1
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Dewangan D, Joshi A, Padhi AK. Long-timescale atomistic simulations uncover loss-of-function mechanisms of uncharacterized Angiogenin mutants associated with ALS. Arch Biochem Biophys 2024; 756:110000. [PMID: 38621442 DOI: 10.1016/j.abb.2024.110000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/19/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disease characterized by progressive degeneration of motor neurons, resulting in respiratory failure and mortality within 3-5 years. Mutations in the Angiogenin (ANG) cause loss of ribonucleolytic and nuclear translocation activities, contributing to ALS pathogenesis. This study focused on investigating two uncharacterized ANG mutations, T11S and R122H, newly identified in the Project Mine consortium. Using extensive computational analysis, including structural modeling and microsecond-timescale molecular dynamics (MD) simulations, we observed conformational changes in the catalytic residue His114 of ANG induced by T11S and R122H mutations. These alterations impaired ribonucleolytic activity, as inferred through molecular docking and binding free energy calculations. Gibbs free energy landscape and residue-residue interaction network analysis further supported our findings, revealing the energetic states and allosteric pathway from the mutated site to His114. Additionally, we assessed the binding of NCI-65828, an inhibitor of ribonucleolytic activity of ANG, and found reduced effectiveness in binding to T11S and R122H mutants when His114 assumed a non-native conformation. This highlights the crucial role of His114 and its association with ALS. Elucidating the relationship between physical structure and functional dynamics of frequently mutated ANG mutants is essential for understanding ALS pathogenesis and developing more effective therapeutic interventions.
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Affiliation(s)
- Deeksha Dewangan
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Aryaman Joshi
- Department of Chemical Engineering & Technology, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Aditya K Padhi
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India.
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2
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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.
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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
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3
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Bernard DN, Narayanan C, Hempel T, Bafna K, Bhojane PP, Létourneau M, Howell EE, Agarwal PK, Doucet N. Conformational exchange divergence along the evolutionary pathway of eosinophil-associated ribonucleases. Structure 2023; 31:329-342.e4. [PMID: 36649708 PMCID: PMC9992247 DOI: 10.1016/j.str.2022.12.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 11/24/2022] [Accepted: 12/20/2022] [Indexed: 01/18/2023]
Abstract
The evolutionary role of conformational exchange in the emergence and preservation of function within structural homologs remains elusive. While protein engineering has revealed the importance of flexibility in function, productive modulation of atomic-scale dynamics has only been achieved on a finite number of distinct folds. Allosteric control of unique members within dynamically diverse structural families requires a better appreciation of exchange phenomena. Here, we examined the functional and structural role of conformational exchange within eosinophil-associated ribonucleases. Biological and catalytic activity of various EARs was performed in parallel to mapping their conformational behavior on multiple timescales using NMR and computational analyses. Despite functional conservation and conformational seclusion to a specific domain, we show that EARs can display similar or distinct motional profiles, implying divergence rather than conservation of flexibility. Comparing progressively more distant enzymes should unravel how this subfamily has evolved new functions and/or altered their behavior at the molecular level.
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Affiliation(s)
- David N Bernard
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Chitra Narayanan
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada; Department of Chemistry, New Jersey City University, Jersey City, NJ 07305, USA
| | - Tim Hempel
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 12, 14195 Berlin, Germany; Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Khushboo Bafna
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Purva Prashant Bhojane
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Myriam Létourneau
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Elizabeth E Howell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Pratul K Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval, 1045 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.
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4
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Panda A, Halder K, Debnath D, De S, Dasgupta S. Thermodynamics of the Association of Aminoglycoside Antibiotics with Human Angiogenin. Protein Pept Lett 2023; 30:92-101. [PMID: 36281865 DOI: 10.2174/0929866530666221021111823] [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: 02/16/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/28/2022]
Abstract
BACKGROUND The body needs to maintain a firm balance between the inducers and inhibitors of angiogenesis, the process of proliferation of blood vessels from pre-existing ones. Human angiogenin (hAng), being a potent inducer of angiogenesis, is a cause of tumor cell proliferation, therefore its inhibition becomes a vital area of research. Aminoglycosides are linked ring systems consisting of amino sugars and an aminocyclitol ring and are in use in clinical practices for a long time. These compounds have found clinical uses as antibacterial agents that inhibit bacterial protein synthesis. OBJECTIVE Gentamycin C1, Kanamycin A, Neomycin B, Paromomycin I, and Streptomycin A are commonly used aminoglycoside antibiotics that have been used for the present study. Among these, Neomycin has reported inhibitory activity against angiogenin-induced angiogenesis on the chicken chorioallantoic membrane. This study focuses on the thermodynamic parameters involved in the interactions of these antibiotics with hAng. METHODS Agarose gel-based assay, Fluorescence quenching studies and Docking studies. RESULTS Anti-ribonucleolytic effect of the antibiotics was observed qualitatively using an agarose gelbased assay, which shows that Neomycin exhibits the most efficient inhibition of hAng. Fluorescence quenching studies at different temperatures, using Stern-Volmer and van't Hoff equations provide information about the thermodynamics of binding, which furthermore highlights the higher binding constant of Neomycin. Docking studies showed that the antibiotics preferably interact with the nuclear translocation site, except Streptomycin, which shows affinity towards the ribonucleolytic site of the protein with very less affinity value. CONCLUSION The study has shown the highly spontaneous formation of Neomycin-hAng complex, giving an exothermic reaction with increase in the degree of freedom of the protein-ligand complex.
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Affiliation(s)
- Atashi Panda
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Krishna Halder
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Debkumar Debnath
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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5
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Ahmad F, Lakshmi PTV, Arunachalam A. An in silico comparative study of curcumin and 2-deoxyuridine nucleoside derivatives: Reveals the role of angiogenin in ER stress-induced apoptosis signaling. Chem Biol Drug Des 2022; 101:1048-1081. [PMID: 36412086 DOI: 10.1111/cbdd.14184] [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: 10/31/2021] [Revised: 09/06/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
Angiogenin (ANG) protein plays a crucial role in angiogenesis, neovascularization, and cancer metastasis in NSCLC (non-small cell lung cancer) via non-coding tiRNA. It protects the cell under ER (endoplasmic reticulum) stress-induced apoptosis through the translational reprogramming process. Although B82 (Curcumin derivatives) induces ER stress-induced apoptosis, its mechanism of action was not studied. Therefore, it was hypothesized that the ribonucleolytic activity of ANG may be regulated by B82, resulting in modulated ER stress signaling for apoptosis. Hence, we designed and proposed a synthesis scheme for RNA-based anti-angiogenic derivatives of 2-deoxyuridine nucleoside forming peptide bond with amino acids like serine (Ser-3) and para-hydroxy-phenyl glycine (Normtyr-1) and compared B82 with them to know the binding affinity with ANG, anti-angiogenic potential, and its probable mechanism of anti-RNase activity through MD simulation study. Therefore, using Gromos96 43a1 and 43a2 force fields, MD simulation was performed to investigate binding affinity, ligand-induced molecular surface area change, conformational change, and dynamics of catalytic site residues to predict ligand binding to ANG in this study. The obtained binding free energy (∆Gbind ) result showed the total average ∆Gbind as -113.480 ± 1.682 (Normtyr-1) > -53.038 ± 33.069 (B82) > -27.909 ± 16.438 (Ser-3) kJ/mole specify role of B82 in regulating ER stress signaling induced apoptosis through ANG ribonucleolytic activity inhibition, suitability of 43a2 force fields and methodology in ligand screening. It shows the crucial role of Leu115 and His13 residue involvement in total ∆Gbind contribution. Hence, based on the MD result, novel conformation of catalytic residues, and ∆Gbind , a promising combination candidate could be proposed for metastatic NSCLC therapy.
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Affiliation(s)
- Faizan Ahmad
- Department of Bioinformatics, Pondicherry University, Pondicherry, India
| | | | - Annamalai Arunachalam
- PG and Research Department of Botany Arignar Anna Government Arts College Villupuram Tamil Nadu India
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6
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Sultana MF, Abo H, Kawashima H. Human and mouse angiogenins: Emerging insights and potential opportunities. Front Microbiol 2022; 13:1022945. [PMID: 36466652 PMCID: PMC9714274 DOI: 10.3389/fmicb.2022.1022945] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/01/2022] [Indexed: 12/27/2023] Open
Abstract
Angiogenin, a well-known angiogenic factor, is crucial to the angiogenesis in gastrointestinal tumors. Human angiogenin has only one gene, whereas the murine angiogenin family has extended to incorporate six genes. Evolutionary studies have suggested functional variations among murine angiogenin paralogs, even though the three-dimensional structures of angiogenin proteins are remarkably similar. In addition to angiogenesis, the ubiquitous pattern of angiogenin expression suggests a variety of functions, such as tumorigenesis, neuroprotective, antimicrobial activity, and innate immunity. Here, we comprehensively reviewed studies on the structures and functions of human and mouse angiogenins. Understanding the structure and function of angiogenins from a broader perspective could facilitate future research related to development of novel therapeutics on its biological processes, especially in gastrointestinal cancers.
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Affiliation(s)
- Mst. Farzana Sultana
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
- Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Hirohito Abo
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Hiroto Kawashima
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
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7
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Sievers K, Ficner R. Structure of angiogenin dimer bound to double-stranded RNA. Acta Crystallogr F Struct Biol Commun 2022; 78:330-337. [PMID: 36048083 PMCID: PMC9435672 DOI: 10.1107/s2053230x22008317] [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: 07/28/2022] [Accepted: 08/20/2022] [Indexed: 11/23/2022] Open
Abstract
Angiogenin is a pathologically relevant but little understood ribonuclease, the interactions of which with RNA are structurally unknown. Here, the first crystal structure of human angiogenin bound to RNA is presented. Angiogenin is an unusual member of the RNase A family and is of great interest in multiple pathological contexts. Although it has been assigned various regulatory roles, its core catalytic function is that of an RNA endonuclease. However, its catalytic efficiency is comparatively low and this has been linked to a unique C-terminal helix which partially blocks its RNA-binding site. Assuming that binding to its RNA substrate could trigger a conformational rearrangement, much speculation has arisen on the topic of the interaction of angiogenin with RNA. To date, no structural data on angiogenin–RNA interactions have been available. Here, the structure of angiogenin bound to a double-stranded RNA duplex is reported. The RNA does not reach the active site of angiogenin and no structural arrangement of the C-terminal domain is observed. However, angiogenin forms a previously unobserved crystallographic dimer that makes several backbone interactions with the major and minor grooves of the RNA double helix.
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8
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Culurciello R, Bosso A, Troisi R, Barrella V, Di Nardo I, Borriello M, Gaglione R, Pistorio V, Aceto S, Cafaro V, Notomista E, Sica F, Arciello A, Pizzo E. Protective Effects of Recombinant Human Angiogenin in Keratinocytes: New Insights on Oxidative Stress Response Mediated by RNases. Int J Mol Sci 2022; 23:ijms23158781. [PMID: 35955913 PMCID: PMC9369303 DOI: 10.3390/ijms23158781] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/27/2022] [Accepted: 08/05/2022] [Indexed: 11/23/2022] Open
Abstract
Human angiogenin (ANG) is a 14-kDa ribonuclease involved in different pathophysiological processes including tumorigenesis, neuroprotection, inflammation, innate immunity, reproduction, the regeneration of damaged tissues and stress cell response, depending on its intracellular localization. Under physiological conditions, ANG moves to the cell nucleus where it enhances rRNA transcription; conversely, recent reports indicate that under stress conditions, ANG accumulates in the cytoplasmic compartment and modulates the production of tiRNAs, a novel class of small RNAs that contribute to the translational inhibition and recruitment of stress granules (SGs). To date, there is still limited and controversial experimental evidence relating to a hypothetical role of ANG in the epidermis, the outermost layer of human skin, which is continually exposed to external stressors. The present study collects compelling evidence that endogenous ANG is able to modify its subcellular localization on HaCaT cells, depending on different cellular stresses. Furthermore, the use of recombinant ANG allowed to determine as this special enzyme is effectively able to counter at various levels the alterations of cellular homeostasis in HaCaT cells, actually opening a new vision on the possible functions that this special enzyme can support also in the stress response of human skin.
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Affiliation(s)
- Rosanna Culurciello
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
- Centro Servizi Metrologici e Tecnologici Avanzati (CeSMA), University of Naples Federico II, 80126 Naples, Italy
| | - Andrea Bosso
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Valentina Barrella
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Ilaria Di Nardo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Margherita Borriello
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy
| | - Rosa Gaglione
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Valeria Pistorio
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Serena Aceto
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Valeria Cafaro
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Eugenio Notomista
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Elio Pizzo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
- Centro Servizi Metrologici e Tecnologici Avanzati (CeSMA), University of Naples Federico II, 80126 Naples, Italy
- Correspondence: ; Tel.: +39-081679151
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9
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β-cyclodextrin encapsulation of curcumin elicits an altered mode of angiogenin inhibition: In vitro and in vivo studies. Int J Biol Macromol 2022; 208:654-666. [PMID: 35341883 DOI: 10.1016/j.ijbiomac.2022.03.127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/13/2022] [Accepted: 03/20/2022] [Indexed: 12/29/2022]
Abstract
The interaction of curcumin (Cur) with human angiogenin (hAng), a potent blood vessel inducer responsible for angiogenesis is found to change following encapsulation within the β-cyclodextrin (βCD) cavity. The enhanced bioavailability and increase in the binding stoichiometry of hAng:Cur-βCD (1:2) leads to increased affinity, hence an increase in the association constant. The altered mode of hAng inhibition of Cur from a non-competitive (KI = 23.7 ± 2.2 μM) to a mixed type (KI = 19.8 ± 1.4 μM), after encapsulation provides an insight into interaction patterns. Isothermal titration calorimetry (ITC) experiments indicate the formation of multiple favorable non-covalent interactions (also confirmed by docking studies), which implies negative enthalpy changes (-ΔHo) and restriction in the dynamic mobility of the free protein molecule resulting in a very less positive entropy change (TΔSo). This leads to a medium magnitude for the spontaneous free energy change associated with the interaction/binding process. The spontaneity of binding indicates a more favorable value for the Cur-βCD (ΔGo = -7.75 kcal/mol) compared to Cur (ΔGo = -7.49 kcal/mol). In vivo studies also demonstrate the anti-angiogenic effect of Cur/Cur-βCD confirmed by the significant decrease in blood vessel density and branching index.
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10
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Padhi AK, Shukla R, Narain P, Gomes J. A distant angiogenin variant causes amyotrophic lateral sclerosis through loss-of-function mechanisms: Insights from long-timescale atomistic simulations and conformational dynamics. Comput Biol Med 2021; 135:104602. [PMID: 34214939 DOI: 10.1016/j.compbiomed.2021.104602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/17/2021] [Accepted: 06/20/2021] [Indexed: 01/01/2023]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a progressive and incurable neurodegenerative disorder characterized by the degeneration of motor neurons leading to severe muscle atrophy, respiratory failure and death within 3-5 years of disease onset. Missense mutations in Angiogenin (ANG) cause ALS through loss of either ribonucleolytic activity or nuclear translocation activity or both of these functions. Although loss-of-function mechanisms of several rare and ALS-causing ANG variants have been studied before, the structure-function relationship and subsequent functional loss mechanisms of certain novel and uncharacterized rare variants have not been deciphered hitherto. In this study, the structural and dynamic properties of the distantly-located I71V variant, on the functional sites of ANG have been investigated to understand its role in ALS etiology and progression. The I71V variant has a minor allele frequency of <0.06% and thus is classified as a rare variant. Our extensive in silico investigation comprising 1-μs molecular dynamics (MD) simulations, conformational dynamics and related integrated analyses reveal that the I71V variant induces a characteristic conformational switching of catalytic His114 residue resulting in loss of ribonucleolytic activity. Molecular docking and a residue-residue interaction network propagated by an allosteric pathway further support these findings. Moreover, while no conformational alteration of nuclear localization signal governing the nuclear translocation activity was observed, an escalation in mutant plasticity was detected in the structural and essential dynamics simulations. Overall, our study emphasizes that the structure-function relationship of frequently mutating novel ANG variants needs to be established and prioritized in order to advance the pathophysiology and therapeutics of ALS.
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Affiliation(s)
- Aditya K Padhi
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
| | - Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, H.P., 173234, India
| | - Priyam Narain
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - James Gomes
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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11
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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.
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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
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12
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Panda A, Karhadkar S, Acharya B, Banerjee A, De S, Dasgupta S. Enhancement of angiogenin inhibition by polyphenol-capped gold nanoparticles. Biopolymers 2021; 112:e23429. [PMID: 33851721 DOI: 10.1002/bip.23429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/27/2021] [Accepted: 03/22/2021] [Indexed: 11/10/2022]
Abstract
Angiogenin (Ang), is a ribonucleolytic protein that is associated with angiogenesis, the formation of blood vessels. The involvement of Ang in vascularisation makes it a potential target for the identification of compounds that have the potential to inhibit the process. The compounds may be assessed for their ability to inhibit the ribonucleolytic activity of the protein and subsequently blood vessel formation, a crucial requirement for tumor formation. We report an inhibition of the ribonucleolytic activity of Ang with the gallate containing green tea polyphenols, ECG and EGCG that exhibits an increased efficacy upon forming polyphenol-capped gold nanoparticles (ECG-AuNPs and EGCG-AuNPs). The extent of inhibition was confirmed using an agarose gel-based assay followed by fluorescence titration studies that indicated a hundred fold stronger binding of polyphenol-capped gold nanoparticles (GTP-AuNPs) compared to the bare polyphenols. Interestingly, we found a change in the mode of inhibition from a noncompetitive type to a competitive mode of inhibition in case of the GTP-AuNPs, which is in agreement with the 'n' values obtained from the fluorescence quenching studies. The effect on angiogenesis has also been assessed by the chorioallantoic membrane (CAM) assay. We find an increase in the inhibition potency of GTP-AuNPs that could find applications in the development of anti-angiogenic compounds.
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Affiliation(s)
- Atashi Panda
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Siddhant Karhadkar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Bidisha Acharya
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Anwesha Banerjee
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
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13
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Pillon MC, Frazier MN, Dillard LB, Williams JG, Kocaman S, Krahn JM, Perera L, Hayne CK, Gordon J, Stewart ZD, Sobhany M, Deterding LJ, Hsu AL, Dandey VP, Borgnia MJ, Stanley RE. Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics. Nat Commun 2021; 12:636. [PMID: 33504779 PMCID: PMC7840905 DOI: 10.1038/s41467-020-20608-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Nsp15, a uridine specific endoribonuclease conserved across coronaviruses, processes viral RNA to evade detection by host defense systems. Crystal structures of Nsp15 from different coronaviruses have shown a common hexameric assembly, yet how the enzyme recognizes and processes RNA remains poorly understood. Here we report a series of cryo-EM reconstructions of SARS-CoV-2 Nsp15, in both apo and UTP-bound states. The cryo-EM reconstructions, combined with biochemistry, mass spectrometry, and molecular dynamics, expose molecular details of how critical active site residues recognize uridine and facilitate catalysis of the phosphodiester bond. Mass spectrometry revealed the accumulation of cyclic phosphate cleavage products, while analysis of the apo and UTP-bound datasets revealed conformational dynamics not observed by crystal structures that are likely important to facilitate substrate recognition and regulate nuclease activity. Collectively, these findings advance understanding of how Nsp15 processes viral RNA and provide a structural framework for the development of new therapeutics.
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Affiliation(s)
- Monica C Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA.
| | - Meredith N Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Lucas B Dillard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Jason G Williams
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Seda Kocaman
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Cassandra K Hayne
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Jacob Gordon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
- Cambridge Institute for Medical Research, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Zachary D Stewart
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Mack Sobhany
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Leesa J Deterding
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Venkata P Dandey
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
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14
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Lasch M, Kumaraswami K, Nasiscionyte S, Kircher S, van den Heuvel D, Meister S, Ishikawa-Ankerhold H, Deindl E. RNase A Treatment Interferes With Leukocyte Recruitment, Neutrophil Extracellular Trap Formation, and Angiogenesis in Ischemic Muscle Tissue. Front Physiol 2020; 11:576736. [PMID: 33240100 PMCID: PMC7677187 DOI: 10.3389/fphys.2020.576736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/16/2020] [Indexed: 01/13/2023] Open
Abstract
Background: RNase A (the bovine equivalent to human RNase 1) and RNase 5 (angiogenin) are two closely related ribonucleases. RNase 5 is described as a powerful angiogenic factor. Whether RNase A shares the same angiogenic characteristic, or interferes with vessel growth as demonstrated for arteriogenesis, has never been investigated and is the topic of this present study. Methods and Results: To investigate whether RNase A shows a pro‐ or anti-angiogenic effect, we employed a murine hindlimb model, in which femoral artery ligation (FAL) results in arteriogenesis in the upper leg, and, due to provoked ischemia, in angiogenesis in the lower leg. C57BL/6J male mice underwent unilateral FAL, whereas the contralateral leg was sham operated. Two and seven days after the surgery and intravenous injection of RNase A (50 μg/kg dissolved in saline) or saline (control), the gastrocnemius muscles of mice were isolated from the lower legs for (immuno-) histological analyses. Hematoxylin and Eosin staining evidenced that RNase A treatment resulted in a higher degree of ischemic tissue damage. This was, however, associated with reduced angiogenesis, as evidenced by a reduced capillary/muscle fiber ratio. Moreover, RNase A treatment was associated with a significant reduction in leukocyte infiltration as shown by CD45+ (pan-leukocyte marker), Ly6G+ or MPO+ (neutrophils), MPO+/CitH3+ [neutrophil extracellular traps (NETs)], and CD68+ (macrophages) staining. CD68/MRC1 double staining revealed that RNase A treated mice showed a reduced percentage of M1-like polarized (CD68+/MRC1−) macrophages whereas the percentage of M2-like polarized (CD68+/MRC1+) macrophages was increased. Conclusion: In contrast to RNase 5, RNase A interferes with angiogenesis, which is linked to reduced leukocyte infiltration and NET formation.
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Affiliation(s)
- Manuel Lasch
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.,Biomedical Center, Institute of Cardiovascular Physiology and Pathophysiology, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Konda Kumaraswami
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.,Biomedical Center, Institute of Cardiovascular Physiology and Pathophysiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Simona Nasiscionyte
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Susanna Kircher
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.,Biomedical Center, Institute of Cardiovascular Physiology and Pathophysiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dominic van den Heuvel
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sarah Meister
- Department of Obstetrics and Gynaecology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hellen Ishikawa-Ankerhold
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Internal Medicine I, Faculty of Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Elisabeth Deindl
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.,Biomedical Center, Institute of Cardiovascular Physiology and Pathophysiology, Ludwig-Maximilians-Universität München, Munich, Germany
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15
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Pillon MC, Frazier MN, Dillard LB, Williams JG, Kocaman S, Krahn JM, Perera L, Hayne CK, Gordon J, Stewart ZD, Sobhany M, Deterding LJ, Hsu AL, Dandey VP, Borgnia MJ, Stanley RE. Cryo-EM Structures of the SARS-CoV-2 Endoribonuclease Nsp15. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.11.244863. [PMID: 32803198 PMCID: PMC7427136 DOI: 10.1101/2020.08.11.244863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
New therapeutics are urgently needed to inhibit SARS-CoV-2, the virus responsible for the on-going Covid-19 pandemic. Nsp15, a uridine-specific endoribonuclease found in all coronaviruses, processes viral RNA to evade detection by RNA-activated host defense systems, making it a promising drug target. Previous work with SARS-CoV-1 established that Nsp15 is active as a hexamer, yet how Nsp15 recognizes and processes viral RNA remains unknown. Here we report a series of cryo-EM reconstructions of SARS-CoV-2 Nsp15. The UTP-bound cryo-EM reconstruction at 3.36 Å resolution provides molecular details into how critical residues within the Nsp15 active site recognize uridine and facilitate catalysis of the phosphodiester bond, whereas the apo-states reveal active site conformational heterogeneity. We further demonstrate the specificity and mechanism of nuclease activity by analyzing Nsp15 products using mass spectrometry. Collectively, these findings advance understanding of how Nsp15 processes viral RNA and provide a structural framework for the development of new therapeutics.
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Affiliation(s)
- Monica C. Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Meredith N. Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Lucas B. Dillard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jason G. Williams
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Seda Kocaman
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Juno M. Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Cassandra K. Hayne
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jacob Gordon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Zachary D. Stewart
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mack Sobhany
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Leesa J. Deterding
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Allen L. Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Venkata P. Dandey
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mario J. Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E. Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
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16
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D'Abadia PL, BailÃo EFLC, Lino JÚnior RS, Oliveira MG, Silva VB, Oliveira LAR, ConceiÇÃo EC, Melo-Reis PR, Borges LL, GonÇalves PJ, Almeida LM. Hancornia speciosa serum fraction latex stimulates the angiogenesis and extracellular matrix remodeling processes. AN ACAD BRAS CIENC 2020; 92:e20190107. [PMID: 32556049 DOI: 10.1590/0001-3765202020190107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/03/2019] [Indexed: 11/21/2022] Open
Abstract
The Hancornia speciosa latex reveals angiogenic, osteogenic, and anti-inflammatory properties, which present its potential for developing of wound healing drugs; however, the latex compounds responsible for angiogenesis remain unknown. One strategy to screen these active compounds is evaluation of latex fractions. This study aimed to obtain different fractions of latex and evaluate its angiogenic activity separately using the chick chorioallantoic membrane (CAM) assay. The serum (SE) fraction was responsible for angiogenesis, which was subject to biochemical characterization and computational simulations in order to understand the contribution of H. speciosa latex in wound healing process. Our results revealed weak antioxidant potential and absence of antimicrobial activity in the SE fraction. Phytochemical analysis identified chlorogenic acids (CGA) as the main compound of SE fraction. CGA bioactivity predictions identify different molecules associated with extracellular matrix (ECM) remodeling, such as metalloproteinases, which also are overexpressed in our CAM assay experiment. Docking simulations revealed the interactions between CGA and matrix metalloproteinase 2. In conclusion, SE latex fraction stimulates angiogenesis and may influence ECM remodeling. These properties may contribute to the wound healing process, and also confirm the widespread use of this plant.
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Affiliation(s)
- PatrÍcia L D'Abadia
- Universidade Estadual de Goiás, Rodovia BR 153, nº 3105, Fazenda Barreiro do Meio, Campus Henrique Santillo, 75132-400 Anápolis, GO, Brazil
| | - Elisa FlÁvia Luiz C BailÃo
- Universidade Estadual de Goiás, Rodovia BR 153, nº 3105, Fazenda Barreiro do Meio, Campus Henrique Santillo, 75132-400 Anápolis, GO, Brazil
| | - Ruy S Lino JÚnior
- Universidade Federal de Goiás, Instituto de Patologia Tropical e Saúde Pública, Rua 235, s/n, Setor Leste Universitário, 74605-050 Goiânia, GO, Brazil
| | - Matheus Gabriel Oliveira
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas, Farmacêuticas e Biomédicas, Av. Universitária, n 1069, Setor Leste Universitário, 74605-010 Goiânia, GO, Brazil
| | - Vinicius B Silva
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas, Farmacêuticas e Biomédicas, Av. Universitária, n 1069, Setor Leste Universitário, 74605-010 Goiânia, GO, Brazil
| | - Leandra A R Oliveira
- Universidade Federal de Goiás, Laboratório de Pesquisa, Desenvolvimento & Inovação de Bioprodutos, Faculdade de Farmácia, Rua 240, s/n, Setor Leste Universitário, 74605-170 Goiânia, GO, Brazil
| | - Edemilson C ConceiÇÃo
- Universidade Federal de Goiás, Laboratório de Pesquisa, Desenvolvimento & Inovação de Bioprodutos, Faculdade de Farmácia, Rua 240, s/n, Setor Leste Universitário, 74605-170 Goiânia, GO, Brazil
| | - Paulo Roberto Melo-Reis
- Pontifícia Universidade Católica de Goiás, Laboratório de Estudos Experimentais e Biotecnológicos, Rua 232, nº 128, Setor Leste Universitário, 74605-120 Goiânia, GO, Brazil
| | - Leonardo Luiz Borges
- Universidade Estadual de Goiás, Rodovia BR 153, nº 3105, Fazenda Barreiro do Meio, Campus Henrique Santillo, 75132-400 Anápolis, GO, Brazil
| | - Pablo JosÉ GonÇalves
- Universidade Federal de Goiás, Instituto de Física, Av. Esperança, s/n, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Luciane M Almeida
- Universidade Estadual de Goiás, Rodovia BR 153, nº 3105, Fazenda Barreiro do Meio, Campus Henrique Santillo, 75132-400 Anápolis, GO, Brazil
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17
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Padhi AK, Narain P, Gomes J. Rare Angiogenin and Ribonuclease 4 variants associated with amyotrophic lateral sclerosis exhibit loss-of-function: a comprehensive in silico study. Metab Brain Dis 2019; 34:1661-1677. [PMID: 31368019 DOI: 10.1007/s11011-019-00473-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/18/2019] [Indexed: 12/12/2022]
Abstract
Amyotrophic Lateral Sclerosis (ALS), a debilitating neurodegenerative disorder is related to mutations in a number of genes, and certain genes of the Ribonuclease (RNASE) superfamily trigger ALS more frequently. Even though missense mutations in Angiogenin (ANG) and Ribonuclease 4 (RNASE4) have been previously shown to cause ALS through loss-of-function mechanisms, understanding the role of rare variants with a plausible explanation of their functional loss mechanisms is an important mission. The study aims to understand if any of the rare ANG and RNASE4 variants catalogued in Project MinE consortium caused ALS due to loss of ribonucleolytic or nuclear translocation or both these activities. Several in silico analyses in combination with extensive molecular dynamics (MD) simulations were performed on wild-type ANG and RNASE4, along with six rare variants (T11S-ANG, R122H-ANG, D2E-RNASE4, N26K-RNASE4, T79A-RNASE4 and G119S-RNASE4) to study the structural and dynamic changes in the catalytic triad and nuclear localization signal residues responsible for ribonucleolytic and nuclear translocation activities respectively. Our comprehensive analyses comprising 1.2 μs simulations with a focus on physicochemical, structural and dynamic properties reveal that T11S-ANG, N26K-RNASE4 and T79A-RNASE4 variants would result in loss of ribonucleolytic activity due to conformational switching of catalytic His114 and His116 respectively but none of the variants would lose their nuclear translocation activity. Our study not only highlights the importance of rare variants but also demonstrates that elucidating the structure-function relationship of mutant effectors is crucial to gain insights into ALS pathophysiology and in developing effective therapeutics.
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Affiliation(s)
- Aditya K Padhi
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
- Laboratory for Structural Bioinformatics, Field for Structural Molecular Biology, Centre for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
| | - Priyam Narain
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - James Gomes
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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18
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High-throughput genome-wide phenotypic screening via immunomagnetic cell sorting. Nat Biomed Eng 2019; 3:796-805. [DOI: 10.1038/s41551-019-0454-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023]
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19
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Tripolszki K, Danis J, Padhi AK, Gomes J, Bozó R, Nagy ZF, Nagy D, Klivényi P, Engelhardt JI, Széll M. Angiogenin mutations in Hungarian patients with amyotrophic lateral sclerosis: Clinical, genetic, computational, and functional analyses. Brain Behav 2019; 9:e01293. [PMID: 31025543 PMCID: PMC6576160 DOI: 10.1002/brb3.1293] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/28/2019] [Accepted: 04/03/2019] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Mutations in the angiogenin (ANG) gene are known to be associated with both familial and sporadic amyotrophic lateral sclerosis (ALS). The majority of disease-causing mutations of ANG result in loss of either ribonucleolytic activity, nuclear translocation activity or both. METHODS We sequenced ANG gene from a total of 136 sporadic ALS patients and 112 healthy controls of Hungarian origin. To elucidate the role of the R33W mutation in the disease mechanism, computational, and functional analyses were performed. RESULTS Mutation screening revealed a mutation located in the signal peptide (M-24I) and two mutations that affect the mature protein (R33W, V103I). The R33W mutation, which has not been previously detected in ALS patients, affects the key amino acid of the nuclear translocation signal of the ANG protein. Molecular dynamics simulations suggested that the R33W mutation results in partial loss of ribonucleolytic activity and reduced nuclear translocation activity. The ribonucleolytic assay and nuclear translocation assay of the R33W ANG protein confirmed the molecular dynamics results. CONCLUSIONS In the Hungarian ALS population, the observed frequency of ANG mutations was 2.9%, which is higher than previously reported for sporadic cohorts. The evidence from computational and functional analyses support the deleterious effect of the novel R33W variant detected in this study.
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Affiliation(s)
| | - Judit Danis
- MTA-SZTE Dermatological Research Group, Szeged, Hungary
| | - Aditya K Padhi
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi, India
| | - James Gomes
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi, India
| | - Renáta Bozó
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | - Zsófia F Nagy
- Department of Medical Genetics, University of Szeged, Szeged, Hungary
| | - Dóra Nagy
- Department of Medical Genetics, University of Szeged, Szeged, Hungary
| | - Péter Klivényi
- Department of Neurology, University of Szeged, Szeged, Hungary
| | | | - Márta Széll
- Department of Medical Genetics, University of Szeged, Szeged, Hungary.,MTA-SZTE Dermatological Research Group, Szeged, Hungary
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20
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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.
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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
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21
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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.
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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
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22
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Chatzileontiadou DSM, Samiotaki M, Alexopoulou AN, Cotsiki M, Panayotou G, Stamatiadi M, Balatsos NAA, Leonidas DD, Kontou M. Proteomic Analysis of Human Angiogenin Interactions Reveals Cytoplasmic PCNA as a Putative Binding Partner. J Proteome Res 2017; 16:3606-3622. [PMID: 28777577 DOI: 10.1021/acs.jproteome.7b00335] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human Angiogenin (hAng) is a member of the ribonuclease A superfamily and a potent inducer of neovascularization. Protein interactions of hAng in the nucleus and cytoplasm of the human umbilical vein cell line EA.hy926 have been investigated by mass spectroscopy. Data are available via ProteomeXchange with identifiers PXD006583 and PXD006584. The first gel-free analysis of hAng immunoprecipitates revealed many statistically significant potential hAng-interacting proteins involved in crucial biological pathways. Surprisingly, proliferating cell nuclear antigen (PCNA), was found to be immunoprecipitated with hAng only in the cytoplasm. The hAng-PCNA interaction and colocalization in the specific cellular compartment was validated with immunoprecipitation, immunoblotting, and immunocytochemistry. The results revealed that PCNA is predominantly localized in the cytoplasm, while hAng is distributed both in the nucleus and in the cytoplasm. hAng and PCNA colocalize in the cytoplasm, suggesting that they may interact in this compartment.
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Affiliation(s)
| | - Martina Samiotaki
- Biomedical Sciences Research Center "Alexander Fleming" , Vari 16672, Greece
| | | | - Marina Cotsiki
- Biomedical Sciences Research Center "Alexander Fleming" , Vari 16672, Greece
| | - George Panayotou
- Biomedical Sciences Research Center "Alexander Fleming" , Vari 16672, Greece
| | - Melina Stamatiadi
- Department of Biochemistry and Biotechnology, University of Thessaly , Biopolis, 41500 Larissa, Greece
| | - Nikolaos A A Balatsos
- Department of Biochemistry and Biotechnology, University of Thessaly , Biopolis, 41500 Larissa, Greece
| | - Demetres D Leonidas
- Department of Biochemistry and Biotechnology, University of Thessaly , Biopolis, 41500 Larissa, Greece
| | - Maria Kontou
- Department of Biochemistry and Biotechnology, University of Thessaly , Biopolis, 41500 Larissa, Greece
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23
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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.
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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
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Tsika AC, Chatzileontiadou DSM, Leonidas DD, Spyroulias GA. NMR study of Met-1 human Angiogenin: (1)H, (13)C, (15)N backbone and side-chain resonance assignment. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:379-383. [PMID: 27624767 DOI: 10.1007/s12104-016-9704-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 08/31/2016] [Indexed: 06/06/2023]
Abstract
Here, we report the high yield expression and preliminary structural analysis via solution hetero-nuclear NMR spectroscopy of the recombinant Met-1 human Angiogenin. The analysis reveals a well folded as well as, a monomeric polypeptide. Τhe sequence-specific assignment of its (1)H, (15)N and (13)C resonances at high percentage was obtained. Also, using TALOS+ its secondary structure elements were determined.
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Affiliation(s)
| | | | - Demetres D Leonidas
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece.
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25
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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.
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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
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26
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Sheng J, Xu Z. Three decades of research on angiogenin: a review and perspective. Acta Biochim Biophys Sin (Shanghai) 2016; 48:399-410. [PMID: 26705141 DOI: 10.1093/abbs/gmv131] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/23/2015] [Indexed: 01/17/2023] Open
Abstract
As a member of the vertebrate-specific secreted ribonucleases, angiogenin (ANG) was first isolated and identified solely by its ability to induce new blood vessel formation, and now, it has been recognized to play important roles in various physiological and pathological processes through regulating cell proliferation, survival, migration, invasion, and/or differentiation. ANG exhibits very weak ribonucleolytic activity that is critical for its biological functions, and exerts its functions through activating different signaling transduction pathways in different target cells. A series of recent studies have indicated that ANG contributes to cellular nucleic acid metabolism. Here, we comprehensively review the results of studies regarding the structure, mechanism, and function of ANG over the past three decades. Moreover, current problems and future research directions of ANG are discussed. The understanding of the function and mechanism of ANG in a wide context will help to better delineate its roles in diseases, especially in cancer and neurodegenerative diseases.
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Affiliation(s)
- Jinghao Sheng
- Institute of Environmental Health, Zhejiang University School of Public Health, Hangzhou 310058, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhengping Xu
- Institute of Environmental Health, Zhejiang University School of Public Health, Hangzhou 310058, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
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27
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Liang S, Acharya KR. Structural basis of substrate specificity in porcine RNase 4. FEBS J 2016; 283:912-28. [PMID: 26748441 DOI: 10.1111/febs.13646] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/26/2015] [Accepted: 01/06/2016] [Indexed: 01/01/2023]
Abstract
UNLABELLED RNase 4, a member of the RNase A superfamily with substrate preference for uridine, has roles in host defence, angiogenesis and neurodegenerative diseases. It also exhibits the highest interspecies amino acid sequence similarity amongst RNase A family members. However, compared to other members of the RNase A family, including eosinophil-derived neurotoxin, eosinophil cationic protein and angiogenin, little is known about the molecular basis of substrate specificity in RNase 4. Here we report high to medium resolution structures of native porcine RNase 4 (PL3), a 'substrate-specificity' determining mutant D80A and their respective complexes with deoxyuridine 5'-monophosphate (dUMP) and deoxycytidine 5'-monophosphate (dCMP). These structures provide insight into the structural basis of the uridine versus cytosine substrate specificity in RNase 4: in the D80A mutant (D80A•dCMP), the side chain of Arg101 is positioned further away from the substrate-binding pocket due to the loss of the Asp80 side chain, reducing the repulsion force on the less favoured dCMP from Arg101 and allowing the ligand to occupy the binding pocket. This can also explain the observation that the ligand in the D80A•dCMP complex is stabilized only by a small number of hydrogen bonds. Compared to the previously reported structure of the human RNase 4•2'-deoxyuridine 3'-phosphate complex, the structure of PL3•dUMP complex shows additional hydrogen bonds between the ligand and the protein. In addition, the interaction between Arg101 and the dUMP ligand is absent. These observed differences are probably the result of the flexibility and different 'positioning' of the phosphate group among the mononucleotide ligands. DATABASE The atomic coordinates and structure factors for PL3 (5AR6), D80A (5ARJ), PL3∙dUMP (5ARK) and D80A∙dCMP (5ARL) complexes have been deposited with the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ, USA (http://www.rcsb.org/).
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Affiliation(s)
- Shutian Liang
- Department of Biology and Biochemistry, University of Bath, UK
| | - K Ravi Acharya
- Department of Biology and Biochemistry, University of Bath, UK
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28
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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.
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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.
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29
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Analysis of single nucleotide polymorphism in human angiogenin using droplet-based microfluidics. BIOCHIP JOURNAL 2014. [DOI: 10.1007/s13206-014-8103-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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30
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Padhi AK, Vasaikar SV, Jayaram B, Gomes J. ANGDelMut - a web-based tool for predicting and analyzing functional loss mechanisms of amyotrophic lateral sclerosis-associated angiogenin mutations. F1000Res 2013; 2:227. [PMID: 24555108 PMCID: PMC3901456 DOI: 10.12688/f1000research.2-227.v3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/10/2014] [Indexed: 01/24/2023] Open
Abstract
ANGDelMut is a web-based tool for predicting the functional consequences of missense mutations in the angiogenin (ANG) protein, which is associated with amyotrophic lateral sclerosis (ALS). Missense mutations in ANG result in loss of either ribonucleolytic activity or nuclear translocation activity or both of these functions, and in turn cause ALS. However, no web-based tools are available to predict whether a newly identified ANG mutation will possibly lead to ALS. More importantly, no web-implemented method is currently available to predict the mechanisms of loss-of-function(s) of ANG mutants. In light of this observation, we developed the ANGDelMut web-based tool, which predicts whether an ANG mutation is deleterious or benign. The user selects certain attributes from the input panel, which serves as a query to infer whether a mutant will exhibit loss of ribonucleolytic activity or nuclear translocation activity or whether the overall stability will be affected. The output states whether the mutation is deleterious or benign, and if it is deleterious, gives the possible mechanism(s) of loss-of-function. This web-based tool, freely available at
http://bioschool.iitd.ernet.in/DelMut/, is the first of its kind to provide a platform for researchers and clinicians, to infer the functional consequences of ANG mutations and correlate their possible association with ALS ahead of experimental findings.
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Affiliation(s)
- Aditya K Padhi
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Suhas V Vasaikar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Bhyravabhotla Jayaram
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India ; Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, 110016, India ; Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - James Gomes
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
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31
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Padhi AK, Vasaikar SV, Jayaram B, Gomes J. ANGDelMut - a web-based tool for predicting and analyzing functional loss mechanisms of amyotrophic lateral sclerosis-associated angiogenin mutations. F1000Res 2013; 2:227. [PMID: 24555108 DOI: 10.12688/f1000research.2-227.v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/20/2013] [Indexed: 12/15/2022] Open
Abstract
ANGDelMut is a web-based tool for predicting the functional consequences of missense mutations in the angiogenin (ANG) protein, which is associated with amyotrophic lateral sclerosis (ALS). Missense mutations in ANG result in loss of either ribonucleolytic activity or nuclear translocation activity or both of these functions, and in turn cause ALS. However, no web-based tools are available to predict whether a newly identified ANG mutation will possibly lead to ALS. More importantly, no web-implemented method is currently available to predict the mechanisms of loss-of-function(s) of ANG mutants. In light of this observation, we developed the ANGDelMut web-based tool, which predicts whether an ANG mutation is deleterious or benign. The user selects certain attributes from the input panel, which serves as a query to infer whether a mutant will exhibit loss of ribonucleolytic activity or nuclear translocation activity or whether the overall stability will be affected. The output states whether the mutation is deleterious or benign, and if it is deleterious, gives the possible mechanism(s) of loss-of-function. This web-based tool, freely available at http://bioschool.iitd.ernet.in/DelMut/, is the first of its kind to provide a platform for researchers and clinicians, to infer the functional consequences of ANG mutations and correlate their possible association with ALS ahead of experimental findings.
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Affiliation(s)
- Aditya K Padhi
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Suhas V Vasaikar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Bhyravabhotla Jayaram
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India ; Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, 110016, India ; Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - James Gomes
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
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32
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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.
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33
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Padhi AK, Vasaikar SV, Jayaram B, Gomes J. Fast prediction of deleterious angiogenin mutations causing amyotrophic lateral sclerosis. FEBS Lett 2013; 587:1762-6. [PMID: 23665167 DOI: 10.1016/j.febslet.2013.04.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/15/2013] [Accepted: 04/22/2013] [Indexed: 12/11/2022]
Abstract
Certain single nucleotide polymorphisms causing missense mutations in angiogenin result in its loss-of-function and onset of amyotrophic lateral sclerosis (ALS). Although several such associations are reported across diverse ethnic groups, no method is available for predicting if a new mutation is deleterious. We present here a fast molecular dynamics based method for determining the mechanisms of functional loss caused by mutations, and attributes to ascertain whether a mutation causes ALS.
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Affiliation(s)
- Aditya K Padhi
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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Prediction of functional loss of human angiogenin mutants associated with ALS by molecular dynamics simulations. Sci Rep 2013; 3:1225. [PMID: 23393617 PMCID: PMC3566597 DOI: 10.1038/srep01225] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 01/18/2013] [Indexed: 12/11/2022] Open
Abstract
Several missense mutations in the coding region of angiogenin (ANG) gene have been identified in Amyotrophic Lateral Sclerosis (ALS) patients. These mutations lead to loss of either ribonucleolytic activity or nuclear translocation activity or both of ANG (protein encoded by ANG gene) causing ALS. We present here a cohesive and comprehensive picture of the molecular origins of functional loss of all ALS associated ANG mutants, emerging via extensive molecular dynamics simulations. Our method effectively predicts that conformational change of His114 results in loss of ribonucleolytic activity and that reduction of solvent accessible surface area of nuclear localization signal residues 31RRR33 results in loss of nuclear translocation activity. These predictions hold true, without exception, for all ANG mutants studied and can be employed to infer whether a new ANG mutation is causative of ALS or benign ahead of experimental findings.
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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.
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Affiliation(s)
| | - K. Ravi Acharya
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
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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.
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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:
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Li Z, Ender C, Meister G, Moore PS, Chang Y, John B. Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Res 2012; 40:6787-99. [PMID: 22492706 PMCID: PMC3413118 DOI: 10.1093/nar/gks307] [Citation(s) in RCA: 238] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 03/22/2012] [Indexed: 01/09/2023] Open
Abstract
Deep sequencing studies frequently identify small RNA fragments of abundant RNAs. These fragments are thought to represent degradation products of their precursors. Using sequencing, computational analysis, and sensitive northern blot assays, we show that constitutively expressed non-coding RNAs such as tRNAs, snoRNAs, rRNAs and snRNAs preferentially produce small 5' and 3' end fragments. Similar to that of microRNA processing, these terminal fragments are generated in an asymmetric manner that predominantly favors either the 5' or 3' end. Terminal-specific and asymmetric processing of these small RNAs occurs in both mouse and human cells. In addition to the known processing of some 3' terminal tRNA-derived fragments (tRFs) by the RNase III endonuclease Dicer, we show that several RNase family members can produce tRFs, including Angiogenin that cleaves the TψC loop to generate 3' tRFs. The 3' terminal tRFs but not the 5' tRFs are highly complementary to human endogenous retroviral sequences in the genome. Despite their independence from Dicer processing, these tRFs associate with Ago2 and are capable of down regulating target genes by transcript cleavage in vitro. We suggest that endogenous 3' tRFs have a role in regulating the unwarranted expression of endogenous viruses through the RNA interference pathway.
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MESH Headings
- Animals
- Argonaute Proteins/metabolism
- Endogenous Retroviruses/genetics
- Humans
- Mice
- Proteins/physiology
- RNA Cleavage
- RNA Processing, Post-Transcriptional
- RNA, Messenger/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/metabolism
- RNA, Small Untranslated/chemistry
- RNA, Small Untranslated/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA-Binding Proteins
- Ribonuclease III/physiology
- Ribonuclease, Pancreatic/metabolism
- Ribonucleases/metabolism
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Affiliation(s)
- Zhihua Li
- School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, Cancer Virology Program, Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA 15213, USA and Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christine Ender
- School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, Cancer Virology Program, Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA 15213, USA and Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Gunter Meister
- School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, Cancer Virology Program, Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA 15213, USA and Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Patrick S. Moore
- School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, Cancer Virology Program, Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA 15213, USA and Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Yuan Chang
- School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, Cancer Virology Program, Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA 15213, USA and Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Bino John
- School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, Cancer Virology Program, Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA 15213, USA and Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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The sulfate-binding site structure of the human eosinophil cationic protein as revealed by a new crystal form. J Struct Biol 2012; 179:1-9. [DOI: 10.1016/j.jsb.2012.04.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 04/25/2012] [Accepted: 04/26/2012] [Indexed: 01/05/2023]
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Padhi AK, Kumar H, Vasaikar SV, Jayaram B, Gomes J. Mechanisms of loss of functions of human angiogenin variants implicated in amyotrophic lateral sclerosis. PLoS One 2012; 7:e32479. [PMID: 22384259 PMCID: PMC3288110 DOI: 10.1371/journal.pone.0032479] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 01/31/2012] [Indexed: 12/11/2022] Open
Abstract
Background Mutations in the coding region of angiogenin (ANG) gene have been found in patients suffering from Amyotrophic Lateral Sclerosis (ALS). Neurodegeneration results from the loss of angiogenic ability of ANG (protein coded by ANG). In this work, we performed extensive molecular dynamics (MD) simulations of wild-type ANG and disease associated ANG variants to elucidate the mechanism behind the loss of ribonucleolytic activity and nuclear translocation activity, functions needed for angiogenesis. Methodology/Principal Findings MD simulations were carried out to study the structural and dynamic differences in the catalytic site and nuclear localization signal residues between WT-ANG (Wild-type ANG) and six mutants. Variants K17I, S28N, P112L and V113I have confirmed association with ALS, while T195C and A238G single nucleotide polymorphisms (SNPs) encoding L35P and K60E mutants respectively, have not been associated with ALS. Our results show that loss of ribonucleolytic activity in K17I is caused by conformational switching of the catalytic residue His114 by 99°. The loss of nuclear translocation activity of S28N and P112L is caused by changes in the folding of the residues 31RRR33 that result in the reduction in solvent accessible surface area (SASA). Consequently, we predict that V113I will exhibit loss of angiogenic properties by loss of nuclear translocation activity and L35P by loss of both ribonucleolytic activity and nuclear translocation activity. No functional loss was inferred for K60E. The MD simulation results were supported by hydrogen bond interaction analyses and molecular docking studies. Conclusions/Significance Conformational switching of catalytic residue His114 seems to be the mechanism causing loss of ribonucleolytic activity and reduction in SASA of nuclear localization signal residues 31RRR33 results in loss of nuclear translocation activity in ANG mutants. Therefore, we predict that L35P mutant, would exhibit loss of angiogenic functions, and hence would correlate with ALS while K60E would not show any loss.
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Affiliation(s)
- Aditya K Padhi
- School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
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40
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Pyatibratov MG, Kostyukova AS. New insights into the role of angiogenin in actin polymerization. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2012; 295:175-98. [PMID: 22449490 DOI: 10.1016/b978-0-12-394306-4.00011-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Angiogenin is a potent stimulator of angiogenesis. It interacts with endothelial cells and induces a wide range of cellular responses initiating a process of blood vessel formation. One important target of angiogenin is endothelial cell-surface actin, and their interaction might be one of crucial steps in angiogenin-induced neovascularization. Recently, it was shown that angiogenin inhibits polymerization of G-actin and changes the physical properties of F-actin. These observations suggest that angiogenin may cause changes in the cell cytoskeleton. This chapter reviews the current state of the literature regarding angiogenin structure and function and discusses the relationship between the angiogenin and actin and possible functional roles of their interaction.
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Affiliation(s)
- Mikhail G Pyatibratov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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41
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Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis. PLoS Biol 2011; 9:e1001193. [PMID: 22087074 PMCID: PMC3210774 DOI: 10.1371/journal.pbio.1001193] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 09/27/2011] [Indexed: 11/19/2022] Open
Abstract
Proteins are intrinsically flexible molecules. The role of internal motions in a protein's designated function is widely debated. The role of protein structure in enzyme catalysis is well established, and conservation of structural features provides vital clues to their role in function. Recently, it has been proposed that the protein function may involve multiple conformations: the observed deviations are not random thermodynamic fluctuations; rather, flexibility may be closely linked to protein function, including enzyme catalysis. We hypothesize that the argument of conservation of important structural features can also be extended to identification of protein flexibility in interconnection with enzyme function. Three classes of enzymes (prolyl-peptidyl isomerase, oxidoreductase, and nuclease) that catalyze diverse chemical reactions have been examined using detailed computational modeling. For each class, the identification and characterization of the internal protein motions coupled to the chemical step in enzyme mechanisms in multiple species show identical enzyme conformational fluctuations. In addition to the active-site residues, motions of protein surface loop regions (>10 Å away) are observed to be identical across species, and networks of conserved interactions/residues connect these highly flexible surface regions to the active-site residues that make direct contact with substrates. More interestingly, examination of reaction-coupled motions in non-homologous enzyme systems (with no structural or sequence similarity) that catalyze the same biochemical reaction shows motions that induce remarkably similar changes in the enzyme–substrate interactions during catalysis. The results indicate that the reaction-coupled flexibility is a conserved aspect of the enzyme molecular architecture. Protein motions in distal areas of homologous and non-homologous enzyme systems mediate similar changes in the active-site enzyme–substrate interactions, thereby impacting the mechanism of catalyzed chemistry. These results have implications for understanding the mechanism of allostery, and for protein engineering and drug design.
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42
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The eight human "canonical" ribonucleases: molecular diversity, catalytic properties, and special biological actions of the enzyme proteins. FEBS Lett 2010; 584:2194-200. [PMID: 20388512 DOI: 10.1016/j.febslet.2010.04.018] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 04/07/2010] [Accepted: 04/07/2010] [Indexed: 01/25/2023]
Abstract
Human ribonucleases (RNases) are members of a large superfamily of rapidly evolving homologous proteins. Upon completion of the human genome, eight catalytically active RNases (numbered 1-8) were identified. These structurally distinct RNases, characterized by their various catalytic differences on different RNA substrates, constitute a gene family that appears to be the sole vertebrate-specific enzyme family. Apart from digestion of dietary RNA, a wide variety of biological actions, including neurotoxicity, angiogenesis, immunosuppressivity, and anti-pathogen activity, have been recently reported for almost all members of the family. Recent evolutionary studies suggest that RNases started off in vertebrates as host defence or angiogenic proteins.
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Kaposi's sarcoma-associated herpesvirus upregulates angiogenin during infection of human dermal microvascular endothelial cells, which induces 45S rRNA synthesis, antiapoptosis, cell proliferation, migration, and angiogenesis. J Virol 2009; 83:3342-64. [PMID: 19158252 DOI: 10.1128/jvi.02052-08] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Kaposi's sarcoma (KS)-associated herpesvirus (KSHV) is associated with the angioproliferative KS lesions characterized by spindle-shaped endothelial cells, inflammatory cells, cytokines, growth factors, and angiogenic factors. De novo KSHV infection of human microvascular dermal endothelial cells results in increased secretion of several growth factors, cytokines, chemokines, and angiogenic factors, and the multifunctional angiogenic protein angiogenin is one of them. KS tissue sections were positive for angiogenin, highlighting the importance of angiogenin in KS pathogenesis. Examination of KSHV-mediated angiogenin upregulation and secretion and potential outcomes revealed that during infection of primary endothelial cells, KSHV induced a time- and dose-dependent increase in angiogenin gene expression and protein secretion beginning as early as 8 h postinfection and lasting until the fifth day of our observation period. TIVE latently transformed cells (TIVE-LTC) latently infected with KSHV secreted high levels of angiogenin. Angiogenin was also detected in BCBL-1 cells (human B cells) carrying KSHV in a latent state. Significant induction of angiogenin was observed in cells expressing KSHV ORF73 (LANA-1; latent) and ORF74 (lytic) genes alone, and moderate induction was seen with the lytic KSHV ORF50 gene. Angiogenin bound to surface actin, internalized in a microtubule-independent manner, and translocated into the nucleus and nucleolus of infected cells. In addition, it increased 45S rRNA gene transcription, antiapoptosis, and proliferation of infected cells, thus demonstrating the multifunctional nature of KSHV-induced angiogenin. These activities were dependent on angiogenin nuclear translocation, which was inhibited by neomycin. Upregulation of angiogenin led to increased activation of urokinase plasminogen activator and generation of active plasmin, which facilitated the migration of endothelial cells toward chemoattractants, including angiogenin, and chemotaxis was prevented by the inhibition of angiogenin nuclear translocation. Treatment of KSHV-infected cell supernatants with antiangiogenin antibodies significantly inhibited endothelial tube formation, and inhibition of nuclear translocation of angiogenin also blocked the expression of KSHV-induced vascular endothelial growth factor C. Collectively, these results strongly suggest that by increasing infected endothelial cell 45S rRNA synthesis, proliferation, migration, and angiogenesis, KSHV-induced angiogenin could be playing a pivotal role in the pathogenesis of KSHV infection, including a contribution to the angioproliferative nature of KS lesions. Our studies suggested that LANA-1 and vGPCR play roles in KSHV-induced angiogenesis and that the angiogenic potential of vGPCR might also be due to its ability to induce angiogenin.
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Harder J, Gläser R, Schröder JM. Human antimicrobial proteins effectors of innate immunity. ACTA ACUST UNITED AC 2008; 13:317-38. [PMID: 18182460 DOI: 10.1177/0968051907088275] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We live in a world populated by an enormous number of micro-organisms. This necessitates the existence of highly effective mechanisms to control microbial growth. Through many research efforts, a chemical defense system based on the production of antimicrobial proteins (AMPs) has been identified. AMPs are endogenous, small proteins exhibiting antimicrobial activity against a wide variety of micro-organisms. The wide distribution of these molecules in the plant and animal kingdom reflects their biological significance. Various human AMPs show a potent effect on pathogenic micro-organisms including antibiotic-resistant bacteria. Thus, there is great interest in understanding the role of AMPs within innate immunity and evaluating their use and/or specific induction to fend off infections. In this review, we provide an overview of the characteristics of human AMPs and discuss examples where AMPs may be involved in the pathogenesis of infectious and inflammatory diseases.
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Affiliation(s)
- Jürgen Harder
- Clinical Research Unit, Department of Dermatology, University Hospital Schleswig-Holstein, Kiel, Germany.
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45
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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.
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Crabtree B, Thiyagarajan N, Prior SH, Wilson P, Iyer S, Ferns T, Shapiro R, Brew K, Subramanian V, Acharya KR. Characterization of Human Angiogenin Variants Implicated in Amyotrophic Lateral Sclerosis. Biochemistry 2007; 46:11810-8. [PMID: 17900154 DOI: 10.1021/bi701333h] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human angiogenin (ANG), the first member of the angiogenin family (from the pancreatic ribonuclease A superfamily) to be identified, is an angiogenic factor that induces neovascularization. It has received much attention due to its involvement in the growth of tumors and its elevated expression level in pancreatic and several other cancers. Recently the biological role of ANG has been shown to extend to the nervous system. Mutations in ANG have been linked with familial as well as sporadic forms of amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disorder characterized by selective destruction of motor neurons. Furthermore, mouse angiogenin-1 has been shown to be expressed in the developing nervous system and during the neuronal differentiation of pluripotent stem cells. We have now characterized the seven variants of ANG reported in ALS patients with respect to the known biochemical properties of ANG and further studied the biological properties of three of these variants. Our results show that the ribonucleolytic activity of six of the seven ANG-ALS implicated variants is significantly reduced or lost and some variants also show altered thermal stability. We report a significant reduction in the cell proliferative and angiogenic activities of the three variants that we chose to investigate further. Our studies on the biochemical and structural features of these ANG variants now form the basis for further investigations to determine their role(s) in ALS.
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Affiliation(s)
- Benedict Crabtree
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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Osorio DS, Antunes A, Ramos MJ. Structural and functional implications of positive selection at the primate angiogenin gene. BMC Evol Biol 2007; 7:167. [PMID: 17883850 PMCID: PMC2194721 DOI: 10.1186/1471-2148-7-167] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 09/20/2007] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Angiogenesis, the formation of new blood vessels, is a primordial process in development and its dysregulation has a central role in the pathogenesis of many diseases. Angiogenin (ANG), a peculiar member of the RNase A superfamily, is a potent inducer of angiogenesis involved in many different types of cancer, amyotrophic lateral sclerosis and also with a possible role in the innate immune defense. The evolutionary path of this family has been a highly dynamic one, where positive selection has played a strong role. In this work we used a combined gene and protein level approach to determine the main sites under diversifying selection on the primate ANG gene and analyze its structural and functional implications. RESULTS We obtained evidence for positive selection in the primate ANG gene. Site specific analysis pointed out 15 sites under positive selection, most of which also exhibited drastic changes in amino acid properties. The mapping of these sites in the ANG 3D-structure described five clusters, four of which were located in functional regions: two in the active site region, one in the nucleolar location signal and one in the cell-binding site. Eight of the 15 sites under selection in the primate ANG gene were highly or moderately conserved in the RNase A family, suggesting a directed event and not a simple consequence of local structural or functional permissiveness. Moreover, 11 sites were exposed to the surface of the protein indicating that they may influence the interactions performed by ANG. CONCLUSION Using a maximum likelihood gene level analysis we identified 15 sites under positive selection in the primate ANG genes, that were further corroborated through a protein level analysis of radical changes in amino acid properties. These sites mapped onto the main functional regions of the ANG protein. The fact that evidence for positive selection is present in all ANG regions required for angiogenesis may be a good indication that angiogenesis is the process under selection. However, other possibilities to be considered arise from the possible involvement of ANG in innate immunity and the potential influence or co-evolution with its interacting proteins and ligands.
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Affiliation(s)
- Daniel S Osorio
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
- INSERM UMR S 787-Groupe Myologie, Faculté de Médecine – Pitié-Salpétrière, UPMC Paris VI, 105 bd. de l'Hôpital, 75634, Paris Cedex 13, France
| | - Agostinho Antunes
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
- CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal
| | - Maria J Ramos
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
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Singh UP, Ardelt W, Saxena SK, Holloway DE, Vidunas E, Lee HS, Saxena A, Shogen K, Acharya KR. Enzymatic and Structural Characterisation of Amphinase, a Novel Cytotoxic Ribonuclease from Rana pipiens Oocytes. J Mol Biol 2007; 371:93-111. [PMID: 17560606 DOI: 10.1016/j.jmb.2007.04.071] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 04/26/2007] [Accepted: 04/29/2007] [Indexed: 10/23/2022]
Abstract
Besides Onconase (ONC) and its V11/N20/R103-variant, oocytes of the Northern Leopard frog (Rana pipiens) contain another homologue of ribonuclease A, which we named Amphinase (Amph). Four variants (Amph-1-4) were isolated and sequenced, each 114 amino acid residues in length and N-glycosylated at two positions. Sequence identities (a) among the variants and (b) versus ONC are 86.8-99.1% and 38.2-40.0%, respectively. When compared with other amphibian ribonucleases, a typical pattern of cysteine residues is evident but the N-terminal pyroglutamate residue is replaced by a six-residue extension. Amph variants have relatively weak ribonucleolytic activity that is insensitive to human ribonuclease inhibitor protein (RI). Values of k(cat)/K(M) with hypersensitive fluorogenic substrates are 10(4) and 10(2)-fold lower than the maximum values exhibited by ribonuclease A and ONC, respectively, and there is little cytosine/uracil or adenine/guanine discrimination at the B(1) or B(2) subsites, respectively. Amph variants have cytotoxic activity toward A-253 carcinoma cells that requires intact ribonucleolytic activity. The glycan component has little or no influence over single-stranded RNA cleavage, RI evasion or cytotoxicity. The crystal structures of natural and recombinant Amph-2 (determined at 1.8 and 1.9 A resolution, respectively) reveal that the N terminus is unlikely to play a catalytic role (but an unusual alpha2-beta1 loop may do so) and the B(2) subsite is rudimentary. At the active site, structural features that may contribute to the enzyme's low ribonucleolytic activity are the fixture of Lys14 in an obstructive position, the accompanying ejection of Lys42, and a lack of constraints on the conformations of Lys42 and His107.
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Affiliation(s)
- Umesh P Singh
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
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In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach. BMC STRUCTURAL BIOLOGY 2007; 7:37. [PMID: 17559675 PMCID: PMC1913526 DOI: 10.1186/1472-6807-7-37] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Accepted: 06/08/2007] [Indexed: 11/29/2022]
Abstract
Background Molecular recognition between enzymes and proteic inhibitors is crucial for normal functioning of many biological pathways. Mutations in either the enzyme or the inhibitor protein often lead to a modulation of the binding affinity with no major alterations in the 3D structure of the complex. Results In this study, a rigid body docking-based approach has been successfully probed in its ability to predict the effects of single and multiple point mutations on the binding energetics in three enzyme-proteic inhibitor systems. The only requirement of the approach is an accurate structural model of the complex between the wild type forms of the interacting proteins, with the assumption that the architecture of the mutated complexes is almost the same as that of the wild type and no major conformational changes occur upon binding. The method was applied to 23 variants of the ribonuclease inhibitor-angiogenin complex, to 15 variants of the barnase-barstar complex, and to 8 variants of the bovine pancreatic trypsin inhibitor-β Trypsin system, leading to thermodynamic and kinetic estimates consistent with in vitro data. Furthermore, simulations with and without explicit water molecules at the protein-protein interface suggested that they should be included in the simulations only when their positions are well defined both in the wild type and in the mutants and they result to be relevant for the modulation of mutational effects on the association process. Conclusion The correlative models built in this study allow for predictions of mutational effects on the thermodynamics and kinetics of association of three substantially different systems, and represent important extensions of our computational approach to cases in which it is not possible to estimate the absolute free energies. Moreover, this study is the first example in the literature of an extensive evaluation of the correlative weights of the single components of the ZDOCK score on the thermodynamics and kinetics of binding of protein mutants compared to the native state. Finally, the results of this study corroborate and extend a previously developed quantitative model for in silico predictions of absolute protein-protein binding affinities spanning a wide range of values, i.e. from -10 up to -21 kcal/mol. The computational approach is simple and fast and can be used for structure-based design of protein-protein complexes and for in silico screening of mutational effects on protein-protein recognition.
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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.
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Affiliation(s)
- Vasanta Subramanian
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.
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