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Douglas JT, Johnson DK, Roy A, Park T. Use of phosphotyrosine-containing peptides to target SH2 domains: Antagonist peptides of the Crk/CrkL-p130Cas axis. Methods Enzymol 2024; 698:301-342. [PMID: 38886037 DOI: 10.1016/bs.mie.2024.04.013] [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] [Indexed: 06/20/2024]
Abstract
Protein-protein interactions between SH2 domains and segments of proteins that include a post-translationally phosphorylated tyrosine residue (pY) underpin numerous signal transduction cascades that allow cells to respond to their environment. Dysregulation of the writing, erasing, and reading of these posttranslational modifications is a hallmark of human disease, notably cancer. Elucidating the precise role of the SH2 domain-containing adaptor proteins Crk and CrkL in tumor cell migration and invasion is challenging because there are no specific and potent antagonists available. Crk and CrkL SH2s interact with a region of the docking protein p130Cas containing 15 potential pY-containing tetrapeptide motifs. This chapter summarizes recent efforts toward peptide antagonists for this Crk/CrkL-p130Cas interaction. We describe our protocol for recombinant expression and purification of Crk and CrkL SH2s for functional assays and our procedure to determine the consensus binding motif from the p130Cas sequence. To develop a more potent antagonist, we employ methods often associated with structure-based drug design. Computational docking using Rosetta FlexPepDock, which accounts for peptides having a greater number of conformational degrees of freedom than small organic molecules that typically constitute libraries, provides quantitative docking metrics to prioritize candidate peptides for experimental testing. A battery of biophysical assays, including fluorescence polarization, differential scanning fluorimetry and saturation transfer difference nuclear magnetic resonance spectroscopy, were employed to assess the candidates. In parallel, GST pulldown competition assays characterized protein-protein binding in vitro. Taken together, our methodology yields peptide antagonists of the Crk/CrkL-p130Cas axis that will be used to validate targets, assess druggability, foster in vitro assay development, and potentially serve as lead compounds for therapeutic intervention.
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Affiliation(s)
- Justin T Douglas
- Nuclear Magnetic Resonance Core Lab, University of Kansas, Lawrence, KS, United States
| | - David K Johnson
- Computational Chemical Biology Core, Molecular Graphics and Modeling Laboratory, University of Kansas, Lawrence, Kansas, United States
| | - Anuradha Roy
- High Throughput Screening Laboratory, University of Kansas, Lawrence, KS, United States
| | - Taeju Park
- Department of Pediatrics, Children's Mercy Kansas City and University of Missouri Kansas City School of Medicine, Kansas City, MO, United States
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Sims C, Birkett MA, Oldham NJ, Stockman RA, Withall DM. Pea aphid odorant-binding protein ApisOBP6 discriminates between aphid sex pheromone components, aphid alarm pheromone and a host plant volatile. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 162:104026. [PMID: 37827436 DOI: 10.1016/j.ibmb.2023.104026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/06/2023] [Accepted: 10/08/2023] [Indexed: 10/14/2023]
Abstract
Olfactory perception of pheromones in insects involves odorant-binding proteins (OBPs), relatively small proteins (ca.110-240 amino acid residues) that can bind reversibly to behaviourally active olfactory ligands. In this study, we investigated the binding in silico and in vitro of the aphid sex pheromone components (1R,4aS,7S,7aR)-nepetalactol and (4aS,7S,7aR)-nepetalactone and the aphid alarm pheromone (E)-β-farnesene by OBPs from the pea aphid, Acyrthosiphon pisum. Screening of protein models of ApisOBPs1-11 with the aphid sex pheromone components suggested that ApisOPB6 was a candidate. Fluorescence assays using ApisOBP6 suggested that ApisOBP6 was able to bind both sex pheromone components and discriminate from the aphid alarm pheromone and the generic plant compound (R/S)-linalool. Saturation transfer difference NMR experiments with ApisOBP6 yielded results consistent to those from the fluorescence experiments, with a clear interaction between ApisOBP6 and (4aS,7S,7aR)-nepetalactone. These results describe a novel interaction and potential function for ApisOBP6, point to pre-receptor odorant discrimination by OBPs, and provide a platform for investigating the function of other aphid olfactory proteins involved in aphid chemical ecology.
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Affiliation(s)
- Cassie Sims
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK; School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Michael A Birkett
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Neil J Oldham
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Robert A Stockman
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - David M Withall
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
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Shirakawa A, Manabe Y, Fukase K. Recent Advances in the Chemical Biology of N-Glycans. Molecules 2021; 26:molecules26041040. [PMID: 33669465 PMCID: PMC7920464 DOI: 10.3390/molecules26041040] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/08/2021] [Accepted: 02/14/2021] [Indexed: 12/19/2022] Open
Abstract
Asparagine-linked N-glycans on proteins have diverse structures, and their functions vary according to their structures. In recent years, it has become possible to obtain high quantities of N-glycans via isolation and chemical/enzymatic/chemoenzymatic synthesis. This has allowed for progress in the elucidation of N-glycan functions at the molecular level. Interaction analyses with lectins by glycan arrays or nuclear magnetic resonance (NMR) using various N-glycans have revealed the molecular basis for the recognition of complex structures of N-glycans. Preparation of proteins modified with homogeneous N-glycans revealed the influence of N-glycan modifications on protein functions. Furthermore, N-glycans have potential applications in drug development. This review discusses recent advances in the chemical biology of N-glycans.
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Affiliation(s)
- Asuka Shirakawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan;
| | - Yoshiyuki Manabe
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan;
- Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- Correspondence: (Y.M.); (K.F.); Tel.: +81-6-6850-5391 (Y.M.); +81-6-6850-5388 (K.F.)
| | - Koichi Fukase
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan;
- Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- Correspondence: (Y.M.); (K.F.); Tel.: +81-6-6850-5391 (Y.M.); +81-6-6850-5388 (K.F.)
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4
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Wang Z, Fang L, Zhao J, Gou S. Insight into the antitumor actions of sterically hindered platinum(ii) complexes by a combination of STD NMR and LCMS techniques. Metallomics 2021; 12:427-434. [PMID: 32022072 DOI: 10.1039/c9mt00258h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sterically hindered platinum(ii) complexes have shown great advantages in overcoming platinum drug resistance. In this study, the antitumor actions of sterically hindered platinum(ii) complex 1 (cis-dichloro[(1R,2R)-N1-(2-fluorobenzyl)-1,2-diaminocyclohexane-N,N']platinum(ii), C13H19FPtCl2) were investigated by using saturation transfer difference nuclear magnetic resonance (STD NMR) and liquid chromatography-mass spectrometry (LCMS) techniques. STD NMR was applied to study the HSA (human serum albumin) binding properties, while the interactions between guanosine 5'-monophosphate (5'-GMP) and complex 1 were studied by LCMS. For HSA binding experiments, strong STD signals were observed for protons of sterically hindered parts of carrier ligands, indicating that the sterically hindered moieties of the carrier ligand could be situated inside the binding pocket of HSA. A 19F NMR experiment indicated that complex 1 could interact with HSA. Furthermore, the binding modes of complex 1 with guanosine 5'-monophosphate (5'-GMP) were studied in the absence and presence of glutathione by LCMS. According to the HPLC profiles, a mono-functional binding mode was observed for complex 1 both in the presence and in the absence of glutathione, while a bi-adduct was observed for Pt(DACH)Cl2, which may be one of the reasons for their different biological activities. Hence, this study demonstrated that the NMR method combined with the LCMS technique could provide valuable information to understand the transport and the underlying anticancer mechanisms of the platinum(ii) complex at the molecular level. Moreover, the results reported here can help to reveal the binding mechanisms of the sterically hindered platinum(ii) compounds with biomolecules, which may shed light on the design of novel platinum(ii) anticancer agents with suitable sterically hindered groups.
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Affiliation(s)
- Zhimei Wang
- Research Center and School of Chemistry and Chemical Engineering, and Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, China.
| | - Lei Fang
- Research Center and School of Chemistry and Chemical Engineering, and Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, China.
| | - Jian Zhao
- Research Center and School of Chemistry and Chemical Engineering, and Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, China.
| | - Shaohua Gou
- Research Center and School of Chemistry and Chemical Engineering, and Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, China.
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Small-molecule inhibitors of nisin resistance protein NSR from the human pathogen Streptococcus agalactiae. Bioorg Med Chem 2019; 27:115079. [DOI: 10.1016/j.bmc.2019.115079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/31/2019] [Accepted: 08/25/2019] [Indexed: 11/19/2022]
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Bustamante N, Iglesias-Bexiga M, Bernardo-García N, Silva-Martín N, García G, Campanero-Rhodes MA, García E, Usón I, Buey RM, García P, Hermoso JA, Bruix M, Menéndez M. Deciphering how Cpl-7 cell wall-binding repeats recognize the bacterial peptidoglycan. Sci Rep 2017; 7:16494. [PMID: 29184076 PMCID: PMC5705596 DOI: 10.1038/s41598-017-16392-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 11/13/2017] [Indexed: 12/25/2022] Open
Abstract
Endolysins, the cell wall lytic enzymes encoded by bacteriophages to release the phage progeny, are among the top alternatives to fight against multiresistant pathogenic bacteria; one of the current biggest challenges to global health. Their narrow range of susceptible bacteria relies, primarily, on targeting specific cell-wall receptors through specialized modules. The cell wall-binding domain of Cpl-7 endolysin, made of three CW_7 repeats, accounts for its extended-range of substrates. Using as model system the cell wall-binding domain of Cpl-7, here we describe the molecular basis for the bacterial cell wall recognition by the CW_7 motif, which is widely represented in sequences of cell wall hydrolases. We report the crystal and solution structure of the full-length domain, identify N-acetyl-D-glucosaminyl-(β1,4)-N-acetylmuramyl-L-alanyl-D-isoglutamine (GMDP) as the peptidoglycan (PG) target recognized by the CW_7 motifs, and characterize feasible GMDP-CW_7 contacts. Our data suggest that Cpl-7 cell wall-binding domain might simultaneously bind to three PG chains, and also highlight the potential use of CW_7-containing lysins as novel anti-infectives.
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Affiliation(s)
- Noemí Bustamante
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Manuel Iglesias-Bexiga
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Noelia Bernardo-García
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006, Madrid, Spain
| | - Noella Silva-Martín
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006, Madrid, Spain
| | - Guadalupe García
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - María A Campanero-Rhodes
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Esther García
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Isabel Usón
- Instituto de Biología Molecular de Barcelona, CSIC, Baldiri Reixach 13, 08028, Barcelona, Spain
- ICREA (Institució Catalana de Recerca i Estudis Avançats), Barcelona, Spain
| | - Rubén M Buey
- Metabolic Engineering Group. Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Pedro García
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Juan A Hermoso
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006, Madrid, Spain
| | - Marta Bruix
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006, Madrid, Spain
| | - Margarita Menéndez
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006, Madrid, Spain.
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain.
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7
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Chaves OA, Jesus CSH, Cruz PF, Sant'Anna CMR, Brito RMM, Serpa C. Evaluation by fluorescence, STD-NMR, docking and semi-empirical calculations of the o-NBA photo-acid interaction with BSA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 169:175-181. [PMID: 27376757 DOI: 10.1016/j.saa.2016.06.028] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/03/2016] [Accepted: 06/17/2016] [Indexed: 06/06/2023]
Abstract
Serum albumins present reversible pH dependent conformational transitions. A sudden laser induced pH-jump is a methodology that can provide new insights on localized protein (un)folding processes that occur within the nanosecond to microsecond time scale. To generate the fast pH jump needed to fast-trigger a protein conformational event, a photo-triggered acid generator as o-nitrobenzaldehyde (o-NBA) can be conveniently used. In order to detect potential specific or nonspecific interactions between o-NBA and BSA, we have performed ligand-binding studies using fluorescence spectroscopy, saturation transfer difference (STD) NMR, molecular docking and semi-empirical calculations. Fluorescence quenching indicates the formation of a non-fluorescent complex in the ground-state between the fluorophore and the quencher, but o-NBA does not bind much effectively to the protein (Ka~4.34×10(3)M(-1)) and thus can be considered a relatively weak binder. The corresponding thermodynamic parameters: ΔG°, ΔS° and ΔH° showed that the binding process is spontaneous and entropy driven. Results of (1)H STD-NMR confirm that the photo-acid and BSA interact, and the relative intensities of the signals in the STD spectra show that all o-NBA protons are equally involved in the binding process, which should correspond to a nonspecific interaction. Molecular docking and semi-empirical calculations suggest that the o-NBA binds preferentially to the Trp-212-containing site of BSA (FA7), interacting via hydrogen bonds with Arg-217 and Tyr-149 residues.
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Affiliation(s)
- Otávio A Chaves
- Departament of Chemistry, Universidade Federal Rural do Rio de Janeiro, BR 465, km 47, 23890-000 Seropédica, RJ, Brazil; CQC, Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Catarina S H Jesus
- CQC, Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal; Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Pedro F Cruz
- CQC, Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Carlos M R Sant'Anna
- Departament of Chemistry, Universidade Federal Rural do Rio de Janeiro, BR 465, km 47, 23890-000 Seropédica, RJ, Brazil
| | - Rui M M Brito
- Departament of Chemistry, Universidade Federal Rural do Rio de Janeiro, BR 465, km 47, 23890-000 Seropédica, RJ, Brazil; CQC, Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Carlos Serpa
- CQC, Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal.
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8
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Marchetti R, Perez S, Arda A, Imberty A, Jimenez‐Barbero J, Silipo A, Molinaro A. "Rules of Engagement" of Protein-Glycoconjugate Interactions: A Molecular View Achievable by using NMR Spectroscopy and Molecular Modeling. ChemistryOpen 2016; 5:274-96. [PMID: 27547635 PMCID: PMC4981046 DOI: 10.1002/open.201600024] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 12/20/2022] Open
Abstract
Understanding the dynamics of protein-ligand interactions, which lie at the heart of host-pathogen recognition, represents a crucial step to clarify the molecular determinants implicated in binding events, as well as to optimize the design of new molecules with therapeutic aims. Over the last decade, advances in complementary biophysical and spectroscopic methods permitted us to deeply dissect the fine structural details of biologically relevant molecular recognition processes with high resolution. This Review focuses on the development and use of modern nuclear magnetic resonance (NMR) techniques to dissect binding events. These spectroscopic methods, complementing X-ray crystallography and molecular modeling methodologies, will be taken into account as indispensable tools to provide a complete picture of protein-glycoconjugate binding mechanisms related to biomedicine applications against infectious diseases.
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Affiliation(s)
- Roberta Marchetti
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Serge Perez
- Department Molecular Pharmacochemistry UMR 5063CNRS and University of GrenobleAlpes, BP 5338041 Grenoble cedex 9France
| | - Ana Arda
- Bizkaia Technological ParkCIC bioGUNEBuilding 801A-148160Derio-BizkaiaSpain
| | - Anne Imberty
- Centre de Recherche sur les CNRSand University of Grenoble Macromolécules Végétales, UPR 5301Alpes, BP 5338041Grenoble cedex 9France
| | | | - Alba Silipo
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Antonio Molinaro
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
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Téletchéa S, Stresing V, Hervouet S, Baud'huin M, Heymann MF, Bertho G, Charrier C, Ando K, Heymann D. Novel RANK antagonists for the treatment of bone-resorptive disease: theoretical predictions and experimental validation. J Bone Miner Res 2014; 29:1466-77. [PMID: 24390798 DOI: 10.1002/jbmr.2170] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 12/17/2013] [Accepted: 01/01/2013] [Indexed: 12/15/2022]
Abstract
Receptor activator of nuclear factor-κB (RANK) and RANK ligand (RANKL) play a pivotal role in bone metabolism, and selective targeting of RANK signaling has become a promising therapeutic strategy in the management of resorptive bone diseases. Existing antibody-based therapies and novel inhibitors currently in development were designed to target the ligand, rather than the membrane receptor expressed on osteoclast precursors. We describe here an alternative approach to designing small peptides able to specifically bind to the hinge region of membrane RANK responsible for the conformational change upon RANKL association. A nonapeptide generated by this method was validated for its biological activity in vitro and in vivo and served as a lead compound for the generation of a series of peptide RANK antagonists derived from the original sequence. Our study presents a structure- and knowledge-based strategy for the design of novel effective and affordable small peptide inhibitors specifically targeting the receptor RANK and opens a new therapeutic opportunity for the treatment of resorptive bone disease.
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Affiliation(s)
- Stéphane Téletchéa
- INSERM, UMR 957, Equipe labellisée LIGUE 2012, Université de Nantes, Laboratory of the Physiopathology of Bone Resorption and Therapy of Primary Bone Tumors (LPRO), Nantes, France
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Cruz-Gallardo I, Aroca Á, Gunzburg MJ, Sivakumaran A, Yoon JH, Angulo J, Persson C, Gorospe M, Karlsson BG, Wilce JA, Díaz-Moreno I. The binding of TIA-1 to RNA C-rich sequences is driven by its C-terminal RRM domain. RNA Biol 2014; 11:766-76. [PMID: 24824036 DOI: 10.4161/rna.28801] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
T-cell intracellular antigen-1 (TIA-1) is a key DNA/RNA binding protein that regulates translation by sequestering target mRNAs in stress granules (SG) in response to stress conditions. TIA-1 possesses three RNA recognition motifs (RRM) along with a glutamine-rich domain, with the central domains (RRM2 and RRM3) acting as RNA binding platforms. While the RRM2 domain, which displays high affinity for U-rich RNA sequences, is primarily responsible for interaction with RNA, the contribution of RRM3 to bind RNA as well as the target RNA sequences that it binds preferentially are still unknown. Here we combined nuclear magnetic resonance (NMR) and surface plasmon resonance (SPR) techniques to elucidate the sequence specificity of TIA-1 RRM3. With a novel approach using saturation transfer difference NMR (STD-NMR) to quantify protein-nucleic acids interactions, we demonstrate that isolated RRM3 binds to both C- and U-rich stretches with micromolar affinity. In combination with RRM2 and in the context of full-length TIA-1, RRM3 significantly enhanced the binding to RNA, particularly to cytosine-rich RNA oligos, as assessed by biotinylated RNA pull-down analysis. Our findings provide new insight into the role of RRM3 in regulating TIA-1 binding to C-rich stretches, that are abundant at the 5' TOPs (5' terminal oligopyrimidine tracts) of mRNAs whose translation is repressed under stress situations.
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Affiliation(s)
- Isabel Cruz-Gallardo
- Instituto de Bioquímica Vegetal y Fotosíntesis; Centro de Investigaciones Científicas Isla de la Cartuja; Universidad de Sevilla-CSIC; Sevilla, Spain
| | - Ángeles Aroca
- Instituto de Bioquímica Vegetal y Fotosíntesis; Centro de Investigaciones Científicas Isla de la Cartuja; Universidad de Sevilla-CSIC; Sevilla, Spain
| | - Menachem J Gunzburg
- Department of Biochemistry and Molecular Biology; Monash University; Clayton, Victoria, Australia
| | - Andrew Sivakumaran
- Department of Biochemistry and Molecular Biology; Monash University; Clayton, Victoria, Australia
| | - Je-Hyun Yoon
- Laboratory of Genetics; National Institute on Aging-Intramural Research Program; NIH; Baltimore, MD USA
| | - Jesús Angulo
- Instituto de Investigaciones Químicas; Centro de Investigaciones Científicas Isla de la Cartuja; Universidad de Sevilla-CSIC; Sevilla, Spain; School of Pharmacy; University of East Anglia; Norwich Research Park; Norwich, UK
| | - Cecilia Persson
- Swedish NMR Centre; University of Gothenburg; Gothenburg, Sweden
| | - Myriam Gorospe
- Laboratory of Genetics; National Institute on Aging-Intramural Research Program; NIH; Baltimore, MD USA
| | - B Göran Karlsson
- Swedish NMR Centre; University of Gothenburg; Gothenburg, Sweden
| | - Jacqueline A Wilce
- Department of Biochemistry and Molecular Biology; Monash University; Clayton, Victoria, Australia
| | - Irene Díaz-Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis; Centro de Investigaciones Científicas Isla de la Cartuja; Universidad de Sevilla-CSIC; Sevilla, Spain
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11
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Harris KA, Shekhtman A, Agris PF. Specific RNA-protein interactions detected with saturation transfer difference NMR. RNA Biol 2013; 10:1307-11. [PMID: 23949611 DOI: 10.4161/rna.25948] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
RNA, at the forefront of biochemical research due to its central role in biology, is recognized by proteins through various mechanisms. Analysis of the RNA-protein interface provides insight into the recognition determinants and function. As such, there is a demand for developing new methods to characterize RNA-protein interactions. Saturation transfer difference (STD) NMR can identify binding ligands for proteins in a rather short period of time, with data acquisitions of just a few hours. Two RNA-protein systems involved in RNA modification were studied using STD NMR. The N (6)-threonylcarbamoyltransferase, YrdC, with nucleoside-specific recognition, was shown to bind the anticodon stem-loop of tRNA(Lys)UUU. The points of contact on the RNA were assigned and a binding interface was identified. STD NMR was also applied to the interaction of the archaeal ribosomal protein, L7Ae, with the box C/D K-turn RNA. The distinctiveness of the two RNA-protein interfaces was evident. Both RNAs exhibited strong STD signals indicative of direct contact with the respective protein, but reflected the nature of recognition. Characterization of nucleic acid recognition determinants traditionally involves cost and time prohibitive methods. This approach offers significant insight into interaction interfaces fairly rapidly, and complements existing structural methods.
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Affiliation(s)
- Kimberly A Harris
- The RNA Institute; University at Albany; Albany, NY USA; Department of Biological Sciences; University at Albany; Albany, NY USA
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12
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Sun P, Jiang X, Jiang B, Zhang X, Liu M. Biomolecular ligands screening using radiation damping difference WaterLOGSY spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2013; 56:285-290. [PMID: 23740293 DOI: 10.1007/s10858-013-9748-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 05/28/2013] [Indexed: 06/02/2023]
Abstract
Water-ligand observed via gradient spectroscopy (WaterLOGSY) is a widely used nuclear magnetic resonance method for ligand screening. The crucial procedure for the effectiveness of WaterLOGSY is selective excitation of the water resonance. The selective excitation is conventionally achieved by using long selective pulse, which causes partial saturation of the water magnetization leading to reduction of sensitivity, in addition to time consuming and error prone. Therefore, many improvements have been made to enhance the sensitivity and robustness of the method. Here we propose an alternative selective excitation scheme for WaterLOGSY by utilizing radiation damping effect. The pulse scheme starts simply with a hard inversion pulse, instead of selective pulse or pulse train, followed by a pulse field gradient to control the radiation damping effect. The rest parts of the pulse scheme are similar to conventional WaterLOGSY. When the gradient pulse is applied immediately after the inversion pulse, the radiation damping effect is suppressed, and all of the magnetization is inversed. When the gradient pulse and the inversion pulse are about 10-20 ms apart, the radiation damping effect remains active and drives the water magnetization toward +z-axis, resulting in selective non-inversion of the water magnetization. By taking the differences of the spectra obtained under these two conditions, one should get the result of WaterLOGSY. The method is demonstrated to be simple, robust and sensitive for ligand screening.
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Affiliation(s)
- Peng Sun
- Wuhan Center for Magnetic Resonance, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
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NMR-based analysis of protein-ligand interactions. Anal Bioanal Chem 2013; 406:943-56. [PMID: 23591643 DOI: 10.1007/s00216-013-6931-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/12/2013] [Accepted: 03/19/2013] [Indexed: 10/27/2022]
Abstract
Physiological processes are mainly controlled by intermolecular recognition mechanisms involving protein-protein and protein-ligand (low molecular weight molecules) interactions. One of the most important tools for probing these interactions is high-field solution nuclear magnetic resonance (NMR) through protein-observed and ligand-observed experiments, where the protein receptor or the organic compounds are selectively detected. NMR binding experiments rely on comparison of NMR parameters of the free and bound states of the molecules. Ligand-observed methods are not limited by the protein molecular size and therefore have great applicability for analysing protein-ligand interactions. The use of these NMR techniques has considerably expanded in recent years, both in chemical biology and in drug discovery. We review here three major ligand-observed NMR methods that depend on the nuclear Overhauser effect-transferred nuclear Overhauser effect spectroscopy, saturation transfer difference spectroscopy and water-ligand interactions observed via gradient spectroscopy experiments-with the aim of reporting recent developments and applications for the characterization of protein-ligand complexes, including affinity measurements and structural determination.
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Wagstaff JL, Taylor SL, Howard MJ. Recent developments and applications of saturation transfer difference nuclear magnetic resonance (STD NMR) spectroscopy. ACTA ACUST UNITED AC 2013; 9:571-7. [DOI: 10.1039/c2mb25395j] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Bhunia A, Bhattacharjya S, Chatterjee S. Applications of saturation transfer difference NMR in biological systems. Drug Discov Today 2012; 17:505-13. [DOI: 10.1016/j.drudis.2011.12.016] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 11/10/2011] [Accepted: 12/14/2011] [Indexed: 01/08/2023]
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Ziarelli F, Peng L, Zhang CC, Viel S. High resolution magic angle spinning NMR to investigate ligand–receptor binding events for mass-limited samples in liquids. J Pharm Biomed Anal 2012; 59:13-7. [DOI: 10.1016/j.jpba.2011.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 10/09/2011] [Accepted: 10/10/2011] [Indexed: 11/29/2022]
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