1
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Tsaridou S, Velimezi G, Willenbrock F, Chatzifrangkeskou M, Elsayed W, Panagopoulos A, Karamitros D, Gorgoulis V, Lygerou Z, Roukos V, O'Neill E, Pefani DE. 53BP1-mediated recruitment of RASSF1A to ribosomal DNA breaks promotes local ATM signaling. EMBO Rep 2022; 23:e54483. [PMID: 35758159 PMCID: PMC9346497 DOI: 10.15252/embr.202154483] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/30/2022] [Accepted: 06/03/2022] [Indexed: 12/29/2022] Open
Abstract
DNA lesions occur across the genome and constitute a threat to cell viability; however, damage at specific genomic loci has a relatively greater impact on overall genome stability. The ribosomal RNA gene repeats (rDNA) are emerging fragile sites. Recent progress in understanding how the rDNA damage response is organized has highlighted a key role of adaptor proteins. Here, we show that the scaffold tumor suppressor RASSF1A is recruited to rDNA breaks. RASSF1A recruitment to double-strand breaks is mediated by 53BP1 and depends on RASSF1A phosphorylation at Serine 131 by ATM kinase. Employing targeted rDNA damage, we uncover that RASSF1A recruitment promotes local ATM signaling. RASSF1A silencing, a common epigenetic event during malignant transformation, results in persistent breaks, rDNA copy number alterations and decreased cell viability. Overall, we identify a novel role for RASSF1A at rDNA break sites, provide mechanistic insight into how the DNA damage response is organized in a chromatin context, and provide further evidence for how silencing of the RASSF1A tumor suppressor contributes to genome instability.
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Affiliation(s)
- Stavroula Tsaridou
- Department of Biology, School of Medicine, University of Patras, Patras, Greece
| | - Georgia Velimezi
- Department of Biology, School of Medicine, University of Patras, Patras, Greece.,Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | | | | | | | - Dimitris Karamitros
- Department of Physiology, School of Medicine, University of Patras, Patras, Greece
| | - Vassilis Gorgoulis
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,Laboratory of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, Athens, Greece.,Faculty of Biology, Medicine and Health, Manchester Academic Health Centre, University of Manchester, Manchester, UK.,Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Zoi Lygerou
- Department of Biology, School of Medicine, University of Patras, Patras, Greece
| | - Vassilis Roukos
- Department of Biology, School of Medicine, University of Patras, Patras, Greece.,Institute of Molecular Biology (IMB), Mainz, Germany
| | - Eric O'Neill
- Department of Oncology, University of Oxford, Oxford, UK
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2
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Cairns L, Patterson A, Weingartner KA, Koehler TJ, DeAngelis DR, Tripp KW, Bothner B, Kavran JM. Biophysical characterization of SARAH domain-mediated multimerization of Hippo pathway complexes in Drosophila. J Biol Chem 2020; 295:6202-6213. [PMID: 32213597 DOI: 10.1074/jbc.ra120.012679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/23/2020] [Indexed: 11/06/2022] Open
Abstract
Hippo pathway signaling limits cell growth and proliferation and maintains the stem-cell niche. These cellular events result from the coordinated activity of a core kinase cassette that is regulated, in part, by interactions involving Hippo, Salvador, and dRassF. These interactions are mediated by a conserved coiled-coil domain, termed SARAH, in each of these proteins. SARAH domain-mediated homodimerization of Hippo kinase leads to autophosphorylation and activation. Paradoxically, SARAH domain-mediated heterodimerization between Hippo and Salvador enhances Hippo kinase activity in cells, whereas complex formation with dRassF inhibits it. To better understand the mechanism by which each complex distinctly modulates Hippo kinase and pathway activity, here we biophysically characterized the entire suite of SARAH domain-mediated complexes. We purified the three SARAH domains from Drosophila melanogaster and performed an unbiased pulldown assay to identify all possible interactions, revealing that isolated SARAH domains are sufficient to recapitulate the cellular assemblies and that Hippo is a universal binding partner. Additionally, we found that the Salvador SARAH domain homodimerizes and demonstrate that this interaction is conserved in Salvador's mammalian homolog. Using native MS, we show that each of these complexes is dimeric in solution. We also measured the stability of each SARAH domain complex, finding that despite similarities at both the sequence and structural levels, SARAH domain complexes differ in stability. The identity, stoichiometry, and stability of these interactions characterized here comprehensively reveal the nature of SARAH domain-mediated complex formation and provide mechanistic insights into how SARAH domain-mediated interactions influence Hippo pathway activity.
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Affiliation(s)
- Leah Cairns
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 20215
| | - Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, 59717
| | - Kyler A Weingartner
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 20215
| | - T J Koehler
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 20215
| | - Daniel R DeAngelis
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 20215
| | - Katherine W Tripp
- The T. C. Jenkins Department of Biophysics, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, Maryland, 201218
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, 59717
| | - Jennifer M Kavran
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 20215; Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland 20215; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, 20215.
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3
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Kumar AP, Verma CS, Lukman S. Structural dynamics and allostery of Rab proteins: strategies for drug discovery and design. Brief Bioinform 2020; 22:270-287. [PMID: 31950981 DOI: 10.1093/bib/bbz161] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/29/2019] [Accepted: 11/15/2019] [Indexed: 01/09/2023] Open
Abstract
Rab proteins represent the largest family of the Rab superfamily guanosine triphosphatase (GTPase). Aberrant human Rab proteins are associated with multiple diseases, including cancers and neurological disorders. Rab subfamily members display subtle conformational variations that render specificity in their physiological functions and can be targeted for subfamily-specific drug design. However, drug discovery efforts have not focused much on targeting Rab allosteric non-nucleotide binding sites which are subjected to less evolutionary pressures to be conserved, hence are likely to offer subfamily specificity and may be less prone to undesirable off-target interactions and side effects. To discover druggable allosteric binding sites, Rab structural dynamics need to be first incorporated using multiple experimentally and computationally obtained structures. The high-dimensional structural data may necessitate feature extraction methods to identify manageable representative structures for subsequent analyses. We have detailed state-of-the-art computational methods to (i) identify binding sites using data on sequence, shape, energy, etc., (ii) determine the allosteric nature of these binding sites based on structural ensembles, residue networks and correlated motions and (iii) identify small molecule binders through structure- and ligand-based virtual screening. To benefit future studies for targeting Rab allosteric sites, we herein detail a refined workflow comprising multiple available computational methods, which have been successfully used alone or in combinations. This workflow is also applicable for drug discovery efforts targeting other medically important proteins. Depending on the structural dynamics of proteins of interest, researchers can select suitable strategies for allosteric drug discovery and design, from the resources of computational methods and tools enlisted in the workflow.
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Affiliation(s)
- Ammu Prasanna Kumar
- Department of Chemistry, College of Arts and Sciences, Khalifa University, Abu Dhabi, United Arab Emirates.,Research Unit in Bioinformatics, Department of Biochemistry and Microbiology, Rhodes University, South Africa
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore
| | - Suryani Lukman
- Department of Chemistry, College of Arts and Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
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4
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Chatzifrangkeskou M, Pefani D, Eyres M, Vendrell I, Fischer R, Pankova D, O'Neill E. RASSF1A is required for the maintenance of nuclear actin levels. EMBO J 2019; 38:e101168. [PMID: 31414556 PMCID: PMC6694222 DOI: 10.15252/embj.2018101168] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 04/23/2019] [Accepted: 05/14/2019] [Indexed: 01/19/2023] Open
Abstract
Nuclear actin participates in many essential cellular processes including gene transcription, chromatin remodelling and mRNA processing. Actin shuttles into and out the nucleus through the action of dedicated transport receptors importin-9 and exportin-6, but how this transport is regulated remains unclear. Here, we show that RASSF1A is a novel regulator of actin nucleocytoplasmic trafficking and is required for the active maintenance of nuclear actin levels through supporting binding of exportin-6 (XPO6) to RAN GTPase. RASSF1A (Ras association domain family 1 isoform A) is a tumour suppressor gene frequently silenced by promoter hypermethylation in all major solid cancers. Specifically, we demonstrate that endogenous RASSF1A localises to the nuclear envelope (NE) and is required for nucleocytoplasmic actin transport and the concomitant regulation of myocardin-related transcription factor A (MRTF-A), a co-activator of the transcription factor serum response factor (SRF). The RASSF1A/RAN/XPO6/nuclear actin pathway is aberrant in cancer cells where RASSF1A expression is lost and correlates with reduced MRTF-A/SRF activity leading to cell adhesion defects. Taken together, we have identified a previously unknown mechanism by which the nuclear actin pool is regulated and uncovered a previously unknown link of RASSF1A and MRTF-A/SRF in tumour suppression.
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Affiliation(s)
| | - Dafni‐Eleftheria Pefani
- Department of OncologyUniversity of OxfordOxfordUK
- Laboratory of BiologyMedical SchoolNational and Kapodistrian University of AthensAthensGreece
- Biomedical Research Foundation of the Academy of AthensAthensGreece
| | | | - Iolanda Vendrell
- Department of OncologyUniversity of OxfordOxfordUK
- Nuffield Department of MedicineTarget Discovery InstituteUniversity of OxfordOxfordUK
| | - Roman Fischer
- Nuffield Department of MedicineTarget Discovery InstituteUniversity of OxfordOxfordUK
| | | | - Eric O'Neill
- Department of OncologyUniversity of OxfordOxfordUK
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5
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Liang Z, Verkhivker GM, Hu G. Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications. Brief Bioinform 2019; 21:815-835. [DOI: 10.1093/bib/bbz029] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/04/2019] [Accepted: 02/21/2019] [Indexed: 12/24/2022] Open
Abstract
Abstract
Proteins are dynamical entities that undergo a plethora of conformational changes, accomplishing their biological functions. Molecular dynamics simulation and normal mode analysis methods have become the gold standard for studying protein dynamics, analyzing molecular mechanism and allosteric regulation of biological systems. The enormous amount of the ensemble-based experimental and computational data on protein structure and dynamics has presented a major challenge for the high-throughput modeling of protein regulation and molecular mechanisms. In parallel, bioinformatics and systems biology approaches including genomic analysis, coevolution and network-based modeling have provided an array of powerful tools that complemented and enriched biophysical insights by enabling high-throughput analysis of biological data and dissection of global molecular signatures underlying mechanisms of protein function and interactions in the cellular environment. These developments have provided a powerful interdisciplinary framework for quantifying the relationships between protein dynamics and allosteric regulation, allowing for high-throughput modeling and engineering of molecular mechanisms. Here, we review fundamental advances in protein dynamics, network theory and coevolutionary analysis that have provided foundation for rapidly growing computational tools for modeling of allosteric regulation. We discuss recent developments in these interdisciplinary areas bridging computational biophysics and network biology, focusing on promising applications in allosteric regulations, including the investigation of allosteric communication pathways, protein–DNA/RNA interactions and disease mutations in genomic medicine. We conclude by formulating and discussing future directions and potential challenges facing quantitative computational investigations of allosteric regulatory mechanisms in protein systems.
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Affiliation(s)
- Zhongjie Liang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Gennady M Verkhivker
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, USA
| | - Guang Hu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
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6
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Abstract
Ras oncoproteins can promote or suppress cellular apoptosis, but the mechanisms underlying these varied responses remain incompletely understood. Ras is linked to the Hippo tumor suppressor pathway, a highly conserved signaling cassette that regulates organ size in animals ranging from flies to humans. The proximal members of this pathway, Mammalian Ste20-like kinases (Msts) -1 and -2, self-associate in homodimers and also form heterodimers with other proteins. Formation of such complexes is known to regulate Mst kinase activity and thus, the Hippo pathway. In a manuscript that recently appeared in Current Biology, we showed that activated Hras promotes the formation of Mst1/Mst2 heterodimers, that activation of Erk was required for this event, and that these heterodimers were much less active than Mst1/Mst1 or Mst2/Mst2 homodimers. Interestingly, the formation of such heterodimers was required to deactivate the Hippo pathway and to enable transformation by Hras. In this Commentary, we discuss the background for this study and surprising implications thereof.
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7
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Liao TJ, Jang H, Tsai CJ, Fushman D, Nussinov R. The dynamic mechanism of RASSF5 and MST kinase activation by Ras. Phys Chem Chem Phys 2017; 19:6470-6480. [PMID: 28197608 PMCID: PMC5381522 DOI: 10.1039/c6cp08596b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
As a tumor suppressor, RASSF5 (NORE1A) activates MST1/2 thereby modulating the Hippo pathway. Structurally, activation involves RASSF5 and MST1/2 swapping their SARAH domains to form a SARAH heterodimer. This exposes the MST1/2 kinase domain which homodimerizes, leading to trans-autophosphorylation. The SARAH-SARAH interaction shifts RASSF5 away from its autoinhibited state and relieves MST1/2 autoinhibition. Separate crystal structures are available for the RA (Ras association) domain and SARAH dimer, where SARAH is a long straight α-helix. Using all-atom molecular dynamics simulations, we modeled the RASSF5 RA with a covalently connected SARAH to elucidate the dynamic mechanism of how SARAH mediates between autoinhibition and Ras triggered-activation. Our results show that in inactive RASSF5 the RA domain retains SARAH, yielding a self-associated conformation in which SARAH is in a kinked α-helical motif that increases the binding interface. When RASSF5 binds K-Ras4B-GTP, the equilibrium shifts toward SARAH's interacting with MST. Since the RA/SARAH affinity is relatively low, whereas that of the SARAH heterodimer is in the nM range, we suggest that RASSF5 exerts its tumor suppressor action through competition with other Ras effectors for Ras effector binding site, as well as coincidentally its recruitment to the membrane to help MST activation. Thus, SARAH plays a key role in RASSF5's tumor suppression action by linking the two major pathways in tumor cell proliferation: Ras and the MAPK (tumor cell proliferation-promoting) pathway, and the Hippo (tumor cell proliferation-suppressing) pathway.
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Affiliation(s)
- Tsung-Jen Liao
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA. and Biophysics Program, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
| | - David Fushman
- Biophysics Program, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA and Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA. and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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8
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RASSF5: An MST activator and tumor suppressor in vivo but opposite in vitro. Curr Opin Struct Biol 2016; 41:217-224. [DOI: 10.1016/j.sbi.2016.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 09/01/2016] [Indexed: 01/05/2023]
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9
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SARAH Domain-Mediated MST2-RASSF Dimeric Interactions. PLoS Comput Biol 2016; 12:e1005051. [PMID: 27716844 PMCID: PMC5055338 DOI: 10.1371/journal.pcbi.1005051] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/04/2016] [Indexed: 11/23/2022] Open
Abstract
RASSF enzymes act as key apoptosis activators and tumor suppressors, being downregulated in many human cancers, although their exact regulatory roles remain unknown. A key downstream event in the RASSF pathway is the regulation of MST kinases, which are main effectors of RASSF-induced apoptosis. The regulation of MST1/2 includes both homo- and heterodimerization, mediated by helical SARAH domains, though the underlying molecular interaction mechanism is unclear. Here, we study the interactions between RASSF1A, RASSF5, and MST2 SARAH domains by using both atomistic molecular simulation techniques and experiments. We construct and study models of MST2 homodimers and MST2-RASSF SARAH heterodimers, and we identify the factors that control their high molecular stability. In addition, we also analyze both computationally and experimentally the interactions of MST2 SARAH domains with a series of synthetic peptides particularly designed to bind to it, and hope that our approach can be used to address some of the challenging problems in designing new anti-cancer drugs. We model the conformational changes and protein-protein interactions of enzymes involved in signaling along the Hippo pathway—a key molecular mechanism that controls the process of programmed cell death in eukaryotic cells, including cells affected by cancer. Combining modern computational modeling techniques with experimental information from X-ray crystallography and systems biology studies, can unveil detailed molecular interactions and lead to novel drugs. Here, we study the atomistic mechanisms and interactions between MST2 and RASSF-type kinases, through their respective SARAH domains—highly conserved, long, terminal α-helices, which play essential roles in the activation of MST kinases and, therefore, in modulating apoptosis. In spite of their key roles in mediating cell signaling pathways, there is little structural information available for the RASSF SARAH domains and their dimerization with the MST2 SARAH domains. In particular, the RASSF1A crystal structure is not available yet. Here, we model, refine and validate atomistic structural models of dimers of the RASSF1A and MST2 SARAH domains, studying the interaction and the dynamic behavior of these molecular complexes using homology modeling, docking and full atomistic molecular dynamics simulations. Experimentally, we validate our approach by designing a novel peptide that can disrupt effectively MST2 homo and hetero SARAH dimers.
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10
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Fallahi E, O'Driscoll NA, Matallanas D. The MST/Hippo Pathway and Cell Death: A Non-Canonical Affair. Genes (Basel) 2016; 7:genes7060028. [PMID: 27322327 PMCID: PMC4929427 DOI: 10.3390/genes7060028] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/07/2016] [Accepted: 06/09/2016] [Indexed: 01/06/2023] Open
Abstract
The MST/Hippo signalling pathway was first described over a decade ago in Drosophila melanogaster and the core of the pathway is evolutionary conserved in mammals. The mammalian MST/Hippo pathway regulates organ size, cell proliferation and cell death. In addition, it has been shown to play a central role in the regulation of cellular homeostasis and it is commonly deregulated in human tumours. The delineation of the canonical pathway resembles the behaviour of the Hippo pathway in the fly where the activation of the core kinases of the pathway prevents the proliferative signal mediated by the key effector of the pathway YAP. Nevertheless, several lines of evidence support the idea that the mammalian MST/Hippo pathway has acquired new features during evolution, including different regulators and effectors, crosstalk with other essential signalling pathways involved in cellular homeostasis and the ability to actively trigger cell death. Here we describe the current knowledge of the mechanisms that mediate MST/Hippo dependent cell death, especially apoptosis. We include evidence for the existence of complex signalling networks where the core proteins of the pathway play a central role in controlling the balance between survival and cell death. Finally, we discuss the possible involvement of these signalling networks in several human diseases such as cancer, diabetes and neurodegenerative disorders.
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Affiliation(s)
- Emma Fallahi
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland. emma.fallahi---
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland. emma.fallahi---
| | - Niamh A O'Driscoll
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - David Matallanas
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland.
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11
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Jambrina PG, Rauch N, Pilkington R, Rybakova K, Nguyen LK, Kholodenko BN, Buchete NV, Kolch W, Rosta E. Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation. Angew Chem Int Ed Engl 2015; 55:983-6. [PMID: 26644280 PMCID: PMC4736688 DOI: 10.1002/anie.201509272] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Indexed: 12/19/2022]
Abstract
RAF kinases are key players in the MAPK signaling pathway and are important targets for personalized cancer therapy. RAF dimerization is part of the physiological activation mechanism, together with phosphorylation, and is known to convey resistance to RAF inhibitors. Herein, molecular dynamics simulations are used to show that phosphorylation of a key N-terminal acidic (NtA) motif facilitates RAF dimerization by introducing several interprotomer salt bridges between the αC-helix and charged residues upstream of the NtA motif. Additionally, we show that the R-spine of RAF interacts with a conserved Trp residue in the vicinity of the NtA motif, connecting the active sites of two protomers and thereby modulating the cooperative interactions in the RAF dimer. Our findings provide a first structure-based mechanism for the auto-transactivation of RAF and could be generally applicable to other kinases, opening new pathways for overcoming dimerization-related drug resistance.
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Affiliation(s)
- Pablo G Jambrina
- Department of Chemistry, King's College London, London, SE1 1DB, UK
| | - Nora Rauch
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Ruth Pilkington
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Katja Rybakova
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Lan K Nguyen
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, 4, Ireland.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, 3800, Australia
| | - Boris N Kholodenko
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Nicolae-Viorel Buchete
- School of Physics and Complex and Adaptative Systems Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Walter Kolch
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland. .,School of Medicine & Medical Sciences, University College Dublin, Belfield, Dublin, 4, Ireland.
| | - Edina Rosta
- Department of Chemistry, King's College London, London, SE1 1DB, UK.
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