1
|
Loveland AB, Koh CS, Ganesan R, Jacobson A, Korostelev AA. Structural mechanism of angiogenin activation by the ribosome. Nature 2024; 630:769-776. [PMID: 38718836 DOI: 10.1038/s41586-024-07508-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/02/2024] [Indexed: 05/15/2024]
Abstract
Angiogenin, an RNase-A-family protein, promotes angiogenesis and has been implicated in cancer, neurodegenerative diseases and epigenetic inheritance1-10. After activation during cellular stress, angiogenin cleaves tRNAs at the anticodon loop, resulting in translation repression11-15. However, the catalytic activity of isolated angiogenin is very low, and the mechanisms of the enzyme activation and tRNA specificity have remained a puzzle3,16-23. Here we identify these mechanisms using biochemical assays and cryogenic electron microscopy (cryo-EM). Our study reveals that the cytosolic ribosome is the activator of angiogenin. A cryo-EM structure features angiogenin bound in the A site of the 80S ribosome. The C-terminal tail of angiogenin is rearranged by interactions with the ribosome to activate the RNase catalytic centre, making the enzyme several orders of magnitude more efficient in tRNA cleavage. Additional 80S-angiogenin structures capture how tRNA substrate is directed by the ribosome into angiogenin's active site, demonstrating that the ribosome acts as the specificity factor. Our findings therefore suggest that angiogenin is activated by ribosomes with a vacant A site, the abundance of which increases during cellular stress24-27. These results may facilitate the development of therapeutics to treat cancer and neurodegenerative diseases.
Collapse
Affiliation(s)
- Anna B Loveland
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA.
| | - Cha San Koh
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA
| | - Robin Ganesan
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
| | | |
Collapse
|
2
|
Sica F, Russo Krauss I, Troisi R, Bosso A, Culurciello R, Carluccio C, Trapani M, Merlino A, Mazzarella L, Pizzo E. The structural features of an ancient ribonuclease from Salmo salar reveal an intriguing case of auto-inhibition. Int J Biol Macromol 2021; 182:659-668. [PMID: 33848550 DOI: 10.1016/j.ijbiomac.2021.04.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
The superfamily of vertebrate ribonucleases, a large group of evolutionarily related proteins, continues to provide interesting structural and functional information. In particular, the crystal structure of SS-RNase-2 from Salmo salar (SS2), here presented, has revealed a novel auto-inhibition mechanism that enriches the number of inhibition strategies observed in some members of the family. Within an essentially unmodified RNase folding, the SS2 active site cleft is in part obstructed by the collapse of an extra pentapeptide inserted in the C-terminal region. This unexpected intrusion alters the organization of the catalytic triad by pushing one catalytic histidine off the pocket. Possible mechanisms to remove the active site obstruction have also been studied through the production of two mutants that provide useful information on the functionality of this intriguing version of the ribonuclease superfamily.
Collapse
Affiliation(s)
- Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126 Naples, Italy.
| | - Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126 Naples, Italy; CSGI (Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase), Via della Lastruccia 3, I-50019 Sesto Fiorentino, FI, Italy
| | - Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126 Naples, Italy
| | - Andrea Bosso
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126 Naples, Italy
| | - Rosanna Culurciello
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126 Naples, Italy
| | - Carla Carluccio
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126 Naples, Italy
| | - Mariateresa Trapani
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126 Naples, Italy
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126 Naples, Italy
| | - Lelio Mazzarella
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126 Naples, Italy; Accademia di Scienze Fisiche e Matematiche della Società Nazionale di Scienze, Lettere ed Arti in Napoli, Naples, Italy
| | - Elio Pizzo
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126 Naples, Italy
| |
Collapse
|
3
|
Shigematsu M, Kawamura T, Kirino Y. Generation of 2',3'-Cyclic Phosphate-Containing RNAs as a Hidden Layer of the Transcriptome. Front Genet 2018; 9:562. [PMID: 30538719 PMCID: PMC6277466 DOI: 10.3389/fgene.2018.00562] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/06/2018] [Indexed: 01/03/2023] Open
Abstract
Cellular RNA molecules contain phosphate or hydroxyl ends. A 2′,3′-cyclic phosphate (cP) is one of the 3′-terminal forms of RNAs mainly generated from RNA cleavage by ribonucleases. Although transcriptome profiling using RNA-seq has become a ubiquitous tool in biological and medical research, cP-containing RNAs (cP-RNAs) form a hidden transcriptome layer, which is infrequently recognized and characterized, because standard RNA-seq is unable to capture them. Despite cP-RNAs’ invisibility in RNA-seq data, increasing evidence indicates that they are not accumulated simply as non-functional degradation products; rather, they have physiological roles in various biological processes, designating them as noteworthy functional molecules. This review summarizes our current knowledge of cP-RNA biogenesis pathways and their catalytic enzymatic activities, discusses how the cP-RNA generation affects biological processes, and explores future directions to further investigate cP-RNA biology.
Collapse
Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Takuya Kawamura
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| |
Collapse
|
4
|
Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily. Structure 2018; 26:426-436.e3. [PMID: 29478822 DOI: 10.1016/j.str.2018.01.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/06/2017] [Accepted: 01/24/2018] [Indexed: 11/21/2022]
Abstract
Enzyme superfamily members that share common chemical and/or biological functions also share common features. While the role of structure is well characterized, the link between enzyme function and dynamics is not well understood. We present a systematic characterization of intrinsic dynamics of over 20 members of the pancreatic-type RNase superfamily, which share a common structural fold. This study is motivated by the fact that the range of chemical activity as well as molecular motions of RNase homologs spans over 105 folds. Dynamics was characterized using a combination of nuclear magnetic resonance experiments and computer simulations. Phylogenetic clustering led to the grouping of sequences into functionally distinct subfamilies. Detailed characterization of the diverse RNases showed conserved dynamical traits for enzymes within subfamilies. These results suggest that selective pressure for the conservation of dynamical behavior, among other factors, may be linked to the distinct chemical and biological functions in an enzyme superfamily.
Collapse
|
5
|
Chatzileontiadou DSM, Tsika AC, Diamantopoulou Z, Delbé J, Badet J, Courty J, Skamnaki VT, Parmenopoulou V, Komiotis D, Hayes JM, Spyroulias GA, Leonidas DD. Evidence for Novel Action at the Cell-Binding Site of Human Angiogenin Revealed by Heteronuclear NMR Spectroscopy, in silico and in vivo Studies. ChemMedChem 2018; 13:259-269. [PMID: 29314771 DOI: 10.1002/cmdc.201700688] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/18/2017] [Indexed: 12/11/2022]
Abstract
A member of the ribonuclease A superfamily, human angiogenin (hAng) is a potent angiogenic factor. Heteronuclear NMR spectroscopy combined with induced-fit docking revealed a dual binding mode for the most antiangiogenic compound of a series of ribofuranosyl pyrimidine nucleosides that strongly inhibit hAng's angiogenic activity in vivo. While modeling suggests the potential for simultaneous binding of the inhibitors at the active and cell-binding sites, NMR studies indicate greater affinity for the cell-binding site than for the active site. Additionally, molecular dynamics simulations at 100 ns confirmed the stability of binding at the cell-binding site with the predicted protein-ligand interactions, in excellent agreement with the NMR data. This is the first time that a nucleoside inhibitor is reported to completely inhibit the angiogenic activity of hAng in vivo by exerting dual inhibitory activity on hAng, blocking both the entrance of hAng into the cell and its ribonucleolytic activity.
Collapse
Affiliation(s)
- Demetra S M Chatzileontiadou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece.,Current address: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Australia
| | | | - Zoi Diamantopoulou
- Laboratoire de Recherche sur la Croissance Cellulaire, la Réparation et la Régénération Tissulaires (CRRET), Université Paris-EST Créteil, CNRS ERL 9215, France.,Current address: Cancer Research (UK) Manchester Institute, Manchester, UK
| | - Jean Delbé
- Laboratoire de Recherche sur la Croissance Cellulaire, la Réparation et la Régénération Tissulaires (CRRET), Université Paris-EST Créteil, CNRS ERL 9215, France
| | - Josette Badet
- INSERM U1139, Université Paris Descartes, 4 avenue de l'Observatoire, 75006, Paris, France
| | - José Courty
- Laboratoire de Recherche sur la Croissance Cellulaire, la Réparation et la Régénération Tissulaires (CRRET), Université Paris-EST Créteil, CNRS ERL 9215, France
| | - Vassiliki T Skamnaki
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece
| | - Vanessa Parmenopoulou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece
| | - Dimitri Komiotis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece
| | - Joseph M Hayes
- Centre for Materials Science and School of Physical Sciences & Computing, University of Central Lancashire, Preston, PR1 2HE, UK
| | | | - Demetres D Leonidas
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece
| |
Collapse
|
6
|
Bradshaw WJ, Rehman S, Pham TTK, Thiyagarajan N, Lee RL, Subramanian V, Acharya KR. Structural insights into human angiogenin variants implicated in Parkinson's disease and Amyotrophic Lateral Sclerosis. Sci Rep 2017; 7:41996. [PMID: 28176817 PMCID: PMC5296752 DOI: 10.1038/srep41996] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/04/2017] [Indexed: 12/11/2022] Open
Abstract
Mutations in Angiogenin (ANG), a member of the Ribonuclease A superfamily (also known as RNase 5) are known to be associated with Amyotrophic Lateral Sclerosis (ALS, motor neurone disease) (sporadic and familial) and Parkinson’s Disease (PD). In our previous studies we have shown that ANG is expressed in neurons during neuro-ectodermal differentiation, and that it has both neurotrophic and neuroprotective functions. In addition, in an extensive study on selective ANG-ALS variants we correlated the structural changes to the effects on neuronal survival and the ability to induce stress granules in neuronal cell lines. Furthermore, we have established that ANG-ALS variants which affect the structure of the catalytic site and either decrease or increase the RNase activity affect neuronal survival. Neuronal cell lines expressing the ANG-ALS variants also lack the ability to form stress granules. Here, we report a detailed experimental structural study on eleven new ANG-PD/ALS variants which will have implications in understanding the molecular basis underlying their role in PD and ALS.
Collapse
Affiliation(s)
- William J Bradshaw
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Saima Rehman
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Tram T K Pham
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Nethaji Thiyagarajan
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Rebecca L Lee
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Vasanta Subramanian
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - K Ravi Acharya
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| |
Collapse
|
7
|
Chatzileontiadou DSM, Tsirkone VG, Dossi K, Kassouni AG, Liggri PGV, Kantsadi AL, Stravodimos GA, Balatsos NAA, Skamnaki VT, Leonidas DD. The ammonium sulfate inhibition of human angiogenin. FEBS Lett 2016; 590:3005-18. [PMID: 27483019 DOI: 10.1002/1873-3468.12335] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/17/2016] [Accepted: 07/22/2016] [Indexed: 11/09/2022]
Abstract
In this study, we investigate the inhibition of human angiogenin by ammonium sulfate. The inhibitory potency of ammonium sulfate for human angiogenin (IC50 = 123.5 ± 14.9 mm) is comparable to that previously reported for RNase A (119.0 ± 6.5 mm) and RNase 2 (95.7 ± 9.3 mm). However, analysis of two X-ray crystal structures of human angiogenin in complex with sulfate anions (in acidic and basic pH environments, respectively) indicates an entirely distinct mechanism of inhibition. While ammonium sulfate inhibits the ribonucleolytic activity of RNase A and RNase 2 by binding to the active site of these enzymes, sulfate anions bind only to peripheral substrate anion-binding subsites of human angiogenin, and not to the active site.
Collapse
Affiliation(s)
| | - Vicky G Tsirkone
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Kyriaki Dossi
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aikaterini G Kassouni
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Panagiota G V Liggri
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Anastassia L Kantsadi
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - George A Stravodimos
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Nikolaos A A Balatsos
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Vassiliki T Skamnaki
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Demetres D Leonidas
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| |
Collapse
|
8
|
Cong X, Cremer C, Nachreiner T, Barth S, Carloni P. Engineered human angiogenin mutations in the placental ribonuclease inhibitor complex for anticancer therapy: Insights from enhanced sampling simulations. Protein Sci 2016; 25:1451-60. [PMID: 27110669 PMCID: PMC4972201 DOI: 10.1002/pro.2941] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/20/2016] [Indexed: 01/29/2023]
Abstract
Targeted human cytolytic fusion proteins (hCFPs) represent a new generation of immunotoxins (ITs) for the specific targeting and elimination of malignant cell populations. Unlike conventional ITs, hCFPs comprise a human/humanized target cell-specific binding moiety (e.g., an antibody or a fragment thereof) fused to a human proapoptotic protein as the cytotoxic domain (effector domain). Therefore, hCFPs are humanized ITs expected to have low immunogenicity. This reduces side effects and allows long-term application. The human ribonuclease angiogenin (Ang) has been shown to be a promising effector domain candidate. However, the application of Ang-based hCFPs is largely hampered by the intracellular placental ribonuclease inhibitor (RNH1). It rapidly binds and inactivates Ang. Mutations altering Ang's affinity for RNH1 modulate the cytotoxicity of Ang-based hCFPs. Here we perform in total 2.7 µs replica-exchange molecular dynamics simulations to investigate some of these mutations-G85R/G86R (GGRRmut ), Q117G (QGmut ), and G85R/G86R/Q117G (GGRR/QGmut ). GGRRmut turns out to perturb greatly the overall Ang-RNH1 interactions, whereas QGmut optimizes them. Combining QGmut with GGRRmut compensates the effects of the latter. Our results explain the in vitro finding that, while Ang GGRRmut -based hCFPs resist RNH1 inhibition remarkably, Ang WT- and Ang QGmut -based ones are similarly sensitive to RNH1 inhibition, whereas Ang GGRR/QGmut -based ones are only slightly resistant. This work may help design novel Ang mutants with reduced affinity for RNH1 and improved cytotoxicity.
Collapse
Affiliation(s)
- Xiaojing Cong
- Computational Biophysics, German Research School for Simulation Sciences (Joint Venture of RWTH Aachen University and Forschungszentrum Jülich)Jülich52428Germany
- Computational Biomedicine Section, Institute for Advanced Simulations ‐ 5 (IAS‐5)Jülich52428GermanyForschungszentrum Jülich
- Computational Biomedicine Section, Institute for Neuroscience and Medicine ‐ 9 (INM‐9)Jülich52428GermanyForschungszentrum Jülich
| | - Christian Cremer
- Department of Experimental Medicine and Immunotherapy, Institute for Applied Medical EngineeringUniversity Hospital RWTH AachenAachen52074Germany
| | - Thomas Nachreiner
- Department of Experimental Medicine and Immunotherapy, Institute for Applied Medical EngineeringUniversity Hospital RWTH AachenAachen52074Germany
| | - Stefan Barth
- Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape TownCape Town7925South Africa
- South African Research Chair in Cancer Biotechnology, Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape Town7925Cape TownSouth Africa
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences (Joint Venture of RWTH Aachen University and Forschungszentrum Jülich)Jülich52428Germany
- Computational Biomedicine Section, Institute for Advanced Simulations ‐ 5 (IAS‐5)Jülich52428GermanyForschungszentrum Jülich
- Computational Biomedicine Section, Institute for Neuroscience and Medicine ‐ 9 (INM‐9)Jülich52428GermanyForschungszentrum Jülich
| |
Collapse
|
9
|
Cremer C, Braun H, Mladenov R, Schenke L, Cong X, Jost E, Brümmendorf TH, Fischer R, Carloni P, Barth S, Nachreiner T. Novel angiogenin mutants with increased cytotoxicity enhance the depletion of pro-inflammatory macrophages and leukemia cells ex vivo. Cancer Immunol Immunother 2015; 64:1575-86. [PMID: 26472728 PMCID: PMC11028715 DOI: 10.1007/s00262-015-1763-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/29/2015] [Indexed: 10/22/2022]
Abstract
Immunotoxins are fusion proteins that combine a targeting component such as an antibody fragment or ligand with a cytotoxic effector component that induces apoptosis in specific cell populations displaying the corresponding antigen or receptor. Human cytolytic fusion proteins (hCFPs) are less immunogenic than conventional immunotoxins because they contain human pro-apoptotic enzymes as effectors. However, one drawback of hCFPs is that target cells can protect themselves by expressing endogenous inhibitor proteins. Inhibitor-resistant enzyme mutants that maintain their cytotoxic activity are therefore promising effector domain candidates. We recently developed potent variants of the human ribonuclease angiogenin (Ang) that were either more active than the wild-type enzyme or less susceptible to inhibition because of their lower affinity for the ribonuclease inhibitor RNH1. However, combining the mutations was unsuccessful because although the enzyme retained its higher activity, its susceptibility to RNH1 reverted to wild-type levels. We therefore used molecular dynamic simulations to determine, at the atomic level, why the affinity for RNH1 reverted, and we developed strategies based on the introduction of further mutations to once again reduce the affinity of Ang for RNH1 while retaining its enhanced activity. We were able to generate a novel Ang variant with remarkable in vitro cytotoxicity against HL-60 cells and pro-inflammatory macrophages. We also demonstrated the pro-apoptotic potential of Ang-based hCFPs on cells freshly isolated from leukemia patients.
Collapse
Affiliation(s)
- Christian Cremer
- Department of Experimental Medicine and Immunotherapy, Institute for Applied Medical Engineering, University Hospital RWTH Aachen, Pauwelsstr. 20, 52074, Aachen, Germany
| | - Hanna Braun
- Department of Experimental Medicine and Immunotherapy, Institute for Applied Medical Engineering, University Hospital RWTH Aachen, Pauwelsstr. 20, 52074, Aachen, Germany
| | - Radoslav Mladenov
- Department of Pharmaceutical Product Development, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstr. 6, 52074, Aachen, Germany
| | - Lea Schenke
- Department of Experimental Medicine and Immunotherapy, Institute for Applied Medical Engineering, University Hospital RWTH Aachen, Pauwelsstr. 20, 52074, Aachen, Germany
| | - Xiaojing Cong
- Department of Computational Biophysics, German Research School for Simulation Sciences (Joint Venture of RWTH Aachen University and Forschungszentrum Jülich), 52428, Jülich, Germany
- Institute for Advanced Simulations IAS-5, Computational Biomedicine, Forschungszentrum, Jülich, Germany
| | - Edgar Jost
- Department of Hematology and Oncology (Internal Medicine IV), University Hospital RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Tim H Brümmendorf
- Department of Hematology and Oncology (Internal Medicine IV), University Hospital RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Rainer Fischer
- Department of Pharmaceutical Product Development, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstr. 6, 52074, Aachen, Germany
- Institute for Molecular Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany
| | - Paolo Carloni
- Department of Computational Biophysics, German Research School for Simulation Sciences (Joint Venture of RWTH Aachen University and Forschungszentrum Jülich), 52428, Jülich, Germany
- Institute for Advanced Simulations IAS-5, Computational Biomedicine, Forschungszentrum, Jülich, Germany
| | - Stefan Barth
- Department of Experimental Medicine and Immunotherapy, Institute for Applied Medical Engineering, University Hospital RWTH Aachen, Pauwelsstr. 20, 52074, Aachen, Germany
- South African Research Chair in Cancer Biotechnology, Institute of Infectious Disease and Molecular Medicine (IDM), Anzio Road, Observatory, Cape Town, 7925, South Africa
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa
| | - Thomas Nachreiner
- Department of Experimental Medicine and Immunotherapy, Institute for Applied Medical Engineering, University Hospital RWTH Aachen, Pauwelsstr. 20, 52074, Aachen, Germany.
| |
Collapse
|
10
|
Targeting tumor micro-environment for design and development of novel anti-angiogenic agents arresting tumor growth. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 113:333-54. [PMID: 24139944 DOI: 10.1016/j.pbiomolbio.2013.10.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 10/05/2013] [Accepted: 10/08/2013] [Indexed: 12/12/2022]
Abstract
Angiogenesis: a process of generation of new blood vessels has been proved to be necessary for sustained tumor growth and cancer progression. Inhibiting angiogenesis pathway has long been remained a significant hope for the development of novel, effective and target orientated antitumor agents arresting the tumor proliferation and metastasis. The process of neoangiogenesis as a biological process is regulated by several pro- and anti-angiogenic factors, especially vascular endothelial growth factor, fibroblast growth factor, epidermal growth factor, hypoxia inducible factor 1 and transforming growth factor. Every endothelial cell destined for vessel formation is equipped with receptors for these angiogenic peptides. Moreover, numerous other angiogenic cytokines such as platelet derived growth factor (PGDF), placenta growth factor (PGF), nerve growth factor (NGF), stem-cell factor (SCF), and interleukins-2, 4, 6 etc. These molecular players performs critical role in regulating the angiogenic switch. Couple of decade's research in molecular aspects of tumor biology has unraveled numerous structural and functional mysteries of these angiogenic peptides. In present article, a detailed update on the functional and structural peculiarities of the various angiogenic peptides is described focusing on structural opportunities made available that has potential to be used to modulate function of these angiogenic peptides in developing therapeutic agents targeting neoplastic angiogenesis. The data may be useful in the mainstream of developing novel anticancer agents targeting tumor angiogenesis. We also discuss major therapeutic agents that are currently used in angiogenesis associated therapies as well as those are subject of active research or are in clinical trials.
Collapse
|
11
|
Structural and molecular insights into the mechanism of action of human angiogenin-ALS variants in neurons. Nat Commun 2013; 3:1121. [PMID: 23047679 PMCID: PMC3493651 DOI: 10.1038/ncomms2126] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 09/06/2012] [Indexed: 12/11/2022] Open
Abstract
Mutations in angiogenin (ANG), a member of the ribonuclease A superfamily, are associated with amyotrophic lateral sclerosis (ALS; sporadic and familial) and Parkinson's disease. We have previously shown that ANG is expressed in neurons during neuro-ectodermal differentiation, and that it has both neurotrophic and neuroprotective functions. Here we report the atomic resolution structure of native ANG and 11 ANG-ALS variants. We correlate the structural changes to the effects on neuronal survival and the ability to induce stress granules in neuronal cell lines. ANG-ALS variants that affect the structure of the catalytic site and either decrease or increase the RNase activity affect neuronal survival. Neuronal cell lines expressing the ANG-ALS variants also lack the ability to form stress granules. Our structure–function studies on these ANG-ALS variants are the first to provide insights into the cellular and molecular mechanisms underlying their role in ALS. Mutations in human angiogenin are implicated in the progression of amyotrophic lateral sclerosis. Thiyagarajan and colleagues show that structural differences between angiogenin variants affect neuronal survival, and the ability to induce stress granules in neuronal cell lines.
Collapse
|
12
|
Thiyagarajan N, Acharya KR. Crystal structure of human angiogenin with an engineered loop exhibits conformational flexibility at the functional regions of the molecule. FEBS Open Bio 2012; 3:65-70. [PMID: 23772376 PMCID: PMC3668512 DOI: 10.1016/j.fob.2012.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 12/19/2012] [Accepted: 12/19/2012] [Indexed: 11/18/2022] Open
Abstract
Human angiogenin (ANG) is an angiogenic molecule and a ribonucleolytic enzyme with significant amino acid sequence identity to pancreatic RNase A, plays a critical role in the establishment and growth of tumours. An association between ANG and cancer has been observed in more than 25 clinical studies to date. In addition, ANG has now been shown to be implicated in Amyotrophic Lateral Sclerosis (ALS) and Parkinson's Disease (PD). Structural and biochemical studies so far have showed several distinguishing features of ANG molecule compared to RNase A and provided details of the putative cell binding site, active site, nuclear translocation sequence and the roles of residues in binding and cleaving RNA. A key finding elucidated from the structural study on ANG is the presence of a 'blocked' C-terminus (part of the active site apparatus) compared with RNase A. Here we report the crystal structure of ANG with an 'engineered-loop' from eosinophil derived neurotoxin (a homologue of ANG) which has resulted with local perturbations (conformational flexibility) at the cell binding site and at the C-terminus of the molecule. This experimental observation will now provide a new avenue to design compounds (potent inhibitors) through a structure guided drug design route.
Collapse
Affiliation(s)
| | - K. Ravi Acharya
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| |
Collapse
|
13
|
Iyer S, Holloway DE, Acharya KR. Crystal structures of murine angiogenin-2 and -3-probing 'structure--function' relationships amongst angiogenin homologues. FEBS J 2012; 280:302-18. [PMID: 23170778 PMCID: PMC3572582 DOI: 10.1111/febs.12071] [Citation(s) in RCA: 8] [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: 09/03/2012] [Revised: 11/14/2012] [Accepted: 11/15/2012] [Indexed: 11/26/2022]
Abstract
Angiogenin (Ang) is a potent inducer of neovascularization. Point mutations in human Ang have been linked to cancer progression and two neurodegenerative diseases: amyotrophic lateral sclerosis and Parkinson's disease. Intensive structural and functional analyses of Ang have been paramount in assigning functions to this novel homologue of bovine pancreatic RNase A. However, inhibitor-binding studies with crystalline Ang (for designing potential anti-cancer drugs) have been hampered as a result of the inaccessibility of the active site. Experiments with the murine homologues of Ang have not only overcome the obvious practical limitations encountered when studying the role of a human protein in healthy individuals, but also the crystal structures of murine angiogenins (mAng and mAng-4) have revealed themselves to have greater potential for the visualization of small-molecule inhibitor binding at the active site. In the present study, we report the crystal structures of two more murine Ang paralogues, mAng-2 and mAng-3, at 1.6 and 1.8 Å resolution, respectively. These constitute the first crystal structures of an Ang with a zinc ion bound at the active site and provide some insight into the possible mode of inhibition of the ribonucleolytic activity of the enzyme by these divalent cations. Both structures show that the residues forming the putative P1, B1 and B2 subsites occupy positions similar to their counterparts in human Ang and are likely to have conserved roles. However, a less obtrusive conformation of the C-terminal segment in mAng-3 and the presence of a sulfate ion in the B1 subsite of mAng-2 suggest that these proteins have the potential to be used for inhibitor-binding studies. We also discuss the biological relevance of the structural similarities and differences between the different Ang homologues.
Collapse
Affiliation(s)
- Shalini Iyer
- Department of Biology and Biochemistry, University of BathUK
| | | | - K Ravi Acharya
- Department of Biology and Biochemistry, University of BathUK
- Correspondence K. Ravi Acharya, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK Fax: +44 (0) 1225 386 779 Tel: +44 (0) 1225 386 238 E-mail:
| |
Collapse
|
14
|
Codoñer FM, Alfonso-Loeches S, Fares MA. Mutational dynamics of murine angiogenin duplicates. BMC Evol Biol 2010; 10:310. [PMID: 20950426 PMCID: PMC2964713 DOI: 10.1186/1471-2148-10-310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 10/15/2010] [Indexed: 12/03/2022] Open
Abstract
Background Angiogenin (Ang) is a protein involved in angiogenesis by inducing the formation of blood vessels. The biomedical importance of this protein has come from findings linking mutations in Ang to cancer progression and neurodegenerative diseases. These findings highlight the evolutionary constrain on Ang amino acid sequence. However, previous studies comparing human Angiogenin with homologs from other phylogenetically related organisms have led to the conclusion that Ang presents a striking variability. Whether this variability has an adaptive value per se remains elusive. Understanding why many functional Ang paralogs have been preserved in mouse and rat and identifying functional divergence mutations at these copies may explain the relationship between mutations and function. In spite of the importance of testing this hypothesis from the evolutionarily and biomedical perspectives, this remains yet unaccomplished. Here we test the main mutational dynamics driving the evolution and function of Ang paralogs in mammals. Results We analysed the phylogenetic asymmetries between the different Ang gene copies in mouse and rat in the context of vertebrate Ang phylogeny. This analysis shows strong evidence in support of accelerated evolution in some Ang murine copies (mAng). This acceleration is not due to non-functionalisation because constraints on amino acid replacements remain strong. We identify many of the amino acid sites involved in signal localization and nucleotide binding by Ang to have evolved under diversifying selection. Compensatory effects of many of the mutations at these paralogs and their key structural location in or nearby important functional regions support a possible functional shift (functional divergence) in many Ang copies. Similarities between 3D-structural models for mAng copies suggest that their divergence is mainly functional. Conclusions We identify the main evolutionary dynamics shaping the variability of Angiogenin in vertebrates and highlight the plasticity of this protein after gene duplication. Our results suggest functional divergence among mAng paralogs. This puts forward mAng as a good system candidate for testing functional plasticity of such an important protein while stresses caution when using mouse as a model to infer the consequences of mutations in the single Ang copy of humans.
Collapse
Affiliation(s)
- Francisco M Codoñer
- Evolutionary Genetics and Bioinformatics Laboratory, Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland
| | | | | |
Collapse
|
15
|
Kazakou K, Holloway DE, Prior SH, Subramanian V, Acharya KR. Ribonuclease A homologues of the zebrafish: polymorphism, crystal structures of two representatives and their evolutionary implications. J Mol Biol 2008; 380:206-22. [PMID: 18508078 PMCID: PMC2582337 DOI: 10.1016/j.jmb.2008.04.070] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Revised: 04/24/2008] [Accepted: 04/27/2008] [Indexed: 12/21/2022]
Abstract
The widespread and functionally varied members of the ribonuclease A (RNase A) superfamily provide an excellent opportunity to study evolutionary forces at work on a conserved protein scaffold. Representatives from the zebrafish are of particular interest as the evolutionary distance from non-ichthyic homologues is large. We conducted an exhaustive survey of available zebrafish DNA sequences and found significant polymorphism among its four known homologues. In an extension of previous nomenclature, the variants have been named RNases ZF-1a–c,-2a–d,-3a–e and-4. We present the first X-ray crystal structures of zebrafish ribonucleases, RNases ZF-1a and-3e at 1.35-and 1.85 Å resolution, respectively. Structure-based clustering with ten other ribonuclease structures indicates greatest similarity to mammalian angiogenins and amphibian ribonucleases, and supports the view that all present-day ribonucleases evolved from a progenitor with three disulphide bonds. In their details, the two structures are intriguing melting-pots of features present in ribonucleases from other vertebrate classes. Whereas in RNase ZF-1a the active site is obstructed by the C-terminal segment (as observed in angiogenin), in RNase ZF-3e the same region is open (as observed in more catalytically efficient homologues). The progenitor of present-day ribonucleases is more likely to have had an obstructive C terminus, and the relatively high similarity (late divergence) of RNases ZF-1 and-3 infers that the active site unblocking event has happened independently in different vertebrate lineages.
Collapse
|
16
|
Subramanian V, Feng Y. A new role for angiogenin in neurite growth and pathfinding: implications for amyotrophic lateral sclerosis. Hum Mol Genet 2007; 16:1445-53. [PMID: 17468498 DOI: 10.1093/hmg/ddm095] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mutations in human angiogenin (hANG), an angiogenic member of the RNase A superfamily, have been recently reported in patients with amyotrophic lateral sclerosis (ALS), a progressive late-onset neurodegenerative disorder. However, very little is known about the expression and subcellular distribution of ANG in the nervous system or its role in differentiation. Here we report that mouse angiogenin-1 (mAng-1) is strongly expressed in the developing nervous system during mouse embryogenesis and neuroectodermal differentiation of pluripotent P19 embryonal carcinoma cells. mAng1 is strongly expressed in motor neurons (MNs) in the spinal cord and dorsal root ganglia as well as in post-mitotic MNs derived from P19 cells. We also show for the first time that ANG expression is in the growth cones and neurites. NCI 65828, an inhibitor of the ribonucleolytic activity of hANG, affected pathfinding by P19-derived neurons but not neuronal differentiation. Our findings clearly show that ANG plays an important role in neurite pathfinding and this has implications for ALS.
Collapse
Affiliation(s)
- Vasanta Subramanian
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.
| | | |
Collapse
|
17
|
Holloway DE, Chavali GB, Hares MC, Subramanian V, Acharya KR. Structure of murine angiogenin: features of the substrate- and cell-binding regions and prospects for inhibitor-binding studies. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2005; 61:1568-78. [PMID: 16301790 PMCID: PMC1780170 DOI: 10.1107/s0907444905029616] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 09/18/2005] [Indexed: 11/10/2022]
Abstract
Angiogenin is an unusual member of the pancreatic ribonuclease superfamily that induces blood-vessel formation and is a promising anticancer target. The three-dimensional structure of murine angiogenin (mAng) has been determined by X-ray crystallography. Two structures are presented: one is a complex with sulfate ions (1.5 Angstroms resolution) and the other a complex with phosphate ions (1.6 Angstroms resolution). Residues forming the putative B(1), P(1) and B(2) subsites occupy positions similar to their hAng counterparts and are likely to play similar roles. The anions occupy the P(1) subsite, sulfate binding conventionally and phosphate adopting two orientations, one of which is novel. The B(1) subsite is obstructed by Glu116 and Phe119, with the latter assuming a less invasive position than its hAng counterpart. Hydrophobic interactions between the C-terminal segment and the main body of the protein are more extensive than in hAng and may underly the lower enzymatic activity of the murine protein. Elsewhere, the structure of the H3-B2 loop supports the view that hAng Asn61 interacts directly with cell-surface molecules and does not merely stabilize adjacent regions of the hAng structure. mAng crystals appear to offer small-molecule inhibitors a clear route to the active site and may even withstand a reorientation of the C-terminal segment that provides access to the cryptic B(1) subsite. These features represent considerable advantages over crystalline hAng and bAng.
Collapse
|
18
|
Merlino A, Vitagliano L, Ceruso MA, Mazzarella L. Subtle functional collective motions in pancreatic-like ribonucleases: from ribonuclease A to angiogenin. Proteins 2003; 53:101-10. [PMID: 12945053 DOI: 10.1002/prot.10466] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The analysis of the dynamic behavior of enzymes is fundamental to structural biology. A direct relationship between protein flexibility and biological function has been shown for bovine pancreatic ribonuclease (RNase A) (Rasmussen et al., Nature 1992;357:423-424). More recently, crystallographic studies have shown that functional motions in RNase A involve the enzyme beta-sheet regions that move concertedly on substrate binding and release (Vitagliano et al., Proteins 2002;46:97-104). These motions have been shown to correspond to intrinsic dynamic properties of the native enzyme by molecular dynamics (MD) simulations. To unveil the occurrence of these collective motions in other members of pancreatic-like superfamily, we carried out MD simulations on human angiogenin (Ang). Essential dynamics (ED) analyses performed on the trajectories reveal that Ang exhibits collective motions similar to RNase A, despite the limited sequence identity (33%) of the two proteins. Furthermore, we show that these collective motions are also present in ensembles of experimentally determined structures of both Ang and RNase A. Finally, these subtle concerted beta-sheet motions were also observed for other two members of the pancreatic-like superfamily by comparing the ligand-bound and ligand-free structures of these enzymes. Taken together, these findings suggest that pancreatic-like ribonucleases share an evolutionary conserved dynamic behavior consisting of subtle beta-sheet motions, which are essential for substrate binding and release.
Collapse
Affiliation(s)
- Antonello Merlino
- Dipartimento di Chimica, Università degli Studi di Napoli Federico II, Napoli, Italy
| | | | | | | |
Collapse
|
19
|
Chavali GB, Papageorgiou AC, Olson KA, Fett JW, Hu GF, Shapiro R, Acharya KR. The crystal structure of human angiogenin in complex with an antitumor neutralizing antibody. Structure 2003; 11:875-85. [PMID: 12842050 DOI: 10.1016/s0969-2126(03)00131-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The murine monoclonal antibody 26-2F neutralizes the angiogenic and ribonucleolytic activities of human angiogenin (ANG) and is highly effective in preventing the establishment and metastatic dissemination of human tumors in athymic mice. Here we report a 2.0 A resolution crystal structure for the complex of ANG with the Fab fragment of 26-2F that reveals the detailed interactions between ANG and the complementarity-determining regions (CDRs) of the antibody. Surprisingly, Fab binding induces a dramatic conformational change in the cell binding region of ANG at the opposite end of the molecule from the combining site; crosslinking experiments indicate that this rearrangement also occurs in solution. The ANG-Fab complex structure should be invaluable for designing maximally humanized versions of 26-2F for potential clinical use.
Collapse
Affiliation(s)
- Gayatri B Chavali
- Department of Biology and Biochemistry, University of Bath, Claverton Down, BA2 7AY, Bath, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
20
|
Metzler DE, Metzler CM, Sauke DJ. Growth and Development. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50035-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|