. Biopolymers 2016; 105:449-62. [PMID: 26996924 PMCID: PMC5319639 DOI: 10.1002/bip.22836] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/11/2016] [Accepted: 03/17/2016] [Indexed: 02/02/2023]
Abstract
This review addresses the regulatory consequences of the binding of GTP to the alpha subunits (Gα) of heterotrimeric G proteins, the reaction mechanism of GTP hydrolysis catalyzed by Gα and the means by which GTPase activating proteins (GAPs) stimulate the GTPase activity of Gα. The high energy of GTP binding is used to restrain and stabilize the conformation of the Gα switch segments, particularly switch II, to afford stable complementary to the surfaces of Gα effectors, while excluding interaction with Gβγ, the regulatory binding partner of GDP-bound Gα. Upon GTP hydrolysis, the energy of these conformational restraints is dissipated and the two switch segments, particularly switch II, become flexible and are able to adopt a conformation suitable for tight binding to Gβγ. Catalytic site pre-organization presents a significant activation energy barrier to Gα GTPase activity. The glutamine residue near the N-terminus of switch II (Glncat ) must adopt a conformation in which it orients and stabilizes the γ phosphate and the water nucleophile for an in-line attack. The transition state is probably loose with dissociative character; phosphoryl transfer may be concerted. The catalytic arginine in switch I (Argcat ), together with amide hydrogen bonds from the phosphate binding loop, stabilize charge at the β-γ bridge oxygen of the leaving group. GAPs that harbor "regulator of protein signaling" (RGS) domains, or structurally unrelated domains within G protein effectors that function as GAPs, accelerate catalysis by stabilizing the pre-transition state for Gα-catalyzed GTP hydrolysis, primarily by restraining Argcat and Glncat to their catalytic conformations. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 449-462, 2016.
Collapse
Affiliation(s)
- Stephen R. Sprang
- Center for Biomolecular Structure and Dynamics, Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, Telephone: (406) 243-6028, Fax: (406) 243-6024,
| |
Collapse
|
121
|
Kaya AI, Lokits AD, Gilbert JA, Iverson TM, Meiler J, Hamm HE. A Conserved Hydrophobic Core in Gαi1 Regulates G Protein Activation and Release from Activated Receptor. J Biol Chem 2016; 291:19674-86. [PMID: 27462082 DOI: 10.1074/jbc.m116.745513] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Indexed: 11/06/2022] Open
Abstract
G protein-coupled receptor-mediated heterotrimeric G protein activation is a major mode of signal transduction in the cell. Previously, we and other groups reported that the α5 helix of Gαi1, especially the hydrophobic interactions in this region, plays a key role during nucleotide release and G protein activation. To further investigate the effect of this hydrophobic core, we disrupted it in Gαi1 by inserting 4 alanine amino acids into the α5 helix between residues Gln(333) and Phe(334) (Ins4A). This extends the length of the α5 helix without disturbing the β6-α5 loop interactions. This mutant has high basal nucleotide exchange activity yet no receptor-mediated activation of nucleotide exchange. By using structural approaches, we show that this mutant loses critical hydrophobic interactions, leading to significant rearrangements of side chain residues His(57), Phe(189), Phe(191), and Phe(336); it also disturbs the rotation of the α5 helix and the π-π interaction between His(57) and Phe(189) In addition, the insertion mutant abolishes G protein release from the activated receptor after nucleotide binding. Our biochemical and computational data indicate that the interactions between α5, α1, and β2-β3 are not only vital for GDP release during G protein activation, but they are also necessary for proper GTP binding (or GDP rebinding). Thus, our studies suggest that this hydrophobic interface is critical for accurate rearrangement of the α5 helix for G protein release from the receptor after GTP binding.
Collapse
Affiliation(s)
| | | | | | - T M Iverson
- From the Departments of Pharmacology, Biochemistry, and
| | - Jens Meiler
- From the Departments of Pharmacology, Chemistry, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | | |
Collapse
|
122
|
Allosteric coupling from G protein to the agonist-binding pocket in GPCRs. Nature 2016; 535:182-6. [PMID: 27362234 PMCID: PMC5702553 DOI: 10.1038/nature18324] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 05/13/2016] [Indexed: 12/17/2022]
Abstract
G protein-coupled receptors (GPCRs) remain the primary conduit by which cells detect environmental stimuli and communicate with each other1. Upon activation by extracellular agonists, these seven transmembrane domain (7TM)-containing receptors interact with heterotrimeric G proteins to regulate downstream second messenger and/or protein kinase cascades1. Crystallographic evidence from a prototypic GPCR, the β2-adrenergic receptor (β2AR), in complex with its cognate G protein, Gs, has provided a model for how agonist binding promotes conformational changes that propagate through the GPCR and into the nucleotide binding pocket of the G protein α-subunit to catalyze GDP release, the key step required for GTP binding and activation of G proteins2. The structure also offers hints on how G protein binding may, in turn, allosterically influence ligand binding. Here we provide functional evidence that G protein coupling to β2AR stabilizes a ‘closed’ receptor conformation characterized by restricted access to and egress from the hormone binding site. Surprisingly, the effects of G protein on the hormone binding site can be observed in the absence of a bound agonist, where G protein coupling driven by basal receptor activity impedes the association of agonists, partial agonists, antagonists and inverse agonists. The ability of bound ligands to dissociate from the receptor is also hindered, providing a structural explanation for the G protein-mediated enhancement of agonist affinity, which has been observed for many GPCR-G protein pairs. Our studies also suggest that in contrast to agonist binding alone, coupling of a G protein in the absence of an agonist stabilizes large structural changes in a GPCR. The effects of nucleotide-free G protein on ligand binding kinetics are shared by other members of the superfamily of GPCRs, suggesting that a common mechanism may underlie G protein-mediated enhancement of agonist affinity.
Collapse
|
123
|
Rivoire O, Reynolds KA, Ranganathan R. Evolution-Based Functional Decomposition of Proteins. PLoS Comput Biol 2016; 12:e1004817. [PMID: 27254668 PMCID: PMC4890866 DOI: 10.1371/journal.pcbi.1004817] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 02/15/2016] [Indexed: 11/24/2022] Open
Abstract
The essential biological properties of proteins—folding, biochemical activities, and the capacity to adapt—arise from the global pattern of interactions between amino acid residues. The statistical coupling analysis (SCA) is an approach to defining this pattern that involves the study of amino acid coevolution in an ensemble of sequences comprising a protein family. This approach indicates a functional architecture within proteins in which the basic units are coupled networks of amino acids termed sectors. This evolution-based decomposition has potential for new understandings of the structural basis for protein function. To facilitate its usage, we present here the principles and practice of the SCA and introduce new methods for sector analysis in a python-based software package (pySCA). We show that the pattern of amino acid interactions within sectors is linked to the divergence of functional lineages in a multiple sequence alignment—a model for how sector properties might be differentially tuned in members of a protein family. This work provides new tools for studying proteins and for generally testing the concept of sectors as the principal units of function and adaptive variation. Proteins display the ability to fold, to carry out complex biochemical reactions, and to be adaptive to changing conditions of selection—the essential characteristics contributing to organismal fitness. A major goal is to understand how these properties emerge from the global pattern of interactions between amino acid residues. Here, we describe the principles and implementation of the statistical coupling analysis (SCA), a method to reveal this pattern through analysis of coevolution between amino acids in an ensemble of homologous sequences. The basic result is a decomposition of protein structures into groups of contiguous amino acids called “sectors” which have been linked to conserved functional properties. This work provides conceptual and practical tools for sector analysis in any sufficiently well-represented protein family, and represents a necessary basis for broadly testing the concept of protein sectors.
Collapse
Affiliation(s)
- Olivier Rivoire
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, Grenoble, France
| | - Kimberly A. Reynolds
- The Green Center for Systems Biology, and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Rama Ranganathan
- The Green Center for Systems Biology, and Departments of Biophysics and Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
| |
Collapse
|
124
|
Abstract
SUMMARYCells must respond to a diverse, complex, and ever-changing mix of signals, using a fairly limited set of parts. Changes in protein level, protein localization, protein activity, and protein-protein interactions are critical aspects of signal transduction, allowing cells to respond highly specifically to a nearly limitless set of cues and also to vary the sensitivity, duration, and dynamics of the response. Signal-dependent changes in levels of gene expression and protein synthesis play an important role in regulation of protein levels, whereas posttranslational modifications of proteins regulate their degradation, localization, and functional interactions. Protein ubiquitylation, for example, can direct proteins to the proteasome for degradation or provide a signal that regulates their interactions and/or location within the cell. Similarly, protein phosphorylation by specific kinases is a key mechanism for augmenting protein activity and relaying signals to other proteins that possess domains that recognize the phosphorylated residues.
Collapse
Affiliation(s)
- Michael J Lee
- David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Michael B Yaffe
- David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| |
Collapse
|
125
|
Tunc-Ozdemir M, Urano D, Jaiswal DK, Clouse SD, Jones AM. Direct Modulation of Heterotrimeric G Protein-coupled Signaling by a Receptor Kinase Complex. J Biol Chem 2016; 291:13918-13925. [PMID: 27235398 DOI: 10.1074/jbc.c116.736702] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Indexed: 01/17/2023] Open
Abstract
Plants and some protists have heterotrimeric G protein complexes that activate spontaneously without canonical G protein-coupled receptors (GPCRs). In Arabidopsis, the sole 7-transmembrane regulator of G protein signaling 1 (AtRGS1) modulates the G protein complex by keeping it in the resting state (GDP-bound). However, it remains unknown how a myriad of biological responses is achieved with a single G protein modulator. We propose that in complete contrast to G protein activation in animals, plant leucine-rich repeat receptor-like kinases (LRR RLKs), not GPCRs, provide this discrimination through phosphorylation of AtRGS1 in a ligand-dependent manner. G protein signaling is directly activated by the pathogen-associated molecular pattern flagellin peptide 22 through its LRR RLK, FLS2, and co-receptor BAK1.
Collapse
Affiliation(s)
- Meral Tunc-Ozdemir
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Daisuke Urano
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Dinesh Kumar Jaiswal
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Steven D Clouse
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina 27695-7609
| | - Alan M Jones
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599; Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599.
| |
Collapse
|
126
|
Guilfoyle AP, Deshpande CN, Font Sadurni J, Ash MR, Tourle S, Schenk G, Maher MJ, Jormakka M. A GTPase chimera illustrates an uncoupled nucleotide affinity and release rate, providing insight into the activation mechanism. Biophys J 2016; 107:L45-L48. [PMID: 25517170 DOI: 10.1016/j.bpj.2014.10.064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/27/2014] [Accepted: 10/29/2014] [Indexed: 11/29/2022] Open
Abstract
The release of GDP from GTPases signals the initiation of a GTPase cycle, where the association of GTP triggers conformational changes promoting binding of downstream effector molecules. Studies have implicated the nucleotide-binding G5 loop to be involved in the GDP release mechanism. For example, biophysical studies on both the eukaryotic Gα proteins and the GTPase domain (NFeoB) of prokaryotic FeoB proteins have revealed conformational changes in the G5 loop that accompany nucleotide binding and release. However, it is unclear whether this conformational change in the G5 loop is a prerequisite for GDP release, or, alternatively, the movement is a consequence of release. To gain additional insight into the sequence of events leading to GDP release, we have created a chimeric protein comprised of Escherichia coli NFeoB and the G5 loop from the human Giα1 protein. The protein chimera retains GTPase activity at a similar level to wild-type NFeoB, and structural analyses of the nucleotide-free and GDP-bound proteins show that the G5 loop adopts conformations analogous to that of the human nucleotide-bound Giα1 protein in both states. Interestingly, isothermal titration calorimetry and stopped-flow kinetic analyses reveal uncoupled nucleotide affinity and release rates, supporting a model where G5 loop movement promotes nucleotide release.
Collapse
Affiliation(s)
- Amy P Guilfoyle
- Structural Biology Program, Centenary Institute, Sydney, New South Wales, Australia; Faculty of Medicine, Central Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Chandrika N Deshpande
- Structural Biology Program, Centenary Institute, Sydney, New South Wales, Australia; Faculty of Medicine, Central Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Josep Font Sadurni
- Structural Biology Program, Centenary Institute, Sydney, New South Wales, Australia; Faculty of Medicine, Central Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Miriam-Rose Ash
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Samuel Tourle
- Structural Biology Program, Centenary Institute, Sydney, New South Wales, Australia; Faculty of Medicine, Central Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Megan J Maher
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.
| | - Mika Jormakka
- Structural Biology Program, Centenary Institute, Sydney, New South Wales, Australia; Faculty of Medicine, Central Clinical School, University of Sydney, Sydney, New South Wales, Australia.
| |
Collapse
|
127
|
Puckerin AA, Chang DD, Subramanyam P, Colecraft HM. Similar molecular determinants on Rem mediate two distinct modes of inhibition of Ca V1.2 channels. Channels (Austin) 2016; 10:379-394. [PMID: 27115600 PMCID: PMC4988437 DOI: 10.1080/19336950.2016.1180489] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Rad/Rem/Rem2/Gem (RGK) proteins are Ras-like GTPases that potently inhibit all high-voltage-gated calcium (CaV1/CaV2) channels and are, thus, well-positioned to tune diverse physiological processes. Understanding how RGK proteins inhibit CaV channels is important for perspectives on their (patho)physiological roles and could advance their development and use as genetically-encoded CaV channel blockers. We previously reported that Rem can block surface CaV1.2 channels in 2 independent ways that engage distinct components of the channel complex: (1) by binding auxiliary β subunits (β-binding-dependent inhibition, or BBD); and (2) by binding the pore-forming α1C subunit N-terminus (α1C-binding-dependent inhibition, or ABD). By contrast, Gem uses only the BBD mechanism to block CaV1.2. Rem molecular determinants required for BBD CaV1.2 inhibition are the distal C-terminus and the guanine nucleotide binding G-domain which interact with the plasma membrane and CaVβ, respectively. However, Rem determinants for ABD CaV1.2 inhibition are unknown. Here, combining fluorescence resonance energy transfer, electrophysiology, systematic truncations, and Rem/Gem chimeras we found that the same Rem distal C-terminus and G-domain also mediate ABD CaV1.2 inhibition, but with different interaction partners. Rem distal C-terminus interacts with α1C N-terminus to anchor the G-domain which likely interacts with an as-yet-unidentified site. In contrast to some previous studies, neither the C-terminus of Rem nor Gem was sufficient to inhibit CaV1/CaV2 channels. The results reveal that similar molecular determinants on Rem are repurposed to initiate 2 independent mechanisms of CaV1.2 inhibition.
Collapse
Affiliation(s)
- Akil A Puckerin
- a Department of Pharmacology & Molecular Signaling , Columbia University , New York , NY , USA
| | - Donald D Chang
- b Department of Physiology & Cellular Biophysics , Columbia University , New York , NY , USA
| | - Prakash Subramanyam
- b Department of Physiology & Cellular Biophysics , Columbia University , New York , NY , USA
| | - Henry M Colecraft
- a Department of Pharmacology & Molecular Signaling , Columbia University , New York , NY , USA.,b Department of Physiology & Cellular Biophysics , Columbia University , New York , NY , USA
| |
Collapse
|
128
|
Brouhard GJ. Dynamic instability 30 years later: complexities in microtubule growth and catastrophe. Mol Biol Cell 2016; 26:1207-10. [PMID: 25823928 PMCID: PMC4454169 DOI: 10.1091/mbc.e13-10-0594] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Microtubules are not like other polymers. Whereas polymers such as F-actin will grow continuously as long as the subunit concentration is high enough, a steadily growing microtubule can suddenly shrink even when there is ample αβ-tubulin around. This remarkable behavior was discovered in 1984 when Tim Mitchison and Marc Kirschner deduced that microtubules switch from growth to shrinkage when they lose their GTP caps. Here, I review the canonical explanation of dynamic instability that was fleshed out in the years after its discovery. Many aspects of this explanation have been recently subverted, particularly those related to how GTP-tubulin forms polymers and why GTP hydrolysis disrupts them. I describe these developments and speculate on how our explanation of dynamic instability can be changed to accommodate them.
Collapse
Affiliation(s)
- Gary J Brouhard
- Department of Biology, McGill University, Montréal, QC H3A 1B1, Canada
| |
Collapse
|
129
|
Abstract
[NiFe]-hydrogenases catalyze the reversible conversion of hydrogen gas into protons and electrons and are vital metabolic components of many species of bacteria and archaea. At the core of this enzyme is a sophisticated catalytic center comprising nickel and iron, as well as cyanide and carbon monoxide ligands, which is anchored to the large hydrogenase subunit through cysteine residues. The production of this multicomponent active site is accomplished by a collection of accessory proteins and can be divided into discrete stages. The iron component is fashioned by the proteins HypC, HypD, HypE, and HypF, which functionalize iron with cyanide and carbon monoxide. Insertion of the iron center signals to the metallochaperones HypA, HypB, and SlyD to selectively deliver the nickel to the active site. A specific protease recognizes the completed metal cluster and then cleaves the C-terminus of the large subunit, resulting in a conformational change that locks the active site in place. Finally, the large subunit associates with the small subunit, and the complete holoenzyme translocates to its final cellular position. Beyond this broad overview of the [NiFe]-hydrogenase maturation process, biochemical and structural studies are revealing the fundamental underlying molecular mechanisms. Here, we review recent work illuminating how the accessory proteins contribute to the maturation of [NiFe]-hydrogenase and discuss some of the outstanding questions that remain to be resolved.
Collapse
Affiliation(s)
- Michael J Lacasse
- Department of Chemistry, University of Toronto , Toronto, Ontario, Canada M5S 3H6
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto , Toronto, Ontario, Canada M5S 3H6.,Department of Biochemistry, University of Toronto , Toronto, Ontario, Canada M5S 1A8
| |
Collapse
|
130
|
Cheung MY, Li X, Miao R, Fong YH, Li KP, Yung YL, Yu MH, Wong KB, Chen Z, Lam HM. ATP binding by the P-loop NTPase OsYchF1 (an unconventional G protein) contributes to biotic but not abiotic stress responses. Proc Natl Acad Sci U S A 2016; 113:2648-53. [PMID: 26912459 PMCID: PMC4791026 DOI: 10.1073/pnas.1522966113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
G proteins are involved in almost all aspects of the cellular regulatory pathways through their ability to bind and hydrolyze GTP. The YchF subfamily, interestingly, possesses the unique ability to bind both ATP and GTP, and is possibly an ancestral form of G proteins based on phylogenetic studies and is present in all kingdoms of life. However, the biological significance of such a relaxed ligand specificity has long eluded researchers. Here, we have elucidated the different conformational changes caused by the binding of a YchF homolog in rice (OsYchF1) to ATP versus GTP by X-ray crystallography. Furthermore, by comparing the 3D relationships of the ligand position and the various amino acid residues at the binding sites in the crystal structures of the apo-bound and ligand-bound versions, a mechanism for the protein's ability to bind both ligands is revealed. Mutation of the noncanonical G4 motif of the OsYchF1 to the canonical sequence for GTP specificity precludes the binding/hydrolysis of ATP and prevents OsYchF1 from functioning as a negative regulator of plant-defense responses, while retaining its ability to bind/hydrolyze GTP and its function as a negative regulator of abiotic stress responses, demonstrating the specific role of ATP-binding/hydrolysis in disease resistance. This discovery will have a significant impact on our understanding of the structure-function relationships of the YchF subfamily of G proteins in all kingdoms of life.
Collapse
Affiliation(s)
- Ming-Yan Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR; Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
| | - Xiaorong Li
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Rui Miao
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR; Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
| | - Yu-Hang Fong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR; Center for Protein Sciences and Crystallography, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
| | - Kwan-Pok Li
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR; Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
| | - Yuk-Lin Yung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR; Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
| | - Mei-Hui Yu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR; Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
| | - Kam-Bo Wong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR; Center for Protein Sciences and Crystallography, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
| | - Zhongzhou Chen
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China;
| | - Hon-Ming Lam
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR; Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR;
| |
Collapse
|
131
|
Torres M. Chapter Two - Heterotrimeric G Protein Ubiquitination as a Regulator of G Protein Signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 141:57-83. [PMID: 27378755 DOI: 10.1016/bs.pmbts.2016.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ubiquitin-mediated regulation of G proteins has been known for over 20 years as a result of discoveries made independently in yeast and vertebrate model systems for pheromone and photoreception, respectively. Since that time, several details underlying the cause and effect of G protein ubiquitination have been determined-including the initiating signals, responsible enzymes, trafficking pathways, and their effects on protein structure, function, interactions, and cell signaling. The collective body of evidence suggests that Gα subunits are the primary targets of ubiquitination. However, longstanding and recent results suggest that Gβ and Gγ subunits are also ubiquitinated, in some cases impacting cell polarization-a process essential for chemotaxis and polarized cell growth. More recently, evidence from mass spectrometry (MS)-based proteomics coupled with advances in PTM bioinformatics have revealed that protein families representing G protein subunits contain several structural hotspots for ubiquitination-most of which have not been investigated for a functional role in signal transduction. Taken together, our knowledge and understanding of heterotrimeric G protein ubiquitination as a regulator of G protein signaling-despite 20 years of research-is still emerging.
Collapse
Affiliation(s)
- M Torres
- Georgia Institute of Technology, School of Biology, Atlanta, GA, United States.
| |
Collapse
|
132
|
Yao XQ, Malik RU, Griggs NW, Skjærven L, Traynor JR, Sivaramakrishnan S, Grant BJ. Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins. J Biol Chem 2015; 291:4742-53. [PMID: 26703464 DOI: 10.1074/jbc.m115.702605] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Indexed: 12/21/2022] Open
Abstract
G protein α subunits cycle between active and inactive conformations to regulate a multitude of intracellular signaling cascades. Important structural transitions occurring during this cycle have been characterized from extensive crystallographic studies. However, the link between observed conformations and the allosteric regulation of binding events at distal sites critical for signaling through G proteins remain unclear. Here we describe molecular dynamics simulations, bioinformatics analysis, and experimental mutagenesis that identifies residues involved in mediating the allosteric coupling of receptor, nucleotide, and helical domain interfaces of Gαi. Most notably, we predict and characterize novel allosteric decoupling mutants, which display enhanced helical domain opening, increased rates of nucleotide exchange, and constitutive activity in the absence of receptor activation. Collectively, our results provide a framework for explaining how binding events and mutations can alter internal dynamic couplings critical for G protein function.
Collapse
Affiliation(s)
- Xin-Qiu Yao
- From the Department of Computational Medicine and Bioinformatics
| | - Rabia U Malik
- Cell and Developmental Biology, and the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | | | - Lars Skjærven
- the Department of Biomedicine, University of Bergen, 5020 Bergen, Norway, and
| | - John R Traynor
- Pharmacology, University of Michigan, Ann Arbor, Michigan 48109
| | - Sivaraj Sivaramakrishnan
- the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Barry J Grant
- From the Department of Computational Medicine and Bioinformatics,
| |
Collapse
|
133
|
Lau CKY, Krewulak KD, Vogel HJ. Bacterial ferrous iron transport: the Feo system. FEMS Microbiol Rev 2015; 40:273-98. [PMID: 26684538 DOI: 10.1093/femsre/fuv049] [Citation(s) in RCA: 212] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2015] [Indexed: 01/24/2023] Open
Abstract
To maintain iron homeostasis within the cell, bacteria have evolved various types of iron acquisition systems. Ferric iron (Fe(3+)) is the dominant species in an oxygenated environment, while ferrous iron (Fe(2+)) is more abundant under anaerobic conditions or at low pH. For organisms that must combat oxygen limitation for their everyday survival, pathways for the uptake of ferrous iron are essential. Several bacterial ferrous iron transport systems have been described; however, only the Feo system appears to be widely distributed and is exclusively dedicated to the transport of iron. In recent years, many studies have explored the role of the FeoB and FeoA proteins in ferrous iron transport and their contribution toward bacterial virulence. The three-dimensional structures for the Feo proteins have recently been determined and provide insight into the molecular details of the transport system. A highly select group of bacteria also express the FeoC protein from the same operon. This review will provide a comprehensive look at the structural and functional aspects of the Feo system. In addition, bioinformatics analyses of the feo operon and the Feo proteins have been performed to complement our understanding of this ubiquitous bacterial uptake system, providing a new outlook for future studies.
Collapse
Affiliation(s)
- Cheryl K Y Lau
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Karla D Krewulak
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| |
Collapse
|
134
|
The experimental power of FR900359 to study Gq-regulated biological processes. Nat Commun 2015; 6:10156. [PMID: 26658454 PMCID: PMC4682109 DOI: 10.1038/ncomms10156] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 11/06/2015] [Indexed: 12/13/2022] Open
Abstract
Despite the discovery of heterotrimeric αβγ G proteins ∼25 years ago, their selective perturbation by cell-permeable inhibitors remains a fundamental challenge. Here we report that the plant-derived depsipeptide FR900359 (FR) is ideally suited to this task. Using a multifaceted approach we systematically characterize FR as a selective inhibitor of Gq/11/14 over all other mammalian Gα isoforms and elaborate its molecular mechanism of action. We also use FR to investigate whether inhibition of Gq proteins is an effective post-receptor strategy to target oncogenic signalling, using melanoma as a model system. FR suppresses many of the hallmark features that are central to the malignancy of melanoma cells, thereby providing new opportunities for therapeutic intervention. Just as pertussis toxin is used extensively to probe and inhibit the signalling of Gi/o proteins, we anticipate that FR will at least be its equivalent for investigating the biological relevance of Gq.
Collapse
|
135
|
Coleman BD, Marivin A, Parag-Sharma K, DiGiacomo V, Kim S, Pepper JS, Casler J, Nguyen LT, Koelle MR, Garcia-Marcos M. Evolutionary Conservation of a GPCR-Independent Mechanism of Trimeric G Protein Activation. Mol Biol Evol 2015; 33:820-37. [PMID: 26659249 PMCID: PMC4760084 DOI: 10.1093/molbev/msv336] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Trimeric G protein signaling is a fundamental mechanism of cellular communication in eukaryotes. The core of this mechanism consists of activation of G proteins by the guanine-nucleotide exchange factor (GEF) activity of G protein coupled receptors. However, the duration and amplitude of G protein-mediated signaling are controlled by a complex network of accessory proteins that appeared and diversified during evolution. Among them, nonreceptor proteins with GEF activity are the least characterized. We recently found that proteins of the ccdc88 family possess a Gα-binding and activating (GBA) motif that confers GEF activity and regulates mammalian cell behavior. A sequence similarity-based search revealed that ccdc88 genes are highly conserved across metazoa but the GBA motif is absent in most invertebrates. This prompted us to investigate whether the GBA motif is present in other nonreceptor proteins in invertebrates. An unbiased bioinformatics search in Caenorhabditis elegans identified GBAS-1 (GBA and SPK domain containing-1) as a GBA motif-containing protein with homologs only in closely related worm species. We demonstrate that GBAS-1 has GEF activity for the nematode G protein GOA-1 and that the two proteins are coexpressed in many cells of living worms. Furthermore, we show that GBAS-1 can activate mammalian Gα-subunits and provide structural insights into the evolutionarily conserved determinants of the GBA–G protein interface. These results demonstrate that the GBA motif is a functional GEF module conserved among highly divergent proteins across evolution, indicating that the GBA-Gα binding mode is strongly constrained under selective pressure to mediate receptor-independent G protein activation in metazoans.
Collapse
Affiliation(s)
| | - Arthur Marivin
- Department of Biochemistry, Boston University School of Medicine
| | | | | | - Seongseop Kim
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine
| | - Judy S Pepper
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine
| | - Jason Casler
- Department of Biochemistry, Boston University School of Medicine
| | - Lien T Nguyen
- Department of Biochemistry, Boston University School of Medicine
| | - Michael R Koelle
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine
| | | |
Collapse
|
136
|
Anand R, Eschenburg S, Reubold TF. Crystal structure of the GTPase domain and the bundle signalling element of dynamin in the GDP state. Biochem Biophys Res Commun 2015; 469:76-80. [PMID: 26612256 DOI: 10.1016/j.bbrc.2015.11.074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 11/17/2015] [Indexed: 10/22/2022]
Abstract
Dynamin is the prototype of a family of large multi-domain GTPases. The 100 kDa protein is a key player in clathrin-mediated endocytosis, where it cleaves off vesicles from membranes using the energy from GTP hydrolysis. We have solved the high resolution crystal structure of a fusion protein of the GTPase domain and the bundle signalling element (BSE) of dynamin 1 liganded with GDP. The structure provides a hitherto missing snapshot of the GDP state of the hydrolytic cycle of dynamin and reveals how the switch I region moves away from the active site after GTP hydrolysis and release of inorganic phosphate. Comparing our structure of the GDP state with the known structures of the GTP state, the transition state and the nucleotide-free state of dynamin 1 we describe the structural changes through the hydrolytic cycle.
Collapse
Affiliation(s)
- Roopsee Anand
- Hannover Medical School, Institute for Biophysical Chemistry, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Susanne Eschenburg
- Hannover Medical School, Institute for Biophysical Chemistry, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Thomas F Reubold
- Hannover Medical School, Institute for Biophysical Chemistry, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.
| |
Collapse
|
137
|
Ran Involved in the Development and Reproduction Is a Potential Target for RNA-Interference-Based Pest Management in Nilaparvata lugens. PLoS One 2015; 10:e0142142. [PMID: 26554926 PMCID: PMC4640576 DOI: 10.1371/journal.pone.0142142] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/19/2015] [Indexed: 11/27/2022] Open
Abstract
Ran (RanGTPase) in insects participates in the 20-hydroxyecdysone signal transduction pathway in which downstream genes, FTZ-F1, Krüppel-homolog 1 (Kr-h1) and vitellogenin, are involved. A putative Ran gene (NlRan) was cloned from Nilaparvata lugens, a destructive phloem-feeding pest of rice. NlRan has the typical Ran primary structure features that are conserved in insects. NlRan showed higher mRNA abundance immediately after molting and peaked in newly emerged female adults. Among the examined tissues ovary had the highest transcript level, followed by fat body, midgut and integument, and legs. Three days after dsNlRan injection the NlRan mRNA abundance in the third-, fourth-, and fifth-instar nymphs was decreased by 94.3%, 98.4% and 97.0%, respectively. NlFTZ-F1 expression levels in treated third- and fourth-instar nymphs were reduced by 89.3% and 23.8%, respectively. In contrast, NlKr-h1 mRNA levels were up-regulated by 67.5 and 1.5 folds, respectively. NlRan knockdown significantly decreased the body weights, delayed development, and killed >85% of the nymphs at day seven. Two apparent phenotypic defects were observed: (1) Extended body form, and failed to molt; (2) The cuticle at the notum was split open but cannot completely shed off. The newly emerged female adults from dsNlRan injected fifth-instar nymphs showed lower levels of NlRan and vitellogenin, lower weight gain and honeydew excretion comparing with the blank control, and no offspring. Those results suggest that NlRan encodes a functional protein that was involved in development and reproduction. The study established proof of concept that NlRan could serve as a target for dsRNA-based pesticides for N. lugens control.
Collapse
|
138
|
Srivastava VK, Chandra M, Saito-Nakano Y, Nozaki T, Datta S. Crystal Structure Analysis of Wild Type and Fast Hydrolyzing Mutant of EhRabX3, a Tandem Ras Superfamily GTPase from Entamoeba histolytica. J Mol Biol 2015; 428:41-51. [PMID: 26555751 DOI: 10.1016/j.jmb.2015.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 10/30/2015] [Accepted: 11/04/2015] [Indexed: 10/22/2022]
Abstract
The enteric protozoan parasite, Entamoeba histolytica, is the causative agent of amoebic dysentery, liver abscess and colitis in human. Vesicular trafficking plays a key role in the survival and virulence of the protozoan and is regulated by various Rab GTPases. EhRabX3 is a catalytically inefficient amoebic Rab protein, which is unique among the eukaryotic Ras superfamily by virtue of its tandem domain organization. Here, we report the crystal structures of GDP-bound fast hydrolyzing mutant (V71A/K73Q) and GTP-bound wild type EhRabX3 at 3.1 and 2.8Å resolutions, respectively. Though both G-domains possess "phosphate binding loop containing nucleoside triphosphate hydrolases fold", only the N-terminal domain binds to guanine nucleotide. The relative orientation of the N-terminal domain and C-terminal domain is stabilized by numerous inter-domain interactions. Compared to other Ras superfamily members, both the GTPase domains displayed large deviation in switch II perhaps due to non-conservative substitutions in this region. As a result, entire switch II is restructured and moved away from the nucleotide binding pocket, providing a rationale for the diminished GTPase activity of EhRabX3. The N-terminal GTPase domain possesses unusually large number of cysteine residues. X-ray crystal structure of the fast hydrolyzing mutant of EhRabX3 revealed that C39 and C163 formed an intra-molecular disulfide bond. Subsequent mutational and biochemical studies suggest that C39 and C163 are critical for maintaining the structural integrity and function of EhRabX3. Structure-guided functional investigation of cysteine mutants could provide the physiological implications of the disulfide bond and could allow us to design potential inhibitors for the better treatment of intestinal amebiasis.
Collapse
Affiliation(s)
- Vijay Kumar Srivastava
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal 462023, India
| | - Mintu Chandra
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal 462023, India
| | - Yumiko Saito-Nakano
- Department of Parasitology, National Institute of Infectious Diseases Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tomoyoshi Nozaki
- Department of Parasitology, National Institute of Infectious Diseases Shinjuku-ku, Tokyo 162-8640, Japan
| | - Sunando Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal 462023, India,.
| |
Collapse
|
139
|
Jian X, Tang WK, Zhai P, Roy NS, Luo R, Gruschus JM, Yohe ME, Chen PW, Li Y, Byrd RA, Xia D, Randazzo PA. Molecular Basis for Cooperative Binding of Anionic Phospholipids to the PH Domain of the Arf GAP ASAP1. Structure 2015; 23:1977-88. [PMID: 26365802 PMCID: PMC4788500 DOI: 10.1016/j.str.2015.08.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/12/2015] [Accepted: 08/14/2015] [Indexed: 11/18/2022]
Abstract
We have defined the molecular basis for association of the PH domain of the Arf GAP ASAP1 with phospholipid bilayers. Structures of the unliganded and dibutyryl PtdIns(4,5)P2-bound PH domain were solved. PtdIns(4,5)P2 made contact with both a canonical site (C site) and an atypical site (A site). We hypothesized cooperative binding of PtdIns(4,5)P2 to the C site and a nonspecific anionic phospholipid to the A site. PtdIns(4,5)P2 dependence of binding to large unilamellar vesicles and GAP activity was sigmoidal, consistent with cooperative sites. In contrast, PtdIns(4,5)P2 binding to the PH domain of PLC δ1 was hyperbolic. Mutation of amino acids in either the C or A site resulted in decreased PtdIns(4,5)P2-dependent binding to vesicles and decreased GAP activity. The results support the idea of cooperative phospholipid binding to the C and A sites of the PH domain of ASAP1. We propose that the mechanism underlies rapid switching between active and inactive ASAP1.
Collapse
Affiliation(s)
- Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wai-Kwan Tang
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peng Zhai
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neeladri Sekhar Roy
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruibai Luo
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James M Gruschus
- Laboratory of Structural Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marielle E Yohe
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pei-Wen Chen
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yifei Li
- Structural Biophysics Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - R Andrew Byrd
- Structural Biophysics Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Di Xia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Laboratory of Cell Biology, National Cancer Institute, Building 37, Room 2122, Bethesda, MD 20892, USA.
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Building 37, Room 2042, Bethesda, MD 20892, USA.
| |
Collapse
|
140
|
van Adrichem AJ, Fagerholm A, Turunen L, Lehto A, Saarela J, Koskinen A, Repasky GA, Wennerberg K. Discovery of MINC1, a GTPase-activating protein small molecule inhibitor, targeting MgcRacGAP. Comb Chem High Throughput Screen 2015; 18:3-17. [PMID: 25479424 PMCID: PMC4435052 DOI: 10.2174/1386207318666141205112730] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 11/12/2014] [Accepted: 12/03/2014] [Indexed: 12/02/2022]
Abstract
The Rho family of Ras superfamily small GTPases regulates a broad range of biological processes such as migration, differentiation, cell growth and cell survival. Therefore, the availability of small molecule modulators as tool compounds could greatly enhance research on these proteins and their biological function. To this end, we designed a biochemical, high throughput screening assay with complementary follow-up assays to identify small molecule compounds inhibiting MgcRacGAP, a Rho family GTPase activating protein involved in cytokinesis and transcriptionally upregulated in many cancers. We first performed an in-house screen of 20,480 compounds, and later we tested the assay against 342,046 compounds from the NIH Molecular Libraries Small Molecule Repository. Primary screening hit rates were about 1% with the majority of those affecting the primary readout, an enzyme-coupled GDP detection assay. After orthogonal and counter screens, we identified two hits with high selectivity towards MgcRacGAP, compared with other RhoGAPs, and potencies in the low micromolar range. The most promising hit, termed MINC1, was then examined with cell-based testing where it was observed to induce an increased rate of cytokinetic failure and multinucleation in addition to other cell division defects, suggesting that it may act as an MgcRacGAP inhibitor also in cells.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Krister Wennerberg
- Institute for Molecular Medicine Finland FIMM, Nordic EMBL Partnership for Molecular Medicine, Biomedicum Helsinki 2U, P.O. Box 20 (Tukholmankatu 8), FI- 00014, University of Helsinki, Finland.
| |
Collapse
|
141
|
Litosch I. Regulating G protein activity by lipase-independent functions of phospholipase C. Life Sci 2015; 137:116-24. [DOI: 10.1016/j.lfs.2015.07.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/18/2015] [Accepted: 07/22/2015] [Indexed: 11/27/2022]
|
142
|
Venkatapurapu SP, Kelley JB, Dixit G, Pena M, Errede B, Dohlman HG, Elston TC. Modulation of receptor dynamics by the regulator of G protein signaling Sst2. Mol Biol Cell 2015; 26:4124-34. [PMID: 26310439 PMCID: PMC4710242 DOI: 10.1091/mbc.e14-12-1635] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 08/13/2015] [Indexed: 01/01/2023] Open
Abstract
G protein–coupled receptor signaling is negatively regulated by both receptor internalization and regulator of G protein signaling (RGS) protein–stimulated inactivation of the G protein. The RGS protein can also positively regulate receptor signaling by binding to the receptor, thereby reducing receptor internalization. G protein–coupled receptor (GPCR) signaling is fundamental to physiological processes such as vision, the immune response, and wound healing. In the budding yeast Saccharomyces cerevisiae, GPCRs detect and respond to gradients of pheromone during mating. After pheromone stimulation, the GPCR Ste2 is removed from the cell membrane, and new receptors are delivered to the growing edge. The regulator of G protein signaling (RGS) protein Sst2 acts by accelerating GTP hydrolysis and facilitating pathway desensitization. Sst2 is also known to interact with the receptor Ste2. Here we show that Sst2 is required for proper receptor recovery at the growing edge of pheromone-stimulated cells. Mathematical modeling suggested pheromone-induced synthesis of Sst2 together with its interaction with the receptor function to reestablish a receptor pool at the site of polarized growth. To validate the model, we used targeted genetic perturbations to selectively disrupt key properties of Sst2 and its induction by pheromone. Together our results reveal that a regulator of G protein signaling can also regulate the G protein–coupled receptor. Whereas Sst2 negatively regulates G protein signaling, it acts in a positive manner to promote receptor retention at the growing edge.
Collapse
Affiliation(s)
- Sai Phanindra Venkatapurapu
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Joshua B Kelley
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Gauri Dixit
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Matthew Pena
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Beverly Errede
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Henrik G Dohlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Timothy C Elston
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| |
Collapse
|
143
|
Abstract
Neomorphic moonlighting proteins perform distinct functions under physiological and pathological conditions without alterations at the gene level. The disordered tubulin-polymerization-promoting protein (TPPP/p25), a prototype of neomorphic moonlighting proteins, modulates the dynamics and stability of the microtubule system via its bundling and tubulin acetylation-promoting activities. These physiological functions are mediated by its direct associations with tubulin/microtubules as well as tubulin deacetylases such as histone deacetylase (HDAC) 6. In a normal brain, TPPP/p25 is expressed in oligodendrocytes and plays a crucial role in the formation of projections in the course of differentiation required for axon ensheathment. Under pathological conditions, TPPP/p25 interacts with α-synuclein, an aberrant protein-protein interaction resulting in aggregation leading to the formation of inclusions as clinical symptoms. The co-enrichment and co-localization of TPPP/p25 and α-synuclein were established in human-brain inclusions characteristic of Parkinson's disease (PD) and other synucleinopathies. The binding segments on TPPP/p25 involved in the physiological and the pathological interactions were identified and validated at molecular and cellular levels using recombinant proteins and transfected HeLa and inducible Chinese-hamster ovary (CHO) 10 cells expressing TPPP/p25. Our finding that distinct motifs are responsible for the neomorphic moonlighting feature of TPPP/p25, has powerful innovative effects in anti-Parkinson's disease drug research.
Collapse
|
144
|
Zhou F, Dong C, Davis JE, Wu WH, Surrao K, Wu G. The mechanism and function of mitogen-activated protein kinase activation by ARF1. Cell Signal 2015; 27:2035-2044. [PMID: 26169956 DOI: 10.1016/j.cellsig.2015.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 06/24/2015] [Indexed: 01/25/2023]
Abstract
Mitogen-activated protein kinases (MAPK) can be activated by a number of biochemical pathways through distinct signaling molecules. We have recently revealed a novel function for the Ras-like small GTPase ADP-ribosylation factor 1 (ARF1) in mediating the activation of Raf1-MEK-ERK1/2 pathway by G protein-coupled receptors [Dong C, Li C and Wu G (2011) J Biol Chem 286, 43,361-43,369]. Here, we have further defined the underlying mechanism and the possible function of ARF1-mediated MAPK pathway. We demonstrated that the blockage of ARF1 activation and the disruption of ARF1 localization to the Golgi by mutating Thr48, a highly conserved residue involved in the exchange of GDP for GTP, and the myristoylation site Gly2 abolished ARF1's ability to activate ERK1/2. In addition, treatment with Golgi structure disrupting agents markedly attenuated ARF1-mediated ERK1/2 activation. Furthermore, ARF1 significantly promoted cell proliferation. More interestingly, ARF1 activated 90kDa ribosomal S6 kinase 1 (RSK1) without influencing Elk-1 activation and ERK2 translocation to the nuclei. These data demonstrate that, once activated, ARF1 activates the MAPK pathway likely using the Golgi as a main platform, which in turn activates the cytoplasmic RSK1, leading to cell proliferation.
Collapse
Affiliation(s)
- Fuguo Zhou
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center, 1901 Perdido St, New Orleans, LA 70112, United States
| | - Chunmin Dong
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center, 1901 Perdido St, New Orleans, LA 70112, United States
| | - Jason E Davis
- Department of Pharmacology and Toxicology, Medical College of Georgia, Georgia Regents University, 1459 Laney Walker Blvd., Augusta, GA 30912, United States
| | - William H Wu
- Department of Pharmacology and Toxicology, Medical College of Georgia, Georgia Regents University, 1459 Laney Walker Blvd., Augusta, GA 30912, United States
| | - Kristen Surrao
- Department of Pharmacology and Toxicology, Medical College of Georgia, Georgia Regents University, 1459 Laney Walker Blvd., Augusta, GA 30912, United States
| | - Guangyu Wu
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center, 1901 Perdido St, New Orleans, LA 70112, United States.,Department of Pharmacology and Toxicology, Medical College of Georgia, Georgia Regents University, 1459 Laney Walker Blvd., Augusta, GA 30912, United States
| |
Collapse
|
145
|
Dror RO, Mildorf TJ, Hilger D, Manglik A, Borhani DW, Arlow DH, Philippsen A, Villanueva N, Yang Z, Lerch MT, Hubbell WL, Kobilka BK, Sunahara RK, Shaw DE. SIGNAL TRANSDUCTION. Structural basis for nucleotide exchange in heterotrimeric G proteins. Science 2015; 348:1361-5. [PMID: 26089515 DOI: 10.1126/science.aaa5264] [Citation(s) in RCA: 208] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
G protein-coupled receptors (GPCRs) relay diverse extracellular signals into cells by catalyzing nucleotide release from heterotrimeric G proteins, but the mechanism underlying this quintessential molecular signaling event has remained unclear. Here we use atomic-level simulations to elucidate the nucleotide-release mechanism. We find that the G protein α subunit Ras and helical domains-previously observed to separate widely upon receptor binding to expose the nucleotide-binding site-separate spontaneously and frequently even in the absence of a receptor. Domain separation is necessary but not sufficient for rapid nucleotide release. Rather, receptors catalyze nucleotide release by favoring an internal structural rearrangement of the Ras domain that weakens its nucleotide affinity. We use double electron-electron resonance spectroscopy and protein engineering to confirm predictions of our computationally determined mechanism.
Collapse
Affiliation(s)
- Ron O Dror
- D. E. Shaw Research, New York, NY 10036, USA.
| | | | - Daniel Hilger
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aashish Manglik
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | | | - Nicolas Villanueva
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zhongyu Yang
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Michael T Lerch
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roger K Sunahara
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - David E Shaw
- D. E. Shaw Research, New York, NY 10036, USA. Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
146
|
Dewhurst HM, Choudhury S, Torres MP. Structural Analysis of PTM Hotspots (SAPH-ire)--A Quantitative Informatics Method Enabling the Discovery of Novel Regulatory Elements in Protein Families. Mol Cell Proteomics 2015; 14:2285-97. [PMID: 26070665 PMCID: PMC4528253 DOI: 10.1074/mcp.m115.051177] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Indexed: 11/08/2022] Open
Abstract
Predicting the biological function potential of post-translational modifications (PTMs) is becoming increasingly important in light of the exponential increase in available PTM data from high-throughput proteomics. We developed structural analysis of PTM hotspots (SAPH-ire)—a quantitative PTM ranking method that integrates experimental PTM observations, sequence conservation, protein structure, and interaction data to allow rank order comparisons within or between protein families. Here, we applied SAPH-ire to the study of PTMs in diverse G protein families, a conserved and ubiquitous class of proteins essential for maintenance of intracellular structure (tubulins) and signal transduction (large and small Ras-like G proteins). A total of 1728 experimentally verified PTMs from eight unique G protein families were clustered into 451 unique hotspots, 51 of which have a known and cited biological function or response. Using customized software, the hotspots were analyzed in the context of 598 unique protein structures. By comparing distributions of hotspots with known versus unknown function, we show that SAPH-ire analysis is predictive for PTM biological function. Notably, SAPH-ire revealed high-ranking hotspots for which a functional impact has not yet been determined, including phosphorylation hotspots in the N-terminal tails of G protein gamma subunits—conserved protein structures never before reported as regulators of G protein coupled receptor signaling. To validate this prediction we used the yeast model system for G protein coupled receptor signaling, revealing that gamma subunit–N-terminal tail phosphorylation is activated in response to G protein coupled receptor stimulation and regulates protein stability in vivo. These results demonstrate the utility of integrating protein structural and sequence features into PTM prioritization schemes that can improve the analysis and functional power of modification-specific proteomics data.
Collapse
Affiliation(s)
- Henry M Dewhurst
- From the ‡Georgia Institute of Technology; School of Biology; 310 Ferst Drive; Atlanta, Georgia 30332
| | - Shilpa Choudhury
- From the ‡Georgia Institute of Technology; School of Biology; 310 Ferst Drive; Atlanta, Georgia 30332
| | - Matthew P Torres
- From the ‡Georgia Institute of Technology; School of Biology; 310 Ferst Drive; Atlanta, Georgia 30332
| |
Collapse
|
147
|
Rosler KS, Mercier E, Andrews IC, Wieden HJ. Histidine 114 Is Critical for ATP Hydrolysis by the Universally Conserved ATPase YchF. J Biol Chem 2015; 290:18650-61. [PMID: 26018081 DOI: 10.1074/jbc.m114.598227] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Indexed: 11/06/2022] Open
Abstract
GTPases perform a wide range of functions, ranging from protein synthesis to cell signaling. Of all known GTPases, only eight are conserved across all three domains of life. YchF is one of these eight universally conserved GTPases; however, its cellular function and enzymatic properties are poorly understood. YchF differs from the classical GTPases in that it has a higher affinity for ATP than for GTP and is a functional ATPase. As a hydrophobic amino acid-substituted ATPase, YchF does not possess the canonical catalytic Gln required for nucleotide hydrolysis. To elucidate the catalytic mechanism of ATP hydrolysis by YchF, we have taken a two-pronged approach combining classical biochemical and in silico techniques. The use of molecular dynamics simulations allowed us to complement our biochemical findings with information about the structural dynamics of YchF. We have thereby identified the highly conserved His-114 as critical for the ATPase activity of YchF from Escherichia coli. His-114 is located in a flexible loop of the G-domain, which undergoes nucleotide-dependent conformational changes. The use of a catalytic His is also observed in the hydrophobic amino acid-substituted GTPase RbgA and is an identifier of the translational GTPase family.
Collapse
Affiliation(s)
- Kirsten S Rosler
- From the Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Evan Mercier
- From the Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Ian C Andrews
- From the Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Hans-Joachim Wieden
- From the Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| |
Collapse
|
148
|
Kiani FA, Fischer S. Advances in quantum simulations of ATPase catalysis in the myosin motor. Curr Opin Struct Biol 2015; 31:115-23. [PMID: 26005996 DOI: 10.1016/j.sbi.2015.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 04/17/2015] [Accepted: 04/20/2015] [Indexed: 11/29/2022]
Abstract
During its contraction cycle, the myosin motor catalyzes the hydrolysis of ATP. Several combined quantum/classical mechanics (QM/MM) studies of this step have been published, which substantially contributed to our thinking about the catalytic mechanism. The methodological difficulties encountered over the years in the simulation of this complex reaction are now understood: (a) Polarization of the protein peptide groups surrounding the highly charged ATP(4-) cannot be neglected. (b) Some unsuspected protein groups need to be treated QM. (c) Interactions with the γ-phosphate versus the β-phosphate favor a concurrent versus a sequential mechanism, respectively. Thus, these practical aspects strongly influence the computed mechanism, and should be considered when studying other catalyzed phosphor-ester hydrolysis reactions, such as in ATPases or GTPases.
Collapse
Affiliation(s)
- Farooq Ahmad Kiani
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, Pakistan
| | - Stefan Fischer
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany.
| |
Collapse
|
149
|
Huang YJ, Zhou ZW, Xu M, Ma QW, Yan JB, Wang JY, Zhang QQ, Huang M, Bao L. Alteration of gene expression profiling including GPR174 and GNG2 is associated with vasovagal syncope. Pediatr Cardiol 2015; 36:475-80. [PMID: 25367286 DOI: 10.1007/s00246-014-1036-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 09/27/2014] [Indexed: 11/24/2022]
Abstract
Vasovagal syncope (VVS) causes accidental harm for susceptible patients. However, pathophysiology of this disorder remains largely unknown. In an effort to understanding of molecular mechanism for VVS, genome-wide gene expression profiling analyses were performed on VVS patients at syncope state. A total of 66 Type 1 VVS child patients and the same number healthy controls were enrolled in this study. Peripheral blood RNAs were isolated from all subjects, of which 10 RNA samples were randomly selected from each groups for gene expression profile analysis using Gene ST 1.0 arrays (Affymetrix). The results revealed that 103 genes were differently expressed between the patients and controls. Significantly, two G-proteins related genes, GPR174 and GNG2 that have not been related to VVS were among the differently expressed genes. The microarray results were confirmed by qRT-PCR in all the tested individuals. Ingenuity pathway analysis and gene ontology annotation study showed that the differently expressed genes are associated with stress response and apoptosis, suggesting that the alteration of some gene expression including G-proteins related genes is associated with VVS. This study provides new insight into the molecular mechanism of VVS and would be helpful to further identify new molecular biomarkers for the disease.
Collapse
Affiliation(s)
- Yu-Juan Huang
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,
| | | | | | | | | | | | | | | | | |
Collapse
|
150
|
Yanagisawa T, Ishii R, Hikida Y, Fukunaga R, Sengoku T, Sekine SI, Yokoyama S. A SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA(Cys.). JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2015; 16:25-41. [PMID: 25618148 PMCID: PMC4329189 DOI: 10.1007/s10969-015-9193-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 01/10/2015] [Indexed: 11/15/2022]
Abstract
The putative translation elongation factor Mbar_A0971 from the methanogenic archaeon Methanosarcina barkeri was proposed to be the pyrrolysine-specific paralogue of EF-Tu ("EF-Pyl"). In the present study, the crystal structures of its homologue from Methanosarcina mazei (MM1309) were determined in the GMPPNP-bound, GDP-bound, and apo forms, by the single-wavelength anomalous dispersion phasing method. The three MM1309 structures are quite similar (r.m.s.d. < 0.1 Å). The three domains, corresponding to domains 1, 2, and 3 of EF-Tu/SelB/aIF2γ, are packed against one another to form a closed architecture. The MM1309 structures resemble those of bacterial/archaeal SelB, bacterial EF-Tu in the GTP-bound form, and archaeal initiation factor aIF2γ, in this order. The GMPPNP and GDP molecules are visible in their co-crystal structures. Isothermal titration calorimetry measurements of MM1309·GTP·Mg(2+), MM1309·GDP·Mg(2+), and MM1309·GMPPNP·Mg(2+) provided dissociation constants of 0.43, 26.2, and 222.2 μM, respectively. Therefore, the affinities of MM1309 for GTP and GDP are similar to those of SelB rather than those of EF-Tu. Furthermore, the switch I and II regions of MM1309 are involved in domain-domain interactions, rather than nucleotide binding. The putative binding pocket for the aminoacyl moiety on MM1309 is too small to accommodate the pyrrolysyl moiety, based on a comparison of the present MM1309 structures with that of the EF-Tu·GMPPNP·aminoacyl-tRNA ternary complex. A hydrolysis protection assay revealed that MM1309 binds cysteinyl (Cys)-tRNA(Cys) and protects the aminoacyl bond from non-enzymatic hydrolysis. Therefore, we propose that MM1309 functions as either a guardian protein that protects the Cys moiety from oxidation or an alternative translation factor for Cys-tRNA(Cys).
Collapse
Affiliation(s)
- Tatsuo Yanagisawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Ryohei Ishii
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Yasushi Hikida
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Ryuya Fukunaga
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Present Address: Department of Biochemistry, School of Medicine, Johns Hopkins University, 725 N. Wolfe Street, 521A Physiology Bldg., Baltimore, MD 21205 USA
| | - Toru Sengoku
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Shun-ichi Sekine
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| |
Collapse
|