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Vincenzi M, Mercurio FA, Autiero I, Leone M. Cancer-Related Mutations in the Sam Domains of EphA2 Receptor and Ship2 Lipid Phosphatase: A Computational Study. Molecules 2024; 29:1024. [PMID: 38474536 DOI: 10.3390/molecules29051024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/09/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
The lipid phosphatase Ship2 interacts with the EphA2 receptor by forming a heterotypic Sam (sterile alpha motif)-Sam complex. Ship2 works as a negative regulator of receptor endocytosis and consequent degradation, and anti-oncogenic effects in cancer cells should be induced by hindering its association with EphA2. Herein, a computational approach is presented to investigate the relationship between Ship2-Sam/EphA2-Sam interaction and cancer onset and further progression. A search was first conducted through the COSMIC (Catalogue of Somatic Mutations in Cancer) database to identify cancer-related missense mutations positioned inside or close to the EphA2-Sam and Ship2-Sam reciprocal binding interfaces. Next, potential differences in the chemical-physical properties of mutant and wild-type Sam domains were evaluated by bioinformatics tools based on analyses of primary sequences. Three-dimensional (3D) structural models of mutated EphA2-Sam and Ship2-Sam domains were built as well and deeply analysed with diverse computational instruments, including molecular dynamics, to classify potentially stabilizing and destabilizing mutations. In the end, the influence of mutations on the EphA2-Sam/Ship2-Sam interaction was studied through docking techniques. This in silico approach contributes to understanding, at the molecular level, the mutation/cancer relationship by predicting if amino acid substitutions could modulate EphA2 receptor endocytosis.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
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2
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Ray S, Hewitt K. Sticky, Adaptable, and Many-sided: SAM protein versatility in normal and pathological hematopoietic states. Bioessays 2023; 45:e2300022. [PMID: 37318311 PMCID: PMC10527593 DOI: 10.1002/bies.202300022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
With decades of research seeking to generalize sterile alpha motif (SAM) biology, many outstanding questions remain regarding this multi-tool protein module. Recent data from structural and molecular/cell biology has begun to reveal new SAM modes of action in cell signaling cascades and biomolecular condensation. SAM-dependent mechanisms underlie blood-related (hematologic) diseases, including myelodysplastic syndromes and leukemias, prompting our focus on hematopoiesis for this review. With the increasing coverage of SAM-dependent interactomes, a hypothesis emerges that SAM interaction partners and binding affinities work to fine tune cell signaling cascades in developmental and disease contexts, including hematopoiesis and hematologic disease. This review discusses what is known and remains unknown about the standard mechanisms and neoplastic properties of SAM domains and what the future might hold for developing SAM-targeted therapies.
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Affiliation(s)
- Suhita Ray
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, United States
| | - Kyle Hewitt
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, United States
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3
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Washburn HR, Chander P, Srikanth KD, Dalva MB. Transsynaptic Signaling of Ephs in Synaptic Development, Plasticity, and Disease. Neuroscience 2023; 508:137-152. [PMID: 36460219 DOI: 10.1016/j.neuroscience.2022.11.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022]
Abstract
Synapse formation between neurons is critical for proper circuit and brain function. Prior to activity-dependent refinement of connections between neurons, activity-independent cues regulate the contact and recognition of potential synaptic partners. Formation of a synapse results in molecular recognition events that initiate the process of synaptogenesis. Synaptogenesis requires contact between axon and dendrite, selection of correct and rejection of incorrect partners, and recruitment of appropriate pre- and postsynaptic proteins needed for the establishment of functional synaptic contact. Key regulators of these events are families of transsynaptic proteins, where one protein is found on the presynaptic neuron and the other is found on the postsynaptic neuron. Of these families, the EphBs and ephrin-Bs are required during each phase of synaptic development from target selection, recruitment of synaptic proteins, and formation of spines to regulation of synaptic plasticity at glutamatergic spine synapses in the mature brain. These roles also place EphBs and ephrin-Bs as important regulators of human neurological diseases. This review will focus on the role of EphBs and ephrin-Bs at synapses.
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Affiliation(s)
- Halley R Washburn
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA; Department of Neuroscience, Jefferson Synaptic Biology Center, Sidney Kimmel Medical College at Thomas Jefferson University, 233 South 10th Street, Bluemle Life Sciences Building, Room 324, Philadelphia, PA 19107, USA
| | - Praveen Chander
- Department of Neuroscience, Jefferson Synaptic Biology Center, Sidney Kimmel Medical College at Thomas Jefferson University, 233 South 10th Street, Bluemle Life Sciences Building, Room 324, Philadelphia, PA 19107, USA
| | - Kolluru D Srikanth
- Department of Neuroscience, Jefferson Synaptic Biology Center, Sidney Kimmel Medical College at Thomas Jefferson University, 233 South 10th Street, Bluemle Life Sciences Building, Room 324, Philadelphia, PA 19107, USA
| | - Matthew B Dalva
- Department of Neuroscience, Jefferson Synaptic Biology Center, Sidney Kimmel Medical College at Thomas Jefferson University, 233 South 10th Street, Bluemle Life Sciences Building, Room 324, Philadelphia, PA 19107, USA.
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Hunting for Novel Routes in Anticancer Drug Discovery: Peptides against Sam-Sam Interactions. Int J Mol Sci 2022; 23:ijms231810397. [PMID: 36142306 PMCID: PMC9499636 DOI: 10.3390/ijms231810397] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 01/10/2023] Open
Abstract
Among the diverse protein binding modules, Sam (Sterile alpha motif) domains attract attention due to their versatility. They are present in different organisms and play many functions in physiological and pathological processes by binding multiple partners. The EphA2 receptor contains a Sam domain at the C-terminus (EphA2-Sam) that is able to engage protein regulators of receptor stability (including the lipid phosphatase Ship2 and the adaptor Odin). Ship2 and Odin are recruited by EphA2-Sam through heterotypic Sam-Sam interactions. Ship2 decreases EphA2 endocytosis and consequent degradation, producing chiefly pro-oncogenic outcomes in a cellular milieu. Odin, through its Sam domains, contributes to receptor stability by possibly interfering with ubiquitination. As EphA2 is upregulated in many types of tumors, peptide inhibitors of Sam-Sam interactions by hindering receptor stability could function as anticancer therapeutics. This review describes EphA2-Sam and its interactome from a structural and functional perspective. The diverse design strategies that have thus far been employed to obtain peptides targeting EphA2-mediated Sam-Sam interactions are summarized as well. The generated peptides represent good initial lead compounds, but surely many efforts need to be devoted in the close future to improve interaction affinities towards Sam domains and consequently validate their anticancer properties.
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5
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The Role of RNA-Binding Proteins in Hematological Malignancies. Int J Mol Sci 2022; 23:ijms23179552. [PMID: 36076951 PMCID: PMC9455611 DOI: 10.3390/ijms23179552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
Hematological malignancies comprise a plethora of different neoplasms, such as leukemia, lymphoma, and myeloma, plus a myriad of dysplasia, such as myelodysplastic syndromes or anemias. Despite all the advances in patient care and the development of new therapies, some of these malignancies remain incurable, mainly due to resistance and refractoriness to treatment. Therefore, there is an unmet clinical need to identify new biomarkers and potential therapeutic targets that play a role in treatment resistance and contribute to the poor outcomes of these tumors. RNA-binding proteins (RBPs) are a diverse class of proteins that interact with transcripts and noncoding RNAs and are involved in every step of the post-transcriptional processing of transcripts. Dysregulation of RBPs has been associated with the development of hematological malignancies, making them potential valuable biomarkers and potential therapeutic targets. Although a number of dysregulated RBPs have been identified in hematological malignancies, there is a critical need to understand the biology underlying their contribution to pathology, such as the spatiotemporal context and molecular mechanisms involved. In this review, we emphasize the importance of deciphering the regulatory mechanisms of RBPs to pinpoint novel therapeutic targets that could drive or contribute to hematological malignancy biology.
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Wu J, Zhou Y, Zhang J, Zhang HX, Jia R. Molecular Dynamics Simulation Investigation of the Binding and Interaction of the EphA6-Odin Protein Complex. J Phys Chem B 2022; 126:4914-4924. [PMID: 35732074 DOI: 10.1021/acs.jpcb.2c01492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein-protein interaction plays an important role in the development of almost all cells. Elucidating the dynamic binding and affinity of a protein-protein complex is essential for understanding the biological functions of proteins. EphA6 and Odin proteins are members of the Eph (erythropoietin-producing hepatocyte) receptor family and the Anks (ankyrin repeat and sterile α motif domain-containing) family, respectively. Odin significantly functions in regulating endocytosis, degradation, and stability of EphA receptors. In this work, the key residues of the interaction interface were determined through a hydrogen bond, root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and dynamic correlation analysis of the conventional molecular dynamics (MD) simulations. The calculated standard binding free energy, -7.92 kcal/mol, between EphA6 and Odin is quite consistent with the experimental measurement value, -8.73 kcal/mol. By the combination of several MD simulation techniques, our investigation of the binding process reveals the detailed representative characteristics of the entire binding pathway at the molecular level. Based on the obtained potential of the mean force (PMF) curve, the analysis of the simulation trajectories shows that the residue Arg1013 in the receptor EphA6 is responsible for capturing Asp739 and Asp740 in the ligand Odin during the initial stage of binding. In the later stage of binding, the hydrogen bonds and salt bridges between a series of residues Lys973, Leu1007, Gly1009, His1010, and Arg1012 in the receptor and residues Leu735, Asn736, Asp739, Asp740, and Asp753 in the ligand mainly contribute to the stability of the protein complex. In addition, the specific change process of the receptor-ligand-binding mode is also clarified during the binding process. Our present simulation will promote a deep understanding of the protein-protein interaction, and the identified key interresidue interaction will be theoretical guidance for the design of protein drugs.
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Affiliation(s)
- Jianhua Wu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, Jilin, People's Republic of China
| | - Yu Zhou
- Department of Hepato-Biliary-Pancreatic Surgery, The Second Hospital of Jilin University, Changchun 130041, Jilin, People's Republic of China
| | - Jilong Zhang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, Jilin, People's Republic of China
| | - Hong-Xing Zhang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, Jilin, People's Republic of China
| | - Ran Jia
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, Jilin, People's Republic of China
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Vincenzi M, Anna Mercurio F, Di Natale C, Palumbo R, Pirone L, La Manna S, Marasco D, Maria Pedone E, Leone M. Targeting Ship2-Sam with peptide ligands: Novel insights from a multidisciplinary approach. Bioorg Chem 2022; 122:105680. [DOI: 10.1016/j.bioorg.2022.105680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/24/2022] [Accepted: 02/09/2022] [Indexed: 01/06/2023]
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8
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Li ZL, Mattos C, Buck M. Computational studies of the principle of dynamic-change-driven protein interactions. Structure 2022; 30:909-916.e2. [DOI: 10.1016/j.str.2022.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/08/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
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Neira JL, Rizzuti B, Ortega-Alarcón D, Giudici AM, Abián O, Fárez-Vidal ME, Velázquez-Campoy A. The armadillo-repeat domain of plakophilin 1 binds the C-terminal sterile alpha motif (SAM) of p73. Biochim Biophys Acta Gen Subj 2021; 1865:129914. [PMID: 33872756 DOI: 10.1016/j.bbagen.2021.129914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Plakophilin 1 (PKP1) is a component of desmosomes, which are key structural components for cell-cell adhesion, and can also be found in other cell locations. The p53, p63 and p73 proteins belong to the p53 family of transcription factors, playing crucial roles in tumour suppression. The α-splice variant of p73 (p73α) has at its C terminus a sterile alpha motif (SAM); such domain, SAMp73, is involved in the interaction with other macromolecules. METHODS We studied the binding of SAMp73 with the armadillo domain of PKP1 (ARM-PKP1) in the absence and the presence of 100 mM NaCl, by using several biophysical techniques, namely fluorescence, far-ultraviolet circular dichroism (CD), nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC), and molecular docking and simulations. RESULTS Association was observed between the two proteins, with a dissociation constant of ~5 μM measured by ITC and fluorescence in the absence of NaCl. The binding region of SAMp73 involved residues of the so-called "middle-loop-end-helix" binding region (i.e., comprising the third helix, together with the C terminus of the second one, and the N-cap of the fourth), as shown by 15N, 1H- HSQC-NMR spectra. Molecular modelling provided additional information on the possible structure of the binding complex. CONCLUSIONS This newly-observed interaction could have potential therapeutic relevance in the tumour pathways where PKP1 is involved, and under conditions when there is a possible inactivation of p53. GENERAL SIGNIFICANCE The discovery of the binding between SAMp73 and ARM-PKP1 suggests a functional role for their interaction, including the possibility that SAMp73 could assist PKP1 in signalling pathways.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain.
| | - Bruno Rizzuti
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036 Rende, Italy.
| | - David Ortega-Alarcón
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | | | - Olga Abián
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - María Esther Fárez-Vidal
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Facultad de Medicina, Universidad de Granada, 18016 Granada, Spain; Instituto de Investigación Biomédica IBS, Complejo Hospitalario Universitario de Granada, Universidad de Granada, 18071 Granada, Spain
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; Fundacion ARAID, Government of Aragon, 50009 Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
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10
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Vincenzi M, Mercurio FA, Leone M. Protein Interaction Domains: Structural Features and Drug Discovery Applications (Part 2). Curr Med Chem 2021; 28:854-892. [PMID: 31942846 DOI: 10.2174/0929867327666200114114142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Proteins present a modular organization made up of several domains. Apart from the domains playing catalytic functions, many others are crucial to recruit interactors. The latter domains can be defined as "PIDs" (Protein Interaction Domains) and are responsible for pivotal outcomes in signal transduction and a certain array of normal physiological and disease-related pathways. Targeting such PIDs with small molecules and peptides able to modulate their interaction networks, may represent a valuable route to discover novel therapeutics. OBJECTIVE This work represents a continuation of a very recent review describing PIDs able to recognize post-translationally modified peptide segments. On the contrary, the second part concerns with PIDs that interact with simple peptide sequences provided with standard amino acids. METHODS Crucial structural information on different domain subfamilies and their interactomes was gained by a wide search in different online available databases (including the PDB (Protein Data Bank), the Pfam (Protein family), and the SMART (Simple Modular Architecture Research Tool)). Pubmed was also searched to explore the most recent literature related to the topic. RESULTS AND CONCLUSION PIDs are multifaceted: they have all diverse structural features and can recognize several consensus sequences. PIDs can be linked to different diseases onset and progression, like cancer or viral infections and find applications in the personalized medicine field. Many efforts have been centered on peptide/peptidomimetic inhibitors of PIDs mediated interactions but much more work needs to be conducted to improve drug-likeness and interaction affinities of identified compounds.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
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Stefanski KM, Russell CM, Westerfield JM, Lamichhane R, Barrera FN. PIP 2 promotes conformation-specific dimerization of the EphA2 membrane region. J Biol Chem 2021; 296:100149. [PMID: 33277361 PMCID: PMC7900517 DOI: 10.1074/jbc.ra120.016423] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 12/27/2022] Open
Abstract
The impact of the EphA2 receptor on cancer malignancy hinges on the two different ways it can be activated. EphA2 induces antioncogenic signaling after ligand binding, but ligand-independent activation of EphA2 is pro-oncogenic. It is believed that the transmembrane (TM) domain of EphA2 adopts two alternate conformations in the ligand-dependent and the ligand-independent states. However, it is poorly understood how the difference in TM helical crossing angles found in the two conformations impacts the activity and regulation of EphA2. We devised a method that uses hydrophobic matching to stabilize two conformations of a peptide comprising the EphA2 TM domain and a portion of the intracellular juxtamembrane (JM) segment. The two conformations exhibit different TM crossing angles, resembling the ligand-dependent and ligand-independent states. We developed a single-molecule technique using styrene maleic acid lipid particles to measure dimerization in membranes. We observed that the signaling lipid PIP2 promotes TM dimerization, but only in the small crossing angle state, which we propose corresponds to the ligand-independent conformation. In this state the two TMs are almost parallel, and the positively charged JM segments are expected to be close to each other, causing electrostatic repulsion. The mechanism PIP2 uses to promote dimerization might involve alleviating this repulsion due to its high density of negative charges. Our data reveal a conformational coupling between the TM and JM regions and suggest that PIP2 might directly exert a regulatory effect on EphA2 activation in cells that is specific to the ligand-independent conformation of the receptor.
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Affiliation(s)
- Katherine M Stefanski
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, USA
| | - Charles M Russell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Rajan Lamichhane
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA.
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA.
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12
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Vincenzi M, Mercurio FA, Leone M. Sam Domains in Multiple Diseases. Curr Med Chem 2020; 27:450-476. [PMID: 30306850 DOI: 10.2174/0929867325666181009114445] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 07/26/2018] [Accepted: 08/27/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND The sterile alpha motif (Sam) domain is a small helical protein module, able to undergo homo- and hetero-oligomerization, as well as polymerization, thus forming different types of protein architectures. A few Sam domains are involved in pathological processes and consequently, they represent valuable targets for the development of new potential therapeutic routes. This study intends to collect state-of-the-art knowledge on the different modes by which Sam domains can favor disease onset and progression. METHODS This review was build up by searching throughout the literature, for: a) the structural properties of Sam domains, b) interactions mediated by a Sam module, c) presence of a Sam domain in proteins relevant for a specific disease. RESULTS Sam domains appear crucial in many diseases including cancer, renal disorders, cataracts. Often pathologies are linked to mutations directly positioned in the Sam domains that alter their stability and/or affect interactions that are crucial for proper protein functions. In only a few diseases, the Sam motif plays a kind of "side role" and cooperates to the pathological event by enhancing the action of a different protein domain. CONCLUSION Considering the many roles of the Sam domain into a significant variety of diseases, more efforts and novel drug discovery campaigns need to be engaged to find out small molecules and/or peptides targeting Sam domains. Such compounds may represent the pillars on which to build novel therapeutic strategies to cure different pathologies.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone, 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone, 16, 80134 Naples, Italy
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13
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Cable CJ, Kaplan N, Getsios S, Thomas PM, Perez White BE. Biotin Identification Proteomics in Three-Dimensional Organotypic Human Skin Cultures. Methods Mol Biol 2020; 2109:185-197. [PMID: 31123999 PMCID: PMC6874900 DOI: 10.1007/7651_2019_239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biotin identification (BioID) proteomics facilitates the unbiased detection of protein interaction neighborhoods in live cells. The BioID technique relies on the covalent biotin alteration of vicinal proteins by a modified bacterial biotin ligase. The biotin ligase is fused to a protein of interest to identify putative protein-protein interactions. Here, we describe the adaptation of this technique for use in three-dimensional epidermal cultures. Due to the covalent biotin modification of proteins, our protocol allows for the complete solubilization of the total cellular protein content in differentiated keratinocytes. Thus, a comprehensive network of potential interactors of a protein of interest can be mapped.
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Affiliation(s)
- Calvin J Cable
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| | - Nihal Kaplan
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| | - Spiro Getsios
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| | - Paul M Thomas
- Department of Molecular Biosciences, Northwestern University, Chicago, IL, USA
- Northwestern Proteomics, Northwestern University, Chicago, IL, USA
| | - Bethany E Perez White
- Department of Dermatology, Northwestern University, Chicago, IL, USA.
- Skin Disease Research Center, Northwestern University, Chicago, IL, USA.
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14
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Mercurio FA, Di Natale C, Pirone L, Vincenzi M, Marasco D, De Luca S, Pedone EM, Leone M. Exploring the Ability of Cyclic Peptides to Target SAM Domains: A Computational and Experimental Study. Chembiochem 2019; 21:702-711. [DOI: 10.1002/cbic.201900444] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Flavia A. Mercurio
- Institute of Biostructures and BioimagingNational Research Council Via Mezzocannone 16 80134 Naples Italy
| | - Concetta Di Natale
- Department of PharmacyUniversity of Naples “Federico II” Via Mezzocannone 16 80134 Naples Italy
| | - Luciano Pirone
- Institute of Biostructures and BioimagingNational Research Council Via Mezzocannone 16 80134 Naples Italy
| | - Marian Vincenzi
- Institute of Biostructures and BioimagingNational Research Council Via Mezzocannone 16 80134 Naples Italy
| | - Daniela Marasco
- Institute of Biostructures and BioimagingNational Research Council Via Mezzocannone 16 80134 Naples Italy
- Department of PharmacyUniversity of Naples “Federico II” Via Mezzocannone 16 80134 Naples Italy
| | - Stefania De Luca
- Institute of Biostructures and BioimagingNational Research Council Via Mezzocannone 16 80134 Naples Italy
| | - Emilia M. Pedone
- Institute of Biostructures and BioimagingNational Research Council Via Mezzocannone 16 80134 Naples Italy
| | - Marilisa Leone
- Institute of Biostructures and BioimagingNational Research Council Via Mezzocannone 16 80134 Naples Italy
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15
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Vincenzi M, Mercurio FA, Leone M. About TFE: Old and New Findings. Curr Protein Pept Sci 2019; 20:425-451. [PMID: 30767740 DOI: 10.2174/1389203720666190214152439] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 01/28/2023]
Abstract
The fluorinated alcohol 2,2,2-Trifluoroethanol (TFE) has been implemented for many decades now in conformational studies of proteins and peptides. In peptides, which are often disordered in aqueous solutions, TFE acts as secondary structure stabilizer and primarily induces an α -helical conformation. The exact mechanism through which TFE plays its stabilizing roles is still debated and direct and indirect routes, relying either on straight interaction between TFE and molecules or indirect pathways based on perturbation of solvation sphere, have been proposed. Another still unanswered question is the capacity of TFE to favor in peptides a bioactive or a native-like conformation rather than simply stimulate the raise of secondary structure elements that reflect only the inherent propensity of a specific amino-acid sequence. In protein studies, TFE destroys unique protein tertiary structure and often leads to the formation of non-native secondary structure elements, but, interestingly, gives some hints about early folding intermediates. In this review, we will summarize proposed mechanisms of TFE actions. We will also describe several examples, in which TFE has been successfully used to reveal structural properties of different molecular systems, including antimicrobial and aggregation-prone peptides, as well as globular folded and intrinsically disordered proteins.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia A Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
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16
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Li ZL, Buck M. Modified Potential Functions Result in Enhanced Predictions of a Protein Complex by All-Atom Molecular Dynamics Simulations, Confirming a Stepwise Association Process for Native Protein-Protein Interactions. J Chem Theory Comput 2019; 15:4318-4331. [PMID: 31241940 DOI: 10.1021/acs.jctc.9b00195] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The relative prevalence of native protein-protein interactions (PPIs) are the cornerstone for understanding the structure, dynamics and mechanisms of function of protein complexes. In this study, we develop a scheme for scaling the protein-water interaction in the CHARMM36 force field, in order to better fit the solvation free energy of amino acids side-chain analogues. We find that the molecular dynamics simulation with the scaled force field, CHARMM36s, as well as a recently released version, CHARMM36m, effectively improve on the overly sticky association of proteins, such as ubiquitin. We investigate the formation of a heterodimer protein complex between the SAM domains of the EphA2 receptor and the SHIP2 enzyme by performing a combined total of 48 μs simulations with the different potential functions. While the native SAM heterodimer is only predicted at a low rate of 6.7% with the original CHARMM36 force field, the yield is increased to 16.7% with CHARMM36s, and to 18.3% with CHARMM36m. By analyzing the 25 native SAM complexes formed in the simulations, we find that their formation involves a preorientation guided by Coulomb interactions, consistent with an electrostatic steering mechanism. In 12 cases, the complex could directly transform to the native protein interaction surfaces with only small adjustments in domain orientation. In the other 13 cases, orientational and/or translational adjustments are needed to reach the native complex. Although the tendency for non-native complexes to dissociate has nearly doubled with the modified potential functions, a dissociation followed by a reassociation to the correct complex structure is still rare. Instead, the remaining non-native complexes undergo configurational changes/surface searching, which, however, rarely leads to native structures on a time scale of 250 ns. These observations provide a rich picture of the mechanisms of protein-protein complex formation and suggest that computational predictions of native complex PPIs could be improved further.
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Affiliation(s)
- Zhen-Lu Li
- Department of Physiology and Biophysics , Case Western Reserve University, School of Medicine , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
| | - Matthias Buck
- Department of Physiology and Biophysics , Case Western Reserve University, School of Medicine , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States.,Departments of Pharmacology and Neurosciences, and Case Comprehensive Cancer Center , Case Western Reserve University, School of Medicine , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
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17
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Sporny M, Guez-Haddad J, Lebendiker M, Ulisse V, Volf A, Mim C, Isupov MN, Opatowsky Y. Structural Evidence for an Octameric Ring Arrangement of SARM1. J Mol Biol 2019; 431:3591-3605. [PMID: 31278906 DOI: 10.1016/j.jmb.2019.06.030] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/16/2019] [Accepted: 06/25/2019] [Indexed: 12/11/2022]
Abstract
SARM1 induces axonal degeneration in response to various insults and is therefore considered an attractive drug target for the treatment of neuro-degenerative diseases as well as for brain and spinal cord injuries. SARM1 activity depends on the integrity of the protein's SAM domains, as well as on the enzymatic conversion of NAD+ to ADPR (ADP Ribose) products by the SARM1's TIR domain. Therefore, inhibition of either SAM or TIR functions may constitute an effective therapeutic strategy. However, there is currently no SARM1-directed therapeutic approach available because of an insufficient structural and mechanistic understanding of this protein. In this study, we found that SARM1 assembles into an octameric ring. This arrangement was not described before in other SAM proteins, but is reminiscent of the apoptosome and inflammasome-well-known apoptotic ring-like oligomers. We show that both SARM1 and the isolated tandem SAM1-2 domains form octamers in solution, and electron microscopy analysis reveals an octameric ring of SARM1. We determined the crystal structure of SAM1-2 and found that it also forms a closed octameric ring in the crystal lattice. The SAM1-2 ring interactions are mediated by complementing "lock and key" hydrophobic grooves and inserts and electrostatic charges between the neighboring protomers. We have mutated several interacting SAM1-2 interfaces and measured how these mutations affect SARM1 apoptotic activity in cultured cells, and in this way identified critical oligomerization sites that facilitate cell death. These results highlight the importance of oligomerization for SARM1 function and reveal critical epitopes for future targeted drug development.
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Affiliation(s)
- Michael Sporny
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Julia Guez-Haddad
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Mario Lebendiker
- Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Israel
| | - Valeria Ulisse
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Allison Volf
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Carsten Mim
- Department of Biomedical Engineering and Health Solutions, Royal Technical Institute (KTH), Stockholm, Sweden; Department of Nutrition and Biosciences, Karolinska Institute, Huddinge, Sweden
| | | | - Yarden Opatowsky
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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18
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Neira JL, Díaz-García C, Prieto M, Coutinho A. The C-terminal SAM domain of p73 binds to the N terminus of MDM2. Biochim Biophys Acta Gen Subj 2019; 1863:760-770. [DOI: 10.1016/j.bbagen.2019.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/25/2019] [Accepted: 01/31/2019] [Indexed: 01/10/2023]
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19
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Design and analysis of EphA2-SAM peptide ligands: A multi-disciplinary screening approach. Bioorg Chem 2019; 84:434-443. [DOI: 10.1016/j.bioorg.2018.12.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/22/2018] [Accepted: 12/06/2018] [Indexed: 01/28/2023]
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20
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Mercurio FA, Pirone L, Di Natale C, Marasco D, Pedone EM, Leone M. Sam domain-based stapled peptides: Structural analysis and interaction studies with the Sam domains from the EphA2 receptor and the lipid phosphatase Ship2. Bioorg Chem 2018; 80:602-610. [PMID: 30036816 DOI: 10.1016/j.bioorg.2018.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/06/2018] [Accepted: 07/12/2018] [Indexed: 12/27/2022]
Abstract
Sam (Sterile alpha motif) domains represent small helical protein-protein interaction modules which play versatile functions in different cellular processes. The Sam domain from the EphA2 receptor binds the Sam domain of the lipid phosphatase Ship2 and this interaction modulates receptor endocytosis and degradation primarily generating pro-oncogenic effects in cell. To identify molecule antagonists of the EphA2-Sam/Ship2-Sam complex with anti-cancer activity, we focused on hydrocarbon helical stapled peptides. EphA2-Sam and one of its interactors (i.e., the first Sam domain of the adaptor protein Odin) were used as model systems for peptide design. Increase in helicity in the stapled peptides, with respect to the corresponding linear/native-like regions, was proved by structural studies conducted through CD (Circular Dichroism) and NMR (Nuclear Magnetic Resonance). Interestingly, interaction assays by means of NMR, SPR (Surface Plasmon Resonance) and MST (MicroScale Thermophoresis) techniques led to the discovery of a novel ligand of Ship2-Sam.
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Affiliation(s)
- Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy
| | | | - Daniela Marasco
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy; University of Naples Federico II, Department of Pharmacy, Naples, Italy
| | - Emilia Maria Pedone
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy.
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21
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Wang Y, Shang Y, Li J, Chen W, Li G, Wan J, Liu W, Zhang M. Specific Eph receptor-cytoplasmic effector signaling mediated by SAM-SAM domain interactions. eLife 2018; 7:35677. [PMID: 29749928 PMCID: PMC5993539 DOI: 10.7554/elife.35677] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/10/2018] [Indexed: 02/06/2023] Open
Abstract
The Eph receptor tyrosine kinase (RTK) family is the largest subfamily of RTKs playing critical roles in many developmental processes such as tissue patterning, neurogenesis and neuronal circuit formation, angiogenesis, etc. How the 14 Eph proteins, via their highly similar cytoplasmic domains, can transmit diverse and sometimes opposite cellular signals upon engaging ephrins is a major unresolved question. Here, we systematically investigated the bindings of each SAM domain of Eph receptors to the SAM domains from SHIP2 and Odin, and uncover a highly specific SAM-SAM interaction-mediated cytoplasmic Eph-effector binding pattern. Comparative X-ray crystallographic studies of several SAM-SAM heterodimer complexes, together with biochemical and cell biology experiments, not only revealed the exquisite specificity code governing Eph/effector interactions but also allowed us to identify SAMD5 as a new Eph binding partner. Finally, these Eph/effector SAM heterodimer structures can explain many Eph SAM mutations identified in patients suffering from cancers and other diseases.
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Affiliation(s)
- Yue Wang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Yuan Shang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Kowloon, China
| | - Jianchao Li
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Kowloon, China
| | - Weidi Chen
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Gang Li
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jun Wan
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Kowloon, China
| | - Wei Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Mingjie Zhang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Kowloon, China
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22
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Rothé B, Leettola CN, Leal-Esteban L, Cascio D, Fortier S, Isenschmid M, Bowie JU, Constam DB. Crystal Structure of Bicc1 SAM Polymer and Mapping of Interactions between the Ciliopathy-Associated Proteins Bicc1, ANKS3, and ANKS6. Structure 2018; 26:209-224.e6. [PMID: 29290488 PMCID: PMC6258031 DOI: 10.1016/j.str.2017.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 10/31/2017] [Accepted: 12/01/2017] [Indexed: 01/25/2023]
Abstract
Head-to-tail polymers of sterile alpha motifs (SAM) can scaffold large macromolecular complexes. Several SAM-domain proteins that bind each other are mutated in patients with cystic kidneys or laterality defects, including the Ankyrin (ANK) and SAM domain-containing proteins ANKS6 and ANKS3, and the RNA-binding protein Bicc1. To address how their interactions are regulated, we first determined a high-resolution crystal structure of a Bicc1-SAM polymer, revealing a canonical SAM polymer with a high degree of flexibility in the subunit interface orientations. We further mapped interactions between full-length and distinct domains of Bicc1, ANKS3, and ANKS6. Neither ANKS3 nor ANKS6 alone formed macroscopic homopolymers in vivo. However, ANKS3 recruited ANKS6 to Bicc1, and the three proteins together cooperatively generated giant macromolecular complexes. Thus, the giant assemblies are shaped by SAM domains, their flanking sequences, and SAM-independent protein-protein and protein-mRNA interactions.
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Affiliation(s)
- Benjamin Rothé
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, SV ISREC, Station 19, 1015 Lausanne, Switzerland
| | - Catherine N Leettola
- Department of Chemistry and Biochemistry, UCLA-DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, Boyer Hall, 611 Charles E. Young Drive East, Los Angeles, CA 90095-1570, USA
| | - Lucia Leal-Esteban
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, SV ISREC, Station 19, 1015 Lausanne, Switzerland
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, UCLA-DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, Boyer Hall, 611 Charles E. Young Drive East, Los Angeles, CA 90095-1570, USA
| | - Simon Fortier
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, SV ISREC, Station 19, 1015 Lausanne, Switzerland
| | - Manuela Isenschmid
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, SV ISREC, Station 19, 1015 Lausanne, Switzerland
| | - James U Bowie
- Department of Chemistry and Biochemistry, UCLA-DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, Boyer Hall, 611 Charles E. Young Drive East, Los Angeles, CA 90095-1570, USA
| | - Daniel B Constam
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, SV ISREC, Station 19, 1015 Lausanne, Switzerland.
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23
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Bennett TM, M’Hamdi O, Hejtmancik JF, Shiels A. Germ-line and somatic EPHA2 coding variants in lens aging and cataract. PLoS One 2017; 12:e0189881. [PMID: 29267365 PMCID: PMC5739433 DOI: 10.1371/journal.pone.0189881] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 12/04/2017] [Indexed: 11/18/2022] Open
Abstract
Rare germ-line mutations in the coding regions of the human EPHA2 gene (EPHA2) have been associated with inherited forms of pediatric cataract, whereas, frequent, non-coding, single nucleotide variants (SNVs) have been associated with age-related cataract. Here we sought to determine if germ-line EPHA2 coding SNVs were associated with age-related cataract in a case-control DNA panel (> 50 years) and if somatic EPHA2 coding SNVs were associated with lens aging and/or cataract in a post-mortem lens DNA panel (> 48 years). Micro-fluidic PCR amplification followed by targeted amplicon (exon) next-generation (deep) sequencing of EPHA2 (17-exons) afforded high read-depth coverage (1000x) for > 82% of reads in the cataract case-control panel (161 cases, 64 controls) and > 70% of reads in the post-mortem lens panel (35 clear lens pairs, 22 cataract lens pairs). Novel and reference (known) missense SNVs in EPHA2 that were predicted in silico to be functionally damaging were found in both cases and controls from the age-related cataract panel at variant allele frequencies (VAFs) consistent with germ-line transmission (VAF > 20%). Similarly, both novel and reference missense SNVs in EPHA2 were found in the post-mortem lens panel at VAFs consistent with a somatic origin (VAF > 3%). The majority of SNVs found in the cataract case-control panel and post-mortem lens panel were transitions and many occurred at di-pyrimidine sites that are susceptible to ultraviolet (UV) radiation induced mutation. These data suggest that novel germ-line (blood) and somatic (lens) coding SNVs in EPHA2 that are predicted to be functionally deleterious occur in adults over 50 years of age. However, both types of EPHA2 coding variants were present at comparable levels in individuals with or without age-related cataract making simple genotype-phenotype correlations inconclusive.
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Affiliation(s)
- Thomas M. Bennett
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Oussama M’Hamdi
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alan Shiels
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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24
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Mercurio FA, Di Natale C, Pirone L, Iannitti R, Marasco D, Pedone EM, Palumbo R, Leone M. The Sam-Sam interaction between Ship2 and the EphA2 receptor: design and analysis of peptide inhibitors. Sci Rep 2017; 7:17474. [PMID: 29234063 PMCID: PMC5727260 DOI: 10.1038/s41598-017-17684-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/21/2017] [Indexed: 12/21/2022] Open
Abstract
The lipid phosphatase Ship2 represents a drug discovery target for the treatment of different diseases, including cancer. Its C-terminal sterile alpha motif domain (Ship2-Sam) associates with the Sam domain from the EphA2 receptor (EphA2-Sam). This interaction is expected to mainly induce pro-oncogenic effects in cells therefore, inhibition of the Ship2-Sam/EphA2-Sam complex may represent an innovative route to discover anti-cancer therapeutics. In the present work, we designed and analyzed several peptide sequences encompassing the interaction interface of EphA2-Sam for Ship2-Sam. Peptide conformational analyses and interaction assays with Ship2-Sam conducted through diverse techniques (CD, NMR, SPR and MST), identified a positively charged penta-amino acid native motif in EphA2-Sam, that once repeated three times in tandem, binds Ship2-Sam. NMR experiments show that the peptide targets the negatively charged binding site of Ship2-Sam for EphA2-Sam. Preliminary in vitro cell-based assays indicate that -at 50 µM concentration- it induces necrosis of PC-3 prostate cancer cells with more cytotoxic effect on cancer cells than on normal dermal fibroblasts. This work represents a pioneering study that opens further opportunities for the development of inhibitors of the Ship2-Sam/EphA2-Sam complex for therapeutic applications.
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Affiliation(s)
- Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Concetta Di Natale
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134, Naples, Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Roberta Iannitti
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Daniela Marasco
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy.,Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134, Naples, Italy
| | - Emilia Maria Pedone
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Rosanna Palumbo
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy.
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25
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Mercurio FA, Costantini S, Di Natale C, Pirone L, Guariniello S, Scognamiglio PL, Marasco D, Pedone EM, Leone M. Structural investigation of a C-terminal EphA2 receptor mutant: Does mutation affect the structure and interaction properties of the Sam domain? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1095-1104. [DOI: 10.1016/j.bbapap.2017.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/03/2017] [Accepted: 06/05/2017] [Indexed: 12/25/2022]
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26
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Neira JL, Cámara-Artigas A. Trifluoroethanol-induced conformational transition of the C-terminal sterile alpha motif (SAM) of human p73. Arch Biochem Biophys 2017; 619:1-9. [DOI: 10.1016/j.abb.2017.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 01/03/2023]
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27
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A role of the SAM domain in EphA2 receptor activation. Sci Rep 2017; 7:45084. [PMID: 28338017 PMCID: PMC5364462 DOI: 10.1038/srep45084] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/17/2017] [Indexed: 11/08/2022] Open
Abstract
Among the 20 subfamilies of protein receptor tyrosine kinases (RTKs), Eph receptors are unique in possessing a sterile alpha motif (SAM domain) at their C-terminal ends. However, the functions of SAM domains in Eph receptors remain elusive. Here we report on a combined cell biology and quantitative fluorescence study to investigate the role of the SAM domain in EphA2 function. We observed elevated tyrosine autophosphorylation levels upon deletion of the EphA2 SAM domain (EphA2ΔS) in DU145 and PC3 prostate cancer cells and a skin tumor cell line derived from EphA1/A2 knockout mice. These results suggest that SAM domain deletion induced constitutive activation of EphA2 kinase activity. In order to explain these effects, we applied fluorescence correlation spectroscopy to investigate the lateral molecular organization of EphA2. Our results indicate that SAM domain deletion (EphA2ΔS-GFP) increases oligomerization compared to the full length receptor (EphA2FL-GFP). Stimulation with ephrinA1, a ligand for EphA2, induced further oligomerization and activation of EphA2FL-GFP. The SAM domain deletion mutant, EphA2ΔS-GFP, also underwent further oligomerization upon ephrinA1 stimulation, but the oligomers were larger than those observed for EphA2FL-GFP. Based on these results, we conclude that the EphA2 SAM domain inhibits kinase activity by reducing receptor oligomerization.
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28
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Medina-Carmona E, Neira JL, Salido E, Fuchs JE, Palomino-Morales R, Timson DJ, Pey AL. Site-to-site interdomain communication may mediate different loss-of-function mechanisms in a cancer-associated NQO1 polymorphism. Sci Rep 2017; 7:44532. [PMID: 28291250 PMCID: PMC5349528 DOI: 10.1038/srep44532] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/10/2017] [Indexed: 12/27/2022] Open
Abstract
Disease associated genetic variations often cause intracellular enzyme inactivation, dysregulation and instability. However, allosteric communication of mutational effects to distant functional sites leading to loss-of-function remains poorly understood. We characterize here interdomain site-to-site communication by which a common cancer-associated single nucleotide polymorphism (c.C609T/p.P187S) reduces the activity and stability in vivo of NAD(P)H:quinone oxidoreductase 1 (NQO1). NQO1 is a FAD-dependent, two-domain multifunctional stress protein acting as a Phase II enzyme, activating cancer pro-drugs and stabilizing p53 and p73α oncosuppressors. We show that p.P187S causes structural and dynamic changes communicated to functional sites far from the mutated site, affecting the FAD binding site located at the N-terminal domain (NTD) and accelerating proteasomal degradation through dynamic effects on the C-terminal domain (CTD). Structural protein:protein interaction studies reveal that the cancer-associated polymorphism does not abolish the interaction with p73α, indicating that oncosuppressor destabilization largely mirrors the low intracellular stability of p.P187S. In conclusion, we show how a single disease associated amino acid change may allosterically perturb several functional sites in an oligomeric and multidomain protein. These results have important implications for the understanding of loss-of-function genetic diseases and the identification of novel structural hot spots as targets for pharmacological intervention.
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Affiliation(s)
- Encarnación Medina-Carmona
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
| | - Jose L. Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202, Elche, Alicante, Spain
- Instituto de Biocomputación y Física de los Sistemas Complejos (BIFI), 50009, Zaragoza, Spain
| | - Eduardo Salido
- Hospital Universitario de Canarias, Centre for Biomedical Research on Rare Diseases (CIBERER), Tenerife, Spain
| | - Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Rogelio Palomino-Morales
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
| | - David J. Timson
- School of Pharmacy and Biomolecular Sciences, The University of Brighton, Brighton, UK
| | - Angel L. Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
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29
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Zhang L, Buck M. Molecular Dynamics Simulations Reveal Isoform Specific Contact Dynamics between the Plexin Rho GTPase Binding Domain (RBD) and Small Rho GTPases Rac1 and Rnd1. J Phys Chem B 2017; 121:1485-1498. [PMID: 28103666 DOI: 10.1021/acs.jpcb.6b11022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Plexin family of transmembrane receptors are unique in that their intracellular region interacts directly with small GTPases of the Rho family. The Rho GTPase binding domain of plexin (RBD)-which is responsible for these interactions-can bind with Rac1 as well as Rnd1 GTPases. GTPase complexes have been crystallized with the RBDs of plexinA1, -A2, and -B1. The protein association is thought to elicit different functional responses in a GTPase and plexin isoform specific manner, but the origin of this is unknown. In this project, we investigated complexes between several RBD and Rac1/Rnd1 GTPases using multimicrosecond length all atom molecular dynamics simulations, also with reference to the free forms of the RBDs and GTPases. In accord with the crystallographic data, the RBDs experience more structural changes than Rho-GTPases upon complex formation. Changes in protein dynamics and networks of correlated motions are revealed by analyzing dihedral angle fluctuations in the proteins. The extent of these changes differs between the different RBDs and also between the Rac1 and Rnd1 GTPases. While the RBDs in the free and bound states have similar-if not decreased-correlations, correlations within the GTPases are increased upon binding. Mapping highly correlated residues to the structures, it is found that the plexinA1, -B1, and -A2 RBDs all have similar communication pathways within the ubiquitin fold, but that different residues are involved. Dynamic network analyses indicate that plexinA1 and -B1 RBDs interact with small GTPases in a similar manner, whereas complexes with the plexinA2 RBD display different features. Importantly complexes with Rnd1 have a considerable number of dynamic correlations and network connections between the proteins, whereas such features are missing in the RBD-Rac1 complexes. Overall, the simulations suggest mechanisms that are consistent with the experimental data on plexinB1 and indicate RBD and GTPase isoform specific changes in protein dynamics upon complex formation.
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Affiliation(s)
- Liqun Zhang
- Chemical Engineering Department, Tennessee Technological University , 1 William L Jones Dr., Cookeville, Tennessee 38505, United States
| | - Matthias Buck
- Department of Physiology and Biophysics, Medical School of Case Western Reserve University , Cleveland, Ohio 44106, United States
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30
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Thomas MP, Erneux C, Potter BVL. SHIP2: Structure, Function and Inhibition. Chembiochem 2017; 18:233-247. [DOI: 10.1002/cbic.201600541] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Mark P. Thomas
- Department of Pharmacy and Pharmacology; University of Bath; Claverton Down Bath BA2 7AY UK
| | - Christophe Erneux
- I.R.I.B.H.M.; Université Libre de Bruxelles; Campus Erasme 808 Route de Lennik 1070 Brussels Belgium
| | - Barry V. L. Potter
- Drug Discovery and Medicinal Chemistry; Department of Pharmacology; University of Oxford; Mansfield Road Oxford OX1 3QT UK
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31
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Perez White BE, Ventrella R, Kaplan N, Cable CJ, Thomas PM, Getsios S. EphA2 proteomics in human keratinocytes reveals a novel association with afadin and epidermal tight junctions. J Cell Sci 2016; 130:111-118. [PMID: 27815408 DOI: 10.1242/jcs.188169] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 10/31/2016] [Indexed: 12/13/2022] Open
Abstract
EphA2 is a receptor tyrosine kinase that helps to maintain epidermal tissue homeostasis. A proximity-dependent biotin identification (BioID) approach was used to identify proteins in close proximity to EphA2 within primary human keratinocytes and three-dimensional (3D) reconstituted human epidermis (RHE) cultures to map a putative protein interaction network for this membrane receptor that exhibits a polarized distribution in stratified epithelia. Although a subset of known EphA2 interactors were identified in the BioID screen, >97% were uniquely detected in keratinocytes with over 50% of these vicinal proteins only present in 3D human epidermal culture. Afadin (AFDN), a cytoskeletal and junction-associated protein, was present in 2D and 3D keratinocyte cultures, and validated as a so-far-unknown EphA2-interacting protein. Loss of EphA2 protein disrupted the subcellular distribution of afadin and occludin in differentiated keratinocytes, leading to impairment of tight junctions. Collectively, these studies illustrate the use of the BioID approach in order to map receptor interaction networks in 3D human epithelial cultures, and reveal a positive regulatory role for EphA2 in the organization of afadin and epidermal tight junctions.
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Affiliation(s)
| | - Rosa Ventrella
- Department of Dermatology, Northwestern University, Chicago, IL 60611, USA
| | - Nihal Kaplan
- Department of Dermatology, Northwestern University, Chicago, IL 60611, USA
| | - Calvin J Cable
- Department of Dermatology, Northwestern University, Chicago, IL 60611, USA
| | - Paul M Thomas
- Proteomics Center of Excellence, Northwestern University, Chicago, IL 60611, USA.,Department of Molecular Biosciences, Northwestern University, Chicago, IL 60611, USA
| | - Spiro Getsios
- Department of Dermatology, Northwestern University, Chicago, IL 60611, USA .,Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
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32
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Singh DR, Ahmed F, Paul MD, Gedam M, Pasquale EB, Hristova K. The SAM domain inhibits EphA2 interactions in the plasma membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1864:31-38. [PMID: 27776928 DOI: 10.1016/j.bbamcr.2016.10.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/26/2016] [Accepted: 10/18/2016] [Indexed: 11/18/2022]
Abstract
All members of the Eph receptor family of tyrosine kinases contain a SAM domain near the C terminus, which has been proposed to play a role in receptor homotypic interactions and/or interactions with binding partners. The SAM domain of EphA2 is known to be important for receptor function, but its contribution to EphA2 lateral interactions in the plasma membrane has not been determined. Here we use a FRET-based approach to directly measure the effect of the SAM domain on the stability of EphA2 dimers on the cell surface in the absence of ligand binding. We also investigate the functional consequences of EphA2 SAM domain deletion. Surprisingly, we find that the EphA2 SAM domain inhibits receptor dimerization and decreases EphA2 tyrosine phosphorylation. This role is dramatically different from the role of the SAM domain of the related EphA3 receptor, which we previously found to stabilize EphA3 dimers and increase EphA3 tyrosine phosphorylation in cells in the absence of ligand. Thus, the EphA2 SAM domain likely contributes to a unique mode of EphA2 interaction that leads to distinct signaling outputs.
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Affiliation(s)
- Deo R Singh
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States
| | - Fozia Ahmed
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States
| | - Michael D Paul
- Program in Molecular Biophysics, Johns Hopkins University, 3400 Charles street, Baltimore, MD 21218, United States
| | - Manasee Gedam
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States
| | - Elena B Pasquale
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Road, La Jolla, San Diego, CA 92037, United States
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States; Program in Molecular Biophysics, Johns Hopkins University, 3400 Charles street, Baltimore, MD 21218, United States.
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33
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Mercurio FA, Marasco D, Di Natale C, Pirone L, Costantini S, Pedone EM, Leone M. Targeting EphA2-Sam and Its Interactome: Design and Evaluation of Helical Peptides Enriched in Charged Residues. Chembiochem 2016; 17:2179-2188. [DOI: 10.1002/cbic.201600413] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Flavia A. Mercurio
- Institute of Biostructures and Bioimaging; National Research Council; Via Mezzocannone 16 80134 Naples Italy
| | - Daniela Marasco
- Institute of Biostructures and Bioimaging; National Research Council; Via Mezzocannone 16 80134 Naples Italy
- Department of Pharmacy; University of Naples “Federico II”; Via Mezzocannone 16 80134 Naples Italy
| | - Concetta Di Natale
- Department of Biology; University of Naples “Federico II”; Via Cinthia 4 80126 Naples Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging; National Research Council; Via Mezzocannone 16 80134 Naples Italy
| | - Susan Costantini
- CROM; IRCCS-Istituto Nazionale Tumori “Fondazione G. Pascale”; Via Mariano Semmola 52 80131 Naples Italy
| | - Emilia M. Pedone
- Institute of Biostructures and Bioimaging; National Research Council; Via Mezzocannone 16 80134 Naples Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging; National Research Council; Via Mezzocannone 16 80134 Naples Italy
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34
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Smirnova E, Kwan JJ, Siu R, Gao X, Zoidl G, Demeler B, Saridakis V, Donaldson LW. A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein. Cell Commun Signal 2016; 14:17. [PMID: 27549312 PMCID: PMC4994250 DOI: 10.1186/s12964-016-0140-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/12/2016] [Indexed: 11/18/2022] Open
Abstract
Background CASKIN2 is a homolog of CASKIN1, a scaffolding protein that participates in a signaling network with CASK (calcium/calmodulin-dependent serine kinase). Despite a high level of homology between CASKIN2 and CASKIN1, CASKIN2 cannot bind CASK due to the absence of a CASK Interaction Domain and consequently, may have evolved undiscovered structural and functional distinctions. Results We demonstrate that the crystal structure of the Sterile Alpha Motif (SAM) domain tandem (SAM1-SAM2) oligomer from CASKIN2 is different than CASKIN1, with the minimal repeating unit being a dimer, rather than a monomer. Analytical ultracentrifugation sedimentation velocity methods revealed differences in monomer/dimer equilibria across a range of concentrations and ionic strengths for the wild type CASKIN2 SAM tandem and a structure-directed double mutant that could not oligomerize. Further distinguishing CASKIN2 from CASKIN1, EGFP-tagged SAM tandem proteins expressed in Neuro2a cells produced punctae that were distinct both in shape and size. Conclusions This study illustrates a new way in which neuronal SAM domains can assemble into large macromolecular assemblies that might concentrate and amplify synaptic responses. Electronic supplementary material The online version of this article (doi:10.1186/s12964-016-0140-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ekaterina Smirnova
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Jamie J Kwan
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Ryan Siu
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Xin Gao
- Division of Computer, Computational Bioscience Research Center, Electrical and Mathematical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Georg Zoidl
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.,Department of Psychology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Borries Demeler
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, 7760 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Vivian Saridakis
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Logan W Donaldson
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.
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35
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Systematic biochemical characterization of the SAM domains in Eph receptor family from Mus Musculus. Biochem Biophys Res Commun 2016; 473:1281-1287. [PMID: 27086853 DOI: 10.1016/j.bbrc.2016.04.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 04/12/2016] [Indexed: 12/13/2022]
Abstract
The Eph receptor family is the largest subfamily of receptor tyrosine kinases and well-known for their pivotal roles in axon guidance, synaptogenesis, artery/venous differentiation and tumorigenesis, etc. Activation of the Eph receptor needs multimerization of the receptors. The intracellular C-terminal SAM domain of Eph receptor was reported to mediate self-association of Eph receptors via the homo SAM-SAM interaction. In this study, we systematically expressed and purified the SAM domain proteins of all fourteen Eph receptors of Mus musculus in Escherichia coli. The FPLC (fast protein liquid chromatography) results showed the recombinant SAM domains were highly homogeneous. Using CD (circular dichroism) spectrometry, we found that the secondary structure of all the SAM domains was typically alpha helical folded and remarkably similar. The thermo-stability tests showed that they were quite stable in solution. SEC-MALS (size exclusion chromatography coupled with multiple angle light scattering) results illustrated 200 μM Eph SAM domains behaved as good monomers in the size-exclusion chromatography. More importantly, DLS (dynamic light scattering) results revealed the overwhelming majority of SAM domains was not multimerized in solution either at 200 μM or 2000 μM protein concentration, which indicating the SAM domain alone was not sufficient to mediate the polymerization of Eph receptor. In summary, our studies provided the systematic biochemical characterizations of the Eph receptor SAM domains and implied their roles in Eph receptor mediated signaling pathways.
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36
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Zhang L, Borthakur S, Buck M. Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations. Biophys J 2016; 110:877-86. [PMID: 26910424 PMCID: PMC4776036 DOI: 10.1016/j.bpj.2015.12.036] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/28/2015] [Accepted: 12/01/2015] [Indexed: 12/11/2022] Open
Abstract
The process of protein complex dissociation remains to be understood at the atomic level of detail. Computers now allow microsecond timescale molecular-dynamics simulations, which make the visualization of such processes possible. Here, we investigated the dissociation process of the EphA2-SHIP2 SAM-SAM domain heterodimer complex using unrestrained all-atom molecular-dynamics simulations. Previous studies on this system have shown that alternate configurations are sampled, that their interconversion can be fast, and that the complex is dynamic by nature. Starting from different NMR-derived structures, mutants were designed to stabilize a subset of configurations by swapping ion pairs across the protein-protein interface. We focused on two mutants, K956D/D1235K and R957D/D1223R, with attenuated binding affinity compared with the wild-type proteins. In contrast to calculations on the wild-type complexes, the majority of simulations of these mutants showed protein dissociation within 2.4 μs. During the separation process, we observed domain rotation and pivoting as well as a translation and simultaneous rolling, typically to alternate and weaker binding interfaces. Several unsuccessful recapturing attempts occurred once the domains were moderately separated. An analysis of protein solvation suggests that the dissociation process correlates with a progressive loss of protein-protein contacts. Furthermore, an evaluation of internal protein dynamics using quasi-harmonic and order parameter analyses indicates that changes in protein internal motions are expected to contribute significantly to the thermodynamics of protein dissociation. Considering protein association as the reverse of the separation process, the initial role of charged/polar interactions is emphasized, followed by changes in protein and solvent dynamics. The trajectories show that protein separation does not follow a single distinct pathway, but suggest that the mechanism of dissociation is common in that it initially involves transitions to surfaces with fewer, less favorable contacts compared with those seen in the fully formed complex.
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Affiliation(s)
- Liqun Zhang
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Susmita Borthakur
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio; Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio; Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio; Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, Ohio; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio.
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37
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Chavent M, Seiradake E, Jones EY, Sansom MSP. Structures of the EphA2 Receptor at the Membrane: Role of Lipid Interactions. Structure 2016; 24:337-47. [PMID: 26724997 PMCID: PMC4744086 DOI: 10.1016/j.str.2015.11.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 10/19/2015] [Accepted: 11/13/2015] [Indexed: 11/29/2022]
Abstract
Ephs are transmembrane receptors that mediate cell-cell signaling. The N-terminal ectodomain binds ligands and enables receptor clustering, which activates the intracellular kinase. Relatively little is known about the function of the membrane-proximal fibronectin domain 2 (FN2) of the ectodomain. Multiscale molecular dynamics simulations reveal that FN2 interacts with lipid bilayers via a site comprising K441, R443, R465, Q462, S464, S491, W467, F490, and P459-461. FN2 preferentially binds anionic lipids, a preference that is reduced in the mutant K441E + R443E. We confirm these results by measuring the binding of wild-type and mutant FN2 domains to lipid vesicles. In simulations of the complete EphA2 ectodomain plus the transmembrane region, we show that FN2 anchors the otherwise flexible ectodomain at the surface of the bilayer. Altogether, our data suggest that FN2 serves a dual function of interacting with anionic lipids and constraining the structure of the EphA2 ectodomain to adopt membrane-proximal configurations.
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Affiliation(s)
- Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Elena Seiradake
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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38
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Etheve L, Martin J, Lavery R. Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction. Nucleic Acids Res 2015; 44:1440-8. [PMID: 26721385 PMCID: PMC4756839 DOI: 10.1093/nar/gkv1511] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/15/2015] [Indexed: 11/13/2022] Open
Abstract
Molecular dynamics simulations of the Caenorhabditis elegans transcription factor SKN-1 bound to its cognate DNA site show that the protein–DNA interface undergoes significant dynamics on the microsecond timescale. A detailed analysis of the simulation shows that movements of two key arginine side chains between the major groove and the backbone of DNA generate distinct conformational sub-states that each recognize only part of the consensus binding sequence of SKN-1, while the experimentally observed binding specificity results from a time-averaged view of the dynamic recognition occurring within this complex.
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Affiliation(s)
- Loïc Etheve
- BMSSI UMR 5086 CNRS/Univ. Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
| | - Juliette Martin
- BMSSI UMR 5086 CNRS/Univ. Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
| | - Richard Lavery
- BMSSI UMR 5086 CNRS/Univ. Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
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39
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Singh DR, Cao Q, King C, Salotto M, Ahmed F, Zhou XY, Pasquale EB, Hristova K. Unliganded EphA3 dimerization promoted by the SAM domain. Biochem J 2015; 471:101-9. [PMID: 26232493 PMCID: PMC4692061 DOI: 10.1042/bj20150433] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/28/2015] [Accepted: 07/31/2015] [Indexed: 01/03/2023]
Abstract
The erythropoietin-producing hepatocellular carcinoma A3 (EphA3) receptor tyrosine kinase (RTK) regulates morphogenesis during development and is overexpressed and mutated in a variety of cancers. EphA3 activation is believed to follow a 'seeding mechanism' model, in which ligand binding to the monomeric receptor acts as a trigger for signal-productive receptor clustering. We study EphA3 lateral interactions on the surface of live cells and we demonstrate that EphA3 forms dimers in the absence of ligand binding. We further show that these dimers are stabilized by interactions involving the EphA3 sterile α-motif (SAM) domain. The discovery of unliganded EphA3 dimers challenges the current understanding of the chain of EphA3 activation events and suggests that EphA3 may follow the 'pre-formed dimer' model of activation known to be relevant for other receptor tyrosine kinases. The present work also establishes a new role for the SAM domain in promoting Eph receptor lateral interactions and signalling on the cell surface.
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Affiliation(s)
- Deo R Singh
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21212, U.S.A
| | - QingQing Cao
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21212, U.S.A
| | - Christopher King
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21212, U.S.A
| | - Matt Salotto
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21212, U.S.A
| | - Fozia Ahmed
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21212, U.S.A
| | - Xiang Yang Zhou
- Vaccine Center, The Wistar Institute, Philadelphia, PA 19104, U.S.A
| | - Elena B Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, U.S.A
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21212, U.S.A. Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21212, U.S.A.
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40
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Taylor EB, Nayak DK, Quiniou SMA, Bengten E, Wilson M. Identification of SHIP-1 and SHIP-2 homologs in channel catfish, Ictalurus punctatus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 51:79-87. [PMID: 25743379 DOI: 10.1016/j.dci.2015.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 06/04/2023]
Abstract
Src homology domain 2 (SH2) domain-containing inositol 5'-phosphatases (SHIP) proteins have diverse roles in signal transduction. SHIP-1 and SHIP-2 homologs were identified in channel catfish, Ictalurus punctatus, based on sequence homology to murine and human SHIP sequences. Full-length cDNAs for catfish SHIP-1 and SHIP-2 (IpSHIP-1 and IpSHIP-2) were obtained using 5' and 3' RACE protocols. Catfish SHIP molecules share a high degree of sequence identity to their respective SHIP sequences from diverse taxa and both are encoded by single copy genes. IpSHIP-1 and IpSHIP-2 transcripts were expressed in all catfish tissues analyzed except for skin, and IpSHIP-1 message was more abundant than IpSHIP-2 message in lymphoid tissues. Catfish clonal B, cytotoxic T, and macrophage cell lines also expressed message for both molecules. IpSHIP-1 and IpSHIP-2 SH2 domains were expressed as recombinant proteins and were both found to be bound by cross-reacting rabbit anti-mouse SHIP-1 pAb. The anti-mouse SHIP-1 pAb also reacted with cell lysates from the cytotoxic T cell lines, macrophages and stimulated PBL. SHIP-1 is also phosphorylated at a conserved tyrosine residue, as shown by immunoprecipitation studies.
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Affiliation(s)
- Erin B Taylor
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Deepak K Nayak
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Sylvie M A Quiniou
- Warmwater Aquaculture Research Unit, USDA-ARS, Stoneville, MS 38776, USA
| | - Eva Bengten
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Melanie Wilson
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216, USA.
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41
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Mercurio FA, Di Natale C, Pirone L, Scognamiglio PL, Marasco D, Pedone EM, Saviano M, Leone M. Peptide Fragments of Odin-Sam1: Conformational Analysis and Interaction Studies with EphA2-Sam. Chembiochem 2015; 16:1629-36. [DOI: 10.1002/cbic.201500197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 11/09/2022]
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42
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Neira JL. Structural dissection of the C-terminal sterile alpha motif (SAM) of human p73. Arch Biochem Biophys 2014; 558:133-42. [DOI: 10.1016/j.abb.2014.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/01/2014] [Accepted: 07/06/2014] [Indexed: 10/25/2022]
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43
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Mercurio FA, Scognamiglio PL, Di Natale C, Marasco D, Pellecchia M, Leone M. CD and NMR conformational studies of a peptide encompassing the Mid Loop interface of Ship2-Sam. Biopolymers 2014; 101:1088-98. [DOI: 10.1002/bip.22512] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/23/2014] [Accepted: 05/23/2014] [Indexed: 11/07/2022]
Affiliation(s)
| | - Pasqualina L. Scognamiglio
- Department of Pharmacy; University "Federico II"; Naples Italy
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPEB); Naples Italy
- IIT Italian Institute of Technology; Naples Italy
| | - Concetta Di Natale
- Department of Pharmacy; University "Federico II"; Naples Italy
- IIT Italian Institute of Technology; Naples Italy
| | - Daniela Marasco
- Institute of Biostructures and Bioimaging (CNR); Naples Italy
- Department of Pharmacy; University "Federico II"; Naples Italy
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPEB); Naples Italy
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging (CNR); Naples Italy
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPEB); Naples Italy
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Zhang L, Buck M. Molecular simulations of a dynamic protein complex: role of salt-bridges and polar interactions in configurational transitions. Biophys J 2014; 105:2412-7. [PMID: 24268153 DOI: 10.1016/j.bpj.2013.09.052] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 08/23/2013] [Accepted: 09/24/2013] [Indexed: 12/29/2022] Open
Abstract
Ion charge pairs and hydrogen bonds have been extensively studied for their roles in stabilizing protein complexes and in steering the process of protein association. Recently, it has become clear that some protein complexes are dynamic in that they interconvert between several alternate configurations. We have previously characterized one such system: the EphA2:SHIP2 SAM-SAM heterodimer by solution NMR. Here we carried out extensive all-atom molecular-dynamics simulations on a microsecond time-scale starting with different NMR-derived structures for the complex. Transitions are observed between several discernible configurations at average time intervals of 50-100 ns. The domains reorient relative to one another by substantial rotation and a slight shifting of the interfaces. Bifurcated and intermediary salt-bridge and hydrogen-bond interactions play a role in the transitions in a process that can be described as moving along a "monkey-bar". We notice an increased density of salt bridges near protein interaction surfaces that appear to enable these transitions, also suggesting why the trajectories can become kinetically hindered in regions where fewer of such interactions are possible. In this context, even microsecond molecular-dynamics simulations are not sufficient to sample the energy landscape unless the structures remain close to their experimentally derived low-energy configurations.
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Affiliation(s)
- Liqun Zhang
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio
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Borthakur S, Lee H, Kim S, Wang BC, Buck M. Binding and function of phosphotyrosines of the Ephrin A2 (EphA2) receptor using synthetic sterile α motif (SAM) domains. J Biol Chem 2014; 289:19694-703. [PMID: 24825902 DOI: 10.1074/jbc.m114.567602] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The sterile α motif (SAM) domain of the ephrin receptor tyrosine kinase, EphA2, undergoes tyrosine phosphorylation, but the effect of phosphorylation on the structure and interactions of the receptor is unknown. Studies to address these questions have been hindered by the difficulty of obtaining site-specifically phosphorylated proteins in adequate amounts. Here, we describe the use of chemically synthesized and specifically modified domain-length peptides to study the behavior of phosphorylated EphA2 SAM domains. We show that tyrosine phosphorylation of any of the three tyrosines, Tyr(921), Tyr(930), and Tyr(960), has a surprisingly small effect on the EphA2 SAM structure and stability. However, phosphorylation at Tyr(921) and Tyr(930) enables differential binding to the Src homology 2 domain of the adaptor protein Grb7, which we propose will lead to distinct functional outcomes. Setting up different signaling platforms defined by selective interactions with adaptor proteins thus adds another level of regulation to EphA2 signaling.
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Affiliation(s)
| | - HyeongJu Lee
- From the Departments of Physiology and Biophysics
| | | | - Bing-Cheng Wang
- From the Departments of Physiology and Biophysics, Pharmacology, and the Rammelkamp Center for Research, MetroHealth Medical Center, Cleveland, Ohio 44109the Case Comprehensive Cancer Center, and
| | - Matthias Buck
- From the Departments of Physiology and Biophysics, the Case Comprehensive Cancer Center, and Neurosciences, the Case Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, Ohio 44106 and
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Lisabeth EM, Falivelli G, Pasquale EB. Eph receptor signaling and ephrins. Cold Spring Harb Perspect Biol 2013; 5:5/9/a009159. [PMID: 24003208 DOI: 10.1101/cshperspect.a009159] [Citation(s) in RCA: 281] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The Eph receptors are the largest of the RTK families. Like other RTKs, they transduce signals from the cell exterior to the interior through ligand-induced activation of their kinase domain. However, the Eph receptors also have distinctive features. Instead of binding soluble ligands, they generally mediate contact-dependent cell-cell communication by interacting with surface-associated ligands-the ephrins-on neighboring cells. Eph receptor-ephrin complexes emanate bidirectional signals that affect both receptor- and ephrin-expressing cells. Intriguingly, ephrins can also attenuate signaling by Eph receptors coexpressed in the same cell. Additionally, Eph receptors can modulate cell behavior independently of ephrin binding and kinase activity. The Eph/ephrin system regulates many developmental processes and adult tissue homeostasis. Its abnormal function has been implicated in various diseases, including cancer. Thus, Eph receptors represent promising therapeutic targets. However, more research is needed to better understand the many aspects of their complex biology that remain mysterious.
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Affiliation(s)
- Erika M Lisabeth
- Cancer Center, Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA
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47
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Mercurio FA, Marasco D, Pirone L, Scognamiglio PL, Pedone EM, Pellecchia M, Leone M. Heterotypic Sam-Sam association between Odin-Sam1 and Arap3-Sam: binding affinity and structural insights. Chembiochem 2012; 14:100-6. [PMID: 23239578 DOI: 10.1002/cbic.201200592] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Indexed: 11/07/2022]
Abstract
Arap3 is a phosphatidylinositol 3 kinase effector protein that plays a role as GTPase activator (GAP) for Arf6 and RhoA. Arap3 contains a sterile alpha motif (Sam) domain that has high sequence homology with the Sam domain of the EphA2-receptor (EphA2-Sam). Both Arap3-Sam and EphA2-Sam are able to associate with the Sam domain of the lipid phosphatase Ship2 (Ship2-Sam). Recently, we reported a novel interaction between the first Sam domain of Odin (Odin-Sam1), a protein belonging to the ANKS (ANKyrin repeat and Sam domain containing) family, and EphA2-Sam. In our latest work, we applied NMR spectroscopy, surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) to characterize the association between Arap3-Sam and Odin-Sam1. We show that these two Sam domains interact with low micromolar affinity. Moreover, by means of molecular docking techniques, supported by NMR data, we demonstrate that Odin-Sam1 and Arap3-Sam might bind with a topology that is common to several Sam-Sam complexes. The revealed structural details form the basis for the design of potential peptide antagonists that could be used as chemical tools to investigate functional aspects related to heterotypic Arap3-Sam associations.
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Affiliation(s)
- Flavia A Mercurio
- Department of Biological Sciences, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
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Mercurio FA, Marasco D, Pirone L, Pedone EM, Pellecchia M, Leone M. Solution structure of the first Sam domain of Odin and binding studies with the EphA2 receptor. Biochemistry 2012; 51:2136-45. [PMID: 22332920 DOI: 10.1021/bi300141h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The EphA2 receptor plays key roles in many physiological and pathological events, including cancer. The process of receptor endocytosis and the consequent degradation have attracted attention as possible means of overcoming the negative outcomes of EphA2 in cancer cells and decreasing tumor malignancy. A recent study indicates that Sam (sterile alpha motif) domains of Odin, a member of the ANKS (ankyrin repeat and sterile alpha motif domain-containing) family of proteins, are important for the regulation of EphA2 endocytosis. Odin contains two tandem Sam domains (Odin-Sam1 and -Sam2). Herein, we report on the nuclear magnetic resonance (NMR) solution structure of Odin-Sam1; through a variety of assays (employing NMR, surface plasmon resonance, and isothermal titration calorimetry techniques), we clearly demonstrate that Odin-Sam1 binds to the Sam domain of EphA2 in the low micromolar range. NMR chemical shift perturbation experiments and molecular modeling studies point out that the two Sam domains interact with a head-to-tail topology characteristic of several Sam-Sam complexes. This binding mode is similar to that we have previously proposed for the association between the Sam domains of the lipid phosphatase Ship2 and EphA2. This work further validates structural elements relevant for the heterotypic Sam-Sam interactions of EphA2 and provides novel insights for the design of potential therapeutic compounds that can modulate receptor endocytosis.
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Affiliation(s)
- Flavia Anna Mercurio
- Department of Biological Sciences, University of Naples Federico II, Naples, Italy
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Neira JL, Sevilla P, García-Blanco F. The C-terminal sterile alpha motif (SAM) domain of human p73 is a highly dynamic protein, which acquires high thermal stability through a decrease in backbone flexibility. Phys Chem Chem Phys 2012; 14:10308-23. [DOI: 10.1039/c2cp41179b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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