1
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Morea V, Angelucci F, Bellelli A. Is allostery a fuzzy concept? FEBS Open Bio 2024. [PMID: 38783588 DOI: 10.1002/2211-5463.13794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/30/2024] [Accepted: 03/11/2024] [Indexed: 05/25/2024] Open
Abstract
Allostery is an important property of biological macromolecules which regulates diverse biological functions such as catalysis, signal transduction, transport, and molecular recognition. However, the concept was expressed using two different definitions by J. Monod and, over time, more have been added by different authors, making it fuzzy. Here, we reviewed the different meanings of allostery in the current literature and found that it has been used to indicate that the function of a protein is regulated by heterotropic ligands, and/or that the binding of ligands and substrates presents homotropic positive or negative cooperativity, whatever the hypothesized or demonstrated reaction mechanism might be. Thus, proteins defined to be allosteric include not only those that obey the two-state concerted model, but also those that obey different reaction mechanisms such as ligand-induced fit, possibly coupled to sequential structure changes, and ligand-linked dissociation-association. Since each reaction mechanism requires its own mathematical description and is defined by it, there are many possible 'allosteries'. This lack of clarity is made even fuzzier by the fact that the reaction mechanism is often assigned imprecisely and/or implicitly in the absence of the necessary experimental evidence. In this review, we examine a list of proteins that have been defined to be allosteric and attempt to assign a reaction mechanism to as many as possible.
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Affiliation(s)
- Veronica Morea
- Institute of Molecular Biology and Pathology, CNR, Rome, Italy
| | - Francesco Angelucci
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, Italy
| | - Andrea Bellelli
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
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2
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Takahashi T, Shirai J, Matsuda M, Nakanaga S, Matsushita S, Wakita K, Hayashishita M, Suzuki R, Noguchi A, Yokota N, Kawahara H. Protein quality control machinery supports primary ciliogenesis by eliminating GDP-bound Rab8-family GTPases. iScience 2023; 26:106652. [PMID: 37182096 PMCID: PMC10173616 DOI: 10.1016/j.isci.2023.106652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/27/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023] Open
Abstract
The small GTPase Rab8 plays a vital role in the vesicular trafficking of cargo proteins from the trans-Golgi network to target membranes. Upon reaching its target destination, Rab8 is released from the vesicular membrane into the cytoplasm via guanosine triphosphate (GTP) hydrolysis. The fate of GDP-bound Rab8 released from the destination membranes, however, has not been investigated adequately. In this study, we found that GDP-bound Rab8 subfamily proteins are targeted for immediate degradation, and the pre-emptive quality control machinery is responsible for eliminating these proteins in a nucleotide-specific manner. We provide evidence that components of this quality control machinery have a critical role in vesicular trafficking events, including the formation of primary cilia, a process regulated by the Rab8 subfamily. These results suggest that the protein degradation machinery plays a critical role in the integrity of membrane trafficking by limiting the excessive accumulation of GDP-bound Rab8 subfamily proteins.
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Affiliation(s)
- Toshiki Takahashi
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Jun Shirai
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Miyo Matsuda
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Sae Nakanaga
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Shin Matsushita
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Kei Wakita
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Mizuki Hayashishita
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Rigel Suzuki
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Aya Noguchi
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Naoto Yokota
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Hiroyuki Kawahara
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
- Corresponding author
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3
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Ito G, Tomita T, Utsunomiya-Tate N. LRRK2-mediated phosphorylation and thermal stability of Rab12 are regulated by bound nucleotides. Biochem Biophys Res Commun 2023; 667:43-49. [PMID: 37207563 DOI: 10.1016/j.bbrc.2023.05.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 05/14/2023] [Indexed: 05/21/2023]
Abstract
An abnormal increase in the phosphorylation of Rab12 by leucine-rich repeat kinase 2 (LRRK2), a serine/threonine kinase genetically linked to Parkinson's disease (PD), has been implicated in the pathogenesis of PD, although the underlying mechanism remains unclear. In this report, we show that LRRK2 phosphorylates Rab12 more efficiently in its GDP-bound form than in its GTP-bound form using an in vitro phosphorylation assay. This observation suggests that LRRK2 recognizes the structural difference of Rab12 caused by the bound nucleotide and that Rab12 phosphorylation inhibits its activation. Circular dichroism data revealed that Rab12, in its GDP-bound form, is more susceptible to heat-induced denaturation than its GTP-bound form, which was exacerbated at basic pH. Differential scanning fluorimetry showed that heat-induced denaturation of Rab12 in its GDP-bound form occurs at a lower temperature than in its GTP-bound form. These results suggest that the type of nucleotide bound to Rab12 determines the efficiency of LRRK2-mediated phosphorylation and the thermal stability of Rab12, and provide insights into elucidating the mechanism of the abnormal increase in Rab12 phosphorylation.
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Affiliation(s)
- Genta Ito
- Department of Biomolecular Chemistry, Faculty of Pharma-Sciences, Teikyo University, Japan.
| | - Taisuke Tomita
- Social Cooperation Program of Brain and Neurological Disorders, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Japan; Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Japan
| | - Naoko Utsunomiya-Tate
- Department of Biomolecular Chemistry, Faculty of Pharma-Sciences, Teikyo University, Japan
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4
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Kaspers MS, Pogenberg V, Pett C, Ernst S, Ecker F, Ochtrop P, Groll M, Hedberg C, Itzen A. Dephosphocholination by Legionella effector Lem3 functions through remodelling of the switch II region of Rab1b. Nat Commun 2023; 14:2245. [PMID: 37076474 PMCID: PMC10115812 DOI: 10.1038/s41467-023-37621-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/22/2023] [Indexed: 04/21/2023] Open
Abstract
Bacterial pathogens often make use of post-translational modifications to manipulate host cells. Legionella pneumophila, the causative agent of Legionnaires disease, secretes the enzyme AnkX that uses cytidine diphosphate-choline to post-translationally modify the human small G-Protein Rab1 with a phosphocholine moiety at Ser76. Later in the infection, the Legionella enzyme Lem3 acts as a dephosphocholinase, hydrolytically removing the phosphocholine. While the molecular mechanism for Rab1 phosphocholination by AnkX has recently been resolved, structural insights into the activity of Lem3 remained elusive. Here, we stabilise the transient Lem3:Rab1b complex by substrate mediated covalent capture. Through crystal structures of Lem3 in the apo form and in complex with Rab1b, we reveal Lem3's catalytic mechanism, showing that it acts on Rab1 by locally unfolding it. Since Lem3 shares high structural similarity with metal-dependent protein phosphatases, our Lem3:Rab1b complex structure also sheds light on how these phosphatases recognise protein substrates.
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Affiliation(s)
- Marietta S Kaspers
- Institute of Biochemistry and Signal Transduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistr. 52, 20246, Hamburg, Germany
| | - Vivian Pogenberg
- Institute of Biochemistry and Signal Transduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistr. 52, 20246, Hamburg, Germany
| | - Christian Pett
- Chemical Biology Center (KBC), Department of Chemistry, Umeå University, Linnaeus väg 10, 90187, Umeå, Sweden
| | - Stefan Ernst
- Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Felix Ecker
- Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Philipp Ochtrop
- Chemical Biology Center (KBC), Department of Chemistry, Umeå University, Linnaeus väg 10, 90187, Umeå, Sweden
| | - Michael Groll
- Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Christian Hedberg
- Chemical Biology Center (KBC), Department of Chemistry, Umeå University, Linnaeus väg 10, 90187, Umeå, Sweden
| | - Aymelt Itzen
- Institute of Biochemistry and Signal Transduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistr. 52, 20246, Hamburg, Germany.
- Centre for Structural Systems Biology, University Medical Centre Hamburg-Eppendorf (UKE), Martinistr. 52, 20246, Hamburg, Germany.
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5
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Pfeffer SR. LRRK2
phosphorylation of Rab
GTPases
in Parkinson’s disease. FEBS Lett 2022; 597:811-818. [PMID: 36114007 DOI: 10.1002/1873-3468.14492] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/03/2022] [Accepted: 09/09/2022] [Indexed: 11/08/2022]
Abstract
Rab GTPases comprise a large family of conserved GTPases that are critical regulators of the secretory and endocytic pathways. The human genome encodes ~ 65 Rabs that localize to discrete membrane compartments and, when in their GTP-bound state, bind to effector proteins to carry out diverse functions. Activating mutations in LRRK2 kinase cause Parkinson's disease, and subsets of Rab GTPases are important LRRK2 substrates. LRRK2 phosphorylates a conserved threonine residue that is essential for Rab interaction with guanine nucleotide exchange factors, effectors, and GDI that recycles Rabs between membrane compartments. This brief review will highlight new findings related to LRRK2-mediated phosphorylation of Rab GTPases and its consequences. Remarkably, Rab phosphorylation flips a switch on Rab effector selection with dominant consequences for cell pathophysiology.
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Affiliation(s)
- Suzanne R. Pfeffer
- Department of Biochemistry Stanford University School of Medicine 279 Campus Drive Stanford CA 94305‐5307 USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network Chevy Chase MD USA
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6
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Felline A, Raimondi F, Gentile S, Fanelli F. Structural communication between the GTPase Sec4p and its activator Sec2p: Determinants of GEF activity and early deformations to nucleotide release. Comput Struct Biotechnol J 2022; 20:5162-5180. [PMID: 36187918 PMCID: PMC9508438 DOI: 10.1016/j.csbj.2022.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Ras GTPases are molecular switches that cycle between OFF and ON states depending on the bound nucleotide (i.e. GDP-bound and GTP-bound, respectively). The Rab GTPase, Sec4p, plays regulatory roles in multiple steps of intracellular vesicle trafficking. Nucleotide release is catalyzed by the Guanine Nucleotide Exchange Factor (GEF) Sec2p. Here, the integration of structural information with molecular dynamics (MD) simulations addressed a number of questions concerning the intrinsic and stimulated dynamics of Sec2p and Sec4p as well as the chain of structural deformations leading to GEF-assisted activation of the Rab GTPase. Sec2p holds an intrinsic ability to adopt the conformation found in the crystallographic complexes with Sec4p, thus suggesting that the latter selects and shifts the conformational equilibrium towards a pre-existing bound-like conformation of Sec2p. The anchoring of Sec4p to a suitable conformation of Sec2p favors the Sec2p-assisted pulling on itself of the α1/switch 1 (SWI) loop and of SWI, which loose any contact with GDP. Those deformations of Sec4p would occur earlier. Formation of the final Sec2p-Sec4p hydrophobic interface, accomplishes later. Disruption of the nucleotide cage would cause firstly loss of interactions with the guanine ring and secondly loss of interactions with the phosphates. The ease in sampling the energy landscape and adopting a bound-like conformation likely favors the catalyzing ability of GEFs for Ras GTPases.
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7
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Orr RG, Furt F, Warner EL, Agar EM, Garbarino JM, Cabral SE, Dubuke ML, Butt AM, Munson M, Vidali L. Rab-E and its interaction with myosin XI are essential for polarised cell growth. THE NEW PHYTOLOGIST 2021; 229:1924-1936. [PMID: 33098085 PMCID: PMC8168425 DOI: 10.1111/nph.17023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 10/12/2020] [Indexed: 05/07/2023]
Abstract
The fundamental process of polarised exocytosis requires the interconnected activity of molecular motors trafficking vesicular cargo within a dynamic cytoskeletal network. In plants, few mechanistic details are known about how molecular motors, such as myosin XI, associate with their secretory cargo to support the ubiquitous processes of polarised growth and cell division. Live-cell imaging coupled with targeted gene knockouts and a high-throughput RNAi assay enabled the first characterisation of the loss of Rab-E function. Yeast two-hybrid and subsequent in silico structural prediction uncovered a specific interaction between Rab-E and myosin XI that is conserved between P. patens and A. thaliana. Rab-E co-localises with myosin XI at sites of active exocytosis, and at the growing tip both proteins are spatiotemporally coupled. Rab-E is required for normal plant growth in P. patens and the rab-E and myosin XI phenotypes are rescued by A. thaliana's Rab-E1c and myosin XI-K/E, respectively. Both PpMyoXI and AtMyoXI-K interact with PpRabE14, and the interaction is specifically mediated by PpMyoXI residue V1422. This interaction is required for polarised growth. Our results suggest that the interaction of Rab-E and myosin XI is a conserved feature of polarised growth in plants.
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Affiliation(s)
- Robert G Orr
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Fabienne Furt
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Erin L Warner
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Erin M Agar
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Jennifer M Garbarino
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Sarah E Cabral
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Michelle L Dubuke
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Allison M Butt
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Mary Munson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Luis Vidali
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
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8
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Wong S, Weisman LS. Roles and regulation of myosin V interaction with cargo. Adv Biol Regul 2021; 79:100787. [PMID: 33541831 PMCID: PMC7920922 DOI: 10.1016/j.jbior.2021.100787] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 05/08/2023]
Abstract
A major question in cell biology is, how are organelles and large macromolecular complexes transported within a cell? Myosin V molecular motors play critical roles in the distribution of organelles, vesicles, and mRNA. Mis-localization of organelles that depend on myosin V motors underlie diseases in the skin, gut, and brain. Thus, the delivery of organelles to their proper destination is important for animal physiology and cellular function. Cargoes attach to myosin V motors via cargo specific adaptor proteins, which transiently bridge motors to their cargoes. Regulation of these adaptor proteins play key roles in the regulation of cargo transport. Emerging studies reveal that cargo adaptors play additional essential roles in the activation of myosin V, and the regulation of actin filaments. Here, we review how motor-adaptor interactions are controlled to regulate the proper loading and unloading of cargoes, as well as roles of adaptor proteins in the regulation of myosin V activity and the dynamics of actin filaments.
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Affiliation(s)
- Sara Wong
- Cell and Molecular Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, United States
| | - Lois S Weisman
- Cell and Developmental Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, United States.
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9
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Pechmann S. Programmed Trade-offs in Protein Folding Networks. Structure 2020; 28:1361-1375.e4. [PMID: 33053320 DOI: 10.1016/j.str.2020.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/25/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
Molecular chaperones as specialized protein quality control enzymes form the core of cellular protein homeostasis. How chaperones selectively interact with their substrate proteins thus allocate their overall limited capacity remains poorly understood. Here, I present an integrated analysis of sequence and structural determinants that define interactions of protein domains as the basic protein folding unit with the Saccharomyces cerevisiae Hsp70 Ssb. Structural homologs of single-domain proteins that differentially interact with Ssb for de novo folding were found to systematically differ in complexity of their folding landscapes, selective use of nonoptimal codons, and presence of short discriminative sequences, thus highlighting pervasive trade-offs in chaperone-assisted protein folding landscapes. However, short discriminative sequences were found to contribute by far the strongest signal toward explaining Ssb interactions. This observation suggested that some chaperone interactions may be directly programmed in the amino acid sequences rather than responding to folding challenges, possibly for regulatory advantages.
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Affiliation(s)
- Sebastian Pechmann
- Département de biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada.
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10
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Human Golgi phosphoprotein 3 is an effector of RAB1A and RAB1B. PLoS One 2020; 15:e0237514. [PMID: 32790781 PMCID: PMC7425898 DOI: 10.1371/journal.pone.0237514] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/28/2020] [Indexed: 12/21/2022] Open
Abstract
Golgi phosphoprotein 3 (GOLPH3) is a peripheral membrane protein localized at the trans-Golgi network that is also distributed in a large cytosolic pool. GOLPH3 has been involved in several post-Golgi protein trafficking events, but its precise function at the molecular level is not well understood. GOLPH3 is also considered the first oncoprotein of the Golgi apparatus, with important roles in several types of cancer. Yet, it is unknown how GOLPH3 is regulated to achieve its contribution in the mechanisms that lead to tumorigenesis. Binding of GOLPH3 to Golgi membranes depends on its interaction to phosphatidylinositol-4-phosphate. However, an early finding showed that GTP promotes the binding of GOLPH3 to Golgi membranes and vesicles. Nevertheless, it remains largely unknown whether this response is consequence of the function of GTP-dependent regulatory factors, such as proteins of the RAB family of small GTPases. Interestingly, in Drosophila melanogaster the ortholog of GOLPH3 interacts with- and behaves as effector of the ortholog of RAB1. However, there is no experimental evidence implicating GOLPH3 as a possible RAB1 effector in mammalian cells. Here, we show that human GOLPH3 interacted directly with either RAB1A or RAB1B, the two isoforms of RAB1 in humans. The interaction was nucleotide dependent and it was favored with GTP-locked active state variants of these GTPases, indicating that human GOLPH3 is a bona fide effector of RAB1A and RAB1B. Moreover, the expression in cultured cells of the GTP-locked variants resulted in less distribution of GOLPH3 in the Golgi apparatus, suggesting an intriguing model of GOLPH3 regulation.
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11
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Huntley GW, Benson DL. Origins of Parkinson's Disease in Brain Development: Insights From Early and Persistent Effects of LRRK2-G2019S on Striatal Circuits. Front Neurosci 2020; 14:265. [PMID: 32273839 PMCID: PMC7113397 DOI: 10.3389/fnins.2020.00265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 03/09/2020] [Indexed: 12/20/2022] Open
Abstract
Late-onset Parkinson's disease (PD) is dominated clinically and experimentally by a focus on dopamine neuron degeneration and ensuing motor system abnormalities. There are, additionally, a number of non-motor symptoms - including cognitive and psychiatric - that can appear much earlier in the course of the disease and also significantly impair quality of life. The neurobiology of such cognitive and psychiatric non-motor symptoms is poorly understood. The recognition of genetic forms of late-onset PD, which are clinically similar to idiopathic forms in both motor and non-motor symptoms, raises the perspective that brain cells and circuits - and the behaviors they support - differ in significant ways from normal by virtue of the fact that these mutations are carried throughout life, including especially early developmental critical periods where circuit structure and function is particularly susceptible to the influence of experience-dependent activity. In this focused review, we support this central thesis by highlighting studies of LRRK2-G2019S mouse models. We describe work that shows that in G2019S mutants, corticostriatal activity and plasticity are abnormal by P21, the end of a period of excitatory synaptogenesis in striatum. Moreover, by young adulthood, impaired striatal synaptic and non-synaptic forms of plasticity likely underlie altered and variable performance by mutant mice in validated tasks that test for depression-like and anhedonia-like behaviors. Mechanistically, deficits in cellular, synaptic and behavioral plasticity may be unified by mutation-linked defects in trafficking of AMPAR subunits and other membrane channels, which in turn may reflect impairment in the function of the Rab family of GTPases, a major target of LRRK2 phosphorylation. These findings underscore the need to better understand how PD-related mutant proteins influence brain structure and function during an extended period of brain development, and offer new clues for future therapeutic strategies to target non-motor cognitive or psychiatric symptoms of PD.
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Affiliation(s)
- George W. Huntley
- Nash Family Department of Neuroscience, Friedman Brain Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Deanna L. Benson
- Nash Family Department of Neuroscience, Friedman Brain Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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12
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Structure and mechanism of a redesigned multidrug transporter from the Major Facilitator Superfamily. Sci Rep 2020; 10:3949. [PMID: 32127561 PMCID: PMC7054563 DOI: 10.1038/s41598-020-60332-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/06/2020] [Indexed: 01/07/2023] Open
Abstract
The rapid increase of multidrug resistance poses urgent threats to human health. Multidrug transporters prompt multidrug resistance by exporting different therapeutics across cell membranes, often by utilizing the H+ electrochemical gradient. MdfA from Escherichia coli is a prototypical H+ -dependent multidrug transporter belonging to the Major Facilitator Superfamily. Prior studies revealed unusual flexibility in the coupling between multidrug binding and deprotonation in MdfA, but the mechanistic basis for this flexibility was obscure. Here we report the X-ray structures of a MdfA mutant E26T/D34M/A150E, wherein the multidrug-binding and protonation sites were revamped, separately bound to three different substrates at resolutions up to 2.0 Å. To validate the functional relevance of these structures, we conducted mutational and biochemical studies. Our data elucidated intermediate states during antibiotic recognition and suggested structural changes that accompany the substrate-evoked deprotonation of E26T/D34M/A150E. These findings help to explain the mechanistic flexibility in drug/H+ coupling observed in MdfA and may inspire therapeutic development to preempt efflux-mediated antimicrobial resistance.
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13
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The Emerging Role of Rab5 in Membrane Receptor Trafficking and Signaling Pathways. Biochem Res Int 2020; 2020:4186308. [PMID: 32104603 PMCID: PMC7036122 DOI: 10.1155/2020/4186308] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/16/2019] [Accepted: 12/07/2019] [Indexed: 02/06/2023] Open
Abstract
Ras analog in brain (Rab) proteins are small guanosine triphosphatases (GTPases) that belong to the Ras-like GTPase superfamily, and they can regulate vesicle trafficking. Rab proteins alternate between an activated (GTP-bound) state and an inactivated (GDP-bound) state. Early endosome marker Rab5 GTPase, a key member of the Rab family, plays a crucial role in endocytosis and membrane transport. The activated-state Rab5 recruits its effectors and regulates the internalization and trafficking of membrane receptors by regulating vesicle fusion and receptor sorting in the early endosomes. In this review, we summarize the role of small Rab GTPases Rab5 in membrane receptor trafficking and the activation of signaling pathways, such as Ras/MAPK and PI3K/Akt, which ultimately affect cell growth, apoptosis, tumorigenesis, and tumor development. This review may provide some insights for our future research and novel therapeutic targets for diseases.
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14
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Gomez RC, Wawro P, Lis P, Alessi DR, Pfeffer SR. Membrane association but not identity is required for LRRK2 activation and phosphorylation of Rab GTPases. J Cell Biol 2019; 218:4157-4170. [PMID: 31624137 PMCID: PMC6891090 DOI: 10.1083/jcb.201902184] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/29/2019] [Accepted: 09/06/2019] [Indexed: 01/03/2023] Open
Abstract
Parkinson’s disease–associated LRRK2 kinase is activated on the Golgi by Rab29 but phosphorylates Rab10 there and on other compartments. This study shows that phosphorylation is restricted to membrane surfaces but need not take place on the Golgi. LRRK2 kinase mutations cause familial Parkinson’s disease and increased phosphorylation of a subset of Rab GTPases. Rab29 recruits LRRK2 to the trans-Golgi and activates it there, yet some of LRRK2’s major Rab substrates are not on the Golgi. We sought to characterize the cell biology of LRRK2 activation. Unlike other Rab family members, we show that Rab29 binds nucleotide weakly, is poorly prenylated, and is not bound to GDI in the cytosol; nevertheless, Rab29 only activates LRRK2 when it is membrane bound and GTP bound. Mitochondrially anchored, GTP-bound Rab29 is both a LRRK2 substrate and activator, and it drives accumulation of active LRRK2 and phosphorylated Rab10 on mitochondria. Importantly, mitochondrially anchored LRRK2 is much less capable of phosphorylating plasma membrane–anchored Rab10 than soluble LRRK2. These data support a model in which LRRK2 associates with and dissociates from distinct membrane compartments to phosphorylate Rab substrates; if anchored, LRRK2 can modify misdelivered Rab substrates that then become trapped there because GDI cannot retrieve them.
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Affiliation(s)
- Rachel C Gomez
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA
| | - Paulina Wawro
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA
| | - Pawel Lis
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Dario R Alessi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Suzanne R Pfeffer
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA
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15
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Yan H, Huang J, Zhang H, Shim WB. A Rab GTPase protein FvSec4 is necessary for fumonisin B1 biosynthesis and virulence in Fusarium verticillioides. Curr Genet 2019; 66:205-216. [PMID: 31292685 DOI: 10.1007/s00294-019-01013-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/30/2019] [Accepted: 07/01/2019] [Indexed: 10/26/2022]
Abstract
Rab GTPases are responsible for a variety of membrane trafficking and vesicular transportation in fungi. But the role of Rab GTPases in Fusarium verticillioides, one of the key corn pathogens worldwide, remains elusive. These Small GTPases in fungi, particularly those homologous to Saccharomyces cerevisiae Sec4, are known to be associated with protein secretion, vesicular trafficking, secondary metabolism and pathogenicity. In this study, our aim was to investigate the molecular functions of FvSec4 in F. verticillioides associated with physiology and virulence. Interestingly, the FvSec4 null mutation did not impair the expression of key conidiation-related genes. Also, the mutant did not show any defect in sexual development, including perithecia production. Meanwhile, GFP-FvSec4 localized to growing hyphal tips and raised the possibility that FvSec4 is involved in protein trafficking and endocytosis. The mutant exhibited defect in corn stalk rot virulence and also significant alteration of fumonisin B1 production. The mutation led to higher sensitivity to oxidative and cell wall stress agents, and defects in carbon utilization. Gene complementation fully restored the defects in the mutant demonstrating that FvSec4 plays important roles in these functions. Taken together, our data indicate that FvSec4 is critical in F. verticillioides hyphal development, virulence, mycotoxin production and stress responses.
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Affiliation(s)
- Huijuan Yan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Jun Huang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Huan Zhang
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Won Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA.
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16
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Wu HH, Symersky J, Lu M. Structure of an engineered multidrug transporter MdfA reveals the molecular basis for substrate recognition. Commun Biol 2019; 2:210. [PMID: 31240248 PMCID: PMC6572762 DOI: 10.1038/s42003-019-0446-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/30/2019] [Indexed: 02/05/2023] Open
Abstract
MdfA is a prototypical H+-coupled multidrug transporter that is characterized by extraordinarily broad substrate specificity. The involvement of specific H-bonds in MdfA-drug interactions and the simplicity of altering the substrate specificity of MdfA contradict the promiscuous nature of multidrug recognition, presenting a baffling conundrum. Here we show the X-ray structures of MdfA variant I239T/G354E in complexes with three electrically different ligands, determined at resolutions up to 2.2 Å. Our structures reveal that I239T/G354E interacts with these compounds differently from MdfA and that I239T/G354E possesses two discrete, non-overlapping substrate-binding sites. Our results shed new light on the molecular design of multidrug-binding and protonation sites and highlight the importance of often-neglected, long-range charge-charge interactions in multidrug recognition. Beyond helping to solve the ostensible conundrum of multidrug recognition, our findings suggest the mechanistic difference between substrate and inhibitor for any H+-dependent multidrug transporter, which may open new vistas on curtailing efflux-mediated multidrug resistance.
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Affiliation(s)
- Hsin-Hui Wu
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064 USA
| | - Jindrich Symersky
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064 USA
| | - Min Lu
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064 USA
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17
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Takahashi T, Minami S, Tsuchiya Y, Tajima K, Sakai N, Suga K, Hisanaga SI, Ohbayashi N, Fukuda M, Kawahara H. Cytoplasmic control of Rab family small GTPases through BAG6. EMBO Rep 2019; 20:embr.201846794. [PMID: 30804014 PMCID: PMC6446207 DOI: 10.15252/embr.201846794] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 01/25/2019] [Accepted: 01/29/2019] [Indexed: 11/18/2022] Open
Abstract
Rab family small GTPases are master regulators of distinct steps of intracellular vesicle trafficking in eukaryotic cells. GDP‐bound cytoplasmic forms of Rab proteins are prone to aggregation due to the exposure of hydrophobic groups but the machinery that determines the fate of Rab species in the cytosol has not been elucidated in detail. In this study, we find that BAG6 (BAT3/Scythe) predominantly recognizes a cryptic portion of GDP‐associated Rab8a, while its major GTP‐bound active form is not recognized. The hydrophobic residues of the Switch I region of Rab8a are essential for its interaction with BAG6 and the degradation of GDP‐Rab8a via the ubiquitin‐proteasome system. BAG6 prevents the excess accumulation of inactive Rab8a, whose accumulation impairs intracellular membrane trafficking. BAG6 binds not only Rab8a but also a functionally distinct set of Rab family proteins, and is also required for the correct distribution of Golgi and endosomal markers. From these observations, we suggest that Rab proteins represent a novel set of substrates for BAG6, and the BAG6‐mediated pathway is associated with the regulation of membrane vesicle trafficking events in mammalian cells.
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Affiliation(s)
- Toshiki Takahashi
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Setsuya Minami
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Yugo Tsuchiya
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Kazu Tajima
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Natsumi Sakai
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Kei Suga
- Department of Cell Physiology, Kyorin University School of Medicine, Mitaka, Japan.,Department of Chemistry, Kyorin University School of Medicine, Mitaka, Japan
| | - Shin-Ichi Hisanaga
- Laboratory of Molecular Neuroscience, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Norihiko Ohbayashi
- Department of Physiological Chemistry, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Mitsunori Fukuda
- Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Hiroyuki Kawahara
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
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18
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Yun JS, Ha SC, Kim S, Kim YG, Kim H, Chang JH. Crystal structure of Arabidopsis thaliana RabA1a. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:93-109. [PMID: 30010245 DOI: 10.1111/jipb.12700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/11/2018] [Indexed: 06/08/2023]
Abstract
RabGTPase is a member of the Ras superfamily of small GTPases, which share a GTP-binding pocket containing highly conserved motifs that promote GTP hydrolysis. In Arabidopsis, the RabA group, which corresponds to the Rab11 group in animals, functions in the recycling of endosomes that control docking and fusion during vesicle transport. However, their molecular mechanisms remain unknown. In this study, we determined the crystal structures of the GDP-bound inactive form and both GppNHp- and GTP-bound active forms of RabA1a, at resolutions of 2.8, 2.6, and 2.6 Å, respectively. A bound sulfate ion in the active site of the GDP-bound structure stabilized Switch II by bridging the interaction between a magnesium ion and Arg74. Comparisons of the two states of RabA1a with Rab11 proteins revealed clear differences in the Switch I and II loops. These results suggested that conformational change of the Switch regions of RabA1a, derived by GTP or GDP binding, could maintain subcellular membrane traffic through the specific interaction of effector molecules.
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Affiliation(s)
- Ji-Sook Yun
- Department of Biology Education, Kyungpook National University, Daehak-ro 80, Daegu 41566, South Korea
| | - Sung Chul Ha
- Beamline Science Division, Pohang Accelerator Laboratory, Jigok-ro 127, Pohang 37673, South Korea
| | - Shinae Kim
- Department of Biology Education, Kyungpook National University, Daehak-ro 80, Daegu 41566, South Korea
| | - Yeon-Gil Kim
- Beamline Science Division, Pohang Accelerator Laboratory, Jigok-ro 127, Pohang 37673, South Korea
| | - Hyeran Kim
- Department of Biological Sciences, Kangwon National University, Kangwondaehak-gil 1, Chuncheon 24341, South Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daehak-ro 80, Daegu 41566, South Korea
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19
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Maheshwari D, Yadav R, Rastogi R, Jain A, Tripathi S, Mukhopadhyay A, Arora A. Structural and Biophysical Characterization of Rab5a from Leishmania Donovani. Biophys J 2018; 115:1217-1230. [PMID: 30241678 PMCID: PMC6170798 DOI: 10.1016/j.bpj.2018.08.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/10/2018] [Accepted: 08/15/2018] [Indexed: 12/21/2022] Open
Abstract
Leishmania donovani possess two isoforms of Rab5 (Rab5a and Rab5b), which are involved in fluid phase and receptor-mediated endocytosis, respectively. We have characterized the solution structure and dynamics of a stabilized truncated LdRab5a mutant. For the purpose of NMR structure determination, protein stability was enhanced by systematically introducing various deletions and mutations. Deletion of hypervariable C-terminal and the 20 residues LdRab5a specific insert slightly enhanced the stability, which was further improved by C107S mutation. The final construct, truncated LdRab5a with C107S mutation, was found to be stable for longer durations at higher concentration, with an increase in melting temperature by 10°C. Solution structure of truncated LdRab5a shows the characteristic GTPase fold having nucleotide and effector binding sites. Orientation of switch I and switch II regions match well with that of guanosine 5'-(β, γ-imido)triphosphate (GppNHp)-bound human Rab5a, indicating that the truncated LdRab5a attains the canonical GTP bound state. However, the backbone dynamics of the P-loop, switch I, and switch II regions were slower than that observed for guanosine 5'-(β, γ-imido)triphosphate (GMPPNP)-bound H-Ras. This dynamic profile may further complement the residue-specific complementarity in determining the specificity of interaction with the effectors. In parallel, biophysical investigations revealed the urea induced unfolding of truncated LdRab5a to be a four-state process that involved two intermediates, I1 and I2. The maximal 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (Bis-ANS) binding was observed for I2 state, which was inferred to have molten globule like characteristics. Overall, the strategy presented would have significant impact for studying other Rab and small GTPase proteins by NMR spectroscopy.
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Affiliation(s)
- Diva Maheshwari
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Rahul Yadav
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ruchir Rastogi
- Cell Biology Lab, National Institute of Immunology, New Delhi, India
| | - Anupam Jain
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Sarita Tripathi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | | | - Ashish Arora
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India.
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20
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Pylypenko O, Hammich H, Yu IM, Houdusse A. Rab GTPases and their interacting protein partners: Structural insights into Rab functional diversity. Small GTPases 2018. [PMID: 28632484 DOI: 10.1080/215412481336191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
Rab molecular switches are key players in defining membrane identity and regulating intracellular trafficking events in eukaryotic cells. In spite of their global structural similarity, Rab-family members acquired particular features that allow them to perform specific cellular functions. The overall fold and local sequence conservations enable them to utilize a common machinery for prenylation and recycling; while individual Rab structural differences determine interactions with specific partners such as GEFs, GAPs and effector proteins. These interactions orchestrate the spatiotemporal regulation of Rab localization and their turning ON and OFF, leading to tightly controlled Rab-specific functionalities such as membrane composition modifications, recruitment of molecular motors for intracellular trafficking, or recruitment of scaffold proteins that mediate interactions with downstream partners, as well as actin cytoskeleton regulation. In this review we summarize structural information on Rab GTPases and their complexes with protein partners in the context of partner binding specificity and functional outcomes of their interactions in the cell.
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Affiliation(s)
- Olena Pylypenko
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| | - Hussein Hammich
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
- b Sorbonne Universités , UPMC Univ Paris 06, Sorbonne Universités, IFD , Paris , France
| | - I-Mei Yu
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| | - Anne Houdusse
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
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21
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Ku B, You JA, Oh KJ, Yun HY, Lee HS, Shin HC, Jung J, Shin YB, Kim SJ. Crystal structures of two forms of the Acanthamoeba polyphaga mimivirus Rab GTPase. Arch Virol 2017; 162:3407-3416. [PMID: 28779233 DOI: 10.1007/s00705-017-3510-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/30/2017] [Indexed: 01/09/2023]
Abstract
Acanthamoeba polyphaga mimivirus (APMV) is a member of the family of giant viruses, harboring a 1,200 kbp genome within its 700 nm-diameter viral particle. The R214 gene of the APMV genome was recently shown to encode a homologue of the Rab GTPases, molecular switch proteins known to play a pivotal role in the regulation of membrane trafficking that were considered to exist only in eukaryotes. Herein, we report the first crystal structures of GDP- and GTP-bound forms of APMV Rab GTPase, both of which were determined at high resolution. An in-depth structural comparison of APMV Rab with each other and with mammalian Rab homologues led to an atomic-level elucidation of the inactive-active conformational change upon GDP/GTP exchange. APMV Rab GTPase exhibited considerable structural similarity to human Rab5, as previously predicted based on its amino acid sequence. However, it also contains unique structural features differentiating it from mammalian homologues, such as the functional substitution of a phenylalanine residue for the stabilization of the nucleotide's guanine base.
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Affiliation(s)
- Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
- Department of Bioscience, University of Science and Technology KRIBB School, Daejeon, 34113, Republic of Korea.
| | - Jin A You
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Bioscience, University of Science and Technology KRIBB School, Daejeon, 34113, Republic of Korea
| | - Kyoung-Jin Oh
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Hye-Yeoung Yun
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Bioscience, University of Science and Technology KRIBB School, Daejeon, 34113, Republic of Korea
| | - Hye Seon Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Ho-Chul Shin
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Juyeon Jung
- Hazard Monitoring BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Yong-Beom Shin
- Hazard Monitoring BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
- Department of Bioscience, University of Science and Technology KRIBB School, Daejeon, 34113, Republic of Korea.
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22
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Mulvaney EP, O'Meara F, Khan AR, O'Connell DJ, Kinsella BT. Identification of α-helix 4 (α4) of Rab11a as a novel Rab11-binding domain (RBD): Interaction of Rab11a with the Prostacyclin Receptor. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1819-1832. [PMID: 28739266 DOI: 10.1016/j.bbamcr.2017.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/28/2017] [Accepted: 07/20/2017] [Indexed: 12/29/2022]
Abstract
The cellular trafficking of numerous G protein-coupled receptors (GPCRs) is known to be regulated by Rab proteins that involves a direct protein:protein interaction between the receptor and the GTPase. In the case of the human prostacyclin receptor (hIP), it undergoes agonist-induced internalization and subsequent Rab11a-dependent recyclization involving an interaction between a Rab11-binding domain (RBD) localized within its carboxyl-tail domain with Rab11a. However, the GPCR-interacting domain on Rab11a itself is unknown. Hence, we sought to identify the region within Rab11a that mediates its interaction with the RBD of the hIP. The α4 helix region of Rab11 was identified as a novel binding domain for the hIP, a site entirely distinct from the Switch I/Switch II -regions that act as specific binding domain for most other Rab and Ras-like GTPase interactants. Specifically, Glu138 within α4 helix of Rab11a appears to contact with key residues (e.g. Lys304) within the RBD of the hIP, where such contacts differ depending on the agonist-activated versus -inactive status of the hIP. Through mutational studies, supported by in silico homology modelling of the inactive and active hIP:Rab11a complexes, a mechanism is proposed to explain both the constitutive and agonist-induced binding of Rab11a to regulate intracellular trafficking of the hIP. Collectively, these studies are not only the first to identify α4 helix of Rab11a as a protein binding domain on the GTPase but also reveal novel mechanistic insights into the intracellular trafficking of the hIP, and potentially of other members of the GPCR superfamily, involving Rab11-dependent mechanisms.
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Affiliation(s)
- Eamon P Mulvaney
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Fergal O'Meara
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Amir R Khan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - David J O'Connell
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - B Therese Kinsella
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.
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23
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Pylypenko O, Hammich H, Yu IM, Houdusse A. Rab GTPases and their interacting protein partners: Structural insights into Rab functional diversity. Small GTPases 2017. [PMID: 28632484 PMCID: PMC5902227 DOI: 10.1080/21541248.2017.1336191] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Rab molecular switches are key players in defining membrane identity and regulating intracellular trafficking events in eukaryotic cells. In spite of their global structural similarity, Rab-family members acquired particular features that allow them to perform specific cellular functions. The overall fold and local sequence conservations enable them to utilize a common machinery for prenylation and recycling; while individual Rab structural differences determine interactions with specific partners such as GEFs, GAPs and effector proteins. These interactions orchestrate the spatiotemporal regulation of Rab localization and their turning ON and OFF, leading to tightly controlled Rab-specific functionalities such as membrane composition modifications, recruitment of molecular motors for intracellular trafficking, or recruitment of scaffold proteins that mediate interactions with downstream partners, as well as actin cytoskeleton regulation. In this review we summarize structural information on Rab GTPases and their complexes with protein partners in the context of partner binding specificity and functional outcomes of their interactions in the cell.
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Affiliation(s)
- Olena Pylypenko
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| | - Hussein Hammich
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France.,b Sorbonne Universités , UPMC Univ Paris 06, Sorbonne Universités, IFD , Paris , France
| | - I-Mei Yu
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| | - Anne Houdusse
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
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24
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Lepore D, Spassibojko O, Pinto G, Collins RN. Cell cycle-dependent phosphorylation of Sec4p controls membrane deposition during cytokinesis. J Cell Biol 2017; 214:691-703. [PMID: 27621363 PMCID: PMC5021095 DOI: 10.1083/jcb.201602038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 08/04/2016] [Indexed: 11/22/2022] Open
Abstract
The GTPase Sec4p is a critical regulator of polarized membrane traffic. Lepore et al. show that the polo-like kinase Cdc5p phosphorylates Sec4p, which promotes coordinated membrane deposition during cytokinesis. Intracellular trafficking is an essential and conserved eukaryotic process. Rab GTPases are a family of proteins that regulate and provide specificity for discrete membrane trafficking steps by harnessing a nucleotide-bound cycle. Global proteomic screens have revealed many Rab GTPases as phosphoproteins, but the effects of this modification are not well understood. Using the Saccharomyces cerevisiae Rab GTPase Sec4p as a model, we have found that phosphorylation negatively regulates Sec4p function by disrupting the interaction with the exocyst complex via Sec15p. We demonstrate that phosphorylation of Sec4p is a cell cycle–dependent process associated with cytokinesis. Through a genomic kinase screen, we have also identified the polo-like kinase Cdc5p as a positive regulator of Sec4p phosphorylation. Sec4p spatially and temporally localizes with Cdc5p exclusively when Sec4p phosphorylation levels peak during the cell cycle, indicating Sec4p is a direct Cdc5p substrate. Our data suggest the physiological relevance of Sec4p phosphorylation is to facilitate the coordination of membrane-trafficking events during cytokinesis.
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Affiliation(s)
- Dante Lepore
- Field of Biochemistry, Molecular and Cellular Biology, Cornell University, Ithaca, NY 14853 Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
| | - Olya Spassibojko
- Cornell Undergraduate Biology, Cornell University, Ithaca, NY 14853
| | - Gabrielle Pinto
- Cornell Undergraduate Biology, Cornell University, Ithaca, NY 14853
| | - Ruth N Collins
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
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25
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Shi MM, Shi CH, Xu YM. Rab GTPases: The Key Players in the Molecular Pathway of Parkinson's Disease. Front Cell Neurosci 2017; 11:81. [PMID: 28400718 PMCID: PMC5369176 DOI: 10.3389/fncel.2017.00081] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/09/2017] [Indexed: 11/13/2022] Open
Abstract
Parkinson’s disease (PD) is a progressive movement disorder with multiple non-motor symptoms. Although family genetic mutations only account for a small proportion of the cases, these mutations have provided several lines of evidence for the pathogenesis of PD, such as mitochondrial dysfunction, protein misfolding and aggregation, and the impaired autophagy-lysosome system. Recently, vesicle trafficking defect has emerged as a potential pathogenesis underlying this disease. Rab GTPases, serving as the core regulators of cellular membrane dynamics, may play an important role in the molecular pathway of PD through the complex interplay with numerous factors and PD-related genes. This might shed new light on the potential therapeutic strategies. In this review, we emphasize the important role of Rab GTPases in vesicle trafficking and summarize the interactions between Rab GTPases and different PD-related genes.
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Affiliation(s)
- Meng-Meng Shi
- Department of Neurology, The first affiliated Hospital, Zhengzhou University Zhengzhou, China
| | - Chang-He Shi
- Department of Neurology, The first affiliated Hospital, Zhengzhou University Zhengzhou, China
| | - Yu-Ming Xu
- Department of Neurology, The first affiliated Hospital, Zhengzhou University Zhengzhou, China
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26
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Mishra AK, Lambright DG. Invited review: Small GTPases and their GAPs. Biopolymers 2016; 105:431-48. [PMID: 26972107 PMCID: PMC5439442 DOI: 10.1002/bip.22833] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/16/2016] [Accepted: 03/10/2016] [Indexed: 12/11/2022]
Abstract
Widespread utilization of small GTPases as major regulatory hubs in many different biological systems derives from a conserved conformational switch mechanism that facilitates cycling between GTP-bound active and GDP-bound inactive states under control of guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), which accelerate slow intrinsic rates of activation by nucleotide exchange and deactivation by GTP hydrolysis, respectively. Here we review developments leading to current understanding of intrinsic and GAP catalyzed GTP hydrolytic reactions in small GTPases from structural, molecular and chemical mechanistic perspectives. Despite the apparent simplicity of the GTPase cycle, the structural bases underlying the hallmark hydrolytic reaction and catalytic acceleration by GAPs are considerably more diverse than originally anticipated. Even the most fundamental aspects of the reaction mechanism have been challenging to decipher. Through a combination of experimental and in silico approaches, the outlines of a consensus view have begun to emerge for the best studied paradigms. Nevertheless, recent observations indicate that there is still much to be learned. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 431-448, 2016.
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Affiliation(s)
- Ashwini K Mishra
- Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605
| | - David G Lambright
- Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605
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27
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miR-15b-5p induces endoplasmic reticulum stress and apoptosis in human hepatocellular carcinoma, both in vitro and in vivo, by suppressing Rab1A. Oncotarget 2016; 6:16227-38. [PMID: 26023735 PMCID: PMC4599266 DOI: 10.18632/oncotarget.3970] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/06/2015] [Indexed: 01/01/2023] Open
Abstract
In human hepatocellular carcinoma (HCC), aberrant expression of miRNAs correlates with tumor cell proliferation, apoptosis, invasion, and migration by targeting downstream proteins. miR-15b levels are reported increased in HCC tissues; however, they negatively correlate to HCC recurrence. Our aim was to understand the reason for this phenomenon. We used the reverse transcription-polymerase chain reaction (RT-PCR) to measure miR-15b-5p expression in both HCC tissues and HCC cell lines. Our results were consistent with the report. Using bioinformatics and luciferase reporter assays, we identified Rab1A as a novel and direct target of miR-15b-5p. Inhibiting the function of Rab1A with shRab1A also inhibited the growth of HCC cells and induced endoplasmic reticulum stress (ERS) and apoptosis. Similarly, suppressing Rab1A by overexpression of miR-15b-5p also inhibited cell growth and induced ERS and apoptosis. Moreover, re-expression of Rab1A rescued the miR-15b-5p -induced ERS, apoptosis, and growth inhibition in HCC cells. In vivo assays were further performed to testify them. Taken together, our data suggest that miR-15b-5p induces ERS, apoptosis, and growth inhibition by targeting and suppressing Rab1A, acting as a tumor suppressor gene in HCC. This finding suggests a novel relation among Rabs, miRNAs, and apoptosis.
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Srikanth S, Kim KD, Gao Y, Woo JS, Ghosh S, Calmettes G, Paz A, Abramson J, Jiang M, Gwack Y. A large Rab GTPase encoded by CRACR2A is a component of subsynaptic vesicles that transmit T cell activation signals. Sci Signal 2016; 9:ra31. [PMID: 27016526 DOI: 10.1126/scisignal.aac9171] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
More than 60 members of the Rab family of guanosine triphosphatases (GTPases) exist in the human genome. Rab GTPases are small proteins that are primarily involved in the formation, trafficking, and fusion of vesicles. We showed thatCRACR2A(Ca(2+) release-activated Ca(2+) channel regulator 2A) encodes a lymphocyte-specific large Rab GTPase that contains multiple functional domains, including EF-hand motifs, a proline-rich domain (PRD), and a Rab GTPase domain with an unconventional prenylation site. Through experiments involving gene silencing in cells and knockout mice, we demonstrated a role for CRACR2A in the activation of the Ca(2+) and c-Jun N-terminal kinase signaling pathways in response to T cell receptor (TCR) stimulation. Vesicles containing this Rab GTPase translocated from near the Golgi to the immunological synapse formed between a T cell and a cognate antigen-presenting cell to activate these signaling pathways. The interaction between the PRD of CRACR2A and the guanidine nucleotide exchange factor Vav1 was required for the accumulation of these vesicles at the immunological synapse. Furthermore, we demonstrated that GTP binding and prenylation of CRACR2A were associated with its localization near the Golgi and its stability. Our findings reveal a previously uncharacterized function of a large Rab GTPase and vesicles near the Golgi in TCR signaling. Other GTPases with similar domain architectures may have similar functions in T cells.
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Affiliation(s)
- Sonal Srikanth
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
| | - Kyun-Do Kim
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Yuanyuan Gao
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Jin Seok Woo
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Shubhamoy Ghosh
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Guillaume Calmettes
- Department of Medicine (Cardiology), David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Aviv Paz
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Jeff Abramson
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Meisheng Jiang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Yousang Gwack
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
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Zade A, Sengupta M, Kondabagil K. Extensive in silico analysis of Mimivirus coded Rab GTPase homolog suggests a possible role in virion membrane biogenesis. Front Microbiol 2015; 6:929. [PMID: 26441866 PMCID: PMC4569851 DOI: 10.3389/fmicb.2015.00929] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/24/2015] [Indexed: 11/29/2022] Open
Abstract
Rab GTPases are the key regulators of intracellular membrane trafficking in eukaryotes. Many viruses and intracellular bacterial pathogens have evolved to hijack the host Rab GTPase functions, mainly through activators and effector proteins, for their benefit. Acanthamoeba polyphaga mimivirus (APMV) is one of the largest viruses and belongs to the monophyletic clade of nucleo-cytoplasmic large DNA viruses (NCLDV). The inner membrane lining is integral to the APMV virion structure. APMV assembly involves extensive host membrane modifications, like vesicle budding and fusion, leading to the formation of a membrane sheet that is incorporated into the virion. Intriguingly, APMV and all group I members of the Mimiviridae family code for a putative Rab GTPase protein. APMV is the first reported virus to code for a Rab GTPase (encoded by R214 gene). Our thorough in silico analysis of the subfamily specific (SF) region of Mimiviridae Rab GTPase sequences suggests that they are related to Rab5, a member of the group II Rab GTPases, of lower eukaryotes. Because of their high divergence from the existing three isoforms, A, B, and C of the Rab5-family, we suggest that Mimiviridae Rabs constitute a new isoform, Rab5D. Phylogenetic analysis indicated probable horizontal acquisition from a lower eukaryotic ancestor followed by selection and divergence. Furthermore, interaction network analysis suggests that vps34 (a Class III PI3K homolog, coded by APMV L615), Atg-8 and dynamin (host proteins) are recruited by APMV Rab GTPase during capsid assembly. Based on these observations, we hypothesize that APMV Rab plays a role in the acquisition of inner membrane during virion assembly.
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Affiliation(s)
- Amrutraj Zade
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay Mumbai, India
| | - Malavi Sengupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay Mumbai, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay Mumbai, India
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Rinaldi FC, Packer M, Collins R. New insights into the molecular mechanism of the Rab GTPase Sec4p activation. BMC STRUCTURAL BIOLOGY 2015; 15:14. [PMID: 26263895 PMCID: PMC4531439 DOI: 10.1186/s12900-015-0041-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/08/2015] [Indexed: 11/14/2022]
Abstract
Background Sec4p is a small monomeric Ras-related GTP-binding protein (23 kDa) that regulates polarized exocytosis in S. cerevisiae. In this study we examine the structural effects of a conserved serine residue in the P-loop corresponding to G12 in Ras. Results We show that the Sec4p residue serine 29 forms a hydrogen bond with the nucleotide. Mutations of this residue have a different impact than equivalent mutations in Ras and can form stable associations with the exchange factor allowing us to elucidate the structure of a complex of Sec4p bound to the exchange factor Sec2p representing an early stage of the exchange reaction. Conclusions Our structural investigation of the Sec4p-Sec2p complex reveals the role of the Sec2p coiled-coil domain in facilitating the fast kinetics of the exchange reaction. For Ras-family GTPases, single point mutations that impact the signaling state of the molecule have been well described however less structural information is available for equivalent mutations in the case of Rab proteins. Understanding the structural properties of mutants such as the one described here, provides useful insights into unique aspects of Rab GTPase function.
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Affiliation(s)
- Fabio C Rinaldi
- Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA.
| | - Michael Packer
- Honors Program in Undergraduate Studies, Cornell University, Ithaca, NY, 14853, USA.
| | - Ruth Collins
- Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA.
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Watson K, Rossi G, Temple B, Brennwald P. Structural basis for recognition of the Sec4 Rab GTPase by its effector, the Lgl/tomosyn homologue, Sro7. Mol Biol Cell 2015. [PMID: 26202462 PMCID: PMC4569318 DOI: 10.1091/mbc.e15-04-0228] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Members of the tomosyn/Lgl/Sro7 family play important roles in vesicle trafficking and cell polarity in eukaryotic cells. The yeast homologue, Sro7, is believed to act as a downstream effector of the Sec4 Rab GTPase to promote soluble N-ethylmaleimide-sensitive factor adaptor protein receptor (SNARE) assembly during Golgi-to-cell surface vesicle transport. Here we describe the identification of a Sec4 binding site on the surface of Sro7 that is contained within a cleft created by the junction of two adjacent β-propellers that form the core structure of Sro7. Computational docking experiments suggested four models for interaction of GTP-Sec4 with the Sro7 binding cleft. Further mutational and biochemical analyses confirmed that only one of the four docking arrangements is perfectly consistent with our genetic and biochemical interaction data. Close examination of this docking model suggests a structural basis for the high substrate and nucleotide selectivity in effector binding by Sro7. Finally, analysis of the surface variation within the homologous interaction site on tomosyn-1 and Lgl-1 structural models suggests a possible conserved Rab GTPase effector function in tomosyn vertebrate homologues.
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Affiliation(s)
- Kelly Watson
- Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599 Graduate Program in Cell and Developmental Biology, University of North Carolina School of Medicine, Chapel Hill, NC 27599
| | - Guendalina Rossi
- Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599
| | - Brenda Temple
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599 R. L. Juliano Structural Bioinformatics Core, University of North Carolina School of Medicine, Chapel Hill, NC 27599
| | - Patrick Brennwald
- Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599 Graduate Program in Cell and Developmental Biology, University of North Carolina School of Medicine, Chapel Hill, NC 27599
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Liang P, He L, Yu J, Xie Z, Chen X, Mao Q, Liang C, Huang Y, Lu G, Yu X. Identification and characterization of a member of Rab subfamily, Rab8, from Clonorchis sinensis. Parasitol Res 2015; 114:1857-64. [PMID: 25773178 DOI: 10.1007/s00436-015-4372-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 02/04/2015] [Indexed: 10/23/2022]
Abstract
The Rabs act as a binary molecular switch that utilizes the conformational changes associated with the GTP/GDP cycle to elicit responses from target proteins. It regulates a broad spectrum of cellular processes including cell proliferation, cytoskeletal assembly, and intracellular membrane trafficking in eukaryotes. The Rab8 from Clonorchis sinensis (CsRab8) was composed of 199 amino acids. The deduced amino acid sequence shared above 50% identities with other species from trematode, tapeworm, mammal, insecta, nematode, and reptile, respectively. The homologous analysis of sequences showed the conservative domains: G1 box (GDSGVGKS), G2 box (T), G3 box (DTAG), G4 box (GNKCDL), and G5 box. In addition, the structure modeling had also shown other functional domains: GTP/Mg(2+) binding sites, switch I region, and switch II region. A phylogenic tree analysis indicated that the CsRab8 was clustered with the Rab from Schistosoma japonicum, and trematode and tapeworm came from the same branch, which was different from an evolutional branch built by other species, such as mammal animal, insecta, nematode, and reptile. The recombinant CsRab8 protein was expressed in Escherichia coli and the purified protein was a soluble molecule by 12% sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis. CsRab8 was identified as a component of excretory/secretory products of C. sinensis by western blot analysis. The transcriptional level of CsRab8 at metacercaria stage was the highest at the four stages and higher by 56.49-folds than that at adult worm, 1.23-folds than that at excysted metacercaria, and 2.69-folds than that at egg stage. Immunohistochemical localization analysis showed that CsRab8 was specifically distributed in the tegument, vitellarium, eggs, and testicle of adult worms, and detected on the vitellarium and tegument of metacercaria. Combined with the results, CsRab8 is indispensable for survival and development of parasites, especially for regulating excretory/secretory products secretion.
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Affiliation(s)
- Pei Liang
- Department of Pathogen Biology, Hainan Medical College, Haikou, Hainan, 571199, China
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33
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Rab proteins: the key regulators of intracellular vesicle transport. Exp Cell Res 2014; 328:1-19. [PMID: 25088255 DOI: 10.1016/j.yexcr.2014.07.027] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/06/2014] [Accepted: 07/23/2014] [Indexed: 01/01/2023]
Abstract
Vesicular/membrane trafficking essentially regulates the compartmentalization and abundance of proteins within the cells and contributes in many signalling pathways. This membrane transport in eukaryotic cells is a complex process regulated by a large and diverse array of proteins. A large group of monomeric small GTPases; the Rabs are essential components of this membrane trafficking route. Most of the Rabs are ubiquitously expressed proteins and have been implicated in vesicle formation, vesicle motility/delivery along cytoskeleton elements and docking/fusion at target membranes through the recruitment of effectors. Functional impairments of Rabs affecting transport pathways manifest different diseases. Rab functions are accompanied by cyclical activation and inactivation of GTP-bound and GDP-bound forms between the cytosol and membranes which is regulated by upstream regulators. Rab proteins are characterized by their distinct sub-cellular localization and regulate a wide variety of endocytic, transcytic and exocytic transport pathways. Mutations of Rabs affect cell growth, motility and other biological processes.
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34
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Khan AR, Ménétrey J. Structural biology of Arf and Rab GTPases' effector recruitment and specificity. Structure 2014; 21:1284-97. [PMID: 23931141 DOI: 10.1016/j.str.2013.06.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/30/2013] [Accepted: 06/05/2013] [Indexed: 11/15/2022]
Abstract
Arf and Rab proteins, members of small GTPases superfamily, localize to specific subcellular compartments and regulate intracellular trafficking. To carry out their cellular functions, Arfs/Rabs interact with numerous and structurally diverse effector proteins. Over the years, a number of Arf/Rab:effector complexes have been crystallized and their structures reveal shared binding modes including α-helical packing, β-β complementation, and heterotetrameric assemblies. We review available structural information and provide a framework for in-depth analysis of complexes. The unifying features that we identify are organized into a classification scheme for different modes of Arf/Rab:effector interactions, which includes "all-α-helical," "mixed α-helical," "β-β zipping," and "bivalent" modes of binding. Additionally, we highlight structural determinants that are the basis of effector specificity. We conclude by expanding on functional implications that are emerging from available structural information under our proposed classification scheme.
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Affiliation(s)
- Amir R Khan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland.
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35
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Lall P, Horgan CP, Oda S, Franklin E, Sultana A, Hanscom SR, McCaffrey MW, Khan AR. Structural and functional analysis of FIP2 binding to the endosome-localised Rab25 GTPase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2679-90. [PMID: 24056041 DOI: 10.1016/j.bbapap.2013.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 09/08/2013] [Accepted: 09/12/2013] [Indexed: 11/30/2022]
Abstract
Rab small GTPases are the master regulators of intracellular trafficking in eukaryotes. They mediate spatial and temporal recruitment of effector proteins to distinct cellular compartments through GTP-induced changes in their conformation. Despite numerous structural studies, the molecular basis for Rab/effector specificity and subsequent biological activity remains poorly understood. Rab25, also known as Rab11c, which is epithelial-specific, has been heavily implicated in ovarian cancer development and independently appears to act as a tumour suppressor in the context of a distinct subset of carcinomas. Here, we show that Rab25 associates with FIP2 and can recruit this effector protein to endosomal membranes. We report the crystal structure of Rab25 in complex with the C-terminal region of FIP2, which consists of a central dimeric FIP2 coiled-coil that mediates a heterotetrameric Rab25-(FIP2)2-Rab25 complex. Thermodynamic analyses show that, despite a relatively conserved interface, FIP2 binds to Rab25 with an approximate 3-fold weaker affinity than to Rab11a. Reduced affinity is mainly associated with lower enthalpic gains for Rab25:FIP2 complex formation, and can be attributed to subtle differences in the conformations of switch 1 and switch 2. These cellular, structural and thermodynamic studies provide insight into the Rab11/Rab25 subfamily of small GTPases that regulate endosomal trafficking pathways in eukaryotes.
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Affiliation(s)
- Patrick Lall
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland
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36
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Abstract
Whereas most of what we know today about the Ras-related small GTPases of the Rab family stems from observations made on Golgi complex, endosome and plasma membrane trafficking, a subset of Rabs localizes in part or predominantly to the ER (endoplasmic reticulum). Here, Rabs such as Rab1, Rab2, Rab6 and Rab33 can regulate the anterograde and retrograde trafficking of vesicles between the Golgi complex, the ERGIC (ER-Golgi intermediate compartment) and the ER itself. However, among the ER-associated Rabs, some Rabs appear to perform roles not directly related to trafficking: these Rabs (e.g. Rab32 or Rab24) could aid proteins of the atlastin and reticulon families in determining the extent and direction of ER tubulation. In so doing, these Rabs regulate not only ER contacts with other organelles such as mitochondria, but also the formation of autophagosomes.
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37
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Pfeffer SR. Rab GTPase regulation of membrane identity. Curr Opin Cell Biol 2013; 25:414-9. [PMID: 23639309 DOI: 10.1016/j.ceb.2013.04.002] [Citation(s) in RCA: 258] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 03/25/2013] [Accepted: 04/05/2013] [Indexed: 11/15/2022]
Abstract
A fundamental question in cell biology is how cells determine membrane compartment identity and the directionality with which cargoes pass through the secretory and endocytic pathways. The discovery of so-called 'Rab cascades' provides a satisfying molecular mechanism that helps to resolve this paradox. One Rab GTPase has the ability to template the localization of the subsequent acting Rab GTPase along a given transport pathway. Thus, in addition to determining compartment identity and functionality, Rab GTPases are likely able to order the events of membrane trafficking. This review will highlight recent advances in our understanding of Rabs and Rab cascades.
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Affiliation(s)
- Suzanne R Pfeffer
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive B400, Stanford, CA 94305-5307, USA.
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38
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Kögel T, Rudolf R, Hodneland E, Copier J, Regazzi R, Tooze SA, Gerdes HH. Rab3D is critical for secretory granule maturation in PC12 cells. PLoS One 2013; 8:e57321. [PMID: 23526941 PMCID: PMC3602456 DOI: 10.1371/journal.pone.0057321] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 01/21/2013] [Indexed: 11/19/2022] Open
Abstract
Neuropeptide- and hormone-containing secretory granules (SGs) are synthesized at the trans-Golgi network (TGN) as immature secretory granules (ISGs) and complete their maturation in the F-actin-rich cell cortex. This maturation process is characterized by acidification-dependent processing of cargo proteins, condensation of the SG matrix and removal of membrane and proteins not destined to mature secretory granules (MSGs). Here we addressed a potential role of Rab3 isoforms in these maturation steps by expressing their nucleotide-binding deficient mutants in PC12 cells. Our data show that the presence of Rab3D(N135I) decreases the restriction of maturing SGs to the F-actin-rich cell cortex, blocks the removal of the endoprotease furin from SGs and impedes the processing of the luminal SG protein secretogranin II. This strongly suggests that Rab3D is implicated in the subcellular localization and maturation of ISGs.
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Affiliation(s)
- Tanja Kögel
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Rüdiger Rudolf
- Interdisciplinary Center of Neurobiology, University of Heidelberg, Heidelberg, Germany
| | | | - John Copier
- London Research Institute Cancer Research United Kingdom, Lincoln's Inn Fields Laboratories, London, United Kingdom
| | - Romano Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Sharon A. Tooze
- London Research Institute Cancer Research United Kingdom, Lincoln's Inn Fields Laboratories, London, United Kingdom
| | - Hans-Hermann Gerdes
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Interdisciplinary Center of Neurobiology, University of Heidelberg, Heidelberg, Germany
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39
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Khan AR. Oligomerization of rab/effector complexes in the regulation of vesicle trafficking. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:579-614. [PMID: 23663983 DOI: 10.1016/b978-0-12-386931-9.00021-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Rabs comprise the largest member of the Ras superfamily of small GTPases with over 60 proteins in mammals and 11 proteins in yeast. Like all small GTPases, Rabs oscillate between an inactive GDP-bound conformation and an active GTP-bound state that is tethered to lipid membranes via a C-terminal prenylation site on conserved cysteine residues. In their active state, Rabs regulate various aspects of membrane trafficking, including vesicle formation, transport, docking, and fusion. The critical element of biological activity is the recruitment of cytosolic effector proteins to specific endomembranes by active Rabs. The importance of Rabs in cellular processes is apparent from their links to genetic disorders, immunodeficiency, cancer, and pathogen invasion. During the last decade, numerous structures of complexes have shed light on the molecular basis for Rab/effector specificity and their topological organization on subcellular membranes. Here, I review the known structures of Rab/effector complexes and their modes of oligomerization. This is followed by a brief discussion on the thermodynamics of effector recruitment, which has not been documented sufficiently in previous reviews. A summary of diseases associated with Rab/effector trafficking pathways concludes this chapter.
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Affiliation(s)
- Amir R Khan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
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40
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Raimondi F, Felline A, Portella G, Orozco M, Fanelli F. Light on the structural communication in Ras GTPases. J Biomol Struct Dyn 2012; 31:142-57. [PMID: 22849539 DOI: 10.1080/07391102.2012.698379] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The graph theory was combined with fluctuation dynamics to investigate the structural communication in four small G proteins, Arf1, H-Ras, RhoA, and Sec4. The topology of small GTPases is such that it requires the presence of the nucleotide to acquire a persistent structural network. The majority of communication paths involves the nucleotide and does not exist in the unbound forms. The latter are almost devoid of high-frequency paths. Thus, small Ras GTPases acquire the ability to transfer signals in the presence of nucleotide, suggesting that it modifies the intrinsic dynamics of the protein through the establishment of regions of hyperlinked nodes with high occurrence of correlated motions. The analysis of communication paths in the inactive (S(GDP)) and active (S(GTP)) states of the four G proteins strengthened the separation of the Ras-like domain into two dynamically distinct lobes, i.e. lobes 1 and 2, representing, respectively, the N-terminal and C-terminal halves of the domain. In the framework of this separation, interfunctional states and interfamily differences could be inferred. The structure network undergoes a reshaping depending on the bound nucleotide. Nucleotide-dependent divergences in structural communication reach the maximum in Arf1 and the minimum in RhoA. In Arf1, the nucleotide-dependent paths essentially express a communication between the G box 4 (G4) and distal portions of lobe 1. In the S(GDP) state, the G4 communicates with the N-term, while, in the S(GTP) state, the G4 communicates with the switch II. Clear differences could be also found between Arf1 and the other three G proteins. In Arf1, the nucleotide tends to communicate with distal portions of lobe 1, whereas in H-Ras, RhoA, and Sec4 it tends to communicate with a cluster of aromatic/hydrophobic amino acids in lobe 2. These differences may be linked, at least in part, to the divergent membrane anchoring modes that would involve the N-term for the Arf family and the C-term for the Rab/Ras/Rho families.
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Affiliation(s)
- Francesco Raimondi
- Department of Chemistry, University of Modena and Reggio Emilia, Modena, Italy
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41
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Crystal structure of Rab6A'(Q72L) mutant reveals unexpected GDP/Mg²⁺ binding with opened GTP-binding domain. Biochem Biophys Res Commun 2012; 424:269-73. [PMID: 22750005 DOI: 10.1016/j.bbrc.2012.06.102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 06/20/2012] [Indexed: 01/14/2023]
Abstract
The Ras small G protein-superfamily is a family of GTP hydrolases whose activity is regulated by GTP/GDP binding states. Rab6A, a member of the Ras superfamily, is involved in the regulation of vesicle trafficking, which is critical for endocytosis, biosynthesis, secretion, cell differentiation and cell growth. Rab6A exists in two isoforms, termed RabA and Rab6A'. Substitution of Gln72 to Leu72 (Q72L) at Rab6 family blocks GTP hydrolysis activity and this mutation usually causes the Rab6 protein to be constitutively in an active form. Here, we report the crystal structure of the human Rab6A'(Q72L) mutant form at 1.9Å resolution. Unexpectedly, we found that Rab6A'(Q72L) possesses GDP/Mg(2+) in the GTP binding pockets, which is formed by a flexible switch I and switch II. Large conformational changes were also detected in the switch I and switch II regions. Our structure revealed that the non-hydrolysable, constitutively active form of Rab6A' can accommodate GDP/Mg(2+) in the open conformation.
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42
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Liu S, Storrie B. Are Rab proteins the link between Golgi organization and membrane trafficking? Cell Mol Life Sci 2012; 69:4093-106. [PMID: 22581368 DOI: 10.1007/s00018-012-1021-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 04/18/2012] [Accepted: 04/24/2012] [Indexed: 11/25/2022]
Abstract
The fundamental separation of Golgi function between subcompartments termed cisternae is conserved across all eukaryotes. Likewise, Rab proteins, small GTPases of the Ras superfamily, are putative common coordinators of Golgi organization and protein transport. However, despite sequence conservation, e.g., Rab6 and Ypt6 are conserved proteins between humans and yeast, the fundamental organization of the organelle can vary profoundly. In the yeast Saccharomyces cerevisiae, the Golgi cisternae are physically separated from one another, while in mammalian cells, the cisternae are stacked one upon the other. Moreover, in mammalian cells, many Golgi stacks are typically linked together to generate a ribbon structure. Do evolutionarily conserved Rab proteins regulate secretory membrane trafficking and diverse Golgi organization in a common manner? In mammalian cells, some Golgi-associated Rab proteins function in coordination of protein transport and maintenance of Golgi organization. These include Rab6, Rab33B, Rab1, Rab2, Rab18, and Rab43. In yeast, these include Ypt1, Ypt32, and Ypt6. Here, based on evidence from both yeast and mammalian cells, we speculate on the essential role of Rab proteins in Golgi organization and protein transport.
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Affiliation(s)
- Shijie Liu
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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Arbitrary protein-protein docking targets biologically relevant interfaces. BMC BIOPHYSICS 2012; 5:7. [PMID: 22559010 PMCID: PMC3441232 DOI: 10.1186/2046-1682-5-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 04/11/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUND Protein-protein recognition is of fundamental importance in the vast majority of biological processes. However, it has already been demonstrated that it is very hard to distinguish true complexes from false complexes in so-called cross-docking experiments, where binary protein complexes are separated and the isolated proteins are all docked against each other and scored. Does this result, at least in part, reflect a physical reality? False complexes could reflect possible nonspecific or weak associations. RESULTS In this paper, we investigate the twilight zone of protein-protein interactions, building on an interesting outcome of cross-docking experiments: false complexes seem to favor residues from the true interaction site, suggesting that randomly chosen partners dock in a non-random fashion on protein surfaces. Here, we carry out arbitrary docking of a non-redundant data set of 198 proteins, with more than 300 randomly chosen "probe" proteins. We investigate the tendency of arbitrary partners to aggregate at localized regions of the protein surfaces, the shape and compositional bias of the generated interfaces, and the potential of this property to predict biologically relevant binding sites. We show that the non-random localization of arbitrary partners after protein-protein docking is a generic feature of protein structures. The interfaces generated in this way are not systematically planar or curved, but tend to be closer than average to the center of the proteins. These results can be used to predict biological interfaces with an AUC value up to 0.69 alone, and 0.72 when used in combination with evolutionary information. An appropriate choice of random partners and number of docking models make this method computationally practical. It is also noted that nonspecific interfaces can point to alternate interaction sites in the case of proteins with multiple interfaces. We illustrate the usefulness of arbitrary docking using PEBP (Phosphatidylethanolamine binding protein), a kinase inhibitor with multiple partners. CONCLUSIONS An approach using arbitrary docking, and based solely on physical properties, can successfully identify biologically pertinent protein interfaces.
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Cheng W, Yin K, Lu D, Li B, Zhu D, Chen Y, Zhang H, Xu S, Chai J, Gu L. Structural insights into a unique Legionella pneumophila effector LidA recognizing both GDP and GTP bound Rab1 in their active state. PLoS Pathog 2012; 8:e1002528. [PMID: 22416225 PMCID: PMC3295573 DOI: 10.1371/journal.ppat.1002528] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 12/26/2011] [Indexed: 01/07/2023] Open
Abstract
The intracellular pathogen Legionella pneumophila hijacks the endoplasmic reticulum (ER)-derived vesicles to create an organelle designated Legionella-containing vacuole (LCV) required for bacterial replication. Maturation of the LCV involved acquisition of Rab1, which is mediated by the bacterial effector protein SidM/DrrA. SidM/DrrA is a bifunctional enzyme having the activity of both Rab1-specific GDP dissociation inhibitor (GDI) displacement factor (GDF) and guanine nucleotide exchange factor (GEF). LidA, another Rab1-interacting bacterial effector protein, was reported to promote SidM/DrrA-mediated recruitment of Rab1 to the LCV as well. Here we report the crystal structures of LidA complexes with GDP- and GTP-bound Rab1 respectively. Structural comparison revealed that GDP-Rab1 bound by LidA exhibits an active and nearly identical conformation with that of GTP-Rab1, suggesting that LidA can disrupt the switch function of Rab1 and render it persistently active. As with GTP, LidA maintains GDP-Rab1 in the active conformation through interaction with its two conserved switch regions. Consistent with the structural observations, biochemical assays showed that LidA binds to GDP- and GTP-Rab1 equally well with an affinity approximately 7.5 nM. We propose that the tight interaction with Rab1 allows LidA to facilitate SidM/DrrA-catalyzed release of Rab1 from GDIs. Taken together, our results support a unique mechanism by which a bacterial effector protein regulates Rab1 recycling.
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Affiliation(s)
- Wei Cheng
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
| | - Kun Yin
- Key Laboratory for Protein Sciences of Ministry of Education, School of Biological Sciences, Tsinghua University, Beijing, China
- Shandong Institute of Parasitical Diseases, Shandong Academy of Medical Sciences, Jining, Shandong, China
| | - Defen Lu
- Key Laboratory for Protein Sciences of Ministry of Education, School of Biological Sciences, Tsinghua University, Beijing, China
| | - Bingqing Li
- Key Laboratory for Protein Sciences of Ministry of Education, School of Biological Sciences, Tsinghua University, Beijing, China
| | - Deyu Zhu
- Key Laboratory for Protein Sciences of Ministry of Education, School of Biological Sciences, Tsinghua University, Beijing, China
| | - Yuzhen Chen
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Hao Zhang
- Key Laboratory for Protein Sciences of Ministry of Education, School of Biological Sciences, Tsinghua University, Beijing, China
| | - Sujuan Xu
- Key Laboratory for Protein Sciences of Ministry of Education, School of Biological Sciences, Tsinghua University, Beijing, China
| | - Jijie Chai
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
- * E-mail: (LG); (JC)
| | - Lichuan Gu
- Key Laboratory for Protein Sciences of Ministry of Education, School of Biological Sciences, Tsinghua University, Beijing, China
- * E-mail: (LG); (JC)
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Hu YH, Deng T, Sun L. The Rab1 GTPase of Sciaenops ocellatus modulates intracellular bacterial infection. FISH & SHELLFISH IMMUNOLOGY 2011; 31:1005-1012. [PMID: 21889593 DOI: 10.1016/j.fsi.2011.08.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 08/21/2011] [Accepted: 08/22/2011] [Indexed: 05/31/2023]
Abstract
The Rab family proteins belong to the Ras-like GTPase superfamily and play important roles in intracellular membrane trafficking. To date no studies on fish Rab have been documented, though rab-like sequences have been found in a number of teleosts. In this study, we identified and analyzed a Rab homologue, SoRab1, from red drum, Sciaenops ocellatus. The cDNA of SoRab1 contains a 5'- untranslated region (UTR) of 358 bp, an open reading frame (ORF) of 612 bp, and a 3'-UTR of 265 bp. The ORF encodes a putative protein of 203 residues, which shares 92-99% overall sequence identities with the Rab1 from fish, human, and mouse. SoRab1 possesses a typical Rab1 GTPase domain with the conserved G box motifs and the switch I and switch II regions. Recombinant SoRab1 purified from Escherichia coli exhibits apparent GTPase activity. Quantitative real time RT-PCR analysis showed that SoRab1 expression was detected in a number of tissues, with the lowest expression found in blood and highest expression found in muscle. Bacterial and lipopolysaccharide challenges significantly upregulated SoRab1 expression in liver, kidney, and spleen in time-dependent manners. Transient overexpression of SoRab1 in primary hepatocytes reduced intracellular bacterial infection, whereas interference with SoRab1 expression by RNAi enhanced intracellular bacterial invasion. These results provide the first indication that a fish Rab1 GTPase, SoRab1, regulates intracellular bacterial infection and thus is likely to play a role in bacteria-induced host immune defense.
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Affiliation(s)
- Yong-hua Hu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
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The activation cycle of Rab GTPase Ypt32 reveals structural determinants of effector recruitment and GDI binding. FEBS Lett 2011; 585:3520-7. [PMID: 22024479 DOI: 10.1016/j.febslet.2011.10.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 10/09/2011] [Accepted: 10/11/2011] [Indexed: 02/02/2023]
Abstract
Rab GTPases localize to distinct sub-cellular compartments and regulate vesicle trafficking in eukaryotic cells. Yeast Rabs Ypt31/32 and Sec4 have 68% homology and bind to common interactors, yet play distinct roles in the transport of exocytic vesicles. The structures of Ypt31/32 have not previously been reported in the uncomplexed state. We describe the crystal structures of GTP and GDP forms of Ypt32 to understand the molecular basis for Rab function. The structure of Ypt32(GTP) reveals that the switch II conformation is distinct from Sec4(GTP) in spite of a highly conserved amino acid sequence. Also, Ypt32(GDP) reveals a remarkable change in conformation of the switch II helix induced by binding to GDI, which has not been described previously.
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Heger CD, Wrann CD, Collins RN. Phosphorylation provides a negative mode of regulation for the yeast Rab GTPase Sec4p. PLoS One 2011; 6:e24332. [PMID: 21931684 PMCID: PMC3171412 DOI: 10.1371/journal.pone.0024332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 08/06/2011] [Indexed: 12/31/2022] Open
Abstract
The Rab family of Ras-related GTPases are part of a complex signaling circuitry in eukaryotic cells, yet we understand little about the mechanisms that underlie Rab protein participation in such signal transduction networks, or how these networks are integrated at the physiological level. Reversible protein phosphorylation is widely used by cells as a signaling mechanism. Several phospho-Rabs have been identified, however the functional consequences of the modification appear to be diverse and need to be evaluated on an individual basis. In this study we demonstrate a role for phosphorylation as a negative regulatory event for the action of the yeast Rab GTPase Sec4p in regulating polarized growth. Our data suggest that the phosphorylation of the Rab Sec4p prevents interactions with its effector, the exocyst component Sec15p, and that the inhibition may be relieved by a PP2A phosphatase complex containing the regulatory subunit Cdc55p.
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Affiliation(s)
- Christopher D. Heger
- Graduate Program in Pharmacology, Cornell University, Ithaca, New York, United States of America
- Department of Molecular Medicine, Cornell University, Ithaca, New York, United States of America
| | - Christiane D. Wrann
- Leadership Program for Veterinary Students, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Ruth N. Collins
- Department of Molecular Medicine, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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Raimondi F, Portella G, Orozco M, Fanelli F. Nucleotide binding switches the information flow in ras GTPases. PLoS Comput Biol 2011; 7:e1001098. [PMID: 21390270 PMCID: PMC3048383 DOI: 10.1371/journal.pcbi.1001098] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 01/28/2011] [Indexed: 12/12/2022] Open
Abstract
The Ras superfamily comprises many guanine nucleotide-binding proteins (G proteins) that are essential to intracellular signal transduction. The guanine nucleotide-dependent intrinsic flexibility patterns of five G proteins were investigated in atomic detail through Molecular Dynamics simulations of the GDP- and GTP-bound states (SGDP and SGTP, respectively). For all the considered systems, the intrinsic flexibility of SGDP was higher than that of SGTP, suggesting that Guanine Exchange Factor (GEF) recognition and nucleotide switch require higher amplitude motions than effector recognition or GTP hydrolysis. Functional mode, dynamic domain, and interaction energy correlation analyses highlighted significant differences in the dynamics of small G proteins and Gα proteins, especially in the inactive state. Indeed, SGDP of Gαt, is characterized by a more extensive energy coupling between nucleotide binding site and distal regions involved in GEF recognition compared to small G proteins, which attenuates in the active state. Moreover, mechanically distinct domains implicated in nucleotide switch could be detected in the presence of GDP but not in the presence of GTP. Finally, in small G proteins, functional modes are more detectable in the inactive state than in the active one and involve changes in solvent exposure of two highly conserved amino acids in switches I and II involved in GEF recognition. The average solvent exposure of these amino acids correlates in turn with the rate of GDP release, suggesting for them either direct or indirect roles in the process of nucleotide switch. Collectively, nucleotide binding changes the information flow through the conserved Ras-like domain, where GDP enhances the flexibility of mechanically distinct portions involved in nucleotide switch, and favors long distance allosteric communication (in Gα proteins), compared to GTP. The Ras superfamily comprises many guanine nucleotide-binding proteins (G proteins) that are essential to intracellular signal transduction. These proteins act biologically as molecular switches cycling between ON and OFF states, thereby controlling a variety of processes ranging from cell growth and differentiation to vesicular and nuclear transport. In spite of the extremely high biological and medical relevance of the Ras GTPase superfamily, a comprehensive structural/dynamic view of the trans-family and family-specific functioning mechanisms is still lacking. In this study, we gained insights into the functional dynamics of Ras GTPases by deciphering the dynamic information encrypted in the topology of these proteins depending on the nucleotide-bound state, i.e. GDP- or GTP-bound (SGDP and SGTP, respectively). Collectively, nucleotide binding changes the information flow through the conserved Ras-like domain, where GDP enhances the flexibility of mechanically distinct portions involved in nucleotide switch, and favors long distance allosteric communication (in Gα proteins), compared to GTP. Functional dynamics is instrumental in GDP switch, which for the members of the Gα family, different from small G proteins, requires allosteric communication between nucleotide and Guanine Exchange Factor binding sites.
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Affiliation(s)
- Francesco Raimondi
- Department of Chemistry, University of Modena and Reggio Emilia, Modena, Italy
- Dulbecco Telethon Institute (DTI), University of Modena and Reggio Emilia, Modena, Italy
| | - Guillem Portella
- Molecular Modeling and Bioinformatics Unit, IRB-BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine, and Barcelona Supercomputing Center, Barcelona, Spain
| | - Modesto Orozco
- Molecular Modeling and Bioinformatics Unit, IRB-BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine, and Barcelona Supercomputing Center, Barcelona, Spain
- National Institute of Bioinformatics, Parc Científic de Barcelona, Barcelona, Spain
| | - Francesca Fanelli
- Department of Chemistry, University of Modena and Reggio Emilia, Modena, Italy
- Dulbecco Telethon Institute (DTI), University of Modena and Reggio Emilia, Modena, Italy
- * E-mail:
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Vázquez-Martínez R, Malagón MM. Rab proteins and the secretory pathway: the case of rab18 in neuroendocrine cells. Front Endocrinol (Lausanne) 2011; 2:1. [PMID: 22649356 PMCID: PMC3355916 DOI: 10.3389/fendo.2011.00001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 01/03/2011] [Indexed: 11/21/2022] Open
Abstract
The secretory pathway is a process characteristic of cells specialized in secretion such as endocrine cells and neurons. It consists of different stages that are dependent on specific transport of proteins in vesicular-tubular carriers. Biochemical analyses have unveiled a number of protein families that confer identity to carrier vesicles and specificity to their transport. Among them is the family of Rab proteins, Ras-like small GTPases that anchor to the surface of transport vesicles and participate in vesicle formation from the donor compartment, transport along cytoskeletal tracks, and docking and fusion with the acceptor compartment. All of these functions are accomplished through the recruitment of effector proteins, such as sorting adaptors, tethering factors, kinases, phosphatases, and motors. The numerous Rab proteins have distinct subcellular distributions throughout the endomembrane system, which ensures efficient cargo transfer. Rab proteins act as molecular switches that alternate between a cytosolic GDP-bound, inactive form and a membrane-associated GTP-bound, active conformation. Cycling between inactive and active states is a highly regulated process that enables Rabs to confer spatio-temporal precision to the different stages through which a vesicle passes during its lifespan. This review focuses on our current knowledge on Rab functioning, from their structural features to the multiple regulatory proteins and effectors that control Rab activity and translate Rab function. Furthermore, we also summarize the information available on a particular Rab protein, Rab18, which has been linked to the control of secretory granule traffic in neuroendocrine cells.
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Affiliation(s)
- Rafael Vázquez-Martínez
- Department of Cell Biology, Physiology and Immunology, University of CordobaCordoba, Spain
- Instituto Maimónides de Investigación Biomédica, Biomedical Research Center in Red Physiopathology of Obesity and NutritionCordoba, Spain
| | - Maria M. Malagón
- Department of Cell Biology, Physiology and Immunology, University of CordobaCordoba, Spain
- Instituto Maimónides de Investigación Biomédica, Biomedical Research Center in Red Physiopathology of Obesity and NutritionCordoba, Spain
- *Correspondence: Maria M. Malagón, Department of Cell Biology, Physiology and Immunology, Universidad de Córdoba, Campus de Rabanales, Edificio Severo-Ochoa, Planta 3, E-14014 Córdoba, Spain. e-mail:
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Insight into the molecular switch mechanism of human Rab5a from molecular dynamics simulations. Biochem Biophys Res Commun 2009; 390:608-12. [PMID: 19819222 DOI: 10.1016/j.bbrc.2009.10.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 10/05/2009] [Indexed: 11/23/2022]
Abstract
Rab5a is currently a most interesting target because it is responsible for regulating the early endosome fusion in endocytosis and possibly the budding process. We utilized longtime-scale molecular dynamics simulations to investigate the internal motion of the wild-type Rab5a and its A30P mutant. It was observed that, after binding with GTP, the global flexibility of the two proteins is increasing, while the local flexibility in their sensitive sites (P-loop, switch I and II regions) is decreasing. Also, the mutation of Ala30 to Pro30 can cause notable flexibility variations in the sensitive sites. However, this kind of variations is dramatically reduced after binding with GTP. Such a remarkable feature is mainly caused by the water network rearrangements in the sensitive sites. These findings might be of use for revealing the profound mechanism of the displacements of Rab5a switch regions, as well as the mechanism of the GDP dissociation and GTP association.
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