1
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Basith S, Manavalan B, Lee G. Unveiling local and global conformational changes and allosteric communications in SOD1 systems using molecular dynamics simulation and network analyses. Comput Biol Med 2024; 168:107688. [PMID: 37988788 DOI: 10.1016/j.compbiomed.2023.107688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/20/2023] [Accepted: 11/06/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a serious neurodegenerative disorder affecting nerve cells in the brain and spinal cord that is caused by mutations in the superoxide dismutase 1 (SOD1) enzyme. ALS-related mutations cause misfolding, dimerisation instability, and increased formation of aggregates. The underlying allosteric mechanisms, however, remain obscure as far as details of their fundamental atomistic structure are concerned. Hence, this gap in knowledge limits the development of novel SOD1 inhibitors and the understanding of how disease-associated mutations in distal sites affect enzyme activity. METHODS We combined microsecond-scale based unbiased molecular dynamics (MD) simulation with network analysis to elucidate the local and global conformational changes and allosteric communications in SOD1 Apo (unmetallated form), Holo, Apo_CallA (mutant and unmetallated form), and Holo_CallA (mutant form) systems. To identify hotspot residues involved in SOD1 signalling and allosteric communications, we performed network centrality, community network, and path analyses. RESULTS Structural analyses showed that unmetallated SOD1 systems and cysteine mutations displayed large structural variations in the catalytic sites, affecting structural stability. Inter- and intra H-bond analyses identified several important residues crucial for maintaining interfacial stability, structural stability, and enzyme catalysis. Dynamic motion analysis demonstrated more balanced atomic displacement and highly correlated motions in the Holo system. The rationale for structural disparity observed in the disulfide bond formation and R143 configuration in Apo and Holo systems were elucidated using distance and dihedral probability distribution analyses. CONCLUSION Our study highlights the efficiency of combining extensive MD simulations with network analyses to unravel the features of protein allostery.
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Affiliation(s)
- Shaherin Basith
- Department of Physiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea.
| | - Balachandran Manavalan
- Computational Biology and Bioinformatics Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Gwang Lee
- Department of Physiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea; Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea.
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2
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Camponeschi F, Banci L. Metal trafficking in the cell: Combining atomic resolution with cellular dimension. FEBS Lett 2023; 597:122-133. [PMID: 36285633 DOI: 10.1002/1873-3468.14524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 01/14/2023]
Abstract
Metals are widely present in biological systems as simple ions or complex cofactors, and are involved in a variety of processes essential for life. Their transport inside cells and insertion into the binding sites of the proteins that need metals to function occur through complex and selective pathways involving dedicated multiprotein machineries specifically and transiently interacting with each other, often sharing the coordination of metal ions and/or cofactors. The understanding of these machineries requires integrated approaches, ranging from bioinformatics to experimental investigations, possibly in the cellular context. In this review, we report two case studies where the use of integrated in vitro and in cellulo approaches is necessary to clarify at atomic resolution essential aspects of metal trafficking in cells.
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Affiliation(s)
- Francesca Camponeschi
- Magnetic Resonance Center CERM, University of Florence, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Florence, Italy.,Department of Chemistry, University of Florence, Italy
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3
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Baek Y, Woo TG, Ahn J, Lee D, Kwon Y, Park BJ, Ha NC. Structural analysis of the overoxidized Cu/Zn-superoxide dismutase in ROS-induced ALS filament formation. Commun Biol 2022; 5:1085. [PMID: 36224351 PMCID: PMC9556535 DOI: 10.1038/s42003-022-04017-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Eukaryotic Cu, Zn-superoxide dismutase (SOD1) is primarily responsible for cytotoxic filament formation in amyotrophic lateral sclerosis (ALS) neurons. Two cysteine residues in SOD1 form an intramolecular disulfide bond. This study aims to explore the molecular mechanism of SOD1 filament formation by cysteine overoxidation in sporadic ALS (sALS). In this study, we determined the crystal structure of the double mutant (C57D/C146D) SOD1 that mimics the overoxidation of the disulfide-forming cysteine residues. The structure revealed the open and relaxed conformation of loop IV containing the mutated Asp57. The double mutant SOD1 produced more contagious filaments than wild-type protein, promoting filament formation of the wild-type SOD1 proteins. Importantly, we further found that HOCl treatment to the wild-type SOD1 proteins facilitated their filament formation. We propose a feasible mechanism for SOD1 filament formation in ALS from the wild-type SOD1, suggesting that overoxidized SOD1 is a triggering factor of sALS. Our findings extend our understanding of other neurodegenerative disorders associated with ROS stresses at the molecular level. Characterization of the structure of an overoxidation-mimicking double mutant of superoxide dismutase SOD1 shows the production of more cytotoxic filaments seen in amyotrophic lateral sclerosis (ALS) neurons.
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Affiliation(s)
- Yeongjin Baek
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Tae-Gyun Woo
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Jinsook Ahn
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Republic of Korea.,Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Dukwon Lee
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yonghoon Kwon
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Bum-Joon Park
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea. .,Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Republic of Korea.
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4
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Hsueh SCC, Nijland M, Peng X, Hilton B, Plotkin SS. First Principles Calculation of Protein-Protein Dimer Affinities of ALS-Associated SOD1 Mutants. Front Mol Biosci 2022; 9:845013. [PMID: 35402516 PMCID: PMC8988244 DOI: 10.3389/fmolb.2022.845013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/08/2022] [Indexed: 01/03/2023] Open
Abstract
Cu,Zn superoxide dismutase (SOD1) is a 32 kDa homodimer that converts toxic oxygen radicals in neurons to less harmful species. The dimerization of SOD1 is essential to the stability of the protein. Monomerization increases the likelihood of SOD1 misfolding into conformations associated with aggregation, cellular toxicity, and neuronal death in familial amyotrophic lateral sclerosis (fALS). The ubiquity of disease-associated mutations throughout the primary sequence of SOD1 suggests an important role of physicochemical processes, including monomerization of SOD1, in the pathology of the disease. Herein, we use a first-principles statistical mechanics method to systematically calculate the free energy of dimer binding for SOD1 using molecular dynamics, which involves sequentially computing conformational, orientational, and separation distance contributions to the binding free energy. We consider the effects of two ALS-associated mutations in SOD1 protein on dimer stability, A4V and D101N, as well as the role of metal binding and disulfide bond formation. We find that the penalty for dimer formation arising from the conformational entropy of disordered loops in SOD1 is significantly larger than that for other protein-protein interactions previously considered. In the case of the disulfide-reduced protein, this leads to a bound complex whose formation is energetically disfavored. Somewhat surprisingly, the loop free energy penalty upon dimerization is still significant for the holoprotein, despite the increased structural order induced by the bound metal cations. This resulted in a surprisingly modest increase in dimer binding free energy of only about 1.5 kcal/mol upon metalation of the protein, suggesting that the most significant stabilizing effects of metalation are on folding stability rather than dimer binding stability. The mutant A4V has an unstable dimer due to weakened monomer-monomer interactions, which are manifested in the calculation by a separation free energy surface with a lower barrier. The mutant D101N has a stable dimer partially due to an unusually rigid β-barrel in the free monomer. D101N also exhibits anticooperativity in loop folding upon dimerization. These computational calculations are, to our knowledge, the most quantitatively accurate calculations of dimer binding stability in SOD1 to date.
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Affiliation(s)
- Shawn C. C. Hsueh
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
| | - Mark Nijland
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, Netherlands
| | - Xubiao Peng
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
- Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, Beijing, China
| | - Benjamin Hilton
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
- Imperial College London, London, United Kingdom
| | - Steven S. Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
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5
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Peggion C, Scalcon V, Massimino ML, Nies K, Lopreiato R, Rigobello MP, Bertoli A. SOD1 in ALS: Taking Stock in Pathogenic Mechanisms and the Role of Glial and Muscle Cells. Antioxidants (Basel) 2022; 11:614. [PMID: 35453299 PMCID: PMC9032988 DOI: 10.3390/antiox11040614] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/18/2022] [Accepted: 03/19/2022] [Indexed: 12/04/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by the loss of motor neurons in the brain and spinal cord. While the exact causes of ALS are still unclear, the discovery that familial cases of ALS are related to mutations in the Cu/Zn superoxide dismutase (SOD1), a key antioxidant enzyme protecting cells from the deleterious effects of superoxide radicals, suggested that alterations in SOD1 functionality and/or aberrant SOD1 aggregation strongly contribute to ALS pathogenesis. A new scenario was opened in which, thanks to the generation of SOD1 related models, different mechanisms crucial for ALS progression were identified. These include excitotoxicity, oxidative stress, mitochondrial dysfunctions, and non-cell autonomous toxicity, also implicating altered Ca2+ metabolism. While most of the literature considers motor neurons as primary target of SOD1-mediated effects, here we mainly discuss the effects of SOD1 mutations in non-neuronal cells, such as glial and skeletal muscle cells, in ALS. Attention is given to the altered redox balance and Ca2+ homeostasis, two processes that are strictly related with each other. We also provide original data obtained in primary myocytes derived from hSOD1(G93A) transgenic mice, showing perturbed expression of Ca2+ transporters that may be responsible for altered mitochondrial Ca2+ fluxes. ALS-related SOD1 mutants are also responsible for early alterations of fundamental biological processes in skeletal myocytes that may impinge on skeletal muscle functions and the cross-talk between muscle cells and motor neurons during disease progression.
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Affiliation(s)
- Caterina Peggion
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; (C.P.); (V.S.); (K.N.); (R.L.)
| | - Valeria Scalcon
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; (C.P.); (V.S.); (K.N.); (R.L.)
| | | | - Kelly Nies
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; (C.P.); (V.S.); (K.N.); (R.L.)
- Department of Radiology, CARIM School for Cardiovascular Diseases, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Raffaele Lopreiato
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; (C.P.); (V.S.); (K.N.); (R.L.)
| | - Maria Pia Rigobello
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; (C.P.); (V.S.); (K.N.); (R.L.)
| | - Alessandro Bertoli
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; (C.P.); (V.S.); (K.N.); (R.L.)
- CNR—Neuroscience Institute, 35131 Padova, Italy;
- Padova Neuroscience Center, University of Padova, 35131 Padova, Italy
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6
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Nielsen JT, Mulder FAA. CheSPI: chemical shift secondary structure population inference. JOURNAL OF BIOMOLECULAR NMR 2021; 75:273-291. [PMID: 34146207 DOI: 10.1007/s10858-021-00374-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/11/2021] [Indexed: 06/12/2023]
Abstract
NMR chemical shifts (CSs) are delicate reporters of local protein structure, and recent advances in random coil CS (RCCS) prediction and interpretation now offer the compelling prospect of inferring small populations of structure from small deviations from RCCSs. Here, we present CheSPI, a simple and efficient method that provides unbiased and sensitive aggregate measures of local structure and disorder. It is demonstrated that CheSPI can predict even very small amounts of residual structure and robustly delineate subtle differences into four structural classes for intrinsically disordered proteins. For structured regions and proteins, CheSPI provides predictions for up to eight structural classes, which coincide with the well-known DSSP classification. The program is freely available, and can either be invoked from URL www.protein-nmr.org as a web implementation, or run locally from command line as a python program. CheSPI generates comprehensive numeric and graphical output for intuitive annotation and visualization of protein structures. A number of examples are provided.
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Affiliation(s)
- Jakob Toudahl Nielsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark.
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark.
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7
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Proline Rich Peptides of Neurohypophysial Origin: Related Peptides and Possible Functions. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10194-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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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: 2.5] [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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Bonaccorsi M, Knight MJ, Le Marchand T, Dannatt HRW, Schubeis T, Salmon L, Felli IC, Emsley L, Pierattelli R, Pintacuda G. Multimodal Response to Copper Binding in Superoxide Dismutase Dynamics. J Am Chem Soc 2020; 142:19660-19667. [PMID: 33166153 DOI: 10.1021/jacs.0c09242] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Copper/zinc superoxide dismutase (SOD) is a homodimeric metalloenzyme that has been extensively studied as a benchmark for structure-function relationships in proteins, in particular because of its implication in the familial form of the neurodegenerative disease amyotrophic lateral sclerosis. Here, we investigate microcrystalline preparations of two differently metalated forms of SOD, namely, the fully mature functional Cu,Zn state and the E,Zn-SOD state in which the Cu site is empty. By using solid-state NMR with fast magic-angle spinning (MAS) at high magnetic fields (1H Larmor frequency of 800-1000 MHz), we quantify motions spanning a dynamic range from ns to ms. We determine that metal ion uptake does not act as a rigidification element but as a switch redistributing motional processes on different time scales, with coupling of the dynamics of histidine side chains and those of remote key backbone elements of the protein.
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Affiliation(s)
- Marta Bonaccorsi
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Michael J Knight
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Tanguy Le Marchand
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Hugh R W Dannatt
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Loïc Salmon
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Isabella C Felli
- Department of Chemistry "Ugo Schiff" and CERM, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Lyndon Emsley
- Laboratory of Magnetic Resonance, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and CERM, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
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10
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Perri ER, Parakh S, Vidal M, Mehta P, Ma Y, Walker AK, Atkin JD. The Cysteine (Cys) Residues Cys-6 and Cys-111 in Mutant Superoxide Dismutase 1 (SOD1) A4V Are Required for Induction of Endoplasmic Reticulum Stress in Amyotrophic Lateral Sclerosis. J Mol Neurosci 2020; 70:1357-1368. [PMID: 32445072 DOI: 10.1007/s12031-020-01551-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/13/2020] [Indexed: 12/21/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the degeneration of motor neurons. Between 12 and 20% of inherited cases and approximately 1-2% of all cases are caused by mutations in the gene encoding dismutase 1 (SOD1). Mutant SOD1 A4V (alanine to valine) induces endoplasmic reticulum (ER) stress, which is increasingly implicated as a pathway to motor neuron degeneration and death in ALS. However, it remains unclear how ER stress is induced by mutant SOD1 A4V. Previous studies have established that it is induced early in pathophysiology and it precedes the formation of mutant SOD1 inclusions. SOD1 contains four cysteine residues, two of which form an intra-subunit disulphide bond involving Cys-57 and Cys-146. The remaining two cysteines, Cys-6 and Cys-111, remain unpaired and have been implicated in mutant SOD1 aggregation. In this study, we examined the relationship between the SOD1 A4V cysteine residues and aggregation, ER stress induction and toxicity. We report here that mutation of Cys-6 and Cys-111 in mutant SOD1 A4V, but not Cys-57 or Cys-146, ameliorates ER stress, inclusion formation and apoptosis in neuronal cell lines. These results imply that protein misfolding, induced by Cys-6 and Cys-111, is required for these pathological events in neuronal cells.
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Affiliation(s)
- Emma R Perri
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Sonam Parakh
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Marta Vidal
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Prachi Mehta
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Yi Ma
- Department of General Surgery, Monash Health, Melbourne, Victoria, Australia
| | - Adam K Walker
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Julie D Atkin
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia. .,Department of General Surgery, Monash Health, Melbourne, Victoria, Australia.
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11
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Abstract
Few proteins have come under such intense scrutiny as superoxide dismutase-1 (SOD1). For almost a century, scientists have dissected its form, function and then later its malfunction in the neurodegenerative disease amyotrophic lateral sclerosis (ALS). We now know SOD1 is a zinc and copper metalloenzyme that clears superoxide as part of our antioxidant defence and respiratory regulation systems. The possibility of reduced structural integrity was suggested by the first crystal structures of human SOD1 even before deleterious mutations in the sod1 gene were linked to the ALS. This concept evolved in the intervening years as an impressive array of biophysical studies examined the characteristics of mutant SOD1 in great detail. We now recognise how ALS-related mutations perturb the SOD1 maturation processes, reduce its ability to fold and reduce its thermal stability and half-life. Mutant SOD1 is therefore predisposed to monomerisation, non-canonical self-interactions, the formation of small misfolded oligomers and ultimately accumulation in the tell-tale insoluble inclusions found within the neurons of ALS patients. We have also seen that several post-translational modifications could push wild-type SOD1 down this toxic pathway. Recently we have come to view ALS as a prion-like disease where both the symptoms, and indeed SOD1 misfolding itself, are transmitted to neighbouring cells. This raises the possibility of intervention after the initial disease presentation. Several small-molecule and biologic-based strategies have been devised which directly target the SOD1 molecule to change the behaviour thought to be responsible for ALS. Here we provide a comprehensive review of the many biophysical advances that sculpted our view of SOD1 biology and the recent work that aims to apply this knowledge for therapeutic outcomes in ALS.
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12
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Pathways of electron transfer and proton translocation in the action of superoxide dismutase dimer. Biochem Biophys Res Commun 2019; 514:772-776. [DOI: 10.1016/j.bbrc.2019.05.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 05/03/2019] [Indexed: 11/21/2022]
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13
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Huai J, Zhang Z. Structural Properties and Interaction Partners of Familial ALS-Associated SOD1 Mutants. Front Neurol 2019; 10:527. [PMID: 31164862 PMCID: PMC6536575 DOI: 10.3389/fneur.2019.00527] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/02/2019] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common motor neuron degenerative disease in adults and has also been proven to be a type of conformational disease associated with protein misfolding and dysfunction. To date, more than 150 distinct genes have been found to be associated with ALS, among which Superoxide Dismutase 1 (SOD1) is the first and the most extensively studied gene. It has been well-established that SOD1 mutants-mediated toxicity is caused by a gain-of-function rather than the loss of the detoxifying activity of SOD1. Compared with the clear autosomal dominant inheritance of SOD1 mutants in ALS, the potential toxic mechanisms of SOD1 mutants in motor neurons remain incompletely understood. A large body of evidence has shown that SOD1 mutants may adopt a complex profile of conformations and interact with a wide range of client proteins. Here, in this review, we summarize the fundamental conformational properties and the gained interaction partners of the soluble forms of the SOD1 mutants which have been published in the past decades. Our goal is to find clues to the possible internal links between structural and functional anomalies of SOD1 mutants, as well as the relationships between their exposed epitopes and interaction partners, in order to help reveal and determine potential diagnostic and therapeutic targets.
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Affiliation(s)
- Jisen Huai
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China
| | - Zhongjian Zhang
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China
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14
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Sala FA, Wright GSA, Antonyuk SV, Garratt RC, Hasnain SS. Molecular recognition and maturation of SOD1 by its evolutionarily destabilised cognate chaperone hCCS. PLoS Biol 2019; 17:e3000141. [PMID: 30735496 PMCID: PMC6383938 DOI: 10.1371/journal.pbio.3000141] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 02/21/2019] [Accepted: 01/22/2019] [Indexed: 11/19/2022] Open
Abstract
Superoxide dismutase-1 (SOD1) maturation comprises a string of posttranslational modifications which transform the nascent peptide into a stable and active enzyme. The successive folding, metal ion binding, and disulphide acquisition steps in this pathway can be catalysed through a direct interaction with the copper chaperone for SOD1 (CCS). This process confers enzymatic activity and reduces access to noncanonical, aggregation-prone states. Here, we present the functional mechanisms of human copper chaperone for SOD1 (hCCS)-catalysed SOD1 activation based on crystal structures of reaction precursors, intermediates, and products. Molecular recognition of immature SOD1 by hCCS is driven by several interface interactions, which provide an extended surface upon which SOD1 folds. Induced-fit complexation is reliant on the structural plasticity of the immature SOD1 disulphide sub-loop, a characteristic which contributes to misfolding and aggregation in neurodegenerative disease. Complexation specifically stabilises the SOD1 disulphide sub-loop, priming it and the active site for copper transfer, while delaying disulphide formation and complex dissociation. Critically, a single destabilising amino acid substitution within the hCCS interface reduces hCCS homodimer affinity, creating a pool of hCCS available to interact with immature SOD1. hCCS substrate specificity, segregation between solvent and biological membranes, and interaction transience are direct results of this substitution. In this way, hCCS-catalysed SOD1 maturation is finessed to minimise copper wastage and reduce production of potentially toxic SOD1 species.
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Affiliation(s)
- Fernanda A. Sala
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, Brazil
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Gareth S. A. Wright
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Richard C. Garratt
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
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15
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Peng X, Cashman NR, Plotkin SS. Prediction of Misfolding-Specific Epitopes in SOD1 Using Collective Coordinates. J Phys Chem B 2018; 122:11662-11676. [PMID: 30351123 DOI: 10.1021/acs.jpcb.8b07680] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We introduce a global, collective coordinate bias into molecular dynamics simulations that partially unfolds a protein, in order to predict misfolding-specific epitopes based on the regions that locally unfold. Several metrics are used to measure local disorder, including solvent exposed surface area (SASA), native contacts ( Q), and root mean squared fluctuations (RMSF). The method is applied to Cu, Zn superoxide dismutase (SOD1). For this protein, the processes of monomerization, metal loss, and conformational unfolding due to microenvironmental stresses are all separately taken into account. Several misfolding-specific epitopes are predicted, and consensus epitopes are calculated. These predicted epitopes are consistent with the "lower-resolution" peptide sequences used to raise disease-specific antibodies, but the epitopes derived from collective coordinates contain shorter, more refined sequences for the key residues constituting the epitope.
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Affiliation(s)
- Xubiao Peng
- Department of Physics and Astronomy , University of British Columbia , Vancouver , British Columbia V6T 1Z1 , Canada.,Center for Quantum Technology Research, School of Physics , Beijing Institute of Technology , Haidian, Beijing 100081 , China
| | - Neil R Cashman
- Brain Research Centre , University of British Columbia , Vancouver , British Columbia V6T 2B5 , Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, and Genome Sciences and Technology Program , University of British Columbia , Vancouver , British Columbia V6T 1Z1 , Canada
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16
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Abstract
Abstract
Metal ions are essential cofactors required by the proteome of organisms from any kingdom of life to correctly exert their functions. Dedicated cellular import, transport and homeostasis systems assure that the needed metal ion is correctly delivered and inserted into the target proteins and avoid the presence of free metal ions in the cell, preventing oxidative damaging. Among metal ions, in eukaryotic organisms copper and iron are required by proteins involved in absolutely essential functions, such as respiration, oxidative stress protection, catalysis, gene expression regulation. Copper and iron binding proteins are localized in essentially all cellular compartments. Copper is physiologically present mainly as individual metal ion. Iron can be present both as individual metal ion or as part of cofactors, such as hemes and iron-sulfur (Fe-S) clusters. Both metal ions are characterized by the ability to cycle between different oxidation states, which enable them to catalyze redox reactions and to participate in electron transfer processes. Here we describe in detail the main processes responsible for the trafficking of copper and iron sulfur clusters, with particular interest for the structural aspects of the maturation of copper and iron-sulfur-binding proteins.
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17
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Pischedda A, Ramasamy KP, Mangiagalli M, Chiappori F, Milanesi L, Miceli C, Pucciarelli S, Lotti M. Antarctic marine ciliates under stress: superoxide dismutases from the psychrophilic Euplotes focardii are cold-active yet heat tolerant enzymes. Sci Rep 2018; 8:14721. [PMID: 30283056 PMCID: PMC6170424 DOI: 10.1038/s41598-018-33127-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/20/2018] [Indexed: 11/09/2022] Open
Abstract
Oxidative stress is a particularly severe threat to Antarctic marine polar organisms because they are exposed to high dissolved oxygen and to intense UV radiation. This paper reports the features of three superoxide dismutases from the Antarctic psychrophilic ciliate Euplotes focardii that faces two environmental challenges, oxidative stress and low temperature. Two out of these are Cu,Zn superoxide dismutases (named Ef-SOD1a and Ef-SOD1b) and one belongs to the Mn-containing group (Ef-SOD2). Ef-SOD1s and Ef-SOD2 differ in their evolutionary history, expression and overall structural features. Ef-SOD1 genes are expressed at different levels, with Ef-SOD1b mRNA 20-fold higher at the ciliate optimal temperature of growth (4 °C). All Ef-SOD enzymes are active at 4 °C, consistent with the definition of cold-adapted enzymes. At the same time, they display temperatures of melting in the range 50-70 °C and retain residual activity after incubation at 65-75 °C. Supported by data of molecular dynamics simulation, we conclude that the E. focardii SODs combine cold activity, local molecular flexibility and thermo tolerance.
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Affiliation(s)
- Alessandro Pischedda
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | - Kesava Priyan Ramasamy
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino (MC), Italy
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | | | | | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino (MC), Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino (MC), Italy.
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
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18
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Gelsolin-Cu/ZnSOD interaction alters intracellular reactive oxygen species levels to promote cancer cell invasion. Oncotarget 2018; 7:52832-52848. [PMID: 27391159 PMCID: PMC5288152 DOI: 10.18632/oncotarget.10451] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/28/2016] [Indexed: 12/13/2022] Open
Abstract
The actin-binding protein, gelsolin, is a well known regulator of cancer cell invasion. However, the mechanisms by which gelsolin promotes invasion are not well established. As reactive oxygen species (ROS) have been shown to promote cancer cell invasion, we investigated on the hypothesis that gelsolin-induced changes in ROS levels may mediate the invasive capacity of colon cancer cells. Herein, we show that increased gelsolin enhances the invasive capacity of colon cancer cells, and this is mediated via gelsolin's effects in elevating intracellular superoxide (O2.-) levels. We also provide evidence for a novel physical interaction between gelsolin and Cu/ZnSOD, that inhibits the enzymatic activity of Cu/ZnSOD, thereby resulting in a sustained elevation of intracellular O2.-. Using microarray data of human colorectal cancer tissues from Gene Omnibus, we found that gelsolin gene expression positively correlates with urokinase plasminogen activator (uPA), an important matrix-degrading protease invovled in cancer invasion. Consistent with the in vivo evidence, we show that increased levels of O2.- induced by gelsolin overexpression triggers the secretion of uPA. We further observed reduction in invasion and intracellular O2.- levels in colon cancer cells, as a consequence of gelsolin knockdown using two different siRNAs. In these cells, concurrent repression of Cu/ZnSOD restored intracellular O2.- levels and rescued invasive capacity. Our study therefore identified gelsolin as a novel regulator of intracellular O2.- in cancer cells via interacting with Cu/ZnSOD and inhibiting its enzymatic activity. Taken together, these findings provide insight into a novel function of gelsolin in promoting tumor invasion by directly impacting the cellular redox milieu.
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19
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Giuliani ME, Benedetti M, Nigro M, Regoli F. Nrf2 and regulation of the antioxidant system in the Antarctic silverfish, Pleuragramma antarctica: Adaptation to environmental changes of pro-oxidant pressure. MARINE ENVIRONMENTAL RESEARCH 2017; 129:1-13. [PMID: 28416257 DOI: 10.1016/j.marenvres.2017.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 06/07/2023]
Abstract
Despite the key importance of Nrf2-Keap1 in regulating antioxidant system in vertebrates, this system is still poorly investigated in marine species. The present study focused on the Antarctic silverfish Pleuragramma antarctica which, during the final phases of embryo development in platelet ice, is challenged by a sudden enhancement of environmental oxidative conditions associated to ice melting. Partial coding sequences were identified for Nrf2, its repressor Keap1 and for typical Nrf2-target antioxidant genes, like catalase, glutathione peroxidase isoform 1 and Cu/Zn-dependent superoxide dismutase. Compared to temperate homologues, the protein sequences showed an elevated conservation of amino acids essential for catalytic functions, while a few specific substitutions in non-essential regions may represent a molecular adaptation to improve flexibility and accessibility to active site at cold temperatures. The role of the Nrf2-Keap1 pathway in modulating the activation of antioxidant defences was demonstrated at both transcriptional and functional levels with a clear temporal increase of antioxidant protection in embryos before the hatching. Such findings confirm the importance of Nrf2 and highlight regulation of antioxidants as an adaptive strategy in P. antarctica to protect the early life stages toward the environmental changes of pro-oxidant pressure.
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Affiliation(s)
- Maria Elisa Giuliani
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Maura Benedetti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Marco Nigro
- Dipartimento di Medicina Clinica e Sperimentale, Università di Pisa, Italy
| | - Francesco Regoli
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy.
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20
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Yuwen T, Kay LE. Longitudinal relaxation optimized amide 1H-CEST experiments for studying slow chemical exchange processes in fully protonated proteins. JOURNAL OF BIOMOLECULAR NMR 2017; 67:295-307. [PMID: 28357518 DOI: 10.1007/s10858-017-0104-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/06/2017] [Indexed: 06/06/2023]
Abstract
Chemical Exchange Saturation Transfer (CEST) experiments are increasingly used to study slow timescale exchange processes in biomolecules. Although 15N- and 13C-CEST have been the approaches of choice, the development of spin state selective 1H-CEST pulse sequences that separate the effects of chemical and dipolar exchange [T. Yuwen, A. Sekhar and L. E. Kay, Angew Chem Int Ed Engl 2016 doi: 10.1002/anie.201610759 (Yuwen et al. 2017)] significantly increases the utility of 1H-based experiments. Pulse schemes have been described previously for studies of highly deuterated proteins. We present here longitudinal-relaxation optimized amide 1H-CEST experiments for probing chemical exchange in protonated proteins. Applications involving a pair of proteins are presented establishing that accurate 1H chemical shifts of sparsely populated conformers can be obtained from simple analyses of 1H-CEST profiles. A discussion of the inherent differences between 15N-/13C- and 1H-CEST experiments is presented, leading to an optimal strategy for recording 1H-CEST experiments.
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Affiliation(s)
- Tairan Yuwen
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, Canada
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, Canada.
- Hospital for Sick Children, Program in Molecular Structure and Function, Toronto, ON, Canada.
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21
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Amin HK, El-Araby AM, Eid S, Nasr T, Bondock S, Leheta O, Dawoud ME. A Thiazole Analogue Exhibits an Anti-Proliferative Effect in Different Human Carcinoma Cell Lines and Its Mechanism Based on Molecular Modeling. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/abc.2017.71005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Ravera E, Martelli T, Geiger Y, Fragai M, Goobes G, Luchinat C. Biosilica and bioinspired silica studied by solid-state NMR. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Ravera E, Ciambellotti S, Cerofolini L, Martelli T, Kozyreva T, Bernacchioni C, Giuntini S, Fragai M, Turano P, Luchinat C. Solid-State NMR of PEGylated Proteins. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510148] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
| | - Silvia Ciambellotti
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
| | - Tommaso Martelli
- Giotto Biotech S.r.l. Via Madonna del Piano 6; 50019 Sesto Fiorentino FI Italy
| | - Tatiana Kozyreva
- Giotto Biotech S.r.l. Via Madonna del Piano 6; 50019 Sesto Fiorentino FI Italy
| | - Caterina Bernacchioni
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”; University of Florence, and Magnetic Resonance Consortium (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino FI Italy
- Giotto Biotech S.r.l. Via Madonna del Piano 6; 50019 Sesto Fiorentino FI Italy
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24
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Ravera E, Ciambellotti S, Cerofolini L, Martelli T, Kozyreva T, Bernacchioni C, Giuntini S, Fragai M, Turano P, Luchinat C. Solid-State NMR of PEGylated Proteins. Angew Chem Int Ed Engl 2016; 55:2446-9. [PMID: 26756539 DOI: 10.1002/anie.201510148] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Indexed: 11/10/2022]
Abstract
PEGylated proteins are widely used in biomedicine but, in spite of their importance, no atomic-level information is available since they are generally resistant to structural characterization approaches. PEGylated proteins are shown here to yield highly resolved solid-state NMR spectra, which allows assessment of the structural integrity of proteins when PEGylated for therapeutic or diagnostic use.
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Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Silvia Ciambellotti
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Tommaso Martelli
- Giotto Biotech S.r.l. Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Tatiana Kozyreva
- Giotto Biotech S.r.l. Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Caterina Bernacchioni
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, and Magnetic Resonance Consortium (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy. .,Giotto Biotech S.r.l. Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy.
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25
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Long D, Delaglio F, Sekhar A, Kay LE. Probing Invisible, Excited Protein States by Non-Uniformly Sampled Pseudo-4D CEST Spectroscopy. Angew Chem Int Ed Engl 2015; 54:10507-11. [PMID: 26178142 DOI: 10.1002/anie.201504070] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 11/07/2022]
Abstract
Chemical exchange saturation transfer (CEST) NMR spectroscopy is a powerful tool for studies of slow timescale protein dynamics. Typical experiments are based on recording a large number of 2D data sets and quantifying peak intensities in each of the resulting planes. A weakness of the method is that peaks must be resolved in 2D spectra, limiting applications to relatively small proteins. Resolution is significantly improved in 3D spectra but recording uniformly sampled data is time-prohibitive. Here we describe non-uniformly sampled HNCO-based pseudo-4D CEST that provides excellent resolution in reasonable measurement times. Data analysis is done through fitting in the time domain, without the need of reconstructing the frequency dimensions, exploiting previously measured accurate peak positions in reference spectra. The methodology is demonstrated on several protein systems, including a nascent form of superoxide dismutase that is implicated in neurodegenerative disease.
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Affiliation(s)
- Dong Long
- Departments of Molecular Genetics, Biochemistry & Chemistry, University of Toronto, Toronto, Ontario M5S 1A8 (Canada).
| | | | - Ashok Sekhar
- Departments of Molecular Genetics, Biochemistry & Chemistry, University of Toronto, Toronto, Ontario M5S 1A8 (Canada)
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry & Chemistry, University of Toronto, Toronto, Ontario M5S 1A8 (Canada). .,Hospital for Sick Children, Program in Molecular Structure and Function, 555 University Avenue, Toronto, Ontario M5G1X8 (Canada).
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26
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Long D, Delaglio F, Sekhar A, Kay LE. Probing Invisible, Excited Protein States by Non-Uniformly Sampled Pseudo-4D CEST Spectroscopy. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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27
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Sekhar A, Rumfeldt JAO, Broom HR, Doyle CM, Bouvignies G, Meiering EM, Kay LE. Thermal fluctuations of immature SOD1 lead to separate folding and misfolding pathways. eLife 2015; 4:e07296. [PMID: 26099300 PMCID: PMC4475725 DOI: 10.7554/elife.07296] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 05/04/2015] [Indexed: 01/08/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease involving cytotoxic conformations of Cu, Zn superoxide dismutase (SOD1). A major challenge in understanding ALS disease pathology has been the identification and atomic-level characterization of these conformers. Here, we use a combination of NMR methods to detect four distinct sparsely populated and transiently formed thermally accessible conformers in equilibrium with the native state of immature SOD1 (apoSOD1(2SH)). Structural models of two of these establish that they possess features present in the mature dimeric protein. In contrast, the other two are non-native oligomers in which the native dimer interface and the electrostatic loop mediate the formation of aberrant intermolecular interactions. Our results show that apoSOD1(2SH) has a rugged free energy landscape that codes for distinct kinetic pathways leading to either maturation or non-native association and provide a starting point for a detailed atomic-level understanding of the mechanisms of SOD1 oligomerization.
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Affiliation(s)
- Ashok Sekhar
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | | | - Helen R Broom
- Department of Chemistry, University of Waterloo, Waterloo, Canada
| | - Colleen M Doyle
- Department of Chemistry, University of Waterloo, Waterloo, Canada
| | | | | | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
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28
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In-cell NMR reveals potential precursor of toxic species from SOD1 fALS mutants. Nat Commun 2014; 5:5502. [PMID: 25429517 DOI: 10.1038/ncomms6502] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 10/07/2014] [Indexed: 12/20/2022] Open
Abstract
Mutations in the superoxide dismutase 1 (SOD1) gene are related to familial cases of amyotrophic lateral sclerosis (fALS). Here we exploit in-cell NMR to characterize the protein folding and maturation of a series of fALS-linked SOD1 mutants in human cells and to obtain insight into their behaviour in the cellular context, at the molecular level. The effect of various mutations on SOD1 maturation are investigated by changing the availability of metal ions in the cells, and by coexpressing the copper chaperone for SOD1, hCCS. We observe for most of the mutants the occurrence of an unstructured SOD1 species, unable to bind zinc. This species may be a common precursor of potentially toxic oligomeric species, that are associated with fALS. Coexpression of hCCS in the presence of copper restores the correct maturation of the SOD1 mutants and prevents the formation of the unstructured species, confirming that hCCS also acts as a molecular chaperone.
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29
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Mera-Adasme R, Sadeghian K, Sundholm D, Ochsenfeld C. Effect of including torsional parameters for histidine-metal interactions in classical force fields for metalloproteins. J Phys Chem B 2014; 118:13106-11. [PMID: 25410708 DOI: 10.1021/jp5078906] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Classical force-field parameters of the metal site of metalloproteins usually comprise only the partial charges of the involved atoms, as well as the bond-stretching and bending parameters of the metal-ligand interactions. Although for certain metal ligands such as histidine residues, the torsional motions at the metal site play an important role for the dynamics of the protein, no such terms have been considered to be crucial in the parametrization of the force fields, and they have therefore been omitted in the parametrization. In this work, we have optimized AMBER-compatible force-field parameters for the reduced state of the metal site of copper, zinc superoxide dismutase (SOD1) and assessed the effect of including torsional parameters for the histidine-metal interactions in molecular dynamics simulations. On the basis of the obtained results, we recommend that torsion parameters of the metal site are included when processes at the metal site are investigated or when free-energy calculations are performed. As the torsion parameters mainly affect the structure of the metal site, other kinds of structural studies can be performed without considering the torsional parameters of the metal site.
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Affiliation(s)
- Raúl Mera-Adasme
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , München 80539, Germany
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30
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The functional role of MnSOD as a biomarker of human diseases and therapeutic potential of a new isoform of a human recombinant MnSOD. BIOMED RESEARCH INTERNATIONAL 2014; 2014:476789. [PMID: 24511533 PMCID: PMC3913005 DOI: 10.1155/2014/476789] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 11/19/2013] [Indexed: 01/05/2023]
Abstract
Reactive oxygen species (ROS) are generated as a consequence of metabolic reactions in the mitochondria of eukaryotic cells. This work describes the role of the manganese superoxide dismutase (MnSOD) as a biomarker of different human diseases and proposes a new therapeutic application for the prevention of cancer and its treatment. The paper also describes how a new form of human MnSOD was discovered, its initial application, and its clinical potentials. The MnSOD isolated from a human liposarcoma cell line (LSA) was able to kill cancer cells expressing estrogen receptors, but it did not have cytotoxic effects on normal cells. Together with its oncotoxic activity, the recombinant MnSOD (rMnSOD) exerts a radioprotective effect on normal cells irradiated with X-rays. The rMnSOD is characterized by the presence of a leader peptide, which allows the protein to enter cells: this unique property can be used in the radiodiagnosis of cancer or chemotherapy, conjugating radioactive substances or chemotherapic drugs to the leader peptide of the MnSOD. Compared to traditional chemotherapic agents, the drugs conjugated with the leader peptide of MnSOD can selectively reach and enter cancer cells, thus reducing the side effects of traditional treatments.
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Hanashima S, Fujiwara N, Matsumoto K, Iwasaki N, Zheng GQ, Torigoe H, Suzuki K, Taniguchi N, Yamaguchi Y. A solution 17O-NMR approach for observing an oxidized cysteine residue in Cu,Zn-superoxide dismutase. Chem Commun (Camb) 2013; 49:1449-51. [PMID: 23323266 DOI: 10.1039/c2cc36918d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Solution (17)O-NMR application to biological macromolecules is extremely limited. We describe here (17)O-NMR observation of the (17)O(2)-oxidized cysteine side chain of human Cu,Zn-superoxide dismutase in solution using selective (17)O(2) oxidation. (17)O-NMR with the aid of (17)O-labeling has wide potential to probe the environment and dynamics of oxidizable functionalities in proteins.
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Affiliation(s)
- Shinya Hanashima
- Structural Glycobiology Team, RIKEN ASI, 2-1 Hirosawa, Wako-shi, 351-0198 Saitama, Japan
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Barbet-Massin E, Pell AJ, Knight MJ, Webber AL, Felli IC, Pierattelli R, Emsley L, Lesage A, Pintacuda G. 13C-Detected Through-Bond Correlation Experiments for Protein Resonance Assignment by Ultra-Fast MAS Solid-State NMR. Chemphyschem 2013; 14:3131-7. [DOI: 10.1002/cphc.201201097] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/02/2013] [Indexed: 11/11/2022]
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Kline CD, Mayfield M, Blackburn NJ. HHM motif at the CuH-site of peptidylglycine monooxygenase is a pH-dependent conformational switch. Biochemistry 2013; 52:2586-96. [PMID: 23530865 DOI: 10.1021/bi4002248] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidylglycine monooxygenase is a copper-containing enzyme that catalyzes the amidation of neuropeptides hormones, the first step of which is the conversion of a glycine-extended pro-peptide to its α-hydroxyglcine intermediate. The enzyme contains two mononuclear Cu centers termed CuM (ligated to imidazole nitrogens of H242, H244 and the thioether S of M314) and CuH (ligated to imidazole nitrogens of H107, H108, and H172) with a Cu-Cu separation of 11 Å. During catalysis, the M site binds oxygen and substrate, and the H site donates the second electron required for hydroxylation. The WT enzyme shows maximum catalytic activity at pH 5.8 and undergoes loss of activity at lower pHs due to a protonation event with a pKA of 4.6. Low pH also causes a unique structural transition in which a new S ligand coordinates to copper with an identical pKA, manifest by a large increase in Cu-S intensity in the X- ray absorption spectroscopy. In previous work (Bauman, A. T., Broers, B. A., Kline, C. D., and Blackburn, N. J. (2011) Biochemistry 50, 10819-10828), we tentatively assigned the new Cu-S interaction to binding of M109 to the H-site (part of an HHM conserved motif common to all but one member of the family). Here we follow up on these findings via studies on the catalytic activity, pH-activity profiles, and spectroscopic (electron paramagnetic resonance, XAS, and Fourier transform infrared) properties of a number of H-site variants, including H107A, H108A, H172A, and M109I. Our results establish that M109 is indeed the coordinating ligand and confirm the prediction that the low pH structural transition with associated loss of activity is abrogated when the M109 thioether is absent. The histidine mutants show more complex behavior, but the almost complete lack of activity in all three variants coupled with only minor differences in their spectroscopic properties suggests that unique structural elements at H are critical for functionality. The data suggest a more general utility for the HHM motif as a copper- and pH-dependent conformational switch.
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Affiliation(s)
- Chelsey D Kline
- Institute of Environmental, Health, Oregon Health and Sciences University, Beaverton, Oregon 97006, USA
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Fujisawa T, Homma K, Yamaguchi N, Kadowaki H, Tsuburaya N, Naguro I, Matsuzawa A, Takeda K, Takahashi Y, Goto J, Tsuji S, Nishitoh H, Ichijo H. A novel monoclonal antibody reveals a conformational alteration shared by amyotrophic lateral sclerosis-linked SOD1 mutants. Ann Neurol 2013; 72:739-49. [PMID: 23280792 DOI: 10.1002/ana.23668] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 04/29/2012] [Accepted: 05/04/2012] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that is characterized by the selective loss of upper and lower motoneurons. Although >100 different Cu, Zn superoxide dismutase (SOD1) mutations have been identified in ALS patients, it remains controversial whether all of them are disease-causative mutations. Therefore, it is necessary to develop molecular mechanism-based diagnosis and treatment of ALS caused by SOD1 mutations. METHODS We previously reported that 3 pathogenic mutations of SOD1 cause chronic endoplasmic reticulum (ER) stress by inducing the binding of SOD1 to Derlin-1, a component of the ER homeostatic machinery. Here, we systematically analyzed 132 SOD1 mutants and found that most have a constitutively exposed Derlin-1-binding region (DBR) that is occluded in the wild-type protein. To develop the novel molecular mechanism-based antibody that can specifically recognize the aberrant structure of toxic SOD1 mutants, we generated the monoclonal antibody against the DBR. RESULTS MS785, a monoclonal antibody generated against the DBR, distinguished most ALS-causative SOD1 mutants from both wild-type and nontoxic mutants. Moreover, MS785 recognized endogenous SOD1 in B lymphocytes derived from 14 ALS patients carrying SOD1 mutations but not from 11 healthy controls. INTERPRETATION This is the first study to address the common property of all ALS-causative SOD1 mutants. MS785 is the first molecular mechanism-based antibody that was shown to be able to distinguish ALS-linked toxic SOD1 mutants from both wild-type and nontoxic mutants. MS785 may thus become an innovative tool for the diagnosis of ALS.
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Affiliation(s)
- Takao Fujisawa
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, Global Center of Education and Research for Chemical Biology of the Diseases, University of Tokyo, Hongo, Tokyo, Japan
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Human superoxide dismutase 1 (hSOD1) maturation through interaction with human copper chaperone for SOD1 (hCCS). Proc Natl Acad Sci U S A 2012; 109:13555-60. [PMID: 22869735 DOI: 10.1073/pnas.1207493109] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Copper chaperone for superoxide dismutase 1 (SOD1), CCS, is the physiological partner for the complex mechanism of SOD1 maturation. We report an in vitro model for human CCS-dependent SOD1 maturation based on the study of the interactions of human SOD1 (hSOD1) with full-length WT human CCS (hCCS), as well as with hCCS mutants and various truncated constructs comprising one or two of the protein's three domains. The synergy between electrospray ionization mass spectrometry (ESI-MS) and NMR is fully exploited. This is an in vitro study of this process at the molecular level. Domain 1 of hCCS is necessary to load hSOD1 with Cu(I), requiring the heterodimeric complex formation with hSOD1 fostered by the interaction with domain 2. Domain 3 is responsible for the catalytic formation of the hSOD1 Cys-57-Cys-146 disulfide bond, which involves both hCCS Cys-244 and Cys-246 via disulfide transfer.
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Matés JM, Segura JA, Alonso FJ, Márquez J. Oxidative stress in apoptosis and cancer: an update. Arch Toxicol 2012; 86:1649-65. [PMID: 22811024 DOI: 10.1007/s00204-012-0906-3] [Citation(s) in RCA: 246] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 07/03/2012] [Indexed: 02/07/2023]
Abstract
The oxygen paradox tells us that oxygen is both necessary for aerobic life and toxic to all life forms. Reactive oxygen species (ROS) touch every biological and medical discipline, especially those involving proliferative status, supporting the idea that active oxygen may be increased in tumor cells. In fact, metabolism of oxygen and the resulting toxic byproducts can cause cancer and death. Efforts to counteract the damage caused by ROS are gaining acceptance as a basis for novel therapeutic approaches, and the field of prevention of cancer is experiencing an upsurge of interest in medically useful antioxidants. Apoptosis is an important means of regulating cell numbers in the developing cell system, but it is so important that it must be controlled. Normal cell death in homeostasis of multicellular organisms is mediated through tightly regulated apoptotic pathways that involve oxidative stress regulation. Defective signaling through these pathways can contribute to both unbalance in apoptosis and development of cancer. Finally, in this review, we discuss new knowledge about recent tools that provide powerful antioxidant strategies, and designing methods to deliver to target cells, in the prevention and treatment of cancer.
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Affiliation(s)
- José M Matés
- Department of Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Málaga, Spain.
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Bauman AT, Broers BA, Kline CD, Blackburn NJ. A copper-methionine interaction controls the pH-dependent activation of peptidylglycine monooxygenase. Biochemistry 2011; 50:10819-28. [PMID: 22080626 DOI: 10.1021/bi201193j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The pH dependence of native peptidylglycine monooxygenase (PHM) and its M314H variant has been studied in detail. For wild-type (WT) PHM, the intensity of the Cu-S interaction visible in the Cu(I) extended X-ray absorption fine structure (EXAFS) data is inversely proportional to catalytic activity over the pH range of 3-8. A previous model based on more limited data was interpreted in terms of two protein conformations involving an inactive Met-on form and an active flexible Met-off form [Bauman, A. T., et al. (2006) Biochemistry 45, 11140-11150] that derived its catalytic activity from the ability to couple into vibrational modes critical for proton tunneling. The new studies comparing the WT and M314H variant have led to the evolution of this model, in which the Met-on form has been found to be derived from coordination of an additional Met residue, rather than a more rigid conformer of M314 as previously proposed. The catalytic activity of the mutant decreased by 96% because of effects on both k(cat) and K(M), but it displayed the same activity-pH profile with a maximum around pH 6. At pH 8, the reduced Cu(I) form gave spectra that could be simulated by replacement of the Cu(M) Cu-S(Met) interaction with a Cu-N/O interaction, but the data did not unambiguously assign the ligand to the imidazole side chain of H314. At pH 3.5, the EXAFS still showed the presence of a strong Cu-S interaction, establishing that the Met-on form observed at low pH in WT cannot be due to a strengthening of the Cu(M)-methionine interaction but must arise from a different Cu-S interaction. Therefore, lowering the pH causes a conformational change at one of the Cu centers that brings a new S donor residue into a favorable orientation for coordination to copper and generates an inactive form. Cys coordination is unlikely because all Cys residues in PHM are engaged in disulfide cross-links. Sequence comparison with the PHM homologues tyramine β-monooxygenase and dopamine β-monooxygenase suggests that M109 (adjacent to H site ligands H107 and H108) is the most likely candidate. A model is presented in which H108 is protonated with a pK(a) of 4.6 to generate the inactive low-pH form with Cu(H) coordinated by M109, H107, and H172.
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Affiliation(s)
- Andrew T Bauman
- Institute of Environmental Health, Oregon Health and Sciences University, Beaverton, Oregon 97006, United States
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38
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Couch V, Stuchebrukhov A. Histidine in continuum electrostatics protonation state calculations. Proteins 2011; 79:3410-9. [PMID: 22072521 DOI: 10.1002/prot.23114] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 04/15/2011] [Accepted: 06/08/2011] [Indexed: 11/10/2022]
Abstract
A modification to the standard continuum electrostatics approach to calculate protein pK(a)s, which allows for the decoupling of histidine tautomers within a two-state model, is presented. Histidine with four intrinsically coupled protonation states cannot be easily incorporated into a two-state formalism, because the interaction between the two protonatable sites of the imidazole ring is not purely electrostatic. The presented treatment, based on a single approximation of the interrelation between histidine's charge states, allows for a natural separation of the two protonatable sites associated with the imidazole ring as well as the inclusion of all protonation states within the calculation.
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Affiliation(s)
- Vernon Couch
- Department of Chemistry, University of California, Davis, California 95616, USA
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Marboutin L, Petitjean H, Xerri B, Vita N, Dupeyrat F, Flament JP, Berthomieu D, Berthomieu C. Profiling the Active Site of a Copper Enzyme through Its Far-Infrared Fingerprint. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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40
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Marboutin L, Petitjean H, Xerri B, Vita N, Dupeyrat F, Flament JP, Berthomieu D, Berthomieu C. Profiling the Active Site of a Copper Enzyme through Its Far-Infrared Fingerprint. Angew Chem Int Ed Engl 2011; 50:8062-6. [DOI: 10.1002/anie.201102014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Indexed: 12/16/2022]
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41
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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: 0.7] [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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42
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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: 336] [Impact Index Per Article: 22.4] [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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Museth AK, Brorsson AC, Lundqvist M, Tibell LAE, Jonsson BH. The ALS-associated mutation G93A in human copper-zinc superoxide dismutase selectively destabilizes the remote metal binding region. Biochemistry 2009; 48:8817-29. [PMID: 19655787 DOI: 10.1021/bi900703v] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
More than 100 distinct mutations in the gene (SOD1) for human copper-zinc superoxide dismutase (CuZnSOD) have been associated with familial amyotrophic lateral sclerosis (fALS). Studies of these mutant proteins, which often have been performed under far from physiological conditions, have indicated effects on protein stabilities, catalytic activity, and metal binding affinities but with no common pattern. Also, with the knowledge that ALS is a late onset disease it is apparent that protein interactions which contribute to the disorder might, in the natural cellular milieu, depend on a delicate balance between intrinsic protein properties. In this study, we have used experimental conditions as near as possible to the in vivo conditions to reduce artifacts emanating from the experimental setup. Using 1H-15N HSQC NMR spectroscopy, we have analyzed hydrogen exchange at the amide groups of wild-type (wt) CuZnSOD and the fALS-associated G93A SOD variant in their fully metalated states. From analyses of the exchange pattern, we have characterized the local dynamics at 64% of all positions in detail in both the wt and G93A protein. The results show that the G93A mutation had no effect on the dynamics at a majority of the investigated positions. However, the mutation results in local destabilization at the site of the mutation and also in stabilization at a few positions that were apparently scattered over the entire protein surface. Most remarkably, the mutation selectively destabilized the remote metal binding region. The results indicate that the metal binding region may affect the intermolecular protein-protein interactions which cause formation of protein aggregates.
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Affiliation(s)
- Anna Katrine Museth
- Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
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Tiwari A, Liba A, Sohn SH, Seetharaman SV, Bilsel O, Matthews CR, Hart PJ, Valentine JS, Hayward LJ. Metal deficiency increases aberrant hydrophobicity of mutant superoxide dismutases that cause amyotrophic lateral sclerosis. J Biol Chem 2009; 284:27746-58. [PMID: 19651777 DOI: 10.1074/jbc.m109.043729] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mechanisms by which mutant variants of Cu/Zn-superoxide dismutase (SOD1) cause familial amyotrophic lateral sclerosis are not clearly understood. Evidence to date suggests that altered conformations of amyotrophic lateral sclerosis mutant SOD1s trigger perturbations of cellular homeostasis that ultimately cause motor neuron degeneration. In this study we correlated the metal contents and disulfide bond status of purified wild-type (WT) and mutant SOD1 proteins to changes in electrophoretic mobility and surface hydrophobicity as detected by 1-anilinonaphthalene-8-sulfonic acid (ANS) fluorescence. As-isolated WT and mutant SOD1s were copper-deficient and exhibited mobilities that correlated with their expected negative charge. However, upon disulfide reduction and demetallation at physiological pH, both WT and mutant SOD1s underwent a conformational change that produced a slower mobility indicative of partial unfolding. Furthermore, although ANS did not bind appreciably to the WT holoenzyme, incubation of metal-deficient WT or mutant SOD1s with ANS increased the ANS fluorescence and shifted its peak toward shorter wavelengths. This increased interaction with ANS was greater for the mutant SOD1s and could be reversed by the addition of metal ions, especially Cu(2+), even for SOD1 variants incapable of forming the disulfide bond. Overall, our findings support the notion that misfolding associated with metal deficiency may facilitate aberrant interactions of SOD1 with itself or with other cellular constituents and may thereby contribute to neuronal toxicity.
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Affiliation(s)
- Ashutosh Tiwari
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.
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45
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Chen S, Li X, Ma H. New Approach for Local Structure Analysis of the Tyrosine Domain in Proteins by Using a Site-Specific and Polarity-Sensitive Fluorescent Probe. Chembiochem 2009; 10:1200-7. [DOI: 10.1002/cbic.200900003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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46
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Banci L, Bertini I, Ciofi-Baffoni S. Copper trafficking in biology: an NMR approach. HFSP JOURNAL 2009; 3:165-75. [PMID: 19949444 DOI: 10.2976/1.3078306] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Accepted: 01/15/2009] [Indexed: 11/19/2022]
Abstract
Copper ions are essential for living organisms because they are involved in several fundamental biological processes. Biomolecules interacting with copper ions have to be characterized as such, when bound to the metal ion, and when they interact with other biomolecules or substrates. The characterization is both structural and dynamic. In this context, NMR is a preferred tool of investigation because it allows shedding light on what happens in solution. Here, the NMR contribution to the copper trafficking is described, providing precious information on biochemical pathways, which are essential to understand the mechanisms of life at the molecular level.
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Affiliation(s)
- Lucia Banci
- Department of Chemistry, and Magnetic Resonance Center CERM, University of Florence, Scientific Campus, 50019, Sesto Fiorentino, Florence, Italy
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47
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Shin DS, DiDonato M, Barondeau DP, Hura GL, Hitomi C, Berglund JA, Getzoff ED, Cary SC, Tainer JA. Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis. J Mol Biol 2009; 385:1534-55. [PMID: 19063897 PMCID: PMC2669833 DOI: 10.1016/j.jmb.2008.11.031] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 11/07/2008] [Accepted: 11/11/2008] [Indexed: 01/07/2023]
Abstract
Prokaryotic thermophiles supply stable human protein homologs for structural biology; yet, eukaryotic thermophiles would provide more similar macromolecules plus those missing in microbes. Alvinella pompejana is a deep-sea hydrothermal-vent worm that has been found in temperatures averaging as high as 68 degrees C, with spikes up to 84 degrees C. Here, we used Cu,Zn superoxide dismutase (SOD) to test if this eukaryotic thermophile can provide insights into macromolecular mechanisms and stability by supplying better stable mammalian homologs for structural biology and other biophysical characterizations than those from prokaryotic thermophiles. Identification, cloning, characterization, X-ray scattering (small-angle X-ray scattering, SAXS), and crystal structure determinations show that A. pompejana SOD (ApSOD) is superstable, homologous, and informative. SAXS solution analyses identify the human-like ApSOD dimer. The crystal structure shows the active site at 0.99 A resolution plus anchoring interaction motifs in loops and termini accounting for enhanced stability of ApSOD versus human SOD. Such stabilizing features may reduce movements that promote inappropriate intermolecular interactions, such as amyloid-like filaments found in SOD mutants causing the neurodegenerative disease familial amyotrophic lateral sclerosis or Lou Gehrig's disease. ApSOD further provides the structure of a long-sought SOD product complex at 1.35 A resolution, suggesting a unified inner-sphere mechanism for catalysis involving metal ion movement. Notably, this proposed mechanism resolves apparent paradoxes regarding electron transfer. These results extend knowledge of SOD stability and catalysis and suggest that the eukaryote A. pompejana provides macromolecules highly similar to those from humans, but with enhanced stability more suitable for scientific and medical applications.
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Affiliation(s)
- David S. Shin
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael DiDonato
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David P. Barondeau
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Greg L. Hura
- Advanced Light Source, Lawrence Berkeley National Laboratory, CA 94720, USA
| | - Chiharu Hitomi
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - J. Andrew Berglund
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Elizabeth D. Getzoff
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - S. Craig Cary
- College of Marine Studies, University of Delaware, Lewes, DE 19958, USA, Department of Biological Sciences, University of Waikato, Hamilton 3240, New Zealand,Corresponding authors. E-mail addresses: and
| | - John A. Tainer
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA,Corresponding authors. E-mail addresses: and
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Rumfeldt JA, Lepock JR, Meiering EM. Unfolding and Folding Kinetics of Amyotrophic Lateral Sclerosis-Associated Mutant Cu,Zn Superoxide Dismutases. J Mol Biol 2009; 385:278-98. [DOI: 10.1016/j.jmb.2008.10.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 09/26/2008] [Accepted: 10/01/2008] [Indexed: 02/06/2023]
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Mori M, Jiménez B, Piccioli M, Battistoni A, Sette M. The Solution Structure of the Monomeric Copper, Zinc Superoxide Dismutase from Salmonella enterica: Structural Insights To Understand the Evolution toward the Dimeric Structure. Biochemistry 2008; 47:12954-63. [DOI: 10.1021/bi801252e] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mirko Mori
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino (FI), Italy, Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy, National Institute of Biostructures and Biosystems (INBB), Viale delle Medaglie d’Oro 305, 00136 Rome, Italy, and Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Beatriz Jiménez
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino (FI), Italy, Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy, National Institute of Biostructures and Biosystems (INBB), Viale delle Medaglie d’Oro 305, 00136 Rome, Italy, and Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Mario Piccioli
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino (FI), Italy, Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy, National Institute of Biostructures and Biosystems (INBB), Viale delle Medaglie d’Oro 305, 00136 Rome, Italy, and Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Andrea Battistoni
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino (FI), Italy, Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy, National Institute of Biostructures and Biosystems (INBB), Viale delle Medaglie d’Oro 305, 00136 Rome, Italy, and Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Marco Sette
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino (FI), Italy, Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy, National Institute of Biostructures and Biosystems (INBB), Viale delle Medaglie d’Oro 305, 00136 Rome, Italy, and Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy
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Lin YC, Vaseeharan B, Chen JC. Identification of the extracellular copper–zinc superoxide dismutase (ecCuZnSOD) gene of the mud crab Scylla serrata and its expression following β-glucan and peptidoglycan injections. Mol Immunol 2008; 45:1346-55. [DOI: 10.1016/j.molimm.2007.09.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Revised: 09/05/2007] [Accepted: 09/06/2007] [Indexed: 10/22/2022]
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