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Sureshan M, Prabhu D, Kadhirvel S. Computational identification and experimental validation of anti-filarial lead molecules targeting metal binding/substrate channel residues of Cu/Zn SOD1 from Wuchereria bancrofti. J Biomol Struct Dyn 2023; 41:8715-8728. [PMID: 36305196 DOI: 10.1080/07391102.2022.2136245] [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: 08/05/2022] [Accepted: 10/10/2022] [Indexed: 10/31/2022]
Abstract
Lymphatic filariasis (LF) is a neglected mosquito-borne parasitic disease, widely caused by Wuchereria bancrofti (Wb) in tropical and sub-tropical countries. During a blood meal, the filarial nematodes are transmitted to humans by the infected mosquito. To counter attack the invaded nematodes, the human immune system produces reactive oxygen species. However, the anti-oxidant enzymes of nematodes counteract the host oxidative cytotoxicity. Cu/Zn Superoxide dismutase (SOD1), a member of antioxidant enzymes and are widely used by the nematodes to sustain the host oxidative stress across its lifecycle, hence targeting SOD1 to develop suitable drug molecules would help to overcome the problems related to efficacy and activity of drugs upon different stages of nematodes. In order to find the potent inhibitors, a three-dimensional structure of Cu/Zn WbSOD1 was modelled and the structural stability was analysed through simulation studies. The structure-guided virtual screening approach has been used to identify lead molecules from the ChemBridge based on the docking score, ADMET properties and protein-ligand complex stability analysis. The identified compounds were observed to interact with the copper, metal binding residues (His48, His63, His80 and His120) and catalytically important residue Arg146, which play a crucial role in the disproportionation of incoming superoxide radicals of Cu/Zn WbSOD1. Further, in vitro validation of the selected leads in the filarial worm Setaria digitata exhibited higher inhibition and better IC50 compared to the standard drug ivermectin. Thus, the identified leads could potentially inhibit enzyme activity, which could subsequently act as drug candidates to control LF.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muthusamy Sureshan
- Biomolecular Crystallography Lab, Department of Bioinformatics, School of Chemical & Biotechnology, SASTRA Deemed University, Thanjavur, India
| | - Dhamodharan Prabhu
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education and Research (BIHER), Chennai, Tamil Nadu, India
| | - Saraboji Kadhirvel
- Biomolecular Crystallography Lab, Department of Bioinformatics, School of Chemical & Biotechnology, SASTRA Deemed University, Thanjavur, India
- Department of Computational Sciences, Central University of Punjab, Bathinda, Punjab, India
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2
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Mavadat E, Seyedalipour B, Hosseinkhani S, Colagar AH. Role of charged residues of the "electrostatic loop" of hSOD1 in promotion of aggregation: Implications for the mechanism of ALS-associated mutations under amyloidogenic conditions. Int J Biol Macromol 2023:125289. [PMID: 37307969 DOI: 10.1016/j.ijbiomac.2023.125289] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/14/2022] [Accepted: 06/07/2023] [Indexed: 06/14/2023]
Abstract
Protein misfolding and amyloid formation are hallmarks of numerous diseases, including amyotrophic lateral sclerosis (ALS), in which hSOD1 aggregation is involved in pathogenesis. We used two point mutations in the electrostatic loop, G138E and T137R, to analyze charge distribution under destabilizing circumstances to gain more about how ALS-linked mutations affect SOD1 protein stability or net repulsive charge. We show that protein charge is important in the ALS disease process using bioinformatics and experiments. The MD simulation findings demonstrate that the mutant protein differs significantly from WT SOD1, which is consistent with the experimental evidence. The specific activity of the wild type was 1.61 and 1.48 times higher than that of the G138E and T137R mutants, respectively. Under amyloid induction conditions, the intensity of intrinsic and ANS fluorescence in both mutants reduced. Increasing the content of β-sheet structures in mutants can be attributed to aggregation propensity, which was confirmed using CD polarimetry and FTIR spectroscopy. Our findings show that two ALS-related mutations promote the formation of amyloid-like aggregates at near physiological pH under destabilizing conditions, which were detected using spectroscopic probes such as Congo red and ThT fluorescence, and also further confirmation of amyloid-like species by TEM. Overall, our results provide evidence supporting the notion that negative charge changes combined with other destabilizing factors play an important role in increasing protein aggregation by reducing repulsive negative charges.
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Affiliation(s)
- Elaheh Mavadat
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Bagher Seyedalipour
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran.
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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3
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Zaji HD, Seyedalipour B, Hanun HM, Baziyar P, Hosseinkhani S, Akhlaghi M. Computational insight into in silico analysis and molecular dynamics simulation of the dimer interface residues of ALS-linked hSOD1 forms in apo/holo states: a combined experimental and bioinformatic perspective. 3 Biotech 2023; 13:92. [PMID: 36845075 PMCID: PMC9944573 DOI: 10.1007/s13205-023-03514-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/03/2023] [Indexed: 02/23/2023] Open
Abstract
The aggregation of misfolded SOD1 proteins in neurodegenerative illnesses is a key pathological hallmark in amyotrophic lateral sclerosis (ALS). SOD1 is stabilized and enzymatically activated after binding to Cu/Zn and forming intramolecular disulfide. SOD1 aggregation/oligomerization is triggered by the dissociation of Cu and/or Zn ions. Therefore, we compared the possible effects of ALS-associated point mutations of the holo/apo forms of WT/I149T/V148G SOD1 variants located at the dimer interface to determine structural characterization using spectroscopic methods, computational approaches as well as molecular dynamics (MD) simulations. Predictive results of computational analysis of single-nucleotide polymorphisms (SNPs) suggested that mutant SOD1 has a deleterious effect on activity and structure destabilization. MD data analysis indicated that changes in flexibility, stability, hydrophobicity of the protein as well as increased intramolecular interactions of apo-SOD1 were more than holo-SOD1. Furthermore, a decrease in enzymatic activity in apo-SOD1 was observed compared to holo-SOD1. Comparative intrinsic and ANS fluorescence results of holo/apo-WT-hSOD1 and mutants indicated structural alterations in the local environment of tryptophan residue and hydrophobic patches, respectively. Experimental and MD data supported that substitution effect and metal deficiency of mutants (apo forms) in the dimer interface may promote the tendency to protein mis-folding and aggregation, consequently disrupting the dimer-monomer equilibrium and increased propensity to dissociation dimer into SOD-monomer ultimately leading to loss of stability and function. Overall, data analysis of apo/holo SOD1 forms on protein structure and function using computational and experimental studies will contribute to a better understanding of ALS pathogenicity.
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Affiliation(s)
- Hamza Dakhil Zaji
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Bagher Seyedalipour
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Haider Munzer Hanun
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Payam Baziyar
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mona Akhlaghi
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
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4
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Brown ML, McAlary L, Lum JS, Farrawell NE, Yerbury JJ. Cells Overexpressing ALS-Associated SOD1 Variants Are Differentially Susceptible to CuATSM-Associated Toxicity. ACS Chem Neurosci 2022; 13:2371-2379. [PMID: 35900338 DOI: 10.1021/acschemneuro.2c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
CuATSM has repeatedly demonstrated to be therapeutically effective in SOD1 mouse models of amyotrophic lateral sclerosis (ALS), leading to current clinical trials. CuATSM acts to stabilize ALS-associated mutant SOD1 protein by supplying copper. However, in vitro work has demonstrated that CuATSM is only therapeutic for wild-type-like SOD1 mutants, not metal-binding-region mutants, suggesting that CuATSM may have genotype-specific effects. Furthermore, relatively high doses of CuATSM have been shown to produce adverse events in humans and mice. Here, we investigated the genotype-specific therapeutic window of CuATSM. NSC-34 cells transiently expressing copper-binding or non-binding mutations of SOD1 were treated with a broad range of CuATSM concentrations and examined for survival via time-lapse microscopy. Determination of the no-observed-adverse-effect level and the LC50 suggest that CuATSM-associated toxicity is dependent on the amount of copper-depleted SOD1 available as well as the mutant's ability to bind copper. Our results suggest that the particular variant of SOD1 mutant is crucial in not only determining the level of efficacy achieved but also potential adverse events.
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Affiliation(s)
- Mikayla L Brown
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Luke McAlary
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Jeremy S Lum
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Natalie E Farrawell
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
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5
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Kolkwitz PE, Mohrlüder J, Willbold D. Inhibition of Polyglutamine Misfolding with D-Enantiomeric Peptides Identified by Mirror Image Phage Display Selection. Biomolecules 2022; 12:biom12020157. [PMID: 35204656 PMCID: PMC8961585 DOI: 10.3390/biom12020157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/07/2022] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
Nine heritable diseases are known that are caused by unphysiologically elongated polyglutamine tracts in human proteins leading to misfolding, aggregation and neurodegeneration. Current therapeutic strategies include efforts to inhibit the expression of the respective gene coding for the polyglutamine-containing proteins. There are, however, concerns that this may interfere with the physiological function of the respective protein. We aim to stabilize the protein’s native conformation by D-enantiomeric peptide ligands to prevent misfolding and aggregation, shift the equilibrium between aggregates and monomers towards monomers and dissolve already existing aggregates into non-toxic and functional monomers. Here, we performed a mirror image phage display selection on the polyglutamine containing a fragment of the androgen receptor. An elongated polyglutamine tract in the androgen receptor causes spinal and bulbar muscular atrophy (SBMA). The selected D-enantiomeric peptides were tested for their ability to inhibit polyglutamine-induced androgen receptor aggregation. We identified D-enantiomeric peptide QF2D-2 (sqsqwstpqGkwshwprrr) as the most promising candidate. It binds to an androgen receptor fragment with 46 consecutive glutamine residues and decelerates its aggregation, even in seeded experiments. Therefore, QF2D-2 may be a promising drug candidate for SBMA treatment or even for all nine heritable polyglutamine diseases, since its aggregation-inhibiting property was shown also for a more general polyglutamine target.
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Affiliation(s)
- Pauline Elisabeth Kolkwitz
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; (P.E.K.); (J.M.)
| | - Jeannine Mohrlüder
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; (P.E.K.); (J.M.)
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; (P.E.K.); (J.M.)
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Correspondence:
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6
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Kumar S, Kumar Bhardwaj V, Singh R, Purohit R. Explicit-solvent molecular dynamics simulations revealed conformational regain and aggregation inhibition of I113T SOD1 by Himalayan bioactive molecules. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116798] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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7
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Bella ED, Bersano E, Antonini G, Borghero G, Capasso M, Caponnetto C, Chiò A, Corbo M, Filosto M, Giannini F, Spataro R, Lunetta C, Mandrioli J, Messina S, Monsurrò MR, Mora G, Riva N, Rizzi R, Siciliano G, Silani V, Simone I, Sorarù G, Tugnoli V, Verriello L, Volanti P, Furlan R, Nolan JM, Abgueguen E, Tramacere I, Lauria G. The unfolded protein response in amyotrophic later sclerosis: results of a phase 2 trial. Brain 2021; 144:2635-2647. [PMID: 33905493 PMCID: PMC8557337 DOI: 10.1093/brain/awab167] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/26/2021] [Accepted: 04/16/2021] [Indexed: 11/14/2022] Open
Abstract
Strong evidence suggests that endoplasmic reticulum (ER) stress plays a critical role in the pathogenesis of amyotrophic lateral sclerosis (ALS) through an altered regulation of proteostasis. Robust preclinical findings demonstrated that guanabenz selectively inhibits ER stress-induced eIF2α-phosphatase allowing misfolded protein clearance, reduces neuronal death and prolongs survival in in vitro and in vivo models. Its efficacy and safety in ALS patients are unknown. To address these issues, we conducted a multicentre, randomised, double-blind trial, with futility design. ALS patients with onset of symptoms within the previous 18 months were randomly assigned to receive in a 1:1:1:1 ratio guanabenz 64 mg, 32 mg, 16 mg or placebo daily for 6 months as add-on therapy to riluzole. The purpose of the placebo group blinding was safety but not efficacy. The primary outcome was the proportion of patients progressing to higher stages of disease in 6 months as measured by the ALS Milano-Torino staging compared to a historical cohort of 200 ALS patients. The secondary outcomes were the rate of decline in ALSFRS-R total score, slow vital capacity change, time to death, tracheotomy or permanent ventilation and serum light neurofilament level at 6 months. The primary analysis of efficacy was performed by intention-to-treat. Guanabenz 64 mg and 32 mg arms, both alone and combined, reached the primary hypothesis of non-futility with proportions of patients who progressed to higher stage of disease at 6 months significantly lower than that expected under the hypothesis of non-futility and significantly lower difference in the median rate of change of the ALSFRS-R total score. This effect was driven by patients with bulbar onset, none of whom (0/18) progressed to a higher stage of disease at 6 months compared with those in guanabenz 16 mg (4/8; 50%), historical cohort alone (21/49; 43%; p = 0.001) or plus placebo (25/60; 42%; p = 0.001). The proportion of patients who experienced at least one adverse event was higher in any guanabenz arm than in the placebo arm, with higher dosing arms having significantly higher proportion of drug-related side effects and the 64 mg arm significantly higher drop-out rate. The number of serious adverse events did not significantly differ between guanabenz arms and placebo. Our findings indicate that a larger trial with a molecule targeting the UPR pathway without the alpha-2 adrenergic related side-effect profile of guanabenz is warranted.
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Affiliation(s)
- Eleonora Dalla Bella
- 3rd Neurology Unit and Motor Neuron Disease Centre, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Milan, Italy
| | - Enrica Bersano
- 3rd Neurology Unit and Motor Neuron Disease Centre, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Milan, Italy
| | - Giovanni Antonini
- NESMOS Department, Neuromuscolar Disease Unit, Sant'Andrea Hospital and University of Rome "Sapienza", Rome, Italy
| | | | | | | | - Adriano Chiò
- ALS Centre "Rita Levi Montalcini", Department of Neuroscience, University of Turin, Turin, Italy.,Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Massimo Corbo
- Department of Neurorehabilitaton, Casa Cura Policlinico, Milan, Italy
| | - Massimiliano Filosto
- Department of Clinical and Experimental Sciences, University of Brescia, ASST Spedali Civili Brescia and NeMO-Brescia Clinical Centre for Neuromuscular Diseases, Brescia, Italy
| | - Fabio Giannini
- Department of Medical and Surgery Sciences and Neurosciences, University of Siena, Italy
| | | | | | - Jessica Mandrioli
- Department of Neurosciences, Azienda Ospedaliero Universitaria di Modena, Modena, Italy
| | - Sonia Messina
- Unit of Neurology and Neuromuscular Disorders, Department of Clinical and Experimental Medicine and University of Messina, AOU Policlinico "G. Martino", Messina, Italy.,NEuroMuscular Omnicentre of Messina, University Hospital "G. Martino", Messina, Italy
| | | | | | - Nilo Riva
- Department of Neurology IRCCS "San Raffaele" Hospital, Milan, Italy
| | - Romana Rizzi
- Neurology Unit, Department of Neuro-Motor Diseases, Azienda Unità Sanitaria Locale, IRCCS of Reggio Emilia, Italy
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Italy
| | - Vincenzo Silani
- Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan, Italy.,Department of Pathophysiology and Transplantation, "Dino Ferrari" Centre and Centre for Neurotechnology and Brain Therapeutics, University of Milan, Milan, Italy
| | - Isabella Simone
- Department of Neurology and Psychiatry, University of Bari, Italy
| | - Gianni Sorarù
- Department of Neurosciences, University of Padua, Italy
| | - Valeria Tugnoli
- Department of Neuroscience and Rehabilitation, Division of Neurology, University Hospital of Ferrara, Ferrara, Italy
| | - Lorenzo Verriello
- Neurology Unit, S. Maria della Misericordia University Hospital, Udine, Italy
| | - Paolo Volanti
- Intensive Neurorehabilitation Unit, ICS Maugeri IRCCS, Mistretta, Italy
| | - Roberto Furlan
- Clinical Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - John M Nolan
- Drew University, Caspersen School of Graduate Studies, Madison, NJ, USA
| | | | - Irene Tramacere
- Scientific Directorate, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Milan, Italy
| | - Giuseppe Lauria
- 3rd Neurology Unit and Motor Neuron Disease Centre, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Milan, Italy.,Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
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8
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Butler KE, Takinami Y, Rainczuk A, Baker ES, Roberts BR. Utilizing Ion Mobility-Mass Spectrometry to Investigate the Unfolding Pathway of Cu/Zn Superoxide Dismutase. Front Chem 2021; 9:614595. [PMID: 33634076 PMCID: PMC7900566 DOI: 10.3389/fchem.2021.614595] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/08/2021] [Indexed: 11/30/2022] Open
Abstract
Native mass spectrometry has emerged as a powerful tool for structural biology as it enables the evaluation of molecules as they occur in their physiological conditions. Ion mobility spectrometry-mass spectrometry (IMS-MS) has shown essential in these analyses as it allows the measurement of the shape of a molecule, denoted as its collision cross section (CCS), and mass. The structural information garnered from native IMS-MS provides insight into the tertiary and quaternary structure of proteins and can be used to validate NMR or crystallographic X-ray structures. Additionally, due to the rapid nature (millisecond measurements) and ability of IMS-MS to analyze heterogeneous solutions, it can be used to address structural questions not possible with traditional structural approaches. Herein, we applied multiple solution conditions to systematically denature bovine Cu/Zn-superoxide dismutase (SOD1) and assess its unfolding pathway from the holo-dimer to the holo-monomer, single-metal monomer, and apo-monomer. Additionally, we compared and noted 1–2% agreement between CCS values from both drift tube IMS and trapped IMS for the SOD1 holo-monomer and holo-dimer. The observed CCS values were in excellent agreement with computational CCS values predicted from the homo-dimer crystal structure, showcasing the ability to use both IMS-MS platforms to provide valuable structural information for molecular modeling of protein interactions and structural assessments.
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Affiliation(s)
- Karen E Butler
- Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | | | | | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Blaine R Roberts
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States.,Department of Neuroscience, Emory University School of Medicine, Atlanta, GA, United States
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9
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Cveticanin J, Mondal T, Meiering EM, Sharon M, Horovitz A. Insight into the Autosomal-Dominant Inheritance Pattern of SOD1-Associated ALS from Native Mass Spectrometry. J Mol Biol 2020; 432:5995-6002. [PMID: 33058881 DOI: 10.1016/j.jmb.2020.09.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 02/05/2023]
Abstract
About 20% of all familial amyotrophic lateral sclerosis (ALS) cases are associated with mutations in superoxide dismutase (SOD1), a homodimeric protein. The disease has an autosomal-dominant inheritance pattern. It is, therefore, important to determine whether wild-type and mutant SOD1 subunits self-associate randomly or preferentially. A measure for the extent of bias in subunit association is the coupling constant determined in a double-mutant cycle type analysis. Here, cell lysates containing co-expressed wild-type and mutant SOD1 subunits were analyzed by native mass spectrometry to determine these coupling constants. Strikingly, we find a linear positive correlation between the coupling constant and the reported average duration of the disease. Our results indicate that inter-subunit communication and a preference for heterodimerization greatly increase the disease severity.
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Affiliation(s)
- Jelena Cveticanin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tridib Mondal
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Amnon Horovitz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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10
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Dantas LS, Viviani LG, Inague A, Piccirillo E, Rezende LD, Ronsein GE, Augusto O, Medeiros MHG, Amaral ATD, Miyamoto S. Lipid aldehyde hydrophobicity affects apo-SOD1 modification and aggregation. Free Radic Biol Med 2020; 156:157-167. [PMID: 32598986 DOI: 10.1016/j.freeradbiomed.2020.05.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/30/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022]
Abstract
Unsaturated lipids are oxidized by reactive oxygen species and enzymes, leading to the increased formation of lipid hydroperoxides and several electrophilic products. Lipid-derived electrophiles can modify macromolecules, such as proteins, resulting in the loss of function and/or aggregation. The accumulation of Cu,Zn-superoxide dismutase (SOD1) aggregates has been associated with familial cases of amyotrophic lateral sclerosis (ALS). The protein aggregation mechanisms in motor neurons remain unclear, although recent studies have shown that lipids and oxidized lipid derivatives may play roles in this process. Here, we aimed to compare the effects of different lipid aldehydes on the induction of SOD1 modifications and aggregation, in vitro. Human recombinant apo-SOD1 was incubated with 4-hydroxy-2-hexenal (HHE), 4-hydroxy-2-nonenal (HNE), 2-hexen-1-al (HEX), 2,4-nonadienal (NON), 2,4-decadienal (DEC), or secosterol aldehydes (SECO-A or SECO-B). High-molecular-weight apo-SOD1 aggregates dramatically increased in the presence of highly hydrophobic aldehydes (LogPcalc > 3). Notably, several Lys residues were modified by exposure to all aldehydes. The observed modifications were primarily observed on Lys residues located near the dimer interface (K3 and K9) and at the electrostatic loop (K122, K128, and K136). Moreover, HHE and HNE induced extensive apo-SOD1 modifications, by forming Schiff bases or Michael adducts with Lys, His, and Cys residues. However, these aldehydes were unable to induce large protein aggregates. Overall, our data shed light on the importance of lipid aldehyde hydrophobicity on the induction of apo-SOD1 aggregation and identified preferential sites of lipid aldehyde-induced modifications.
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Affiliation(s)
- Lucas S Dantas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Lucas G Viviani
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Alex Inague
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Erika Piccirillo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil; Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Leandro de Rezende
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Graziella E Ronsein
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ohara Augusto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Marisa H G Medeiros
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Antonia T do Amaral
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Sayuri Miyamoto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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11
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Tompa DR, Muthusamy S, Srikanth S, Kadhirvel S. Molecular dynamics of far positioned surface mutations of Cu/Zn SOD1 promotes altered structural stability and metal-binding site: Structural clues to the pathogenesis of amyotrophic lateral sclerosis. J Mol Graph Model 2020; 100:107678. [PMID: 32768728 DOI: 10.1016/j.jmgm.2020.107678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/18/2020] [Accepted: 06/26/2020] [Indexed: 10/23/2022]
Abstract
Cu/Zn superoxide dismutase (SOD1) mutations are associated to the motor neuron disorder, amyotrophic lateral sclerosis (ALS), which is characterized by aggregates of the misfolded proteins. The distribution of mutations all over the three-dimensional structure of SOD1 makes it complex to determine the exact molecular mechanism underlying SOD1 destabilization and the associated ALS pathology. In this study, we have examined structure and dynamics of SOD1 protein upon two ALS associated point mutations at the surface residue Glu100 (E100G and E100K), which is located far from the Cu and Zn sites and dimer interface. The molecular dynamics simulations were performed for these mutants for 50ns using GROMACS package. Our results indicate that the mutations result in structural destabilization by affecting the gate keeping role of Glu100 and loss of electrostatic interactions on the protein surface which stabilizes the β-barrel structure of the native form. Further, these mutations could increase the fluctuations in the zinc-binding loop (loop IV), primarily due to loss of hydrogen bond between Asp101 and Arg79. The relaxed conformation of Arg79 further affects the native conformation of His80 and Asp83, that results in altered zinc site geometry and the structure of the substrate channel. Our results clearly suggest that, similar to the mutations located at metal sites/dimer interface/disulfide regions, the mutations at the far positioned site (Glu100) also induce significant conformational changes that could affect the metallation and structure of SOD1 molecule, resulting in formation of toxic intermediate species that cause ALS.
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Affiliation(s)
- Dharma Rao Tompa
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India
| | - Sureshan Muthusamy
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India
| | - Srimari Srikanth
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India
| | - Saraboji Kadhirvel
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India.
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Computational prediction of protein aggregation: Advances in proteomics, conformation-specific algorithms and biotechnological applications. Comput Struct Biotechnol J 2020; 18:1403-1413. [PMID: 32637039 PMCID: PMC7322485 DOI: 10.1016/j.csbj.2020.05.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/16/2022] Open
Abstract
Protein aggregation is a widespread phenomenon that stems from the establishment of non-native intermolecular contacts resulting in protein precipitation. Despite its deleterious impact on fitness, protein aggregation is a generic property of polypeptide chains, indissociable from protein structure and function. Protein aggregation is behind the onset of neurodegenerative disorders and one of the serious obstacles in the production of protein-based therapeutics. The development of computational tools opened a new avenue to rationalize this phenomenon, enabling prediction of the aggregation propensity of individual proteins as well as proteome-wide analysis. These studies spotted aggregation as a major force driving protein evolution. Actual algorithms work on both protein sequences and structures, some of them accounting also for conformational fluctuations around the native state and the protein microenvironment. This toolbox allows to delineate conformation-specific routines to assist in the identification of aggregation-prone regions and to guide the optimization of more soluble and stable biotherapeutics. Here we review how the advent of predictive tools has change the way we think and address protein aggregation.
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13
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Computational prediction and redesign of aberrant protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:43-83. [DOI: 10.1016/bs.pmbts.2019.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Wells C, Brennan SE, Keon M, Saksena NK. Prionoid Proteins in the Pathogenesis of Neurodegenerative Diseases. Front Mol Neurosci 2019; 12:271. [PMID: 31780895 PMCID: PMC6861308 DOI: 10.3389/fnmol.2019.00271] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
There is a growing body of evidence that prionoid protein behaviors are a core element of neurodegenerative diseases (NDs) that afflict humans. Common elements in pathogenesis, pathological effects and protein-level behaviors exist between Alzheimer's Disease (AD), Parkinson's Disease (PD), Huntington's Disease (HD) and Amyotrophic Lateral Sclerosis (ALS). These extend beyond the affected neurons to glial cells and processes. This results in a complicated system of disease progression, which often takes advantage of protective processes to promote the propagation of pathological protein aggregates. This review article provides a current snapshot of knowledge on these proteins and their intrinsic role in the pathogenesis and disease progression seen across NDs.
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Bunck DN, Atsavapranee B, Museth AK, VanderVelde D, Heath JR. Modulating the Folding Landscape of Superoxide Dismutase 1 with Targeted Molecular Binders. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- David N. Bunck
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 East California Boulevard MC 172-27 USA
| | - Beatriz Atsavapranee
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 East California Boulevard MC 172-27 USA
| | - Anna K. Museth
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 East California Boulevard MC 172-27 USA
| | - David VanderVelde
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 East California Boulevard MC 172-27 USA
| | - James R. Heath
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 East California Boulevard MC 172-27 USA
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Bunck DN, Atsavapranee B, Museth AK, VanderVelde D, Heath JR. Modulating the Folding Landscape of Superoxide Dismutase 1 with Targeted Molecular Binders. Angew Chem Int Ed Engl 2018; 57:6212-6215. [PMID: 29645329 DOI: 10.1002/anie.201802269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Indexed: 01/20/2023]
Abstract
Amyotrophic lateral sclerosis, or Lou Gehrig's disease, is characterized by motor neuron death, with average survival times of two to five years. One cause of this disease is the misfolding of superoxide dismutase 1 (SOD1), a phenomenon influenced by point mutations spanning the protein. Herein, we used an epitope-specific high-throughput screen to identify a peptide ligand that stabilizes the SOD1 native conformation and accelerates its folding by a factor of 2.5. This strategy may be useful for fundamental studies of protein energy landscapes as well as designing new classes of therapeutics.
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Affiliation(s)
- David N Bunck
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC, 172-27, USA
| | - Beatriz Atsavapranee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC, 172-27, USA
| | - Anna K Museth
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC, 172-27, USA
| | - David VanderVelde
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC, 172-27, USA
| | - James R Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC, 172-27, USA
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Tompa DR, Kadhirvel S. Molecular dynamics of a far positioned SOD1 mutant V14M reveals pathogenic misfolding behavior. J Biomol Struct Dyn 2017; 36:4085-4098. [PMID: 29157189 DOI: 10.1080/07391102.2017.1407675] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Human superoxide dismutase (Cu/Zn SOD1) is a homodimeric enzyme. Mutations in Cu/Zn SOD1 causes a familial form of amyotrophic lateral sclerosis (fALS), and aggregation of mutant SOD1 has been proposed to play a role in neurodegeneration. Though a majority of the mutations are point substitutions, there are a few changes that result in amino acid deletions or truncations of the polypeptide. These pathogenic mutations are scattered throughout the three-dimensional structure of the dimeric enzyme, which creates a puzzling pattern to investigate the molecular determinants of fALS. The most common hypothesis proposed that the misfolding of SOD1 mutants are primarily triggered by decreased affinity for metal ions. However, this hypothesis is challenging, as a significant number of disease-causing mutations are located far away from the metal-binding site and dimer interface. So in the present study, we have investigated the influence of such a far positioned pathogenic mutation, V14M, in altering the stability and folding of the Cu/Zn SOD1. Though the location of Val14 is far positioned, it has a vital role in the stability of SOD1 by preserving its hydrophobic cluster at one end of the β barrel domain. We have performed MD simulations of the V14M mutant for 80 ns timescale. The results reveal the fact that irrespective of its location, V14M mutation triggers a conformational change that is more similar to that of the metal-deficient holo form and could resemble an intermediate state in the folding reaction which results in protein misfolding and aggregation.
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Affiliation(s)
- Dharma Rao Tompa
- a Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology , SASTRA University , Thanjavur 613 401 , India
| | - Saraboji Kadhirvel
- a Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology , SASTRA University , Thanjavur 613 401 , India
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Sibilla C, Bertolotti A. Prion Properties of SOD1 in Amyotrophic Lateral Sclerosis and Potential Therapy. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a024141. [PMID: 28096265 DOI: 10.1101/cshperspect.a024141] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating and rapidly progressive neurodegenerative disease caused by the deterioration of motor neurons. The first symptoms of ALS always begin at a focal but variable site and consistently spread to neighboring regions, suggesting that neurodegeneration in ALS is an orderly and propagating process. Like other neurodegenerative diseases, misfolding of a specific protein is central to ALS. SOD1, the major constituent of the protein deposits in some familial and sporadic forms of ALS, propagates its misfolded conformation like prions, providing a plausible molecular basis for the focality and spreading of muscle weakness in ALS. Because protein misfolding is a common cause of diverse neurodegenerative diseases, strategies aimed at boosting a cell's ability to cope with misfolded proteins could lead to therapeutics to combat these devastating age-related proteinopathies.
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Affiliation(s)
- Caroline Sibilla
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Anne Bertolotti
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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Prakash A, Kumar V, Pandey P, Bharti DR, Vishwakarma P, Singh R, Hassan MI, Lynn AM. Solvent sensitivity of protein aggregation in Cu, Zn superoxide dismutase: a molecular dynamics simulation study. J Biomol Struct Dyn 2017; 36:2605-2617. [PMID: 28782426 DOI: 10.1080/07391102.2017.1364670] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Misfolding and aggregation of Cu, Zn Superoxide Dismutase (SOD1) is often found in amyotrophic lateral sclerosis (ALS) patients. The central apo SOD1 barrel was involved in protein maturation and pathological aggregation in ALS. In this work, we employed atomistic molecular dynamics (MD) simulations to study the conformational dynamics of SOD1barrel monomer in different concentrations of trifluoroethanol (TFE). We find concentration dependence unusual structural and dynamical features, characterized by the local unfolding of SOD1barrel. This partially unfolded structure is characterized by the exposure of hydrophobic core, is highly dynamic in nature, and is the precursor of aggregation seen in SOD1barrel. Our computational studies supports the hypothesis of the formation of aggregation 'building blocks' by means of local unfolding of apo monomer as the mechanism of SOD1 fibrillar aggregation. The non-monotonic TFE concentration dependence of protein conformational changes was explored through simulation studies. Our results suggest that altered protein conformation and dynamics within its structure may underlie the aggregation of SOD1 in ALS.
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Affiliation(s)
- Amresh Prakash
- a School of Computational & Integrative Sciences , Jawaharlal Nehru University , New Delhi , 110067 , India
| | - Vijay Kumar
- b Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi , 110025 , India
| | - Preeti Pandey
- a School of Computational & Integrative Sciences , Jawaharlal Nehru University , New Delhi , 110067 , India
| | - Deepak R Bharti
- a School of Computational & Integrative Sciences , Jawaharlal Nehru University , New Delhi , 110067 , India
| | - Poonam Vishwakarma
- a School of Computational & Integrative Sciences , Jawaharlal Nehru University , New Delhi , 110067 , India
| | - Ruhar Singh
- a School of Computational & Integrative Sciences , Jawaharlal Nehru University , New Delhi , 110067 , India
| | - Md Imtaiyaz Hassan
- b Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi , 110025 , India
| | - Andrew M Lynn
- a School of Computational & Integrative Sciences , Jawaharlal Nehru University , New Delhi , 110067 , India
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Bella ED, Tramacere I, Antonini G, Borghero G, Capasso M, Caponnetto C, Chiò A, Corbo M, Eleopra R, Filosto M, Giannini F, Granieri E, Bella VL, Lunetta C, Mandrioli J, Mazzini L, Messina S, Monsurrò MR, Mora G, Riva N, Rizzi R, Siciliano G, Silani V, Simone I, Sorarù G, Volanti P, Lauria G. Protein misfolding, amyotrophic lateral sclerosis and guanabenz: protocol for a phase II RCT with futility design (ProMISe trial). BMJ Open 2017; 7:e015434. [PMID: 28801400 PMCID: PMC5724081 DOI: 10.1136/bmjopen-2016-015434] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Recent studies suggest that endoplasmic reticulum stress may play a critical role in the pathogenesis of amyotrophic lateral sclerosis (ALS) through an altered regulation of the proteostasis, the cellular pathway-balancing protein synthesis and degradation. A key mechanism is thought to be the dephosphorylation of eIF2α, a factor involved in the initiation of protein translation. Guanabenz is an alpha-2-adrenergic receptor agonist safely used in past to treat mild hypertension and is now an orphan drug. A pharmacological action recently discovered is its ability to modulate the synthesis of proteins by the activation of translational factors preventing misfolded protein accumulation and endoplasmic reticulum overload. Guanabenz proved to rescue motoneurons from misfolding protein stress both in in vitro and in vivo ALS models, making it a potential disease-modifying drug in patients. It is conceivable investigating whether its neuroprotective effects based on the inhibition of eIF2α dephosphorylation can change the progression of ALS. METHODS AND ANALYSES Protocolised Management In Sepsis is a multicentre, randomised, double-blind, placebo-controlled phase II clinical trial with futility design. We will investigate clinical outcomes, safety, tolerability and biomarkers of neurodegeneration in patients with ALS treated with guanabenz or riluzole alone for 6 months. The primary aim is to test if guanabenz can reduce the proportion of patients progressed to a higher stage of disease at 6 months compared with their baseline stage as measured by the ALS Milano-Torino Staging (ALS-MITOS) system and to the placebo group. Secondary aims are safety, tolerability and change in at least one biomarker of neurodegeneration in the guanabenz arm compared with the placebo group. Findings will provide reliable data on the likelihood that guanabenz can slow the course of ALS in a phase III trial. ETHICS AND DISSEMINATION The study protocol was approved by the Ethics Committee of IRCCS 'Carlo Besta Foundation' of Milan (Eudract no. 2014-005367-32 Pre-results) based on the Helsinki declaration.
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Affiliation(s)
- Eleonora Dalla Bella
- 3rd Neurology Unit and ALS Centre, IRCCS ‘Carlo Besta’ Neurological Institute, Milan, Italy
| | - Irene Tramacere
- Scientific Direction, IRCCS ‘Carlo Besta’ Neurological Institute, Milan, Italy
| | - Giovanni Antonini
- Neuromuscular Disease Unit, Sant’Andrea Hospital and University of Rome ‘Sapienza’, Rome, Italy
| | - Giuseppe Borghero
- Neurologic Unit, Monserrato University Hospital, Cagliari University, Cagliari, Italy
| | | | - Claudia Caponnetto
- Department of Neurosciences, Rehabilitatioņ Ophthalmology, Genetics, Mother and Child Disease, IRCCS University Hospital San Martino IST, Genova, Italy
| | - Adriano Chiò
- Department of Neurosciences, ALS Centre, ‘Rita Levi Montalcini’, University of Turin and Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Massimo Corbo
- Department of Neurorehabilitation, Casa Cura Policlinico, Milan, Italy
| | - Roberto Eleopra
- Neurology Unit, S Maria della Misericordia University Hospital, Udine, Italy
| | | | - Fabio Giannini
- Department of Medical and Surgery Sciences and Neurosciences, University of Siena, Siena, Italy
| | | | | | | | - Jessica Mandrioli
- Department of Neurosciences, S Agostino-Estense Hospital, Modena, Italy
| | - Letizia Mazzini
- ALS Centre, Neurologic Clinic, Maggiore della Carità University Hospital, Novara;, Italy
| | | | | | - Gabriele Mora
- ALS Center, ‘Salvatore Maugeri’ Clinical-Scientific Institutes, Milan, Italy
| | - Nilo Riva
- Department of Neurology IRCCS ‘San Raffaele’ Hospital, Milan, Italy
| | - Romana Rizzi
- Neurology Unit, Department of Neuro-Motor Diseases, IRCCS Arcispedale Santa Maria Nuova, Reggio Emilia, Italy
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Pisa, Italy
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano - Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milan, Italy
| | - Isabella Simone
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari, Bari, Italy
| | - Gianni Sorarù
- Department of Neurosciences, University of Padua, Padua, Italy
| | - Paolo Volanti
- Intensive Neurorehabilitation Unit, IRCCS ‘Salvatore Maugeri’ Foundation, Mistretta, Italy
| | - Giuseppe Lauria
- 3rd Neurology Unit and ALS Centre, IRCCS ‘Carlo Besta’ Neurological Institute, Milan, Italy
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Danielsson J, Oliveberg M. Comparing protein behaviour in vitro and in vivo , what does the data really tell us? Curr Opin Struct Biol 2017; 42:129-135. [DOI: 10.1016/j.sbi.2017.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/04/2017] [Indexed: 10/20/2022]
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McAlary L, Aquilina JA, Yerbury JJ. Susceptibility of Mutant SOD1 to Form a Destabilized Monomer Predicts Cellular Aggregation and Toxicity but Not In vitro Aggregation Propensity. Front Neurosci 2016; 10:499. [PMID: 27867347 PMCID: PMC5095133 DOI: 10.3389/fnins.2016.00499] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 10/20/2016] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the rapid and progressive degeneration of upper and lower motor neurons in the spinal cord, brain stem and motor cortex. The first gene linked to ALS was the gene encoding the free radical scavenging enzyme superoxide dismutase-1 (SOD1) that currently has over 180, mostly missense, ALS-associated mutations identified. SOD1-associated fALS patients show remarkably broad mean survival times (<1 year to ~17 years death post-diagnosis) that are mutation dependent. A hallmark of SOD1-associated ALS is the deposition of SOD1 into large insoluble aggregates in motor neurons. This is thought to be a consequence of mutation induced structural destabilization and/or oxidative damage leading to the misfolding and aggregation of SOD1 into a neurotoxic species. Here we aim to understand the relationship between SOD1 variant toxicity, structural stability, and aggregation propensity using a combination of cell culture and purified protein assays. Cell based assays indicated that aggregation of SOD1 variants correlate closely to cellular toxicity. However, the relationship between cellular toxicity and disease severity was less clear. We next utilized mass spectrometry to interrogate the structural consequences of metal loss and disulfide reduction on fALS-associated SOD1 variant structure. All variants showed evidence of unfolded, intermediate, and compact conformations, with SOD1G37R, SOD1G93A and SOD1V148G having the greatest abundance of intermediate and unfolded SOD1. SOD1G37R was an informative outlier as it had a high propensity to unfold and form oligomeric aggregates, but it did not aggregate to the same extent as SOD1G93A and SOD1V148G in in vitro aggregation assays. Furthermore, seeding the aggregation of DTT/EDTA-treated SOD1G37R with preformed SOD1G93A fibrils elicited minimal aggregation response, suggesting that the arginine substitution at position-37 blocks the templating of SOD1 onto preformed fibrils. We propose that this difference may be explained by multiple strains of SOD1 aggregate and this may also help explain the slow disease progression observed in patients with SOD1G37R.
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Affiliation(s)
- Luke McAlary
- Lab 210, Illawarra Health and Medical Research InstituteWollongong, NSW, Australia; Science Medicine and Health Faculty, School of Biological Sciences, University of WollongongWollongong, NSW, Australia
| | - J Andrew Aquilina
- Science Medicine and Health Faculty, School of Biological Sciences, University of Wollongong Wollongong, NSW, Australia
| | - Justin J Yerbury
- Lab 210, Illawarra Health and Medical Research InstituteWollongong, NSW, Australia; Science Medicine and Health Faculty, School of Biological Sciences, University of WollongongWollongong, NSW, Australia
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Lei XG, Zhu JH, Cheng WH, Bao Y, Ho YS, Reddi AR, Holmgren A, Arnér ESJ. Paradoxical Roles of Antioxidant Enzymes: Basic Mechanisms and Health Implications. Physiol Rev 2016; 96:307-64. [PMID: 26681794 DOI: 10.1152/physrev.00010.2014] [Citation(s) in RCA: 247] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are generated from aerobic metabolism, as a result of accidental electron leakage as well as regulated enzymatic processes. Because ROS/RNS can induce oxidative injury and act in redox signaling, enzymes metabolizing them will inherently promote either health or disease, depending on the physiological context. It is thus misleading to consider conventionally called antioxidant enzymes to be largely, if not exclusively, health protective. Because such a notion is nonetheless common, we herein attempt to rationalize why this simplistic view should be avoided. First we give an updated summary of physiological phenotypes triggered in mouse models of overexpression or knockout of major antioxidant enzymes. Subsequently, we focus on a series of striking cases that demonstrate "paradoxical" outcomes, i.e., increased fitness upon deletion of antioxidant enzymes or disease triggered by their overexpression. We elaborate mechanisms by which these phenotypes are mediated via chemical, biological, and metabolic interactions of the antioxidant enzymes with their substrates, downstream events, and cellular context. Furthermore, we propose that novel treatments of antioxidant enzyme-related human diseases may be enabled by deliberate targeting of dual roles of the pertaining enzymes. We also discuss the potential of "antioxidant" nutrients and phytochemicals, via regulating the expression or function of antioxidant enzymes, in preventing, treating, or aggravating chronic diseases. We conclude that "paradoxical" roles of antioxidant enzymes in physiology, health, and disease derive from sophisticated molecular mechanisms of redox biology and metabolic homeostasis. Simply viewing antioxidant enzymes as always being beneficial is not only conceptually misleading but also clinically hazardous if such notions underpin medical treatment protocols based on modulation of redox pathways.
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Affiliation(s)
- Xin Gen Lei
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing,China; Department of Animal Science, Cornell University, Ithaca, New York; Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Food Science, Nutrition and Health Promotion, Mississippi State University, Mississippi State, Mississippi; Department of Nutrition, Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom; Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan; Georgia Institute of Technology, School of Chemistry and Biochemistry, Parker Petit Institute for Bioengineering and Biosciences, Atlanta, Georgia; and Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jian-Hong Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing,China; Department of Animal Science, Cornell University, Ithaca, New York; Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Food Science, Nutrition and Health Promotion, Mississippi State University, Mississippi State, Mississippi; Department of Nutrition, Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom; Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan; Georgia Institute of Technology, School of Chemistry and Biochemistry, Parker Petit Institute for Bioengineering and Biosciences, Atlanta, Georgia; and Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Wen-Hsing Cheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing,China; Department of Animal Science, Cornell University, Ithaca, New York; Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Food Science, Nutrition and Health Promotion, Mississippi State University, Mississippi State, Mississippi; Department of Nutrition, Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom; Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan; Georgia Institute of Technology, School of Chemistry and Biochemistry, Parker Petit Institute for Bioengineering and Biosciences, Atlanta, Georgia; and Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yongping Bao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing,China; Department of Animal Science, Cornell University, Ithaca, New York; Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Food Science, Nutrition and Health Promotion, Mississippi State University, Mississippi State, Mississippi; Department of Nutrition, Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom; Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan; Georgia Institute of Technology, School of Chemistry and Biochemistry, Parker Petit Institute for Bioengineering and Biosciences, Atlanta, Georgia; and Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ye-Shih Ho
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing,China; Department of Animal Science, Cornell University, Ithaca, New York; Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Food Science, Nutrition and Health Promotion, Mississippi State University, Mississippi State, Mississippi; Department of Nutrition, Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom; Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan; Georgia Institute of Technology, School of Chemistry and Biochemistry, Parker Petit Institute for Bioengineering and Biosciences, Atlanta, Georgia; and Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Amit R Reddi
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing,China; Department of Animal Science, Cornell University, Ithaca, New York; Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Food Science, Nutrition and Health Promotion, Mississippi State University, Mississippi State, Mississippi; Department of Nutrition, Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom; Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan; Georgia Institute of Technology, School of Chemistry and Biochemistry, Parker Petit Institute for Bioengineering and Biosciences, Atlanta, Georgia; and Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Arne Holmgren
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing,China; Department of Animal Science, Cornell University, Ithaca, New York; Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Food Science, Nutrition and Health Promotion, Mississippi State University, Mississippi State, Mississippi; Department of Nutrition, Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom; Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan; Georgia Institute of Technology, School of Chemistry and Biochemistry, Parker Petit Institute for Bioengineering and Biosciences, Atlanta, Georgia; and Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Elias S J Arnér
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing,China; Department of Animal Science, Cornell University, Ithaca, New York; Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Food Science, Nutrition and Health Promotion, Mississippi State University, Mississippi State, Mississippi; Department of Nutrition, Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom; Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan; Georgia Institute of Technology, School of Chemistry and Biochemistry, Parker Petit Institute for Bioengineering and Biosciences, Atlanta, Georgia; and Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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24
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Broom HR, Rumfeldt JAO, Vassall KA, Meiering EM. Destabilization of the dimer interface is a common consequence of diverse ALS-associated mutations in metal free SOD1. Protein Sci 2015; 24:2081-9. [PMID: 26362407 DOI: 10.1002/pro.2803] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/02/2015] [Accepted: 09/11/2015] [Indexed: 11/08/2022]
Abstract
Neurotoxic misfolding of Cu, Zn-superoxide dismutase (SOD1) is implicated in causing amyotrophic lateral sclerosis, a devastating and incurable neurodegenerative disease. Disease-linked mutations in SOD1 have been proposed to promote misfolding and aggregation by decreasing protein stability and increasing the proportion of less folded forms of the protein. Here we report direct measurement of the thermodynamic effects of chemically and structurally diverse mutations on the stability of the dimer interface for metal free (apo) SOD1 using isothermal titration calorimetry and size exclusion chromatography. Remarkably, all mutations studied, even ones distant from the dimer interface, decrease interface stability, and increase the population of monomeric SOD1. We interpret the thermodynamic data to mean that substantial structural perturbations accompany dimer dissociation, resulting in the formation of poorly packed and malleable dissociated monomers. These findings provide key information for understanding the mechanisms and energetics underlying normal maturation of SOD1, as well as toxic SOD1 misfolding pathways associated with disease. Furthermore, accurate prediction of protein-protein association remains very difficult, especially when large structural changes are involved in the process, and our findings provide a quantitative set of data for such cases, to improve modelling of protein association.
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Affiliation(s)
- Helen R Broom
- Department of Chemistry, Guelph-Waterloo Centre for Graduate Work in Chemistry and Biochemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Jessica A O Rumfeldt
- Department of Chemistry, Guelph-Waterloo Centre for Graduate Work in Chemistry and Biochemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Kenrick A Vassall
- Department of Chemistry, Guelph-Waterloo Centre for Graduate Work in Chemistry and Biochemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Elizabeth M Meiering
- Department of Chemistry, Guelph-Waterloo Centre for Graduate Work in Chemistry and Biochemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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25
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Das I, Krzyzosiak A, Schneider K, Wrabetz L, D'Antonio M, Barry N, Sigurdardottir A, Bertolotti A. Preventing proteostasis diseases by selective inhibition of a phosphatase regulatory subunit. Science 2015; 348:239-42. [PMID: 25859045 DOI: 10.1126/science.aaa4484] [Citation(s) in RCA: 312] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein phosphorylation regulates virtually all biological processes. Although protein kinases are popular drug targets, targeting protein phosphatases remains a challenge. Here, we describe Sephin1 (selective inhibitor of a holophosphatase), a small molecule that safely and selectively inhibited a regulatory subunit of protein phosphatase 1 in vivo. Sephin1 selectively bound and inhibited the stress-induced PPP1R15A, but not the related and constitutive PPP1R15B, to prolong the benefit of an adaptive phospho-signaling pathway, protecting cells from otherwise lethal protein misfolding stress. In vivo, Sephin1 safely prevented the motor, morphological, and molecular defects of two otherwise unrelated protein-misfolding diseases in mice, Charcot-Marie-Tooth 1B, and amyotrophic lateral sclerosis. Thus, regulatory subunits of phosphatases are drug targets, a property exploited here to safely prevent two protein misfolding diseases.
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Affiliation(s)
- Indrajit Das
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Agnieszka Krzyzosiak
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Kim Schneider
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Lawrence Wrabetz
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Maurizio D'Antonio
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Nicholas Barry
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Anna Sigurdardottir
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Anne Bertolotti
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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26
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Estácio SG, Leal SS, Cristóvão JS, Faísca PFN, Gomes CM. Calcium binding to gatekeeper residues flanking aggregation-prone segments underlies non-fibrillar amyloid traits in superoxide dismutase 1 (SOD1). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:118-26. [PMID: 25463043 DOI: 10.1016/j.bbapap.2014.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/14/2014] [Accepted: 11/18/2014] [Indexed: 12/26/2022]
Abstract
Calcium deregulation is a central feature among neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Calcium accumulates in the spinal and brain stem motor neurons of ALS patients triggering multiple pathophysiological processes which have been recently shown to include direct effects on the aggregation cascade of superoxide dismutase 1 (SOD1). SOD1 is a Cu/Zn enzyme whose demetallated form is implicated in ALS protein deposits, contributing to toxic gain of function phenotypes. Here we undertake a combined experimental and computational study aimed at establishing the molecular details underlying the regulatory effects of Ca(2+) over SOD1 aggregation potential. Isothermal titration calorimetry indicates entropy driven low affinity association of Ca(2+) ions to apo SOD1, at pH7.5 and 37°C. Molecular dynamics simulations denote a noticeable loss of native structure upon Ca(2+) association that is especially prominent at the zinc-binding and electrostatic loops, whose decoupling is known to expose the central SOD1 β-barrel triggering aggregation. Structural mapping of the preferential apo SOD1 Ca(2+) binding locations reveals that among the most frequent ligands for Ca(2+) are negatively-charged gatekeeper residues located in boundary positions with respect to segments highly prone to edge-to-edge aggregation. Calcium interactions thus diminish gatekeeping roles of these residues, by shielding repulsive interactions via stacking between aggregating β-sheets, partly blocking fibril formation and promoting amyloidogenic oligomers such as those found in ALS inclusions. Interestingly, many fALS mutations occur at these positions, disclosing how Ca(2+) interactions recreate effects similar to those of genetic defects, a finding with relevance to understand sporadic ALS pathomechanisms.
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Affiliation(s)
- Sílvia G Estácio
- Centro de Física da Matéria Condensada, Universidade de Lisboa, Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
| | - Sónia S Leal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Joana S Cristóvão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Patrícia F N Faísca
- Centro de Física da Matéria Condensada, Universidade de Lisboa, Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
| | - Cláudio M Gomes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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27
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Pey AL, Megarity CF, Timson DJ. FAD binding overcomes defects in activity and stability displayed by cancer-associated variants of human NQO1. Biochim Biophys Acta Mol Basis Dis 2014; 1842:2163-73. [PMID: 25179580 DOI: 10.1016/j.bbadis.2014.08.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/08/2014] [Accepted: 08/20/2014] [Indexed: 01/24/2023]
Abstract
NAD(P)H quinone oxidoreductase 1 is involved in antioxidant defence and protection from cancer, stabilizing the apoptosis regulator p53 towards degradation. Here, we studied the enzymological, biochemical and biophysical properties of two cancer-associated variants (p.R139W and p.P187S). Both variants (especially p.187S) have lower thermal stability and greater susceptibility to proteolysis compared to the wild-type. p.P187S also has reduced activity due to a lower binding affinity for the FAD cofactor as assessed by activity measurements and direct titrations. Native gel electrophoresis and dynamic light scattering also suggest that p.P187S has a higher tendency to populate unfolded states under native conditions. Detailed thermal stability studies showed that all variants irreversibly denature causing dimer dissociation, while addition of FAD restores the stability of the polymorphic forms to wild-type levels. The kinetic destabilization induced by polymorphisms as well as the kinetic protection exerted by FAD was confirmed by measuring denaturation kinetics at temperatures close to physiological. Our data suggest that the main molecular mechanisms associated with these cancer-related variants are their low binding affinity for FAD and/or kinetic instability. Thus, pharmacological chaperones may be useful in the treatment of patients bearing these polymorphisms.
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Affiliation(s)
- Angel L Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Spain.
| | - Clare F Megarity
- School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - David J Timson
- School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK; Institute for Global Food Security, Queen's University Belfast, 18-30 Malone Road, Belfast BT9 5BN, UK.
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28
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Pey AL. Protein homeostasis disorders of key enzymes of amino acids metabolism: mutation-induced protein kinetic destabilization and new therapeutic strategies. Amino Acids 2013; 45:1331-41. [PMID: 24178766 DOI: 10.1007/s00726-013-1609-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 10/19/2013] [Indexed: 12/31/2022]
Abstract
Many inborn errors of amino acids metabolism are caused by single point mutations affecting the ability of proteins to fold properly (i.e., protein homeostasis), thus leading to enzyme loss-of-function. Mutations may affect protein homeostasis by altering intrinsic physical properties of the polypeptide (folding thermodynamics, and rates of folding/unfolding/misfolding) as well as the interaction of partially folded states with elements of the protein homeostasis network (such as molecular chaperones and proteolytic machineries). Understanding these mutational effects on protein homeostasis is required to develop new therapeutic strategies aimed to target specific features of the mutant polypeptide. Here, I review recent work in three different diseases of protein homeostasis associated to inborn errors of amino acids metabolism: phenylketonuria, inherited homocystinuria and primary hyperoxaluria type I. These three different genetic disorders involve proteins operating in different cell organelles and displaying different structural complexities. Mutations often decrease protein kinetic stability of the native state (i.e., its half-life for irreversible denaturation), which can be studied using simple kinetic models amenable to biophysical and biochemical characterization. Natural ligands and pharmacological chaperones are shown to stabilize mutant enzymes, thus supporting their therapeutic application to overcome protein kinetic destabilization. The role of molecular chaperones in protein folding and misfolding is also discussed as well as their potential pharmacological modulation as promising new therapeutic approaches. Since current available treatments for these diseases are either burdening or only successful in a fraction of patients, alternative treatments must be considered covering studies from protein structure and biophysics to studies in animal models and patients.
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Affiliation(s)
- Angel L Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Granada, Spain,
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29
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Schmidlin T, Ploeger K, Jonsson AL, Daggett V. Early steps in thermal unfolding of superoxide dismutase 1 are similar to the conformational changes associated with the ALS-associated A4V mutation. Protein Eng Des Sel 2013; 26:503-13. [PMID: 23784844 DOI: 10.1093/protein/gzt030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
There are over 100 mutations in Cu/Zn superoxide dismutase (SOD1) that result in a subset of familial amyotrophic lateral sclerosis (fALS) cases. The hypothesis that dissociation of the dimer, misfolding of the monomer and subsequent aggregation of mutant SOD1 leads to fALS has been gaining support as an explanation for how these disparate missense mutations cause the same disease. These forms are only responsible for a fraction of the ALS cases; however, the rest are sporadic. Starting with a folded apo monomer, the species considered most likely to be involved in misfolding, we used high-temperature all-atom molecular dynamics simulations to explore the events of the wild-type protein unfolding through the denatured state. All simulations showed early loss of structure along the β5-β6 edge of the β-sandwich, supporting earlier findings of instability in this region. Transition state structures identified from the simulations are in good agreement with experiment, providing detailed, validated molecular models for this elusive state. Furthermore, we compare the process of thermal unfolding investigated here to that of the lethal A4V mutant-induced unfolding at physiological temperature and find that the pathways are very similar.
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Affiliation(s)
- Tom Schmidlin
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA
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30
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Pey AL, Mesa-Torres N, Chiarelli LR, Valentini G. Structural and energetic basis of protein kinetic destabilization in human phosphoglycerate kinase 1 deficiency. Biochemistry 2013; 52:1160-70. [PMID: 23336698 DOI: 10.1021/bi301565m] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein kinetic destabilization is a common feature of many human genetic diseases. Human phosphoglycerate kinase 1 (PGK1) deficiency is a rare genetic disease caused by mutations in the PGK1 protein, which often shows reduced kinetic stability. In this work, we have performed an in-depth characterization of the thermal stability of the wild type and four disease-causing mutants (I47N, L89P, E252A, and T378P) of human PGK1. PGK1 thermal denaturation is a process under kinetic control, and it is described well by a two-state irreversible denaturation model. Kinetic analysis of differential scanning calorimetry profiles shows that the disease-causing mutations decrease PGK1 kinetic stability from ~5-fold (E252A) to ~100000-fold (L89P) compared to that of wild-type PGK1, and in some cases, mutant enzymes are denatured on a time scale of a few minutes at physiological temperature. We show that changes in protein kinetic stability are associated with large differences in enthalpic and entropic contributions to denaturation free energy barriers. It is also shown that the denaturation transition state becomes more nativelike in terms of solvent exposure as the protein is destabilized by mutations (Hammond effect). Unfolding experiments with urea further suggest a scenario in which the thermodynamic stability of PGK1 at least partly determines its kinetic stability. ATP and ADP kinetically stabilize PGK1 enzymes, and kinetic stabilization is nucleotide- and mutant-selective. Overall, our data provide insight into the structural and energetic basis underlying the low kinetic stability displayed by some mutants causing human PGK1 deficiency, which may have important implications for the development of native state kinetic stabilizers for the treatment of this disease.
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Affiliation(s)
- Angel L Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Granada, Spain.
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31
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Burns JN, Turnage KC, Walker CA, Lieberman RL. The stability of myocilin olfactomedin domain variants provides new insight into glaucoma as a protein misfolding disorder. Biochemistry 2011; 50:5824-33. [PMID: 21612213 DOI: 10.1021/bi200231x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Myocilin variants, localized to the olfactomedin (OLF) domain, are linked to early-onset, inherited forms of open-angle glaucoma. Disease-causing myocilin variants accumulate within trabecular meshwork cells instead of being secreted to the trabecular extracellular matrix of the eye. We hypothesize that, like in other diseases of protein misfolding, aggregation and downstream pathogenesis originate from the compromised thermal stability of mutant myocilins. In an expansion of our pilot study of four mutants, we compare 21 additional purified OLF variants by using a fluorescence stability assay and investigate the secondary structure of the most stable variants by circular dichroism. Variants with lower melting temperatures are correlated with earlier glaucoma diagnoses. The chemical chaperone trimethylamine N-oxide is capable of restoring the stability of most, but not all, variants to wild-type (WT) levels. Interestingly, three reported OLF disease variants, A427T, G246R, and A445V, exhibited properties indistinguishable from those of WT OLF, but an increased apparent aggregation propensity in vitro relative to that of WT OLF suggests that biophysical factors other than thermal stability, such as kinetics and unfolding pathways, may also be involved in myocilin glaucoma pathogenesis. Similarly, no changes from WT OLF stability and secondary structure were detected for three annotated single-nucleotide polymorphism variants. Our work provides the first quantitative demonstration of compromised stability among many identified OLF variants and places myocilin glaucoma in the context of other diseases of protein misfolding.
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Affiliation(s)
- J Nicole Burns
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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32
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Banci L, Bertini I, Blaževitš O, Cantini F, Lelli M, Luchinat C, Mao J, Vieru M. NMR characterization of a "fibril-ready" state of demetalated wild-type superoxide dismutase. J Am Chem Soc 2010; 133:345-9. [PMID: 21162535 DOI: 10.1021/ja1069689] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Demetalated superoxide dismutase (SOD1) is a transient species, fibrillogenic in nature and of biomedical interest. It is a conformationally disordered protein difficult to characterize. We have developed a strategy based on the NMR investigation of a crystalline species characterized by X-ray crystallography and on the comparison of the solid-state-solution-state chemical shifts. The solid-state assignment has been also helpful in assigning the solution spectra. The solution NMR spectra presumably detect species that are the result of equilibria among multiple species. From the differences in chemical shifts between the two forms, we learned that a β-sheet becomes conformationally labile and two loops in the same sheet show propensity to take a β conformation. This strategy, which exploits solution and solid-state NMR spectra in a synergistic way, thus provides information on the species that are prone to oligomerize.
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Affiliation(s)
- Lucia Banci
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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33
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Ricci C, Benigni M, Battistini S, Greco G, Torzini A, Giannini F. A novel exon 1 mutation (G10R) in the SOD1 gene in a patient with familial ALS. AMYOTROPHIC LATERAL SCLEROSIS : OFFICIAL PUBLICATION OF THE WORLD FEDERATION OF NEUROLOGY RESEARCH GROUP ON MOTOR NEURON DISEASES 2010; 11:481-485. [PMID: 20331403 DOI: 10.3109/17482960903480383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Mutations in the superoxide dismutase-1 (SOD1) gene have been found in 12-23% of patients with a diagnosis of ALS. Although the mechanism by which mutant SOD1 causes neural death remains elusive, several lines of evidence suggest that ALS is a protein-folding disease. Here we report a novel missense mutation in exon 1 of the SOD1 gene in a 68-year-old female with familial ALS characterized by spinal onset with upper and lower motor neuron signs and early neuroimaging evidence of corticospinal tract involvement. Molecular analysis identified a heterozygous mutation in codon 10, with substitution of a highly conserved glycine with arginine (G10R). Modelling of the mutant SOD1 showed a strong destabilization of the protein secondary structure that could influence the strength of the dimer interface. This property can result in a failure of the protein to fold and generation of toxic intracellular aggregates, suggesting a pathogenic role for the mutation.
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Affiliation(s)
- Claudia Ricci
- Department of Neuroscience, University of Siena, Italy.
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34
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Bento-Abreu A, Van Damme P, Van Den Bosch L, Robberecht W. The neurobiology of amyotrophic lateral sclerosis. Eur J Neurosci 2010; 31:2247-65. [PMID: 20529130 DOI: 10.1111/j.1460-9568.2010.07260.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Amyotrophic lateral sclerosis is a degenerative disease affecting the motor neurons. In spite of our growing insights into its biology, it remains a lethal condition. The identification of the cause of several of the familial forms of ALS allowed generation of models to study this disease both in vitro and in vivo. Here, we summarize what is known about the pathogenic mechanisms of ALS induced by hereditary mutations, and attempt to identify the relevance of these findings for understanding the pathogenic mechanisms of the sporadic form of this disease.
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Affiliation(s)
- André Bento-Abreu
- Laboratory for Neurobiology, Experimental Neurology, K.U.Leuven, Herestraat, 3000 Leuven, Belgium.
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35
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Münch C, Bertolotti A. Exposure of hydrophobic surfaces initiates aggregation of diverse ALS-causing superoxide dismutase-1 mutants. J Mol Biol 2010; 399:512-25. [PMID: 20399791 PMCID: PMC2927901 DOI: 10.1016/j.jmb.2010.04.019] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 04/12/2010] [Accepted: 04/13/2010] [Indexed: 11/09/2022]
Abstract
The copper-zinc superoxide dismutase-1 (SOD1) is a highly structured protein and, a priori, one of the least likely proteins to be involved in a misfolding disease. However, more than 140, mostly missense, mutations in the SOD1 gene cause aggregation of the affected protein in familial forms of amyotrophic lateral sclerosis (ALS). The remarkable diversity of the effects of these mutations on SOD1 properties has suggested that they promote aggregation by a variety of mechanisms. Experimental assessment of surface hydrophobicity using a sensitive fluorescent-based assay, revealed that diverse ALS-causing mutations provoke SOD1 aggregation by increasing their propensity to expose hydrophobic surfaces. These findings could not be anticipated from analysis of the amino acid sequence. Our results uncover the biochemical nature of the misfolded aggregation-prone intermediate and reconcile the seemingly diverse effects of ALS-causing mutations into a unifying mechanism. Furthermore, the method we describe here will be useful for investigating and interfering with aggregation of various proteins and thereby provide insight into the molecular mechanisms underlying many neurodegenerative diseases.
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Affiliation(s)
- Christian Münch
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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36
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Perry J, Shin D, Getzoff E, Tainer J. The structural biochemistry of the superoxide dismutases. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1804:245-62. [PMID: 19914407 PMCID: PMC3098211 DOI: 10.1016/j.bbapap.2009.11.004] [Citation(s) in RCA: 322] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2009] [Revised: 11/04/2009] [Accepted: 11/05/2009] [Indexed: 01/11/2023]
Abstract
The discovery of superoxide dismutases (SODs), which convert superoxide radicals to molecular oxygen and hydrogen peroxide, has been termed the most important discovery of modern biology never to win a Nobel Prize. Here, we review the reasons this discovery has been underappreciated, as well as discuss the robust results supporting its premier biological importance and utility for current research. We highlight our understanding of SOD function gained through structural biology analyses, which reveal important hydrogen-bonding schemes and metal-binding motifs. These structural features create remarkable enzymes that promote catalysis at faster than diffusion-limited rates by using electrostatic guidance. These architectures additionally alter the redox potential of the active site metal center to a range suitable for the superoxide disproportionation reaction and protect against inhibition of catalysis by molecules such as phosphate. SOD structures may also control their enzymatic activity through product inhibition; manipulation of these product inhibition levels has the potential to generate therapeutic forms of SOD. Markedly, structural destabilization of the SOD architecture can lead to disease, as mutations in Cu,ZnSOD may result in familial amyotrophic lateral sclerosis, a relatively common, rapidly progressing and fatal neurodegenerative disorder. We describe our current understanding of how these Cu,ZnSOD mutations may lead to aggregation/fibril formation, as a detailed understanding of these mechanisms provides new avenues for the development of therapeutics against this so far untreatable neurodegenerative pathology.
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Affiliation(s)
- J.J.P. Perry
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The School of Biotechnology, Amrita University, Kollam, Kerala 690525, India
| | - D.S. Shin
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - E.D. Getzoff
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - J.A. Tainer
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Life Sciences Division, Department of Molecular Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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