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Corrales-Guerrero L, Prischi F, Díaz-Moreno I. Editorial: Weak interactions in molecular machinery volume II. Front Mol Biosci 2023; 10:1284353. [PMID: 37790878 PMCID: PMC10542395 DOI: 10.3389/fmolb.2023.1284353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 10/05/2023] Open
Affiliation(s)
- Laura Corrales-Guerrero
- cicCartuja, Institute for Chemical Research (IIQ), University of Seville—CSIC, Seville, Spain
| | - Filippo Prischi
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Irene Díaz-Moreno
- cicCartuja, Institute for Chemical Research (IIQ), University of Seville—CSIC, Seville, Spain
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2
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Trampari E, Prischi F, Vargiu AV, Abi-Assaf J, Bavro VN, Webber MA. Functionally distinct mutations within AcrB underpin antibiotic resistance in different lifestyles. NPJ Antimicrob Resist 2023; 1:2. [PMID: 38686215 PMCID: PMC11057200 DOI: 10.1038/s44259-023-00001-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/27/2023] [Indexed: 05/02/2024]
Abstract
Antibiotic resistance is a pressing healthcare challenge and is mediated by various mechanisms, including the active export of drugs via multidrug efflux systems, which prevent drug accumulation within the cell. Here, we studied how Salmonella evolved resistance to two key antibiotics, cefotaxime and azithromycin, when grown planktonically or as a biofilm. Resistance to both drugs emerged in both conditions and was associated with different substitutions within the efflux-associated transporter, AcrB. Azithromycin exposure selected for an R717L substitution, while cefotaxime for Q176K. Additional mutations in ramR or envZ accumulated concurrently with the R717L or Q176K substitutions respectively, resulting in clinical resistance to the selective antibiotics and cross-resistance to other drugs. Structural, genetic, and phenotypic analysis showed the two AcrB substitutions confer their benefits in profoundly different ways. R717L reduces steric barriers associated with transit through the substrate channel 2 of AcrB. Q176K increases binding energy for cefotaxime, improving recognition in the distal binding pocket, resulting in increased efflux efficiency. Finally, we show the R717 substitution is present in isolates recovered around the world.
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Affiliation(s)
- Eleftheria Trampari
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ UK
| | - Filippo Prischi
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ UK
| | - Attilio V. Vargiu
- Department of Physics, University of Cagliari, S. P. 8, km. 0.700, 09042 Monserrato, Italy
| | - Justin Abi-Assaf
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ UK
| | - Vassiliy N. Bavro
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ UK
| | - Mark A. Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ UK
- Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7UA UK
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3
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Hough MA, Prischi F, Worrall JAR. Perspective: Structure determination of protein-ligand complexes at room temperature using X-ray diffraction approaches. Front Mol Biosci 2023; 10:1113762. [PMID: 36756363 PMCID: PMC9899996 DOI: 10.3389/fmolb.2023.1113762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/12/2023] [Indexed: 01/24/2023] Open
Abstract
The interaction between macromolecular proteins and small molecule ligands is an essential component of cellular function. Such ligands may include enzyme substrates, molecules involved in cellular signalling or pharmaceutical drugs. Together with biophysical techniques used to assess the thermodynamic and kinetic properties of ligand binding to proteins, methodology to determine high-resolution structures that enable atomic level interactions between protein and ligand(s) to be directly visualised is required. Whilst such structural approaches are well established with high throughput X-ray crystallography routinely used in the pharmaceutical sector, they provide only a static view of the complex. Recent advances in X-ray structural biology methods offer several new possibilities that can examine protein-ligand complexes at ambient temperature rather than under cryogenic conditions, enable transient binding sites and interactions to be characterised using time-resolved approaches and combine spectroscopic measurements from the same crystal that the structures themselves are determined. This Perspective reviews several recent developments in these areas and discusses new possibilities for applications of these advanced methodologies to transform our understanding of protein-ligand interactions.
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Affiliation(s)
- Michael A. Hough
- School of Life Sciences, University of Essex, Colchester, United Kingdom,Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, United Kingdom,*Correspondence: Michael A. Hough, ; Jonathan A. R. Worrall,
| | - Filippo Prischi
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Jonathan A. R. Worrall
- School of Life Sciences, University of Essex, Colchester, United Kingdom,*Correspondence: Michael A. Hough, ; Jonathan A. R. Worrall,
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4
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Chrysostomou S, Roy R, Prischi F, Thamlikitkul L, Chapman KL, Mufti U, Peach R, Ding L, Hancock D, Moore C, Molina-Arcas M, Mauri F, Pinato DJ, Abrahams JM, Ottaviani S, Castellano L, Giamas G, Pascoe J, Moonamale D, Pirrie S, Gaunt C, Billingham L, Steven NM, Cullen M, Hrouda D, Winkler M, Post J, Cohen P, Salpeter SJ, Bar V, Zundelevich A, Golan S, Leibovici D, Lara R, Klug DR, Yaliraki SN, Barahona M, Wang Y, Downward J, Skehel JM, Ali MMU, Seckl MJ, Pardo OE. Repurposed floxacins targeting RSK4 prevent chemoresistance and metastasis in lung and bladder cancer. Sci Transl Med 2021; 13:eaba4627. [PMID: 34261798 PMCID: PMC7611705 DOI: 10.1126/scitranslmed.aba4627] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 10/26/2020] [Accepted: 06/09/2021] [Indexed: 12/20/2022]
Abstract
Lung and bladder cancers are mostly incurable because of the early development of drug resistance and metastatic dissemination. Hence, improved therapies that tackle these two processes are urgently needed to improve clinical outcome. We have identified RSK4 as a promoter of drug resistance and metastasis in lung and bladder cancer cells. Silencing this kinase, through either RNA interference or CRISPR, sensitized tumor cells to chemotherapy and hindered metastasis in vitro and in vivo in a tail vein injection model. Drug screening revealed several floxacin antibiotics as potent RSK4 activation inhibitors, and trovafloxacin reproduced all effects of RSK4 silencing in vitro and in/ex vivo using lung cancer xenograft and genetically engineered mouse models and bladder tumor explants. Through x-ray structure determination and Markov transient and Deuterium exchange analyses, we identified the allosteric binding site and revealed how this compound blocks RSK4 kinase activation through binding to an allosteric site and mimicking a kinase autoinhibitory mechanism involving the RSK4's hydrophobic motif. Last, we show that patients undergoing chemotherapy and adhering to prophylactic levofloxacin in the large placebo-controlled randomized phase 3 SIGNIFICANT trial had significantly increased (P = 0.048) long-term overall survival times. Hence, we suggest that RSK4 inhibition may represent an effective therapeutic strategy for treating lung and bladder cancer.
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Affiliation(s)
- Stelios Chrysostomou
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Rajat Roy
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Filippo Prischi
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Lucksamon Thamlikitkul
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Kathryn L Chapman
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
- Assay Biology, Domainex Ltd, Cambridge CB10 1XL, UK
| | - Uwais Mufti
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Robert Peach
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
- Department of Neurology, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Laifeng Ding
- Key Laboratory of Magnetic Resonance in Biological Systems, National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - David Hancock
- Oncogene Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Christopher Moore
- Oncogene Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Miriam Molina-Arcas
- Oncogene Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Francesco Mauri
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - David J Pinato
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Joel M Abrahams
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Silvia Ottaviani
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Leandro Castellano
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Georgios Giamas
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Jennifer Pascoe
- Department of Oncology, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TH, UK
| | - Devmini Moonamale
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Sarah Pirrie
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham B15 2TT, UK
| | - Claire Gaunt
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham B15 2TT, UK
| | - Lucinda Billingham
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham B15 2TT, UK
| | - Neil M Steven
- Department of Oncology, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TH, UK
| | - Michael Cullen
- Department of Oncology, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TH, UK
| | - David Hrouda
- Department Urology, Charing Cross Hospital, London W6 8RF, UK
| | - Mathias Winkler
- Department Urology, Charing Cross Hospital, London W6 8RF, UK
| | - John Post
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH. UK
| | - Philip Cohen
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH. UK
| | | | - Vered Bar
- Curesponse, 6 Weizmann Street, 6423906 Tel Aviv, Israel
| | | | - Shay Golan
- Department of Urology, Rabin Medical Center, Jabotinsky St. 39, 4941492 Petah Tikva, Israel
| | - Dan Leibovici
- Department of Urology, Kaplan Medical Center, 7610001 Rehovot, Israel
| | - Romain Lara
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
- AstraZeneca, Discovery Science, R&D, Discovery Biology, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, UK
| | - David R Klug
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
| | - Sophia N Yaliraki
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, London SW7 2AZ, UK
| | - Yulan Wang
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
| | - Julian Downward
- Oncogene Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - J Mark Skehel
- Biological Mass Spectrometry and Proteomics, MRC LMB, Cambridge CB2 0QH, UK
| | - Maruf M U Ali
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
| | - Michael J Seckl
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK.
| | - Olivier E Pardo
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK.
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Cronin R, Brooke GN, Prischi F. The role of the p90 ribosomal S6 kinase family in prostate cancer progression and therapy resistance. Oncogene 2021; 40:3775-3785. [PMID: 33972681 PMCID: PMC8175238 DOI: 10.1038/s41388-021-01810-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/08/2021] [Accepted: 04/20/2021] [Indexed: 02/06/2023]
Abstract
Prostate cancer (PCa) is the second most commonly occurring cancer in men, with over a million new cases every year worldwide. Tumor growth and disease progression is mainly dependent on the Androgen Receptor (AR), a ligand dependent transcription factor. Standard PCa therapeutic treatments include androgen-deprivation therapy and AR signaling inhibitors. Despite being successful in controlling the disease in the majority of men, the high frequency of disease progression to aggressive and therapy resistant stages (termed castrate resistant prostate cancer) has led to the search for new therapeutic targets. The p90 ribosomal S6 kinase (RSK1-4) family is a group of highly conserved Ser/Thr kinases that holds promise as a novel target. RSKs are effector kinases that lay downstream of the Ras/Raf/MEK/ERK signaling pathway, and aberrant activation or expression of RSKs has been reported in several malignancies, including PCa. Despite their structural similarities, RSK isoforms have been shown to perform nonredundant functions and target a wide range of substrates involved in regulation of transcription and translation. In this article we review the roles of the RSKs in proliferation and motility, cell cycle control and therapy resistance in PCa, highlighting the possible interplay between RSKs and AR in mediating disease progression. In addition, we summarize the current advances in RSK inhibitor development and discuss their potential clinical benefits.
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Affiliation(s)
- Ryan Cronin
- School of Life Sciences, University of Essex, Colchester, UK
| | - Greg N Brooke
- School of Life Sciences, University of Essex, Colchester, UK.
| | - Filippo Prischi
- School of Life Sciences, University of Essex, Colchester, UK.
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6
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Prischi F, Filippakopoulos P. Editorial: Structural Studies of Protein Complexes in Signaling Pathways. Front Mol Biosci 2021; 8:641932. [PMID: 33996897 PMCID: PMC8119893 DOI: 10.3389/fmolb.2021.641932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/05/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Filippo Prischi
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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7
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Obomighie I, Lapenas K, Murphy BE, Bowles AMC, Bechtold U, Prischi F. The Role of Ribosomal Protein S6 Kinases in Plant Homeostasis. Front Mol Biosci 2021; 8:636560. [PMID: 33778006 PMCID: PMC7988200 DOI: 10.3389/fmolb.2021.636560] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/11/2021] [Indexed: 01/11/2023] Open
Abstract
The p70 ribosomal S6 kinase (S6K) family is a group of highly conserved kinases in eukaryotes that regulates cell growth, cell proliferation, and stress response via modulating protein synthesis and ribosomal biogenesis. S6Ks are downstream effectors of the Target of Rapamycin (TOR) pathway, which connects nutrient and energy signaling to growth and homeostasis, under normal and stress conditions. The plant S6K family includes two isoforms, S6K1 and S6K2, which, despite their high level of sequence similarity, have distinct functions and regulation mechanisms. Significant advances on the characterization of human S6Ks have occurred in the past few years, while studies on plant S6Ks are scarce. In this article, we review expression and activation of the two S6K isoforms in plants and we discuss their roles in mediating responses to stresses and developmental cues.
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Affiliation(s)
| | - Kestutis Lapenas
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Billy E Murphy
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | | | - Ulrike Bechtold
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Filippo Prischi
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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Trezza A, Iovinelli D, Santucci A, Prischi F, Spiga O. An integrated drug repurposing strategy for the rapid identification of potential SARS-CoV-2 viral inhibitors. Sci Rep 2020; 10:13866. [PMID: 32807895 PMCID: PMC7431416 DOI: 10.1038/s41598-020-70863-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/31/2020] [Indexed: 12/23/2022] Open
Abstract
The Coronavirus disease 2019 (COVID-19) is an infectious disease caused by the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). The virus has rapidly spread in humans, causing the ongoing Coronavirus pandemic. Recent studies have shown that, similarly to SARS-CoV, SARS-CoV-2 utilises the Spike glycoprotein on the envelope to recognise and bind the human receptor ACE2. This event initiates the fusion of viral and host cell membranes and then the viral entry into the host cell. Despite several ongoing clinical studies, there are currently no approved vaccines or drugs that specifically target SARS-CoV-2. Until an effective vaccine is available, repurposing FDA approved drugs could significantly shorten the time and reduce the cost compared to de novo drug discovery. In this study we attempted to overcome the limitation of in silico virtual screening by applying a robust in silico drug repurposing strategy. We combined and integrated docking simulations, with molecular dynamics (MD), Supervised MD (SuMD) and Steered MD (SMD) simulations to identify a Spike protein - ACE2 interaction inhibitor. Our data showed that Simeprevir and Lumacaftor bind the receptor-binding domain of the Spike protein with high affinity and prevent ACE2 interaction.
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Affiliation(s)
- Alfonso Trezza
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100, Siena, Italy
| | - Daniele Iovinelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100, Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100, Siena, Italy
| | - Filippo Prischi
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK.
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100, Siena, Italy.
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9
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Spiga O, Cicaloni V, Fiorini C, Trezza A, Visibelli A, Millucci L, Bernardini G, Bernini A, Marzocchi B, Braconi D, Prischi F, Santucci A. Machine learning application for development of a data-driven predictive model able to investigate quality of life scores in a rare disease. Orphanet J Rare Dis 2020; 15:46. [PMID: 32050984 PMCID: PMC7017449 DOI: 10.1186/s13023-020-1305-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/14/2020] [Indexed: 01/11/2023] Open
Abstract
Background Alkaptonuria (AKU) is an ultra-rare autosomal recessive disease caused by a mutation in the homogentisate 1,2-dioxygenase (HGD) gene. One of the main obstacles in studying AKU, and other ultra-rare diseases, is the lack of a standardized methodology to assess disease severity or response to treatment. Quality of Life scores (QoL) are a reliable way to monitor patients’ clinical condition and health status. QoL scores allow to monitor the evolution of diseases and assess the suitability of treatments by taking into account patients’ symptoms, general health status and care satisfaction. However, more comprehensive tools to study a complex and multi-systemic disease like AKU are needed. In this study, a Machine Learning (ML) approach was implemented with the aim to perform a prediction of QoL scores based on clinical data deposited in the ApreciseKUre, an AKU- dedicated database. Method Data derived from 129 AKU patients have been firstly examined through a preliminary statistical analysis (Pearson correlation coefficient) to measure the linear correlation between 11 QoL scores. The variable importance in QoL scores prediction of 110 ApreciseKUre biomarkers has been then calculated using XGBoost, with K-nearest neighbours algorithm (k-NN) approach. Due to the limited number of data available, this model has been validated using surrogate data analysis. Results We identified a direct correlation of 6 (age, Serum Amyloid A, Chitotriosidase, Advanced Oxidation Protein Products, S-thiolated proteins and Body Mass Index) out of 110 biomarkers with the QoL health status, in particular with the KOOS (Knee injury and Osteoarthritis Outcome Score) symptoms (Relative Absolute Error (RAE) 0.25). The error distribution of surrogate-model (RAE 0.38) was unequivocally higher than the true-model one (RAE of 0.25), confirming the consistency of our dataset. Our data showed that inflammation, oxidative stress, amyloidosis and lifestyle of patients correlates with the QoL scores for physical status, while no correlation between the biomarkers and patients’ mental health was present (RAE 1.1). Conclusions This proof of principle study for rare diseases confirms the importance of database, allowing data management and analysis, which can be used to predict more effective treatments.
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Affiliation(s)
- Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy.
| | - Vittoria Cicaloni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy.,Toscana Life Sciences Foundation, Siena, Italy
| | | | - Alfonso Trezza
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy
| | - Anna Visibelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy.,Department of Information Engineering and Mathematics, University of Siena, Siena, Italy
| | - Lia Millucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy
| | - Giulia Bernardini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy
| | - Andrea Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy
| | - Barbara Marzocchi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy.,UOC Patologia Clinica, Azienda Ospedaliera Senese, Siena, Italy
| | - Daniela Braconi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy
| | - Filippo Prischi
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy
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Trampari E, Holden E, Wickham G, Ravi A, Prischi F, Martins LDO, Savva G, Bavro V, Webber M. Experimental evolution selects clinically relevant antibiotic resistance in biofilms but with collateral tradeoffs. Access Microbiol 2020. [DOI: 10.1099/acmi.mim2019.po0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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11
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Chrysostomou S, Roy R, Prischi F, Chapman K, Mufti U, Mauri F, Bellezza G, Abrahams J, Ottaviani S, Castellano L, Giamas G, Hrouda D, Winkler M, Klug D, Yaliraki S, Barahona M, Wang Y, Ali M, Seckl M, Pardo O. Abstract 1775: Targeting RSK4 prevents both chemoresistance and metastasis in lung cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-1775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Lung cancer is the commonest cause of cancer death worldwide with a five-year survival rate of less than five percent for metastatic tumors. Non-small cell lung cancer (NSCLC) accounts for 80% of lung cancer cases of which adenocarcinoma prevails. Patients almost invariably develop metastatic drug-resistant disease and this is responsible for our failure to provide curative therapy. Hence, a better understanding of the mechanisms underlying these biological processes is urgently required to improve clinical outcome.
The 90-kDa ribosomal S6 kinases (RSKs) are downstream effectors of the RAS/MAPK cascade. RSKs are highly conserved serine/threonine protein kinases implicated in diverse cellular processes, including cell survival, proliferation, migration and invasion. Four isoforms exist in humans (RSK1-4) and are uniquely characterized by the presence of two non-identical N- and C-terminal kinase domains. RSK isoforms are 73-80% identical at protein level and this has been thought to suggest overlapping functions.
However, through functional genomic kinome screens, we show that RSK4, contrary to RSK1, promotes both drug resistance and metastasis in lung cancer. This kinase is overexpressed in the majority (57%) of NSCLC biopsies and this correlates with poor overall survival in lung adenocarcinoma patients. Genetic silencing of RSK4 sensitizes lung cancer cells to chemotherapy and prevents their migration and invasiveness in vitro and in vivo. RSK4 downregulation decreases the anti-apoptotic proteins Bcl2 and cIAP1/2 which correlates with increased apoptotic signalling, whilst it also induces mesenchymal-epithelial transition (MET) through inhibition of NFκB activity. A small-molecule inhibitor screen identified several floxacins, including trovafloxacin, as potent allosteric inhibitors of RSK4 activation. Trovafloxacin reproduced all biological and molecular effects of RSK4 silencing in vitro and in vivo, and is predicted to bind a novel allosteric site revealed by our RSK4 N-terminal kinase domain crystal structure and mathematical Markov Transient Analysis.
Taken together, our data demonstrate that RSK4 represents a promising novel therapeutic target in lung cancer.
Citation Format: Stelios Chrysostomou, Rajat Roy, Filippo Prischi, Katie Chapman, Uwais Mufti, Francesco Mauri, Guido Bellezza, Joel Abrahams, Silvia Ottaviani, Leandro Castellano, Georgios Giamas, David Hrouda, Mathias Winkler, David Klug, Sophia Yaliraki, Mauricio Barahona, Yulan Wang, Maruf Ali, Michael Seckl, Olivier Pardo. Targeting RSK4 prevents both chemoresistance and metastasis in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1775.
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Affiliation(s)
| | - Rajat Roy
- 1Imperial College London, London, United Kingdom
| | | | | | - Uwais Mufti
- 4Harrogate and District NHS Foundation Trust, Harrogate, United Kingdom
| | | | | | | | | | | | | | - David Hrouda
- 7Charing Cross Hospital, Imperial College NHS Trust, London, United Kingdom
| | - Mathias Winkler
- 7Charing Cross Hospital, Imperial College NHS Trust, London, United Kingdom
| | - David Klug
- 1Imperial College London, London, United Kingdom
| | | | | | - Yulan Wang
- 8Wuhan Institute of Physics and Mathematics, Wuhan, China
| | - Maruf Ali
- 1Imperial College London, London, United Kingdom
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12
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Zabet N, Catoni M, Prischi F, Paszkowski J. Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies. Nucleic Acids Res 2017; 45:3777-3784. [PMID: 28053115 PMCID: PMC5397141 DOI: 10.1093/nar/gkw1330] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/22/2016] [Indexed: 12/29/2022] Open
Abstract
Methylation of cytosine is an epigenetic mark involved in the regulation of transcription, usually associated with transcriptional repression. In mammals, methylated cytosines are found predominantly in CpGs but in plants non-CpG methylation (in the CpHpG or CpHpH contexts, where H is A, C or T) is also present and is associated with the transcriptional silencing of transposable elements. In addition, CpG methylation is found in coding regions of active genes. In the absence of the demethylase of lysine 9 of histone 3 (IBM1), a subset of body-methylated genes acquires non-CpG methylation. This was shown to alter their expression and affect plant development. It is not clear why only certain body-methylated genes gain non-CpG methylation in the absence of IBM1 and others do not. Here we describe a link between CpG methylation and the establishment of methylation in the CpHpG context that explains the two classes of body-methylated genes. We provide evidence that external cytosines of CpCpG sites can only be methylated when internal cytosines are methylated. CpCpG sites methylated in both cytosines promote spreading of methylation in the CpHpG context in genes protected by IBM1. In contrast, CpCpG sites remain unmethylated in IBM1-independent genes and do not promote spread of CpHpG methylation.
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Affiliation(s)
- Nicolae Radu Zabet
- The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK
- To whom correspondence should be addressed. Tel: +44 0 1206872630; Fax: +44 0 01206872592; . Correspondence may also be addressed to Jerzy Paszkowski. Tel: +44 0 1223761159; Fax: +44 0 1223761100;
| | - Marco Catoni
- The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Filippo Prischi
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Jerzy Paszkowski
- The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
- To whom correspondence should be addressed. Tel: +44 0 1206872630; Fax: +44 0 01206872592; . Correspondence may also be addressed to Jerzy Paszkowski. Tel: +44 0 1223761159; Fax: +44 0 1223761100;
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13
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Abstract
Hybrid methods, which combine and integrate several biochemical and biophysical techniques, have rapidly caught up in the last twenty years to provide a way to obtain a fuller description of proteins and molecular complexes with sizes and complexity otherwise not easily affordable. Here, we review the use of a robust hybrid methodology based on a mixture of NMR, SAXS, site directed mutagenesis and molecular docking which we have developed to determine the structure of weakly interacting molecular complexes. We applied this technique to gain insights into the structure of complexes formed amongst proteins involved in the molecular machine, which produces the essential iron-sulfur cluster prosthetic groups. Our results were validated both by X-ray structures and by other groups who adopted the same approach. We discuss the advantages and the limitations of our methodology and propose new avenues, which could improve it.
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Affiliation(s)
- Filippo Prischi
- School of Biological Sciences, University of Essex Colchester, UK
| | - Annalisa Pastore
- Maurice Wohl Institute, King's College LondonLondon, UK; Molecular Medicine Department, University of PaviaPavia, Italy
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14
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Prischi F, Pastore A. Application of Nuclear Magnetic Resonance and Hybrid Methods to Structure Determination of Complex Systems. Adv Exp Med Biol 2016; 896:351-68. [PMID: 27165336 DOI: 10.1007/978-3-319-27216-0_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The current main challenge of Structural Biology is to undertake the structure determination of increasingly complex systems in the attempt to better understand their biological function. As systems become more challenging, however, there is an increasing demand for the parallel use of more than one independent technique to allow pushing the frontiers of structure determination and, at the same time, obtaining independent structural validation. The combination of different Structural Biology methods has been named hybrid approaches. The aim of this review is to critically discuss the most recent examples and new developments that have allowed structure determination or experimentally-based modelling of various molecular complexes selecting them among those that combine the use of nuclear magnetic resonance and small angle scattering techniques. We provide a selective but focused account of some of the most exciting recent approaches and discuss their possible further developments.
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Affiliation(s)
- Filippo Prischi
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Annalisa Pastore
- Department of Clinical Neurosciences, King's College London, Denmark Hill Campus, London, UK.
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15
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Popovic M, Sanfelice D, Pastore C, Prischi F, Temussi PA, Pastore A. Selective observation of the disordered import signal of a globular protein by in-cell NMR: the example of frataxins. Protein Sci 2015; 24:996-1003. [PMID: 25772583 PMCID: PMC4456112 DOI: 10.1002/pro.2679] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/08/2015] [Indexed: 01/16/2023]
Abstract
We have exploited the capability of in-cell NMR to selectively observe flexible regions within folded proteins to carry out a comparative study of two members of the highly conserved frataxin family which are found both in prokaryotes and in eukaryotes. They all contain a globular domain which shares more than 50% identity, which in eukaryotes is preceded by an N-terminal tail containing the mitochondrial import signal. We demonstrate that the NMR spectrum of the bacterial ortholog CyaY cannot be observed in the homologous E. coli system, although it becomes fully observable as soon as the cells are lysed. This behavior has been observed for several other compact globular proteins as seems to be the rule rather than the exception. The NMR spectrum of the yeast ortholog Yfh1 contains instead visible signals from the protein. We demonstrate that they correspond to the flexible N-terminal tail indicating that this is flexible and unfolded. This flexibility of the N-terminus agrees with previous studies of human frataxin, despite the extensive sequence diversity of this region in the two proteins. Interestingly, the residues that we observe in in-cell experiments are not visible in the crystal structure of a Yfh1 mutant designed to destabilize the first helix. More importantly, our results show that, in cell, the protein is predominantly present not as an aggregate but as a monomeric species.
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Affiliation(s)
- Matija Popovic
- National Institute for Medical Research, MRC, The RidgewayLondon, United Kingdom
| | - Domenico Sanfelice
- Department of Clinical Neuroscience, King's College London, Denmark Hill CampusLondon, United Kingdom
| | - Chiara Pastore
- Department of Life Sciences, Centre for Structural Biology, Sir Ernst Chain Building, Imperial College LondonLondon, SW7 2AZ, United Kingdom
| | - Filippo Prischi
- Department of Life Sciences, Centre for Structural Biology, Sir Ernst Chain Building, Imperial College LondonLondon, SW7 2AZ, United Kingdom
| | - Piero Andrea Temussi
- National Institute for Medical Research, MRC, The RidgewayLondon, United Kingdom
| | - Annalisa Pastore
- Department of Clinical Neuroscience, King's College London, Denmark Hill CampusLondon, United Kingdom
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16
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Carrara M, Prischi F, Nowak PR, Ali MM. Crystal structures reveal transient PERK luminal domain tetramerization in endoplasmic reticulum stress signaling. EMBO J 2015; 34:1589-600. [PMID: 25925385 PMCID: PMC4474532 DOI: 10.15252/embj.201489183] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 04/13/2015] [Indexed: 11/25/2022] Open
Abstract
Stress caused by accumulation of misfolded proteins within the endoplasmic reticulum (ER) elicits a cellular unfolded protein response (UPR) aimed at maintaining protein-folding capacity. PERK, a key upstream component, recognizes ER stress via its luminal sensor/transducer domain, but the molecular events that lead to UPR activation remain unclear. Here, we describe the crystal structures of mammalian PERK luminal domains captured in dimeric state as well as in a novel tetrameric state. Small angle X-ray scattering analysis (SAXS) supports the existence of both crystal structures also in solution. The salient feature of the tetramer interface, a helix swapped between dimers, implies transient association. Moreover, interface mutations that disrupt tetramer formation in vitro reduce phosphorylation of PERK and its target eIF2α in cells. These results suggest that transient conversion from dimeric to tetrameric state may be a key regulatory step in UPR activation.
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Affiliation(s)
- Marta Carrara
- Department of Life Sciences, Imperial College, London, UK
| | | | - Piotr R Nowak
- Department of Life Sciences, Imperial College, London, UK
| | - Maruf Mu Ali
- Department of Life Sciences, Imperial College, London, UK
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17
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Carrara M, Prischi F, Nowak PR, Kopp MC, Ali MM. Noncanonical binding of BiP ATPase domain to Ire1 and Perk is dissociated by unfolded protein CH1 to initiate ER stress signaling. eLife 2015; 4. [PMID: 25692299 PMCID: PMC4337721 DOI: 10.7554/elife.03522] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 01/29/2015] [Indexed: 12/20/2022] Open
Abstract
The unfolded protein response (UPR) is an essential cell signaling system that detects the accumulation of misfolded proteins within the endoplasmic reticulum (ER) and initiates a cellular response in order to maintain homeostasis. How cells detect the accumulation of misfolded proteins remains unclear. In this study, we identify a noncanonical interaction between the ATPase domain of the ER chaperone BiP and the luminal domains of the UPR sensors Ire1 and Perk that dissociates when authentic ER unfolded protein CH1 binds to the canonical substrate binding domain of BiP. Unlike the interaction between chaperone and substrates, we found that the interaction between BiP and UPR sensors was unaffected by nucleotides. Thus, we discover that BiP is dual functional UPR sensor, sensing unfolded proteins by canonical binding to substrates and transducing this event to noncanonical, signaling interaction to Ire1 and Perk. Our observations implicate BiP as the key component for detecting ER stress and suggest an allosteric mechanism for UPR induction. DOI:http://dx.doi.org/10.7554/eLife.03522.001 Proteins perform many essential tasks in cells, but to be able to work they first have to correctly fold into a specific three-dimensional shape. Within the cell, many proteins are folded with the help of ‘chaperone’ proteins. If any proteins fold incorrectly, the normal workings of the cell can be disturbed, which may damage the cell. This is more likely to happen if a cell suddenly requires a large number of proteins to be made, which can overwhelm the chaperone proteins. In humans and other eukaryotic organisms, many proteins are folded in a compartment within the cell called the endoplasmic reticulum. Inside this compartment there is a system called the unfolded protein response that detects misfolded proteins and boosts the cell's capacity to re-fold them. As part of this system, two sensor proteins detect when misfolded proteins are present, but it is not clear how they do so. It has been suggested that a chaperone protein called BiP may be able to activate these sensor proteins in order to turn on the unfolded protein response. In this study, Carrara et al. studied the sensor proteins and BiP using an artificial set-up in the laboratory. The experiments show that both of the sensor proteins can bind to a section of the BiP chaperone called the ATPase domain. However, in the presence of an unfolded protein, BiP stopped interacting with the sensor proteins, which could allow the sensor proteins to activate the unfolded protein response. The experiments also show that BiP must bind to the unfolded protein to activate the unfolded protein response. Carrara et al.'s findings suggest that BiP has a dual role in cells: to sense unfolded proteins by binding to them, and then to activate the sensor proteins that trigger the unfolded protein response. Together, these results suggest a new model for how cells detect and respond to misfolded proteins within the endoplasmic reticulum, and may provide new targets for therapies to treat diseases caused by defects in protein folding. DOI:http://dx.doi.org/10.7554/eLife.03522.002
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Affiliation(s)
- Marta Carrara
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Filippo Prischi
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Piotr R Nowak
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Megan C Kopp
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Maruf Mu Ali
- Department of Life Sciences, Imperial College, London, United Kingdom
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18
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Carrara M, Prischi F, Ali MMU. UPR Signal Activation by Luminal Sensor Domains. Int J Mol Sci 2013; 14:6454-66. [PMID: 23519110 PMCID: PMC3634511 DOI: 10.3390/ijms14036454] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/15/2013] [Accepted: 03/18/2013] [Indexed: 12/23/2022] Open
Abstract
The unfolded protein response (UPR) is a cell-signaling system that detects the accumulation of unfolded protein within the endoplasmic reticulum (ER) and initiates a number of cellular responses to restore ER homeostasis. The presence of unfolded protein is detected by the ER-luminal sensor domains of the three UPR-transducer proteins IRE1, PERK, and ATF6, which then propagate the signal to the cytosol. In this review, we discuss the various mechanisms of action that have been proposed on how the sensor domains detect the presence of unfolded protein to activate downstream UPR signaling.
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Affiliation(s)
- Marta Carrara
- Department of Life Sciences, Centre for Structural Biology, Imperial College London, London SW7 2AZ, UK.
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19
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Bernini A, Spiga O, Venditti V, Prischi F, Botta M, Croce G, Tong APL, Wong WT, Niccolai N. The use of a ditopic Gd(III) paramagnetic probe for investigating α-bungarotoxin surface accessibility. J Inorg Biochem 2012; 112:25-31. [DOI: 10.1016/j.jinorgbio.2012.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 03/02/2012] [Accepted: 03/03/2012] [Indexed: 01/06/2023]
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20
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Prischi F, Konarev PV, Iannuzzi C, Pastore C, Adinolfi S, Martin SR, Svergun DI, Pastore A. Structural bases for the interaction of frataxin with the central components of iron-sulphur cluster assembly. Nat Commun 2010; 1:95. [PMID: 20981023 PMCID: PMC2982165 DOI: 10.1038/ncomms1097] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 09/22/2010] [Indexed: 01/09/2023] Open
Abstract
Reduced levels of frataxin, an essential protein of as yet unknown function, are responsible for causing the neurodegenerative pathology Friedreich's ataxia. Independent reports have linked frataxin to iron-sulphur cluster assembly through interactions with the two central components of this machinery: desulphurase Nfs1/IscS and the scaffold protein Isu/IscU. In this study, we use a combination of biophysical methods to define the structural bases of the interaction of CyaY (the bacterial orthologue of frataxin) with the IscS/IscU complex. We show that CyaY binds IscS as a monomer in a pocket between the active site and the IscS dimer interface. Recognition does not require iron and occurs through electrostatic interactions of complementary charged residues. Mutations at the complex interface affect the rates of enzymatic cluster formation. CyaY binding strengthens the affinity of the IscS/IscU complex. Our data suggest a new paradigm for understanding the role of frataxin as a regulator of IscS functions.
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Affiliation(s)
- Filippo Prischi
- National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Petr V. Konarev
- European Molecular Biology Laboratory, EMBL c/o DESY, Notkestrasse 85, Hamburg D-22603, Germany
| | - Clara Iannuzzi
- National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Chiara Pastore
- National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Salvatore Adinolfi
- National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Stephen R. Martin
- National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, EMBL c/o DESY, Notkestrasse 85, Hamburg D-22603, Germany
| | - Annalisa Pastore
- National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
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21
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Prischi F, Pastore C, Carroni M, Iannuzzi C, Adinolfi S, Temussi P, Pastore A. Of the vulnerability of orphan complex proteins: the case study of the E. coli IscU and IscS proteins. Protein Expr Purif 2010; 73:161-6. [PMID: 20471481 DOI: 10.1016/j.pep.2010.05.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 05/01/2010] [Accepted: 05/03/2010] [Indexed: 11/18/2022]
Abstract
IscS and IscU, the two central protein components of the iron sulfur cluster assembly machinery, form a complex that is still relatively poorly characterized. In an attempt to standardize the purification of these proteins for structural studies we have developed a protocol to produce them individually in high concentration and purity. We show that IscS is a rather robust protein as long as it is produced in a PLP loaded form and that this co-factor is essential for fold stability and enzyme activity. In contrast to previous evidence, we also propose that, in contrast with previous evidence, IscU is a thermodynamically stable protein with a well defined fold but, when produced in isolation, is a 'complex-orphan protein' that is prone to unfolding if not stabilised by a co-factor or a protein partner. Our work will facilitate further structural and functional studies of these proteins and eventually lead to a better understanding of the whole machinery.
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Affiliation(s)
- Filippo Prischi
- MRC National Institute for Medical research, The Ridgeway, London NW7 1AA, UK
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22
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Abstract
Frataxin is a highly conserved nuclear-encoded mitochondrial protein whose deficiency is the primary cause of Friedreich's ataxia, an autosomal recessive neurodegenerative disease. The frataxin structure comprises a well-characterized globular domain that is present in all species and is preceded in eukaryotes by a non-conserved N-terminal tail that contains the mitochondrial import signal. Little is known about the structure and dynamic properties of the N-terminal tail. Here, we show that this region is flexible and intrinsically unfolded in human frataxin. It does not alter the iron-binding or self-aggregation properties of the globular domain. It is therefore very unlikely that this region could be important for the conserved functions of the protein.
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Affiliation(s)
- Filippo Prischi
- Dipartimento di Biologia Molecolare, University of Siena, Siena, Italy
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23
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Bernini A, Venditti V, Spiga O, Ciutti A, Prischi F, Consonni R, Zetta L, Arosio I, Fusi P, Guagliardi A, Niccolai N. NMR studies on the surface accessibility of the archaeal protein Sso7d by using TEMPOL and Gd(III)(DTPA-BMA) as paramagnetic probes. Biophys Chem 2008; 137:71-5. [DOI: 10.1016/j.bpc.2008.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 07/08/2008] [Accepted: 07/08/2008] [Indexed: 11/27/2022]
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Bernini A, Spiga O, Venditti V, Prischi F, Bracci L, Tong APL, Wong WT, Niccolai N. NMR studies of lysozyme surface accessibility by using different paramagnetic relaxation probes. J Am Chem Soc 2007; 128:9290-1. [PMID: 16848438 DOI: 10.1021/ja062109y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Paramagnetic probes, whose approach to proteins can be monitored by nuclear magnetic resonance (NMR) studies, have been found to be of primary relevance for investigating protein surfaces' accessibility. Here, a Gd(III) neutral complex which contains two metal ions, [Gd2(L7)(H2O)2], is suggested as a paramagnetic probe particularly suited for systematic NMR investigation of protein surface accessibility, due to an expected high relaxivity and to the lack of electric charge which could favor specific interactions. Hen egg white lysozyme has been used as a model system to verify the absence of preferential approaches of this paramagnetic probe to specific protein moieties by comparing paramagnetic perturbation profiles of 1H-13C HSQC signals obtained in the presence of TEMPOL and [Gd2(L7)(H2O)2]. From the similarity of the measured paramagnetic perturbation profiles induced by the two different probes, specific interactions of [Gd2(L7)(H2O)2] with the enzyme could be ruled out. The large size of the latter probe is suggested to be responsible for the strong paramagnetic perturbations observed for CalphaH groups which are located in convex surface-exposed regions. The combined use of the two probes reveals fine details of the dynamics controlling their approach toward the protein surface.
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Affiliation(s)
- Andrea Bernini
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, I-53100 Siena, Italy
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25
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Venditti V, Bernini A, De Simone A, Spiga O, Prischi F, Niccolai N. MD and NMR studies of alpha-bungarotoxin surface accessibility. Biochem Biophys Res Commun 2007; 356:114-7. [PMID: 17336923 DOI: 10.1016/j.bbrc.2007.02.094] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 02/20/2007] [Indexed: 11/27/2022]
Abstract
Protein surface accessibility represents a dimension of structural biology which has not been discussed in details so far, in spite of its fundamental role in controlling the molecular recognition process. In the present report the surface accessibility of alpha-bungarotoxin, a small and well characterized protein, has been investigated by analyzing its interaction with solvent and paramagnetic molecules in an integrated way. The presence of strong hydration sites, identified by a combined analysis of MD simulation and NMR results, seems to prevent the access of Gd(III)DTPA-BMA to the protein surface. On the contrary, the limited hydration of the alpha-bungarotoxin active site favors frequent encounters between the paramagnetic probe and the protein in the latter region. All the data obtained here for alpha-bungarotoxin suggest that shape and stability of the solvation shell control its surface accessibility and, hence, intermolecular interactions in a way which could be common to many other proteins.
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Affiliation(s)
- Vincenzo Venditti
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, via A. Fiorentina 1, 53100 Siena, Italy
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26
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Spiga O, Padula MG, Scarselli M, Ciutti A, Bernini A, Venditti V, Prischi F, Falciani C, Lozzi L, Bracci L, Valensin PE, Caudai C, Niccolai N. Structurally Driven Selection of Human Hepatitis C Virus Mimotopes. Antivir Ther 2006. [DOI: 10.1177/135965350601100705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A structural genomics approach is proposed for the development of new diagnostic kits. It combines molecular modelling, peptide synthesis and immunological tests. The preliminary step is the development of a reliable three-dimensional structure of an immunodominant protein of the target pathogenic organism using the various bioinformatic strategies that are now available to structural biologists. Once the protein structure is obtained, the most surface-exposed fragments with minimal sequence variability among the different strains reported in the genomic data bank are reproduced synthetically as linear peptides. These peptides are then tested for immunoreactivity with the plasma of infected patients to determine whether the synthetic molecules have antigenic activity and can therefore be used to detect infecting agents. This structurally driven selection of mimotopes was successfully performed for the human hepatitis C virus, as five peptides that specifically interact with the plasma of HCV-infected patients were identified solely on the basis of the three-dimensional structure predicted for the E2 homodimer of the 1a viral subtype. A similar approach could easily be extended to a large variety of immunogenic proteins from other pathogenic organisms.
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Affiliation(s)
- Ottavia Spiga
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, Siena, Italy
| | - Maria G Padula
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, Siena, Italy
| | - Maria Scarselli
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, Siena, Italy
| | - Arianna Ciutti
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, Siena, Italy
| | - Andrea Bernini
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, Siena, Italy
| | - Vincenzo Venditti
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, Siena, Italy
| | - Filippo Prischi
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, Siena, Italy
| | - Chiara Falciani
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, Siena, Italy
| | - Luisa Lozzi
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, Siena, Italy
| | - Luisa Bracci
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, Siena, Italy
| | - Piero E Valensin
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, Siena, Italy
| | - Cinzia Caudai
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, Siena, Italy
| | - Neri Niccolai
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, Siena, Italy
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27
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Bernini A, Spiga O, Ciutti A, Venditti V, Prischi F, Governatori M, Bracci L, Lelli B, Pileri S, Botta M, Barge A, Laschi F, Niccolai N. NMR studies of BPTI aggregation by using paramagnetic relaxation reagents. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2006; 1764:856-62. [PMID: 16627014 DOI: 10.1016/j.bbapap.2006.02.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Revised: 02/07/2006] [Accepted: 02/27/2006] [Indexed: 11/17/2022]
Abstract
Paramagnetic probes, whose approach to proteins can be monitored by nuclear magnetic resonance (NMR) studies, have been found of primary relevance for investigating protein surfaces accessibility. Here, paramagnetic probes are also suggested for a systematic investigation on protein aggregation. Bovine pancreatic trypsin inhibitor (BPTI) was used as a model system for aggregation by analyzing its interaction with TEMPOL and Gd(III)DTPA-BMA. Some of the measured paramagnetic relaxation rates of BPTI protons exhibited a reverse dependence on protein concentration, which can be attributed to the formation of transient BPTI aggregates.
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Affiliation(s)
- Andrea Bernini
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, Via A. Fiorentina, I-53100 Siena, Italy
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Bernini A, Spiga O, Venditti V, Prischi F, Bracci L, Huang J, Tanner JA, Niccolai N. Tertiary structure prediction of SARS coronavirus helicase. Biochem Biophys Res Commun 2006; 343:1101-4. [PMID: 16579970 PMCID: PMC7092897 DOI: 10.1016/j.bbrc.2006.03.069] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Accepted: 03/11/2006] [Indexed: 11/23/2022]
Abstract
SARS coronavirus, SCV, has been recently responsible of a sudden and widespread infection which caused almost 800 victims. The limited amount of SCV protein structural information is partially responsible of the lack of specific drugs against the virus. Coronavirus helicases are very conserved and peculiar proteins which have been proposed as suitable targets for antiviral drugs, such as bananins, which have been recently shown to inhibit the SCV helicase in vitro. Here, the quaternary structure of SCV helicase has been predicted, which will provide a solid foundation for the rational design of other antiviral helicase inhibitors.
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Affiliation(s)
- Andrea Bernini
- Biomolecular Structure Research Center, Department of Molecular Biology, University of Siena, I-53100 Siena, Italy
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Spiga O, Padula MG, Scarselli M, Ciutti A, Bernini A, Venditti V, Prischi F, Falciani C, Lozzi L, Bracci L, Valensin PE, Caudai C, Niccolai N. Structurally driven selection of human hepatitis C virus mimotopes. Antivir Ther 2006; 11:917-22. [PMID: 17302254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
A structural genomics approach is proposed for the development of new diagnostic kits. It combines molecular modelling, peptide synthesis and immunological tests. The preliminary step is the development of a reliable three-dimensional structure of an immunodominant protein of the target pathogenic organism using the various bioinformatic strategies that are now available to structural biologists. Once the protein structure is obtained, the most surface-exposed fragments with minimal sequence variability among the different strains reported in the genomic data bank are reproduced synthetically as linear peptides. These peptides are then tested for immunoreactivity with the plasma of infected patients to determine whether the synthetic molecules have antigenic activity and can therefore be used to detect infecting agents. This structurally driven selection of mimotopes was successfully performed for the human hepatitis C virus, as five peptides that specifically interact with the plasma of HCV-infected patients were identified solely on the basis of the three-dimensional structure predicted for the E2 homodimer of the la viral subtype. A similar approach could easily be extended to a large variety of immunogenic proteins from other pathogenic organisms.
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Affiliation(s)
- Ottavia Spiga
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, Siena, Italy
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Spiga O, Bernini A, Ciutti A, Chiellini S, Menciassi N, Finetti F, Causarono V, Anselmi F, Prischi F, Niccolai N. Molecular modelling of S1 and S2 subunits of SARS coronavirus spike glycoprotein. Biochem Biophys Res Commun 2003; 310:78-83. [PMID: 14511651 PMCID: PMC7110993 DOI: 10.1016/j.bbrc.2003.08.122] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The S1 and S2 subunits of the spike glycoprotein of the coronavirus which is responsible for the severe acute respiratory syndrome (SARS) have been modelled, even though the corresponding amino acid sequences were not suitable for tertiary structure predictions with conventional homology and/or threading procedures. An indirect search for a protein structure to be used as a template for 3D modelling has been performed on the basis of the genomic organisation similarity generally exhibited by coronaviruses. The crystal structure of Clostridium botulinum neurotoxin B appeared to be structurally adaptable to human and canine coronavirus spike protein sequences and it was successfully used to model the two subunits of SARS coronavirus spike glycoprotein. The overall shape and the surface hydrophobicity of the two subunits in the obtained models suggest the localisation of the most relevant regions for their activity.
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Affiliation(s)
- Ottavia Spiga
- Department of Molecular Biology, University of Siena, I-53100 Siena, Italy
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