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Pazos F. Prediction of Protein Sites and Physicochemical Properties Related to Functional Specificity. Bioengineering (Basel) 2021; 8:bioengineering8120201. [PMID: 34940354 PMCID: PMC8698372 DOI: 10.3390/bioengineering8120201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
Specificity Determining Positions (SDPs) are protein sites responsible for functional specificity within a family of homologous proteins. These positions are extracted from a family’s multiple sequence alignment and complement the fully conserved positions as predictors of functional sites. SDP analysis is now routinely used for locating these specificity-related sites in families of proteins of biomedical or biotechnological interest with the aim of mutating them to switch specificities or design new ones. There are many different approaches for detecting these positions in multiple sequence alignments. Nevertheless, existing methods report the potential SDP positions but they do not provide any clue on the physicochemical basis behind the functional specificity, which has to be inferred a-posteriori by manually inspecting these positions in the alignment. In this work, a new methodology is presented that, concomitantly with the detection of the SDPs, automatically provides information on the amino-acid physicochemical properties more related to the change in specificity. This new method is applied to two different multiple sequence alignments of homologous of the well-studied RasH protein representing different cases of functional specificity and the results discussed in detail.
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Affiliation(s)
- Florencio Pazos
- Computational Systems Biology Group, Systems Biology Department, National Centre for Biotechnology (CNB-CSIC), c/Darwin, 3, 28049 Madrid, Spain
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2
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Pitarch B, Ranea JAG, Pazos F. Protein residues determining interaction specificity in paralogous families. Bioinformatics 2021; 37:1076-1082. [PMID: 33135068 DOI: 10.1093/bioinformatics/btaa934] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 10/06/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023] Open
Abstract
MOTIVATION Predicting the residues controlling a protein's interaction specificity is important not only to better understand its interactions but also to design mutations aimed at fine-tuning or swapping them as well. RESULTS In this work, we present a methodology that combines sequence information (in the form of multiple sequence alignments) with interactome information to detect that kind of residues in paralogous families of proteins. The interactome is used to define pairwise similarities of interaction contexts for the proteins in the alignment. The method looks for alignment positions with patterns of amino-acid changes reflecting the similarities/differences in the interaction neighborhoods of the corresponding proteins. We tested this new methodology in a large set of human paralogous families with structurally characterized interactions, and discuss in detail the results for the RasH family. We show that this approach is a better predictor of interfacial residues than both, sequence conservation and an equivalent 'unsupervised' method that does not use interactome information. AVAILABILITY AND IMPLEMENTATION http://csbg.cnb.csic.es/pazos/Xdet/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Borja Pitarch
- Computational Systems Biology Group, Systems Biology Department, National Centre for Biotechnology (CNB-CSIC), 28049 Madrid, Spain
| | - Juan A G Ranea
- Department of Molecular Biology and Biochemistry, University of Malaga, Malaga 29071, Spain.,CIBER de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain.,Institute of Biomedical Research in Malaga (IBIMA), Malaga, Spain
| | - Florencio Pazos
- Computational Systems Biology Group, Systems Biology Department, National Centre for Biotechnology (CNB-CSIC), 28049 Madrid, Spain
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Rezaei Adariani S, Kazemein Jasemi NS, Bazgir F, Wittich C, Amin E, Seidel CAM, Dvorsky R, Ahmadian MR. A comprehensive analysis of RAS-effector interactions reveals interaction hotspots and new binding partners. J Biol Chem 2021; 296:100626. [PMID: 33930461 PMCID: PMC8163975 DOI: 10.1016/j.jbc.2021.100626] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 02/07/2023] Open
Abstract
RAS effectors specifically interact with GTP-bound RAS proteins to link extracellular signals to downstream signaling pathways. These interactions rely on two types of domains, called RAS-binding (RB) and RAS association (RA) domains, which share common structural characteristics. Although the molecular nature of RAS-effector interactions is well-studied for some proteins, most of the RA/RB-domain-containing proteins remain largely uncharacterized. Here, we searched through human proteome databases, extracting 41 RA domains in 39 proteins and 16 RB domains in 14 proteins, each of which can specifically select at least one of the 25 members in the RAS family. We next comprehensively investigated the sequence–structure–function relationship between different representatives of the RAS family, including HRAS, RRAS, RALA, RAP1B, RAP2A, RHEB1, and RIT1, with all members of RA domain family proteins (RASSFs) and the RB-domain-containing CRAF. The binding affinity for RAS-effector interactions, determined using fluorescence polarization, broadly ranged between high (0.3 μM) and very low (500 μM) affinities, raising interesting questions about the consequence of these variable binding affinities in the regulation of signaling events. Sequence and structural alignments pointed to two interaction hotspots in the RA/RB domains, consisting of an average of 19 RAS-binding residues. Moreover, we found novel interactions between RRAS1, RIT1, and RALA and RASSF7, RASSF9, and RASSF1, respectively, which were systematically explored in sequence–structure–property relationship analysis, and validated by mutational analysis. These data provide a set of distinct functional properties and putative biological roles that should now be investigated in the cellular context.
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Affiliation(s)
- Soheila Rezaei Adariani
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Neda S Kazemein Jasemi
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Farhad Bazgir
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Christoph Wittich
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Ehsan Amin
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany; Medical Faculty, Institute of Neural and Sensory Physiology, Heinrich Heine University, Düsseldorf, Germany
| | - Claus A M Seidel
- Chair of Molecular Physical Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Radovan Dvorsky
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Mohammad R Ahmadian
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany.
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Pontes C, Ruiz-Serra V, Lepore R, Valencia A. Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic β-CoVs. Comput Struct Biotechnol J 2021; 19:759-766. [PMID: 33456724 PMCID: PMC7802526 DOI: 10.1016/j.csbj.2021.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 01/13/2023] Open
Abstract
The recent emergence of the novel SARS-CoV-2 in China and its rapid spread in the human population has led to a public health crisis worldwide. Like in SARS-CoV, horseshoe bats currently represent the most likely candidate animal source for SARS-CoV-2. Yet, the specific mechanisms of cross-species transmission and adaptation to the human host remain unknown. Here we show that the unsupervised analysis of conservation patterns across the β-CoV spike protein family, using sequence information alone, can provide valuable insights on the molecular basis of the specificity of β-CoVs to different host cell receptors. More precisely, our results indicate that host cell receptor usage is encoded in the amino acid sequences of different CoV spike proteins in the form of a set of specificity determining positions (SDPs). Furthermore, by integrating structural data, in silico mutagenesis and coevolution analysis we could elucidate the role of SDPs in mediating ACE2 binding across the Sarbecovirus lineage, either by engaging the receptor through direct intermolecular interactions or by affecting the local environment of the receptor binding motif. Finally, by the analysis of coevolving mutations across a paired MSA we were able to identify key intermolecular contacts occurring at the spike-ACE2 interface. These results show that effective mining of the evolutionary records held in the sequence of the spike protein family can help tracing the molecular mechanisms behind the evolution and host-receptor adaptation of circulating and future novel β-CoVs.
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Key Words
- APC, average product correction
- CoVs, Coronaviruses
- EV, evolutionary rate
- Functional specificity
- MCA, multiple correspondence analysis
- MI, mutual information
- MSA, multiple sequence alignment
- NTD, N-terminal domain
- Phylogenetic analysis
- Protein subfamilies
- RBD, receptor binding domain
- RBM, receptor binding motif
- SARS-CoV-2
- SDPs, specificity determining positions
- Specificity Determining Positions
- Spike protein evolution
- hACE2, human angiotensin converting enzyme 2
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Affiliation(s)
- Camila Pontes
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- University of Brasília (UnB), 70910-900, Brasília - DF, Brazil
| | | | - Rosalba Lepore
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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5
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Exploring the interactions of the RAS family in the human protein network and their potential implications in RAS-directed therapies. Oncotarget 2018; 7:75810-75826. [PMID: 27713118 PMCID: PMC5342780 DOI: 10.18632/oncotarget.12416] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/15/2016] [Indexed: 12/14/2022] Open
Abstract
RAS proteins are the founding members of the RAS superfamily of GTPases. They are involved in key signaling pathways regulating essential cellular functions such as cell growth and differentiation. As a result, their deregulation by inactivating mutations often results in aberrant cell proliferation and cancer. With the exception of the relatively well-known KRAS, HRAS and NRAS proteins, little is known about how the interactions of the other RAS human paralogs affect cancer evolution and response to treatment. In this study we performed a comprehensive analysis of the relationship between the phylogeny of RAS proteins and their location in the protein interaction network. This analysis was integrated with the structural analysis of conserved positions in available 3D structures of RAS complexes. Our results show that many RAS proteins with divergent sequences are found close together in the human interactome. We found specific conserved amino acid positions in this group that map to the binding sites of RAS with many of their signaling effectors, suggesting that these pairs could share interacting partners. These results underscore the potential relevance of cross-talking in the RAS signaling network, which should be taken into account when considering the inhibitory activity of drugs targeting specific RAS oncoproteins. This study broadens our understanding of the human RAS signaling network and stresses the importance of considering its potential cross-talk in future therapies.
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Chagoyen M, García-Martín JA, Pazos F. Practical analysis of specificity-determining residues in protein families. Brief Bioinform 2015; 17:255-61. [DOI: 10.1093/bib/bbv045] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/15/2015] [Indexed: 12/17/2022] Open
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Mott HR, Owen D. Structures of Ras superfamily effector complexes: What have we learnt in two decades? Crit Rev Biochem Mol Biol 2015; 50:85-133. [PMID: 25830673 DOI: 10.3109/10409238.2014.999191] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The Ras superfamily small G proteins are master regulators of a diverse range of cellular processes and act via downstream effector molecules. The first structure of a small G protein-effector complex, that of Rap1A with c-Raf1, was published 20 years ago. Since then, the structures of more than 60 small G proteins in complex with their effectors have been published. These effectors utilize a diverse array of structural motifs to interact with the G protein fold, which we have divided into four structural classes: intermolecular β-sheets, helical pairs, other interactions, and pleckstrin homology (PH) domains. These classes and their representative structures are discussed and a contact analysis of the interactions is presented, which highlights the common effector-binding regions between and within the small G protein families.
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Affiliation(s)
- Helen R Mott
- Department of Biochemistry, University of Cambridge , Cambridge , UK
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Mills RD, Mulhern TD, Liu F, Culvenor JG, Cheng HC. Prediction of the Repeat Domain Structures and Impact of Parkinsonism-Associated Variations on Structure and Function of all Functional Domains of Leucine-Rich Repeat Kinase 2 (LRRK2). Hum Mutat 2014; 35:395-412. [DOI: 10.1002/humu.22515] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 01/08/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Ryan D. Mills
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Parkville Victoria Australia
| | - Terrence D. Mulhern
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Parkville Victoria Australia
| | - Fei Liu
- Department of Chemistry & Biomolecular Sciences; Macquarie University; NSW Australia
| | - Janetta G. Culvenor
- Department of Pathology; University of Melbourne; Parkville Victoria Australia
| | - Heung-Chin Cheng
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Parkville Victoria Australia
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9
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Integrated RAS signaling defined by parallel NMR detection of effectors and regulators. Nat Chem Biol 2014; 10:223-30. [DOI: 10.1038/nchembio.1435] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 11/26/2013] [Indexed: 12/16/2022]
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10
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Monastyrskyy B, D'Andrea D, Fidelis K, Tramontano A, Kryshtafovych A. Evaluation of residue-residue contact prediction in CASP10. Proteins 2013; 82 Suppl 2:138-53. [PMID: 23760879 DOI: 10.1002/prot.24340] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 05/14/2013] [Accepted: 05/21/2013] [Indexed: 12/13/2022]
Abstract
We present the results of the assessment of the intramolecular residue-residue contact predictions from 26 prediction groups participating in the 10th round of the CASP experiment. The most recently developed direct coupling analysis methods did not take part in the experiment likely because they require a very deep sequence alignment not available for any of the 114 CASP10 targets. The performance of contact prediction methods was evaluated with the measures used in previous CASPs (i.e., prediction accuracy and the difference between the distribution of the predicted contacts and that of all pairs of residues in the target protein), as well as new measures, such as the Matthews correlation coefficient, the area under the precision-recall curve and the ranks of the first correctly and incorrectly predicted contact. We also evaluated the ability to detect interdomain contacts and tested whether the difficulty of predicting contacts depends upon the protein length and the depth of the family sequence alignment. The analyses were carried out on the target domains for which structural homologs did not exist or were difficult to identify. The evaluation was performed for all types of contacts (short, medium, and long-range), with emphasis placed on long-range contacts, i.e. those involving residues separated by at least 24 residues along the sequence. The assessment suggests that the best CASP10 contact prediction methods perform at approximately the same level, and comparably to those participating in CASP9.
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Abstract
Co-evolution is a fundamental component of the theory of evolution and is essential for understanding the relationships between species in complex ecological networks. A wide range of co-evolution-inspired computational methods has been designed to predict molecular interactions, but it is only recently that important advances have been made. Breakthroughs in the handling of phylogenetic information and in disentangling indirect relationships have resulted in an improved capacity to predict interactions between proteins and contacts between different protein residues. Here, we review the main co-evolution-based computational approaches, their theoretical basis, potential applications and foreseeable developments.
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Affiliation(s)
- David de Juan
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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12
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Goldfinger LE, Lee S. Emerging treatments in lung cancer - targeting the RLIP76 molecular transporter. LUNG CANCER-TARGETS AND THERAPY 2013; 2013:61-69. [PMID: 25419163 PMCID: PMC4240306 DOI: 10.2147/lctt.s53672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Multidrug resistance in lung cancer cells is a significant obstacle in the treatment of lung cancer. Resistance to chemotherapeutic agents is often the result of efflux of the drugs from cancer cells, mediated by adenosine triphosphate (ATP)-dependent drug transport across the plasma membrane. Thus, identifying molecular targets in the cancer cell transport machinery could be a key factor in successful combinatorial therapy, along with chemotherapeutic drugs. The transport protein Ral-interacting protein of 76 kDa (RLIP76), also known as Ral-binding protein 1 (RalBP1), is a highly promising target for lung cancer treatment. RLIP76 is an ATP-dependent non-ATP-binding cassette (ABC) transporter, responsible for the major transport function in many cells, including many cancer cell lines, causing efflux of glutathione-electrophile conjugates of both endogenous metabolites and environmental toxins. RLIP76 is expressed in most human tissues, and is overexpressed in non-small-cell lung cancer cell lines and in many tumor types. The blockade of RLIP76 by various approaches has been shown to increase the sensitivity to radiation and chemotherapeutic drugs, and leads to apoptosis in cells. In xenograft tumor models in mice, RLIP76 blockade or depletion results in complete and sustained regression across many cancer cell types, including lung cancer cells. In addition to its transport function, RLIP76 has many other cellular and physiological functions based on its domain structure, which includes a unique Ral-binding domain and a Rho GTPase activating protein (RhoGAP)-catalytic domain as well as docking sites for multiple signaling proteins. As a Ral effector, RhoGAP, and adapter protein, RLIP76 has been shown to play important roles in endocytosis, mitochondrial fission, cell spreading and migration, actin dynamics during gastrulation, and Ras-induced tumorigenesis. Additionally, RLIP76 is also important for stromal cell function in tumors, as it was recently shown to be required for efficient endothelial cell function and angiogenesis in solid tumors. However, RLIP76 knockout mice are viable, and blockade effects appear to be selective for implanted tumors in mice, suggesting the possibility that RLIP76-targeting drugs may be successful in clinical trials. In this review, we outline the many cellular and physiological functions of RLIP76 in normal and cancer cells, and discuss the potential for RLIP76-based therapeutics in lung cancer treatment.
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Affiliation(s)
- Lawrence E Goldfinger
- Department of Anatomy and Cell Biology, The Sol Sherry Thrombosis Research Center, Temple University School of Medicine, Philadelphia, PA, USA ; Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Seunghyung Lee
- Department of Anatomy and Cell Biology, The Sol Sherry Thrombosis Research Center, Temple University School of Medicine, Philadelphia, PA, USA
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Aiello D, Caffrey DR. Evolution of specific protein-protein interaction sites following gene duplication. J Mol Biol 2012; 423:257-72. [PMID: 22789570 DOI: 10.1016/j.jmb.2012.06.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 05/16/2012] [Accepted: 06/29/2012] [Indexed: 11/15/2022]
Abstract
Gene duplication is a common evolutionary process that leads to the expansion and functional diversification of protein subfamilies. The evolutionary events that cause paralogous proteins to bind different protein ligands (functionally diverged interfaces) are investigated and compared to paralogous proteins that bind the same protein ligand (functionally preserved interfaces). We find that functionally diverged interfaces possess more subfamily-specific residues than functionally preserved interfaces. These subfamily-specific residues are usually partially buried at the interface rim and achieve specific binding through optimized hydrogen bond geometries. In addition to optimized hydrogen bond geometries, side-chain modeling experiments suggest that steric effects are also important for binding specificity. Residues that are completely buried at the interface hub are also less conserved in functionally diverged interfaces than in functionally preserved interfaces. Consistent with this finding, hub residues contribute less to free energy of binding in functionally diverged interfaces than in functionally preserved interfaces. Therefore, we propose that protein binding is a delicate balance between binding affinity that primarily occurs at the interface hub and binding specificity that primarily occurs at the interface rim.
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Affiliation(s)
- Daniel Aiello
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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14
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Cho B, Fischer JA. Ral inhibits ligand-independent Notch signaling in Drosophila. Small GTPases 2012; 3:186-91. [PMID: 22750761 DOI: 10.4161/sgtp.19802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We discovered recently that the Drosophila Ral GTPase regulates Notch signaling and thereby affects cell patterning in the eye. Although Ral functions in the ligand signaling cells, Ral does not stimulate ligand signaling directly. Rather, in cells that express both Notch receptor and ligand, Ral activity promotes a cell to become the signaler by inhibiting Notch receptor activation in that cell. Moreover, Ral inhibits a particular pathway of Notch activation-receptor activation that occurs independent of ligand binding. In this Commentary, we discuss the phenomenon of ligand-independent Notch receptor activation and how this event might be regulated by Ral.
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Affiliation(s)
- Bomsoo Cho
- Section of Molecular Cell and Developmental Biology, Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
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Neyraud V, Aushev VN, Hatzoglou A, Meunier B, Cascone I, Camonis J. RalA and RalB proteins are ubiquitinated GTPases, and ubiquitinated RalA increases lipid raft exposure at the plasma membrane. J Biol Chem 2012; 287:29397-405. [PMID: 22700969 DOI: 10.1074/jbc.m112.357764] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Ras GTPases signal by orchestrating a balance among several effector pathways, of which those driven by the GTPases RalA and RalB are essential to Ras oncogenic functions. RalA and RalB share the same effectors but support different aspects of oncogenesis. One example is the importance of active RalA in anchorage-independent growth and membrane raft trafficking. This study has shown a new post-translational modification of Ral GTPases: nondegradative ubiquitination. RalA (but not RalB) ubiquitination increases in anchorage-independent conditions in a caveolin-dependent manner and when lipid rafts are endocytosed. Forcing RalA mono-ubiquitination (by expressing a protein fusion consisting of ubiquitin fused N-terminally to RalA) leads to RalA enrichment at the plasma membrane and increases raft exposure. This study suggests the existence of an ubiquitination/de-ubiquitination cycle superimposed on the GDP/GTP cycle of RalA, involved in the regulation of RalA activity as well as in membrane raft trafficking.
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Affiliation(s)
- Vincent Neyraud
- From the Analysis of Transduction Pathways (ATP) Group, Institut Curie, INSERM U830, Paris cedex 05, France
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Rojas AM, Fuentes G, Rausell A, Valencia A. The Ras protein superfamily: evolutionary tree and role of conserved amino acids. ACTA ACUST UNITED AC 2012; 196:189-201. [PMID: 22270915 PMCID: PMC3265948 DOI: 10.1083/jcb.201103008] [Citation(s) in RCA: 280] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Ras superfamily is a fascinating example of functional diversification in the context of a preserved structural framework and a prototypic GTP binding site. Thanks to the availability of complete genome sequences of species representing important evolutionary branch points, we have analyzed the composition and organization of this superfamily at a greater level than was previously possible. Phylogenetic analysis of gene families at the organism and sequence level revealed complex relationships between the evolution of this protein superfamily sequence and the acquisition of distinct cellular functions. Together with advances in computational methods and structural studies, the sequence information has helped to identify features important for the recognition of molecular partners and the functional specialization of different members of the Ras superfamily.
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Affiliation(s)
- Ana Maria Rojas
- Computational Cell Biology Group, Institute for Predictive and Personalized Medicine of Cancer, 08916 Badalona, Barcelona, Spain.
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Muth T, Garcia-Martin JA, Rausell A, Juan D, Valencia A, Pazos F. JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. Bioinformatics 2011; 28:584-6. [DOI: 10.1093/bioinformatics/btr688] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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18
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Rybko VA, Knizhnik AV, Komelkov AV, Aushev VN, Trukhanova LS, Tchevkina EM. Different metastasis promotive potency of small G-proteins RalA and RalB in in vivo hamster tumor model. Cancer Cell Int 2011; 11:22. [PMID: 21714887 PMCID: PMC3135494 DOI: 10.1186/1475-2867-11-22] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 06/29/2011] [Indexed: 01/28/2023] Open
Abstract
Background Previously we have shown that oncogenic Ha-Ras stimulated in vivo metastasis through RalGEF-Ral signaling. RalA and RalB are highly homologous small G proteins belonging to Ras superfamily. They can be activated by Ras-RalGEF signaling pathway and influence cellular growth and survival, motility, vesicular transport and tumor progression in humans and in animal models. Here we first time compared the influence of RalA and RalB on tumorigenic, invasive and metastatic properties of RSV transformed hamster fibroblasts. Methods Retroviral vectors encoding activated forms or effector mutants of RalA or RalB proteins were introduced into the low metastatic HET-SR cell line. Tumor growth and spontaneous metastatic activity (SMA) were evaluated on immunocompetent hamsters after subcutaneous injection of cells. The biological properties of cells, including proliferation, clonogenicity, migration and invasion were determined using MTT, wound healing, colony formation and Boyden chamber assays respectively. Protein expression and phosphorylation was detected by Westen blot analysis. Extracellular proteinases activity was assessed by substrate-specific zymography. Results We have showed that although both Ral proteins stimulated SMA, RalB was more effective in metastasis stimulation in vivo as well as in potentiating of directed movement and invasion in vitro. Simultaneous expression of active RalA and RalB didn't give synergetic effect on metastasis formation. RalB activity decreased expression of Caveolin-1, while active RalA stimulated MMP-1 and uPA proteolytic activity, as well as CD24 expression. Both Ral proteins were capable of Cyclin D1 upregulation, JNK1 kinase activation, and stimulation of colony growth and motility. Among three main RalB effectors (RalBP1, exocyst complex and PLD1), PLD1 was essential for RalB-dependent metastasis stimulation. Conclusions Presented results are the first data on direct comparison of RalA and RalB impact as well as of RalA/RalB simultaneous expression influence on in vivo cell metastatic activity. We showed that RalB activation significantly more than RalA stimulates SMA. This property correlates with the ability of RalB to stimulate in vitro invasion and serum directed cell movement. We also found that RalB-PLD1 interaction is necessary for the acquisition of RalB-dependent high metastatic cell phenotype. These findings contribute to the identification of molecular mechanisms of metastasis and tumor progression.
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Affiliation(s)
- Vera A Rybko
- Department of Oncogenes Regulation, Institute of Carcinogenesis, Russian N,N, Blokhin Cancer Research Center, Kashirskoye shosse 24, 115478, Moscow, Russia.
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Fenwick RB, Campbell LJ, Rajasekar K, Prasannan S, Nietlispach D, Camonis J, Owen D, Mott HR. The RalB-RLIP76 complex reveals a novel mode of ral-effector interaction. Structure 2010; 18:985-95. [PMID: 20696399 DOI: 10.1016/j.str.2010.05.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 04/30/2010] [Accepted: 05/11/2010] [Indexed: 01/08/2023]
Abstract
RLIP76 (RalBP1) is a multidomain protein that interacts with multiple small G protein families: Ral via a specific binding domain, and Rho and R-Ras via a GTPase activating domain. RLIP76 interacts with endocytosis proteins and has also been shown to behave as a membrane ATPase that transports chemotherapeutic agents from the cell. We have determined the structure of the Ral-binding domain of RLIP76 and show that it comprises a coiled-coil motif. The structure of the RLIP76-RalB complex reveals a novel mode of binding compared to the structures of RalA complexed with the exocyst components Sec5 and Exo84. RLIP76 interacts with both nucleotide-sensitive regions of RalB, and key residues in the interface have been identified using affinity measurements of RalB mutants. Sec5, Exo84, and RLIP76 bind Ral proteins competitively and with similar affinities in vitro.
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Affiliation(s)
- R Brynmor Fenwick
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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20
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Valencia A. Multiple sequence alignments as tools for protein structure and function prediction. Comp Funct Genomics 2010; 4:424-7. [PMID: 18629077 PMCID: PMC2447362 DOI: 10.1002/cfg.313] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2003] [Revised: 06/06/2003] [Accepted: 06/06/2003] [Indexed: 11/07/2022] Open
Abstract
Multiple sequence alignments have much to offer to the understanding of protein structure, evolution and function. We are developing approaches to use this information
in predicting protein-binding specificity, intra-protein and protein-protein
interactions, and in reconstructing protein interaction networks.
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Affiliation(s)
- Alfonso Valencia
- Protein Design Group, National Centre for Biotechnology, CNB-CSIC, Madrid, Spain.
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21
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Protein interactions and ligand binding: from protein subfamilies to functional specificity. Proc Natl Acad Sci U S A 2010; 107:1995-2000. [PMID: 20133844 DOI: 10.1073/pnas.0908044107] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The divergence accumulated during the evolution of protein families translates into their internal organization as subfamilies, and it is directly reflected in the characteristic patterns of differentially conserved residues. These specifically conserved positions in protein subfamilies are known as "specificity determining positions" (SDPs). Previous studies have limited their analysis to the study of the relationship between these positions and ligand-binding specificity, demonstrating significant yet limited predictive capacity. We have systematically extended this observation to include the role of differential protein interactions in the segregation of protein subfamilies and explored in detail the structural distribution of SDPs at protein interfaces. Our results show the extensive influence of protein interactions in the evolution of protein families and the widespread association of SDPs with protein interfaces. The combined analysis of SDPs in interfaces and ligand-binding sites provides a more complete picture of the organization of protein families, constituting the necessary framework for a large scale analysis of the evolution of protein function.
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22
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Fenwick RB, Prasannan S, Campbell LJ, Nietlispach D, Evetts KA, Camonis J, Mott HR, Owen D. Solution structure and dynamics of the small GTPase RalB in its active conformation: significance for effector protein binding. Biochemistry 2009; 48:2192-206. [PMID: 19166349 DOI: 10.1021/bi802129d] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The small G proteins RalA/B have a crucial function in the regulatory network that couples extracellular signals with appropriate cellular responses. RalA/B are an important component of the Ras signaling pathway and, in addition to their role in membrane trafficking, are implicated in the initiation and maintenance of tumorigenic transformation of human cells. RalA and RalB share 85% sequence identity and collaborate in supporting cancer cell proliferation but have markedly different effects. RalA is important in mediating proliferation, while depletion of RalB results in transformed cells undergoing apoptosis. Crystal structures of RalA in the free form and in complex with its effectors, Sec5 and Exo84, have been solved. Here we have determined the solution structure of free RalB bound to the GTP analogue GMPPNP to an RMSD of 0.6 A. We show that, while the overall architecture of RalB is very similar to the crystal structure of RalA, differences exist in the switch regions, which are sensitive to the bound nucleotide. Backbone 15N dynamics suggest that there are four regions of disorder in RalB: the P-loop, switch I, switch II, and the loop comprising residues 116-121, which has a single residue insertion compared to RalA. 31P NMR data and the structure of RalB.GMPPNP show that the switch regions predominantly adopt state 1 (Ras nomenclature) in the unbound form, which in Ras is not competent to bind effectors. In contrast, 31P NMR analysis of RalB.GTP reveals that conformations corresponding to states 1 and 2 are both sampled in solution and that addition of an effector protein only partially stabilizes state 2.
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23
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Singhal SS, Yadav S, Roth C, Singhal J. RLIP76: A novel glutathione-conjugate and multi-drug transporter. Biochem Pharmacol 2008; 77:761-9. [PMID: 18983828 DOI: 10.1016/j.bcp.2008.10.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 10/01/2008] [Accepted: 10/02/2008] [Indexed: 11/17/2022]
Abstract
RLIP76, a stress-responsive, multi-functional protein with multi-specific transport activity towards glutathione-conjugates (GS-E) and chemotherapeutic agents, is frequently over-expressed in malignant cells. Our recent studies suggest that it plays a prominent anti-apoptotic role selectively in cancer cells. We have previously shown that RLIP76 accounts for up to 80% of the transport of GS-E and blocking the RLIP76-mediated transport of GS-E in cells results in the accumulation of pro-apoptotic endogenous electrophiles and on-set of apoptosis. Here we demonstrate that when RLIP76 mediate transport of GS-E is abrogated either by anti-RLIP76 IgG or accumulation of 4-hydroxynonenal (4-HNE) and its GSH-conjugate (GS-HNE) occurs and a massive apoptosis is observed in cells, indicate that the inhibition of RLIP76 transport activity at the cell surface is sufficient for observed anti-tumor activity. RLIP76 is linked with certain cellular functions including membrane plasticity and movement (as a primary 'effector' in the Ral pathway, perhaps functioning as a GTPase activating protein, or GAP), and as a component of clathrin-coated pit-mediated receptor-ligand endocytosis-a process that mediates movement of membrane vesicles.
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Affiliation(s)
- Sharad S Singhal
- Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, TX 76107, USA.
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24
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Qiao J, Holian O, Lee BS, Huang F, Zhang J, Lum H. Phosphorylation of GTP dissociation inhibitor by PKA negatively regulates RhoA. Am J Physiol Cell Physiol 2008; 295:C1161-8. [PMID: 18768928 DOI: 10.1152/ajpcell.00139.2008] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The cAMP-PKA cascade is a recognized signaling pathway important in inhibition of inflammatory injury events such as endothelial permeability and leucocyte trafficking, and a critical target of regulation is believed to be inhibition of Rho proteins. Here, we hypothesize that PKA directly phosphorylates GTP dissociation inhibitor (GDI) to negatively regulate Rho activity. Amino acid analysis of GDIalpha showed two potential protein kinase A (PKA) phosphorylation motifs, Ser(174) and Thr(182). Using in vitro kinase assay and mass spectrometry, we found that the purified PKA catalytic subunit phosphorylated GDIalpha-GST fusion protein and PKA motif-containing GDIalpha peptide at Ser(174), but not Thr(182). Transfection of COS-7 cells with mutated full-length GDIalpha at Ser(174) to Ala(174) (GDIalpha-Ser(174A)) abrogated the ability of cAMP to phosphorylate GDIalpha. However, mutation of Thr(182) to Ala(182) (GDIalpha-Thr(182A)) did not abrogate, and cAMP increased phosphorylation of GDIalpha to a similar extent as wild-type GDIalpha transfectants. The mutant GDIalpha-Ser(174A), but not GDIalpha-Thr(182A), was unable to prevent cAMP-mediated inhibition of Rho-dependent serum-response element reporter activity. Furthermore, the mutant GDIalpha-Ser(174A) was unable to prevent the thrombin-induced RhoA activation. Coprecipitation studies indicated that neither mutation of the PKA consensus sites nor phosphorylation alter GDIalpha binding with RhoA, suggesting that phosphorylation of Ser(174) regulated preformed GDIalpha-RhoA complexes. The findings provide strong support that the selective phosphorylation at Ser(174) by PKA is a signaling pathway in the negative regulation of RhoA activity and therefore could be a potential protective mechanism for inflammatory injury.
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Affiliation(s)
- Jing Qiao
- Dept. of Pharmacology, Rush Univ. Medical Center, 1735 W. Harrison St., Cohn Research Bldg.; Rm 416, Chicago, IL 60612, USA
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25
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Cascone I, Selimoglu R, Ozdemir C, Del Nery E, Yeaman C, White M, Camonis J. Distinct roles of RalA and RalB in the progression of cytokinesis are supported by distinct RalGEFs. EMBO J 2008; 27:2375-87. [PMID: 18756269 DOI: 10.1038/emboj.2008.166] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2008] [Accepted: 07/31/2008] [Indexed: 01/03/2023] Open
Abstract
The Ras family G-proteins RalA and RalB make critical non-overlapping contributions to the generation of a tumorigenic regulatory network, supporting bypass of the normal restraints on both cell proliferation and survival. The Sec6/8 complex, or exocyst, has emerged as a principal direct effector complex for Ral GTPases. Here, we show that RalA and RalB support mitotic progression through mobilization of the exocyst for two spatially and kinetically distinct steps of cytokinesis. RalA is required to tether the exocyst to the cytokinetic furrow in early cytokinesis. RalB is then required for recruitment of the exocyst to the midbody of this bridge to drive abscission and completion of cytokinesis. The collaborative action of RalA and RalB is specified by discrete subcellular compartmentalization and unique pairs of RalGEF proteins that provide inputs from both Ras-family protein-dependent and protein-independent regulatory cues. This suggests that Ral GTPases integrate diverse upstream signals to choreograph multiple roles for the exocyst in mitotic progression.
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26
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Goldfinger LE. Choose your own path: specificity in Ras GTPase signaling. MOLECULAR BIOSYSTEMS 2008; 4:293-9. [PMID: 18354782 DOI: 10.1039/b716887j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Ras superfamily of small G proteins contributes importantly to numerous cellular and physiological processes (M. F. Olsen and R. Marais, Semin. Immunol., 2000, 12, 63). This family comprises a large class of proteins (more than 150) which all share a common enzymatic function: hydrolysis of the gamma-phosphate of guanosine triphosphate (GTP) to create the products guanosine diphosphate (GDP) and inorganic phosphate (Y. Takai, T. Sasaki and T. Matozaki, Physiol. Rev., 2001, 81, 153). For this reason Ras family proteins, which include the Ras, Rho, Arf/Sara, Ran and Rab subfamilies, are classified as GTPases (G. W. Reuther and C. J. Der, Curr. Opin. Cell Biol., 2000, 12, 157). Guanine nucleotide coupling is a key regulator of enzymatic function; thus, Ras family GTPases participate in signal transduction. Ras signaling depends on binding to effectors. Many of the known effectors can bind to multiple Ras isotypes, often leading to common cellular outcomes, but each Ras isotype also engages specific effector pathways to mediate unique functions. Further, each Ras isotype can propagate multiple signaling pathways, indicating the presence of cellular determinants which allow for promiscuity in Ras-effector interactions while also maintaining specificity. Small distinctions in sequence, structure, and/or cellular regulation contribute to these differences in Ras-effector binding and subsequent cellular effects. A major focus of investigation in the Ras signaling field is identifying the determinants of these individualized functions. This review will attempt to summarize the current state of understanding of this question (with a particular focus on the Ras subfamily) and the approaches being taken to address it, and will discuss prospective areas for future investigation.
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Affiliation(s)
- Lawrence E Goldfinger
- Department of Medicine, Division of Rheumatology, University of California, San Diego, CA 92093-0726, USA.
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27
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Pirovano W, Feenstra KA, Heringa J. Sequence comparison by sequence harmony identifies subtype-specific functional sites. Nucleic Acids Res 2006; 34:6540-8. [PMID: 17130172 PMCID: PMC1702503 DOI: 10.1093/nar/gkl901] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Multiple sequence alignments are often used to reveal functionally important residues within a protein family. They can be particularly useful for the identification of key residues that determine functional differences between protein subfamilies. We present a new entropy-based method, Sequence Harmony (SH) that accurately detects subfamily-specific positions from a multiple sequence alignment. The SH algorithm implements a novel formula, able to score compositional differences between subfamilies, without imposing conservation, in a simple manner on an intuitive scale. We compare our method with the most important published methods, i.e. AMAS, TreeDet and SDP-pred, using three well-studied protein families: the receptor-binding domain (MH2) of the Smad family of transcription factors, the Ras-superfamily of small GTPases and the MIP-family of integral membrane transporters. We demonstrate that SH accurately selects known functional sites with higher coverage than the other methods for these test-cases. This shows that compositional differences between protein subfamilies provide sufficient basis for identification of functional sites. In addition, SH selects a number of sites of unknown function that could be interesting candidates for further experimental investigation.
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Affiliation(s)
| | | | - Jaap Heringa
- To whom correspondence should be addressed. Tel: +31 20 59 87649; Fax: +31 20 59 87653;
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28
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Goldfinger LE, Ptak C, Jeffery ED, Shabanowitz J, Hunt DF, Ginsberg MH. RLIP76 (RalBP1) is an R-Ras effector that mediates adhesion-dependent Rac activation and cell migration. ACTA ACUST UNITED AC 2006; 174:877-88. [PMID: 16966426 PMCID: PMC2064341 DOI: 10.1083/jcb.200603111] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Ras family of small GTPases regulates cell proliferation, spreading, migration and apoptosis, and malignant transformation by binding to several protein effectors. One such GTPase, R-Ras, plays distinct roles in each of these processes, but to date, identified R-Ras effectors were shared with other Ras family members (e.g., H-Ras). We utilized a new database of Ras-interacting proteins to identify RLIP76 (RalBP1) as a novel R-Ras effector. RLIP76 binds directly to R-Ras in a GTP-dependent manner, but does not physically associate with the closely related paralogues H-Ras and Rap1A. RLIP76 is required for adhesion-induced Rac activation and the resulting cell spreading and migration, as well as for the ability of R-Ras to enhance these functions. RLIP76 regulates Rac activity through the adhesion-induced activation of Arf6 GTPase and activation of Arf6 bypasses the requirement for RLIP76 in Rac activation and cell spreading. Thus, we identify a novel R-Ras effector, RLIP76, which links R-Ras to adhesion-induced Rac activation through a GTPase cascade that mediates cell spreading and migration.
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Affiliation(s)
- Lawrence E Goldfinger
- Division of Rheumatology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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29
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Nadkar A, Pungaliya C, Drake K, Zajac E, Singhal SS, Awasthi S. Therapeutic resistance in lung cancer. Expert Opin Drug Metab Toxicol 2006; 2:753-77. [PMID: 17014393 DOI: 10.1517/17425255.2.5.753] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Despite considerable progress over the last 25 years in the systemic therapy of lung cancer, intrinsic and acquired resistance to chemotherapeutic agents and radiation remains a vexing problem. The number of mechanisms of therapeutic resistance in lung cancer has expanded considerably over the past three decades, and the crucial role of stress resistance pathways is increasingly recognised as a cause of intrinsic and acquired chemo- and radiotherapy resistance. This paper reviews recent evidence for stress defence proteins, particularly RALBP1/RLIP76, in mediating intrinsic and acquired chemotherapy and radiation resistance in human lung cancer.
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Affiliation(s)
- Aalok Nadkar
- Department of Chemistry and Biochemistry, University of Texas at Arlington, 700 Planetarium Place, CPB # 351, 76019-0065, USA.
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30
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Carro A, Tress M, de Juan D, Pazos F, Lopez-Romero P, del Sol A, Valencia A, Rojas AM. TreeDet: a web server to explore sequence space. Nucleic Acids Res 2006; 34:W110-5. [PMID: 16844971 PMCID: PMC1538789 DOI: 10.1093/nar/gkl203] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The TreeDet (Tree Determinant) Server is the first release of a system designed to integrate results from methods that predict functional sites in protein families. These methods take into account the relation between sequence conservation and evolutionary importance. TreeDet fully analyses the space of protein sequences in either user-uploaded or automatically generated multiple sequence alignments. The methods implemented in the server represent three main classes of methods for the detection of family-dependent conserved positions, a tree-based method, a correlation based method and a method that employs a principal component analyses coupled to a cluster algorithm. An additional method is provided to highlight the reliability of the position in the alignments. The server is available at .
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Affiliation(s)
| | | | | | | | | | | | | | - Ana M. Rojas
- To whom correspondence should be addressed at Spanish National Cancer Center (CNIO), Structural Bioinformatics Group, Centro Nacional de Investigaciones Oncológicas (CNIO), C/Melchor Fernandez Almagro 3, 28029 Madrid, Spain. Tel: +34 91 585 46 69; Fax: +34 91 585 45 06;
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31
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Nussbaum M, Collins RN. Use of search algorithms to define specificity in Rab GTPase domain function. Methods Enzymol 2006; 403:10-9. [PMID: 16473573 DOI: 10.1016/s0076-6879(05)03002-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The continuing explosion of sequencing data has inspired a corresponding effort in the annotation and classification of protein families. Within a particular protein family, however, individual members may have distinct functions, although they share a common fold and broadly defined physiological role. Rab GTPases are the largest subfamily of the Ras superfamily, yet from early in their discovery, it was apparent that each Rab protein has a unique subcellular localization and regulates a particular stage(s) membrane traffic. To gain insight into the contribution of individual residues to unique protein functions a general strategy is outlined. This method should allow the cell and molecular biologist with no specialist expertise to implement an algorithm that makes use of a combination of experimental and phylogenetic data. The algorithm is applicable to the analysis of any protein domain and here is illustrated with the analysis of residues contributing to the individual functions of a pair of Rab GTPases.
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32
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Singhal SS, Wickramarachchi D, Singhal J, Yadav S, Awasthi YC, Awasthi S. Determinants of differential doxorubicin sensitivity between SCLC and NSCLC. FEBS Lett 2006; 580:2258-64. [PMID: 16579994 DOI: 10.1016/j.febslet.2006.03.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Revised: 03/06/2006] [Accepted: 03/08/2006] [Indexed: 11/18/2022]
Abstract
Doxorubicin (DOX) transport activity of Ral-interacting protein (RLIP76) in non-small cell lung cancer (NSCLC) is approximately twice that of in small cell lung cancer (SCLC). Since protein-kinase-C (PKC)alpha mediated phosphorylation of RLIP76 causes doubling of the specific activity of RLIP76, and NSCLC cells are known to have greater PKCalpha activity, we examined the contribution of PKC mediated phosphorylation of RLIP76 towards intrinsic DOX-resistance in human NSCLC. Expression of a deletion mutant RLIP76(delPKCalpha-sites) followed by depletion of the wild-type RLIP76 using a siRNA targeted at one of the deleted regions resulted in generation of cells expressing only the mutant protein, which could not be phosphorylated by PKCalpha. DOX-transport activity of the mutant RLIP76 purified from NSCLC and SCLC was similar and comparable to that of RLIP76 purified from the wild-type SCLC. However, this activity was significantly lower than that of RLIP76 purified from the wild-type NSCLC. After siRNA mediated depletion of PKCalpha, DOX-transport activities of RLIP76 purified from SCLC and NSCLC were indistinguishable. Depletion of PKCalpha inhibited the growth of NSCLC more than SCLC cells (70+/-3% vs. 43+/-5%, respectively). PKCalpha-depletion lowered the IC(50) of NSCLC cell lines for DOX to the same level as that observed for SCLC. RLIP76(-/-) mouse embryonic fibroblasts (MEFs) were significantly more sensitive to DOX as compared with RLIP76(+/+) MEFs (IC(50) 25 vs. 125nM, respectively). However, PKCalpha-depletion did not affect DOX-cytotoxicity towards RLIP76(-/-) MEFs, as opposed to RLIP76(+/+) MEFs which were sensitized by 2.2-fold. These results demonstrate that RLIP76 is a primary determinant of DOX-resistance, and that PKCalpha mediated accumulation defect and DOX-resistance in NSCLC is primarily due to differential phosphorylation of RLIP76 in SCLC and NSCLC.
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MESH Headings
- ATP-Binding Cassette Transporters/genetics
- ATP-Binding Cassette Transporters/metabolism
- Animals
- Antibiotics, Antineoplastic/pharmacology
- Antibiotics, Antineoplastic/therapeutic use
- Biological Transport, Active/drug effects
- Biological Transport, Active/genetics
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Small Cell/drug therapy
- Carcinoma, Small Cell/genetics
- Carcinoma, Small Cell/metabolism
- Cell Line, Tumor
- Doxorubicin/pharmacology
- Doxorubicin/therapeutic use
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Embryo, Mammalian/cytology
- Embryo, Mammalian/metabolism
- Enzyme Activation/drug effects
- Enzyme Activation/genetics
- Fibroblasts/cytology
- Fibroblasts/metabolism
- GTPase-Activating Proteins/genetics
- GTPase-Activating Proteins/metabolism
- Humans
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Mice
- Mice, Knockout
- Phosphorylation/drug effects
- Protein Kinase C-alpha/metabolism
- Protein Processing, Post-Translational/drug effects
- Protein Processing, Post-Translational/genetics
- RNA, Small Interfering/genetics
- RNA, Small Interfering/pharmacology
- Sequence Deletion/genetics
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Affiliation(s)
- Sharad S Singhal
- Department of Chemistry and Biochemistry, University of Texas at Arlington, 401 W, 3rd Street, CPB RM # 312, Arlington, TX 76019-0065, USA
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33
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Sacco E, Fantinato S, Manzoni R, Metalli D, De Gioia L, Fantucci P, Alberghina L, Vanoni M. The isolated catalytic hairpin of the Ras-specific guanine nucleotide exchange factor Cdc25Mm retains nucleotide dissociation activity but has impaired nucleotide exchange activity. FEBS Lett 2005; 579:6851-8. [PMID: 16325815 DOI: 10.1016/j.febslet.2005.11.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Revised: 10/10/2005] [Accepted: 11/11/2005] [Indexed: 12/21/2022]
Abstract
Cdc25Mm is a mammalian Ras-specific guanine nucleotide exchange factor (GEF). By homology modeling we show that it shares with Sos-GEF the structure of the putative catalytic HI hairpin where the dominant negative T1184E mutation is located. Similarly to Cdc25MmT1184E, the isolated wild-type and mutant hairpins retain the ability to displace Ras-bound nucleotide, originate a stable Ras/GEF complex and downregulate the Ras pathway in vivo. These results indicate that nucleotide re-entry and Ras/GEF dissociation--final steps in the GEF catalytic cycle--require GEF regions different from the HI hairpin. GEF down-sizing could lead to development of novel Ras inhibitors.
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Affiliation(s)
- Elena Sacco
- Dipartimento di Biotechnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
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34
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Pautsch A, Vogelsgesang M, Tränkle J, Herrmann C, Aktories K. Crystal structure of the C3bot-RalA complex reveals a novel type of action of a bacterial exoenzyme. EMBO J 2005; 24:3670-80. [PMID: 16177825 PMCID: PMC1276701 DOI: 10.1038/sj.emboj.7600813] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Accepted: 08/22/2005] [Indexed: 12/21/2022] Open
Abstract
C3 exoenzymes from bacterial pathogens ADP-ribosylate and inactivate low-molecular-mass GTPases of the Rho subfamily. Ral, a Ras subfamily GTPase, binds the C3 exoenzymes from Clostridium botulinum and C. limosum with high affinity without being a substrate for ADP ribosylation. In the complex, the ADP-ribosyltransferase activity of C3 is blocked, while binding of NAD and NAD-glycohydrolase activity remain. Here we report the crystal structure of C3 from C. botulinum in a complex with GDP-bound RalA at 1.8 A resolution. C3 binds RalA with a helix-loop-helix motif that is adjacent to the active site. A quaternary complex with NAD suggests a mode for ADP-ribosyltransferase inhibition. Interaction of C3 with RalA occurs at a unique interface formed by the switch-II region, helix alpha3 and the P loop of the GTPase. C3-binding stabilizes the GDP-bound conformation of RalA and blocks nucleotide release. Our data indicate that C. botulinum exoenzyme C3 is a single-domain toxin with bifunctional properties targeting Rho GTPases by ADP ribosylation and Ral by a guanine nucleotide dissociation inhibitor-like effect, which blocks nucleotide exchange.
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Affiliation(s)
- Alexander Pautsch
- Structural Research, Department of Integrated Lead Discovery, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Martin Vogelsgesang
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie der Universität Freiburg, Otto-Krayer-Haus, Freiburg, Germany
| | - Jens Tränkle
- Physikalische Chemie I, Ruhr-Universität Bochum, Bochum, Germany
| | | | - Klaus Aktories
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie der Universität Freiburg, Otto-Krayer-Haus, Freiburg, Germany
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie der Universität Freiburg, Otto-Krayer-Haus, Albertstrasse 25, 79104 Freiburg, Germany. Tel.: +49 761 203 5301; Fax: +49 761 203 5311; E-mail:
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Elliot-Smith AE, Mott HR, Lowe PN, Laue ED, Owen D. Specificity Determinants on Cdc42 for Binding Its Effector Protein ACK. Biochemistry 2005; 44:12373-83. [PMID: 16156650 DOI: 10.1021/bi0506021] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cdc42 and Rac are highly homologous members of the Rho family of small G proteins that interact with several downstream effector proteins thereby causing cytoskeletal rearrangements, cell proliferation, and differentiation. While some effectors, such as the tyrosine kinase, ACK, and the scaffold protein, WASP, are unique to Cdc42, others, such as the serine-threonine kinase, PAK, are shared with Rac. Previous mutagenesis studies identified Val42 and Leu174 as residues that selectively affect binding of Cdc42 to ACK and WASP but not to PAK. However, it is unclear whether these discriminatory residues are sufficient determinants of specificity. In this study we sought to introduce "gain-of function" mutations into Rac to allow it to bind to ACK and WASP, thereby revealing all specificity determinants. Thirteen mutations were made changing Rac residues to those in Cdc42. Equilibrium binding constants of all mutant Rac proteins to ACK, WASP, and PAK were measured. A combination of seven mutations (S41A, A42V, N43T, D47G, N52T, W56F, and R174L) was determined to be necessary to change the binding affinity of Rac for ACK from negligible (K(d) < 1 microM) to a comparable affinity to Cdc42 (K(d) 25 nM). These mutations are not confined to interface residues. We interpret these data to indicate the importance of the structure of regions of the protein distinct from the contact residues. None of these mutant Rac proteins bound WASP with a similar affinity to Cdc42. Hence, residues as yet unidentified, outside the interface, must be necessary for binding WASP.
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36
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Singhal SS, Yadav S, Singhal J, Drake K, Awasthi YC, Awasthi S. The role of PKCα and RLIP76 in transport-mediated doxorubicin-resistance in lung cancer. FEBS Lett 2005; 579:4635-41. [PMID: 16087181 DOI: 10.1016/j.febslet.2005.07.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Revised: 07/11/2005] [Accepted: 07/19/2005] [Indexed: 10/25/2022]
Abstract
In deletion mutant analyses of potential phosphorylation sites in RLIP76, we identified T297 and S509 as targets for phosphorylation by PKCalpha. Phosphorylation at T297 increased doxorubicin (DOX)-transport activity approximately 2-fold for RLIP76 purified from recombinant source, or from three small (H69, H1417, H1618) and three non-small cell, one each derived from H226 (squamous), H358 (bronchio alveolar), and H1395 (adenocarcinoma) lung cancer cell lines. T297 phosphorylation conferred sensitivity to tryptic digestion at R293. The specific activity for DOX-transport by RLIP76 purified from non-small cell, which was primarily in the phosphorylated form, was approximately twice that in small cell lung cancer cell lines. These finding offer a novel explanation for the observed intrinsic differences in sensitivity to DOX between non-small cell and small cell lung cancer cell lines.
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Affiliation(s)
- Sharad S Singhal
- Department of Chemistry and Biochemistry, 502 Yates St., Science Hall #223, University of Texas at Arlington, Arlington, TX 76019-0065, USA.
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37
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Sidhu RS, Clough RR, Bhullar RP. Regulation of Phospholipase C-δ1 through Direct Interactions with the Small GTPase Ral and Calmodulin. J Biol Chem 2005; 280:21933-41. [PMID: 15817490 DOI: 10.1074/jbc.m412966200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Second messengers generated from membrane lipids play a critical role in signaling and control diverse cellular processes. Despite being one of the most evolutionarily conserved of all the phosphoinositide-specific phospholipase C (PLC) isoforms, a family of enzymes responsible for hydrolysis of the membrane lipid phosphatidylinositol bisphosphate, the mechanism of PLC-delta1 activation is still poorly understood. Here we report a novel regulatory mechanism for PLC-delta1 activation that involves direct interaction of the small GTPase Ral and the universal calcium-signaling molecule calmodulin (CaM) with PLC-delta1. In addition, we have identified a novel IQ type CaM binding motif within the catalytic region of PLC-delta1 that is not found in other PLC isoforms. Binding of CaM at the IQ motif inhibits PLC-delta1 activity, while addition of Ral reverses the inhibition. The overexpression of various Ral mutants in cells potentiates PLC-delta1 activity. Thus, the Ral-CaM complex defines a multifaceted regulatory mechanism for PLC-delta1 activation.
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Affiliation(s)
- Ranjinder S Sidhu
- Department of Oral Biology, Faculty of Dentistry, University of Manitoba, Winnipeg, Manitoba R3E 0W2, Canada
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38
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Jin R, Junutula JR, Matern HT, Ervin KE, Scheller RH, Brunger AT. Exo84 and Sec5 are competitive regulatory Sec6/8 effectors to the RalA GTPase. EMBO J 2005; 24:2064-74. [PMID: 15920473 PMCID: PMC1150893 DOI: 10.1038/sj.emboj.7600699] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Accepted: 05/06/2005] [Indexed: 12/31/2022] Open
Abstract
The Sec6/8 complex, also known as the exocyst complex, is an octameric protein complex that has been implicated in tethering of secretory vesicles to specific regions on the plasma membrane. Two subunits of the Sec6/8 complex, Exo84 and Sec5, have recently been shown to be effector targets for active Ral GTPases. However, the mechanism by which Ral proteins regulate the Sec6/8 activities remains unclear. Here, we present the crystal structure of the Ral-binding domain of Exo84 in complex with active RalA. The structure reveals that the Exo84 Ral-binding domain adopts a pleckstrin homology domain fold, and that RalA interacts with Exo84 via an extended interface that includes both switch regions. Key residues of Exo84 and RalA were found that determine the specificity of the complex interactions; these interactions were confirmed by mutagenesis binding studies. Structural and biochemical data show that Exo84 and Sec5 competitively bind to active RalA. Taken together, these results further strengthen the proposed role of RalA-regulated assembly of the Sec6/8 complex.
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Affiliation(s)
- Rongsheng Jin
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | | | - Hugo T Matern
- Genentech Inc., 1 DNA Way, South San Francisco, CA, USA
| | - Karen E Ervin
- Genentech Inc., 1 DNA Way, South San Francisco, CA, USA
| | | | - Axel T Brunger
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Science, Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Department of Molecular and Cellular Physiology, Stanford University, James H Clark Center, E300C, 318 Campus Drive, Stanford, CA 94305-5432, USA. Tel.:+1 650 736 1031; Fax: +1 650 736 1961; E-mail:
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39
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Nicely NI, Kosak J, de Serrano V, Mattos C. Crystal structures of Ral-GppNHp and Ral-GDP reveal two binding sites that are also present in Ras and Rap. Structure 2005; 12:2025-36. [PMID: 15530367 DOI: 10.1016/j.str.2004.08.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2004] [Revised: 08/26/2004] [Accepted: 08/28/2004] [Indexed: 11/18/2022]
Abstract
RalA is a GTPase with effectors such as Sec5 and Exo84 in the exocyst complex and RalBP1, a GAP for Rho proteins. We report the crystal structures of Ral-GppNHp and Ral-GDP. Disordered switch I and switch II, located away from crystal contacts, are observed in one of the molecules in the asymmetric unit of the Ral-GppNHp structure. In the other molecule in the asymmetric unit, a second Mg(2+) ion is bound to the GppNHp gamma-phosphate in an environment in which switch I is pulled away from the nucleotide and switch II is found in a tight beta turn. Clustering of conserved residues on the surface of Ral-GppNHp identifies two putative sites for protein-protein interaction. One site is adjacent to switch I. The other is modulated by switch II and is obstructed in Ral-GDP. The Ral structures are discussed in the context of the published structures of the Ral/Sec5 complex, Ras, and Rap.
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Affiliation(s)
- Nathan I Nicely
- Department of Molecular and Structural Biochemistry, 128 Polk Hall-CB 7622, North Carolina State University, Raleigh, NC 27695, USA
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40
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Dransart E, Morin A, Cherfils J, Olofsson B. Uncoupling of Inhibitory and Shuttling Functions of Rho GDP Dissociation Inhibitors. J Biol Chem 2005; 280:4674-83. [PMID: 15513926 DOI: 10.1074/jbc.m409741200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rho GDP dissociation inhibitors (rhoGDIs) are postulated to regulate the activity of small G proteins of the Rho family by a shuttling process involving the extraction of Rho from donor membranes, the formation of the inhibitory cytosolic Rho/rhoGDI complexes, and delivery of Rho to target membranes. However, the role of rhoGDIs in site-specific membrane targeting or extraction of Rho is still poorly understood. Here we investigated the molecular functions of two rhoGDIs, the specific rhoGDI-3 and the less specific but well studied rhoGDI-1, in HeLa cells using structure-based mutagenesis of the rhoGDI protein. We identified two sites in rhoGDI, which form conserved interactions with their Rho target, whose mutation results in the uncoupling of inhibitory and shuttling functions of rhoGDIs: D66GDI-3 (equivalent to D45GDI-1), a conserved residue in the helix-loop-helixGDI/switch 1Rho interface, and D206GDI-3 (equivalent to D185GDI-1) in the beta-sandwichGDI/switch 2Rho interface. Mutations of both sites result in the loss of rhoGDI-3 or rhoGDI-1 inhibitory activity but not of their ability to form cytosolic complexes with RhoG or Cdc42 in vivo. Remarkably, the mutants were detected at Rho-induced membrane ruffles or protrusions where they co-localized with RhoG or Cdc42, likely identifying for the first time the site of extraction of a Rho protein by a rhoGDI in vivo. We propose that these mutations act by modifying the steady-state kinetics of the shuttling process regulated by rhoGDIs, such that transient steps at the cell membranes now become detectable. They should provide valuable tools for future investigations of the dynamics of membrane extraction or delivery of Rho proteins and their regulation by cellular partners.
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Affiliation(s)
- Estelle Dransart
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR 9063, F-91198 Gif-sur-Yvette, France
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41
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Lebreton S, Boissel L, Iouzalen N, Moreau J. RLIP mediates downstream signalling from RalB to the actin cytoskeleton during Xenopus early development. Mech Dev 2004; 121:1481-94. [PMID: 15511640 DOI: 10.1016/j.mod.2004.07.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2004] [Revised: 07/13/2004] [Accepted: 07/26/2004] [Indexed: 10/26/2022]
Abstract
The Ras protein activates at least three different pathways during early development. Two of them regulate mesodermal gene expression and the third is thought to participate in the control of actin cytoskeleton dynamics via the Ral protein. From a yeast two-hybrid screen of a Xenopus maternal cDNA library, we identified the Xenopus orthologue of the Ral interacting protein (RLIP, RIP1 or RalBP1), a putative effector of small G protein Ral. Previously, we observed that a constitutively activated form of Ral GTPase (XralB G23V) induced bleaching of the animal hemisphere and disruption of the cortical actin cytoskeleton. To demonstrate that RLIP is the effector of RalB in early development, we show that the artificial targeting of RLIP to the membrane induces a similar phenotype to that of activated RalB. We show that overexpression of the Ral binding domain (RalBD) of XRLIP, which binds to the effector site of Ral, acts in competition with the endogenous effector of Ral and protects against the destructive effect of XralB G23V on the actin cytoskeleton. In contrast, the XRLIP has a synergistic effect on the activated form of XralB, which is dependent on the RalBD of RLIP. We provide evidence for the involvement of RLIP by way of its RalBD on the dynamics of the actin cytoskeleton and propose that signalling from Ral to RLIP is required for gastrulation.
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Affiliation(s)
- Stéphanie Lebreton
- Mécanismes Moléculaires du Développement, Institut Jacques Monod, CNRS, Universités Paris VI et Paris VII, 2 Place Jussieu, 75251 Paris 05, France
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42
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Yadav S, Singhal SS, Singhal J, Wickramarachchi D, Knutson E, Albrecht TB, Awasthi YC, Awasthi S. Identification of Membrane-Anchoring Domains of RLIP76 Using Deletion Mutant Analyses†. Biochemistry 2004; 43:16243-53. [PMID: 15610018 DOI: 10.1021/bi0482811] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RLIP76 (RALBP1) is a multifunctional transporter involved in signaling and transmembrane movement of solute allocrites, which include glutathione conjugates and several natural product antineoplastic agents [Awasthi, S., et al. (2000) Biochemistry 39, 9327-9334; (2001) Biochemistry 40, 4159-4168]. Our previous studies suggested that the membrane-anchoring domain resides in the N-terminus of RLIP76, despite the lack of identifiable membrane-spanning domains. Amino acid sequence analysis indicated that this region of RLIP76 contains sequences that are similar to those of vector peptides. We, therefore, have studied the effect of a series of deletion mutant proteins on hydrophobicity and transport activity. RLIP76 or one of its derived deletion mutants was expressed in Escherichia coli, and bacteria were lysed and extracted in buffer without or with the nonionic detergent polidocanol. The ratio of RLIP76 in the detergent/aqueous extracts was found to be 2.5 for the wild-type protein, but decreased to 0.7 in the mutant in which amino acids 154-219 were deleted. Deletion of only one segment of this region (amino acids 171-185) alone resulted in a significant decrease in this ratio to 1.0. For the mutants with deletions within the region from amino acid 154 to 219, loss of hydrophobicity correlated with less incorporation of mutants into artificial liposomes, and decreased transport activity toward doxorubicin and dinitrophenyl-S-glutathione. In contrast, deletion of one of the two ATP-binding sites (at amino acids 65-80 or 415-448) or both sites did not affect hydrophobicity but reduced or abrogated transport activity. NSCLC (H358) stably transfected with del171-185 and del154-219 showed that loss of these regions results in a decrease in the extent of membrane association of RLIP76. Confocal laser immunohistochemistry colocalized amino acids 171-185 with her2/neu on the cell surface. Depletion of wild-type RLIP76 using si-RNA directed to this region in cells transfected with del171-185 resulted in the loss of cell surface expression. These finding demonstrate that amino acids 171-185 constitute a cell surface epitope which is necessary for optimal transport of anthracycline and glutathione conjugates by RLIP76, and that this peptide could be a novel target for antineoplastic therapy.
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Affiliation(s)
- Sushma Yadav
- Department of Chemistry and Biochemistry, University of Texas, Arlington, Texas 76019-0065, USA
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43
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Pazos F, Sternberg MJE. Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci U S A 2004; 101:14754-9. [PMID: 15456910 PMCID: PMC522026 DOI: 10.1073/pnas.0404569101] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2004] [Indexed: 11/18/2022] Open
Abstract
Current structural genomics projects are yielding structures for proteins whose functions are unknown. Accordingly, there is a pressing requirement for computational methods for function prediction. Here we present PHUNCTIONER, an automatic method for structure-based function prediction using automatically extracted functional sites (residues associated to functions). The method relates proteins with the same function through structural alignments and extracts 3D profiles of conserved residues. Functional features to train the method are extracted from the Gene Ontology (GO) database. The method extracts these features from the entire GO hierarchy and hence is applicable across the whole range of function specificity. 3D profiles associated with 121 GO annotations were extracted. We tested the power of the method both for the prediction of function and for the extraction of functional sites. The success of function prediction by our method was compared with the standard homology-based method. In the zone of low sequence similarity (approximately 15%), our method assigns the correct GO annotation in 90% of the protein structures considered, approximately 20% higher than inheritance of function from the closest homologue.
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Affiliation(s)
- Florencio Pazos
- Structural Bioinformatics Group, Biochemistry Building, Department of Biological Sciences, Imperial College London, London SW7 2AZ, UK
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44
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Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci 2004; 13:190-202. [PMID: 14691234 PMCID: PMC2286531 DOI: 10.1110/ps.03323604] [Citation(s) in RCA: 226] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Protein interfaces are thought to be distinguishable from the rest of the protein surface by their greater degree of residue conservation. We test the validity of this approach on an expanded set of 64 protein-protein interfaces using conservation scores derived from two multiple sequence alignment types, one of close homologs/orthologs and one of diverse homologs/paralogs. Overall, we find that the interface is slightly more conserved than the rest of the protein surface when using either alignment type, with alignments of diverse homologs showing marginally better discrimination. However, using a novel surface-patch definition, we find that the interface is rarely significantly more conserved than other surface patches when using either alignment type. When an interface is among the most conserved surface patches, it tends to be part of an enzyme active site. The most conserved surface patch overlaps with 39% (+/- 28%) and 36% (+/- 28%) of the actual interface for diverse and close homologs, respectively. Contrary to results obtained from smaller data sets, this work indicates that residue conservation is rarely sufficient for complete and accurate prediction of protein interfaces. Finally, we find that obligate interfaces differ from transient interfaces in that the former have significantly fewer alignment gaps at the interface than the rest of the protein surface, as well as having buried interface residues that are more conserved than partially buried interface residues.
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Affiliation(s)
- Daniel R Caffrey
- Pfizer Discovery Technology Center, Cambridge, Massachusetts 02139, USA
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45
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Vargiu P, De Abajo R, Garcia-Ranea JA, Valencia A, Santisteban P, Crespo P, Bernal J. The small GTP-binding protein, Rhes, regulates signal transduction from G protein-coupled receptors. Oncogene 2004; 23:559-68. [PMID: 14724584 DOI: 10.1038/sj.onc.1207161] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Ras homolog enriched in striatum, Rhes, is the product of a thyroid hormone-regulated gene during brain development. Rhes and the dexamethasone-induced Dexras1 define a novel distinct subfamily of proteins within the Ras family, characterized by an extended variable domain in the carboxyl terminal region. We have carried this study because there is a complete lack of knowledge on Rhes signaling. We show that in PC12 cells, Rhes is targeted to the plasma membrane by farnesylation. We demonstrate that about 30% of the native Rhes protein is bound to GTP and this proportion is unaltered by typical Ras family nucleotide exchange factors. However, Rhes is not transforming in murine fibroblasts. We have also examined the role of Rhes in cell signaling. Rhes does not stimulate the ERK pathway. By contrast, it binds to and activates PI3K. On the other hand, we demonstrate that Rhes impairs the activation of the cAMP/PKA pathway by thyroid-stimulating hormone, and by an activated beta2 adrenergic receptor by a mechanism that suggests uncoupling of the receptor to its cognate heterotrimeric complex. Overall, our results provide the initial insights into the role in signal transduction of this novel Ras family member.
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Affiliation(s)
- Pierfrancesco Vargiu
- Instituto de Investigaciones Biomédicas Alberto Sols. Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28029 Madrid, Spain
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46
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Lebreton S, Boissel L, Moreau J. Control of embryonicXenopusmorphogenesis by a Ral-GDS/Xral branch of the Ras signalling pathway. J Cell Sci 2003; 116:4651-62. [PMID: 14576358 DOI: 10.1242/jcs.00763] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Ras proteins mediate biological responses through various effectors and play a key role in relaying the Fibroblast Growth Factor (FGF) mesoderm induction signal during embryogenesis of the frog, Xenopus laevis. One Ras effector pathway involves the activation of the small G protein Ral. In the present study, we have investigated the role of key components in the Ral branch of FGF and Ras signalling during early Xenopus development. Treatment of animal caps with bFGF, which converts prospective ectoderm to mesoderm, activates Xral. The Ras mutant 12V37G, which can bind to Ral-GDS but not Raf, also activates Xral as well as causing developmental defects and cortical F-actin disassembly. A similar phenotype is induced by Ral-GDS itself. FGF-induced expression of several signature mesodermal genes, by contrast, is independent of Xral signalling. This and other data suggest that the RalB branch of Ras and FGF signalling regulates the actin cytoskeleton and morphogenesis in a transcriptionally independent manner. We also find Xral to be specifically activated in the marginal zone of Xenopus embryos, and find that disruption of the Ral pathway in this region prevents closure of the blastopore during gastrulation. We conclude that Ral signalling is autonomously required by mesodermal cells to effect essential morphogenetic changes during Xenopus gastrulation.
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Affiliation(s)
- Stéphanie Lebreton
- Institut Jacques Monod, CNRS, Universités Paris VI et Paris VII, Mécanismes Moléculaires du Développement, 2 Place Jussieu, 75251 Paris cedex 05, France
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47
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Awasthi S, Singhal SS, Sharma R, Zimniak P, Awasthi YC. Transport of glutathione conjugates and chemotherapeutic drugs by RLIP76 (RALBP1): a novel link between G-protein and tyrosine kinase signaling and drug resistance. Int J Cancer 2003; 106:635-46. [PMID: 12866021 DOI: 10.1002/ijc.11260] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Our studies have shown that RLIP76 (RALBP1), a 76 kDa Ral-binding, Rho/Rac-GAP and Ral effector protein, is a novel multispecific transporter of xenobiotics as well as GS-Es. Like previously characterized ABC transporters, it mediates ATP-dependent transport of structurally unrelated amphiphilic xenobiotics and displays inherent ATPase activity, which is stimulated by its substrate allocrites. It does not have significant sequence homology with ABC transporters and differs from the ABC transporters in several other important aspects, including (i) lack of any close homologs in humans, (ii) lack of a classical Walker domain, (iii) integral membrane association without clearly defined transmembrane domains and (iv) its role as a direct link to Ras/Ral/Rho and EGF-R signaling through its multifunctional nature, including GAP activity, regulation of exocytosis as well as clathrin-coated pit-mediated receptor endocytosis. Its multifunctional nature derives from the presence of multiple motifs, including a Rho/Rac GAP domain, a Ral effector domain binding motif, 2 distinct ATP-binding domains, a H(+)-ATPase domain, PKC and tyrosine kinase phosphorylation sites and the ability to undergo fragmentation into multiple smaller peptides which participate as components of macromolecular functional complexes. One of the physiologic functions of RLIP76 is regulation of intracellular concentration of the electrophilic intermediates of oxidative lipid metabolism by mediating efflux of GS-E formed from oxidative degradation of arachidonic acid, including leukotrienes and the 4HNE-GSH conjugate. RLIP76-mediated transport of amphiphilic chemotherapeutic agents such as anthracyclines and vinca alkaloids as well as GS-E produced during oxidative metabolism places this multifunctional protein in a central role as a resistance mechanism for preventing apoptosis caused by chemotherapeutic agents and a variety of external/internal stressors, including oxidative stress, heat shock and radiation.
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Affiliation(s)
- Sanjay Awasthi
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX 76019, USA.
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48
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Fukai S, Matern HT, Jagath JR, Scheller RH, Brunger AT. Structural basis of the interaction between RalA and Sec5, a subunit of the sec6/8 complex. EMBO J 2003; 22:3267-78. [PMID: 12839989 PMCID: PMC165653 DOI: 10.1093/emboj/cdg329] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2003] [Revised: 05/13/2003] [Accepted: 05/15/2003] [Indexed: 12/21/2022] Open
Abstract
The sec6/8 complex or exocyst is an octameric protein complex that functions during cell polarization by regulating the site of exocytic vesicle docking to the plasma membrane, in concert with small GTP-binding proteins. The Sec5 subunit of the mammalian sec6/8 complex binds Ral in a GTP-dependent manner. Here we report the crystal structure of the complex between the Ral-binding domain of Sec5 and RalA bound to a non-hydrolyzable GTP analog (GppNHp) at 2.1 A resolution, providing the first structural insights into the mechanism and specificity of sec6/8 regulation. The Sec5 Ral-binding domain folds into an immunoglobulin-like beta-sandwich structure, which represents a novel fold for an effector of a GTP-binding protein. The interface between the two proteins involves a continuous antiparallel beta-sheet, similar to that found in other effector/G-protein complexes, such as Ras and Rap1A. Specific interactions unique to the RalA.Sec5 complex include Sec5 Thr11 and Arg27, and RalA Glu38, which we show are required for complex formation by isothermal titration calorimetry. Comparison of the structures of GppNHp- and GDP-bound RalA suggests a nucleotide-dependent switch mechanism for Sec5 binding.
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Affiliation(s)
- Shuya Fukai
- Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University, James H.Clark Center, E300C, 318 Campus Drive, Stanford, CA 94305-5432, USA
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49
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Morillas M, Gómez-Puertas P, Bentebibel A, Sellés E, Casals N, Valencia A, Hegardt FG, Asins G, Serra D. Identification of conserved amino acid residues in rat liver carnitine palmitoyltransferase I critical for malonyl-CoA inhibition. Mutation of methionine 593 abolishes malonyl-CoA inhibition. J Biol Chem 2003; 278:9058-63. [PMID: 12499375 DOI: 10.1074/jbc.m209999200] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carnitine palmitoyltransferase (CPT) I, which catalyzes the conversion of palmitoyl-CoA to palmitoylcarnitine facilitating its transport through the mitochondrial membranes, is inhibited by malonyl-CoA. By using the SequenceSpace algorithm program to identify amino acids that participate in malonyl-CoA inhibition in all carnitine acyltransferases, we found 5 conserved amino acids (Thr(314), Asn(464), Ala(478), Met(593), and Cys(608), rat liver CPT I coordinates) common to inhibitable malonyl-CoA acyltransferases (carnitine octanoyltransferase and CPT I), and absent in noninhibitable malonyl-CoA acyltransferases (CPT II, carnitine acetyltransferase (CAT) and choline acetyltransferase (ChAT)). To determine the role of these amino acid residues in malonyl-CoA inhibition, we prepared the quintuple mutant CPT I T314S/N464D/A478G/M593S/C608A as well as five single mutants CPT I T314S, N464D, A478G, M593S, and C608A. In each case the CPT I amino acid selected was mutated to that present in the same homologous position in CPT II, CAT, and ChAT. Because mutant M593S nearly abolished the sensitivity to malonyl-CoA, two other Met(593) mutants were prepared: M593A and M593E. The catalytic efficiency (V(max)/K(m)) of CPT I in mutants A478G and C608A and all Met(593) mutants toward carnitine as substrate was clearly increased. In those CPT I proteins in which Met(593) had been mutated, the malonyl-CoA sensitivity was nearly abolished. Mutations in Ala(478), Cys(608), and Thr(314) to their homologous amino acid residues in CPT II, CAT, and ChAT caused various decreases in malonyl-CoA sensitivity. Ala(478) is located in the structural model of CPT I near the catalytic site and participates in the binding of malonyl-CoA in the low affinity site (Morillas, M., Gómez-Puertas, P., Rubi, B., Clotet, J., Ariño, J., Valencia, A., Hegardt, F. G., Serra, D., and Asins, G. (2002) J. Biol. Chem. 277, 11473-11480). Met(593) may participate in the interaction of malonyl-CoA in the second affinity site, whose location has not been reported.
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Affiliation(s)
- Montserrat Morillas
- Department of Biochemistry and Molecular Biology, University of Barcelona, School of Pharmacy, E-08028 Barcelona, Spain
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del Sol A, del Sol Mesa A, Pazos F, Valencia A. Automatic methods for predicting functionally important residues. J Mol Biol 2003; 326:1289-302. [PMID: 12589769 DOI: 10.1016/s0022-2836(02)01451-1] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sequence analysis is often the first guide for the prediction of residues in a protein family that may have functional significance. A few methods have been proposed which use the division of protein families into subfamilies in the search for those positions that could have some functional significance for the whole family, but at the same time which exhibit the specificity of each subfamily ("Tree-determinant residues"). However, there are still many unsolved questions like the best division of a protein family into subfamilies, or the accurate detection of sequence variation patterns characteristic of different subfamilies. Here we present a systematic study in a significant number of protein families, testing the statistical meaning of the Tree-determinant residues predicted by three different methods that represent the range of available approaches. The first method takes as a starting point a phylogenetic representation of a protein family and, following the principle of Relative Entropy from Information Theory, automatically searches for the optimal division of the family into subfamilies. The second method looks for positions whose mutational behavior is reminiscent of the mutational behavior of the full-length proteins, by directly comparing the corresponding distance matrices. The third method is an automation of the analysis of distribution of sequences and amino acid positions in the corresponding multidimensional spaces using a vector-based principal component analysis. These three methods have been tested on two non-redundant lists of protein families: one composed by proteins that bind a variety of ligand groups, and the other composed by proteins with annotated functionally relevant sites. In most cases, the residues predicted by the three methods show a clear tendency to be close to bound ligands of biological relevance and to those amino acids described as participants in key aspects of protein function. These three automatic methods provide a wide range of possibilities for biologists to analyze their families of interest, in a similar way to the one presented here for the family of proteins related with ras-p21.
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Affiliation(s)
- Antonio del Sol
- Protein Design Group, National Center for Biotechnology, Cantoblanco, Madrid 28049, Spain
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