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Zaji HD, Seyedalipour B, Hanun HM, Baziyar P, Hosseinkhani S, Akhlaghi M. Computational insight into in silico analysis and molecular dynamics simulation of the dimer interface residues of ALS-linked hSOD1 forms in apo/holo states: a combined experimental and bioinformatic perspective. 3 Biotech 2023; 13:92. [PMID: 36845075 PMCID: PMC9944573 DOI: 10.1007/s13205-023-03514-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/03/2023] [Indexed: 02/23/2023] Open
Abstract
The aggregation of misfolded SOD1 proteins in neurodegenerative illnesses is a key pathological hallmark in amyotrophic lateral sclerosis (ALS). SOD1 is stabilized and enzymatically activated after binding to Cu/Zn and forming intramolecular disulfide. SOD1 aggregation/oligomerization is triggered by the dissociation of Cu and/or Zn ions. Therefore, we compared the possible effects of ALS-associated point mutations of the holo/apo forms of WT/I149T/V148G SOD1 variants located at the dimer interface to determine structural characterization using spectroscopic methods, computational approaches as well as molecular dynamics (MD) simulations. Predictive results of computational analysis of single-nucleotide polymorphisms (SNPs) suggested that mutant SOD1 has a deleterious effect on activity and structure destabilization. MD data analysis indicated that changes in flexibility, stability, hydrophobicity of the protein as well as increased intramolecular interactions of apo-SOD1 were more than holo-SOD1. Furthermore, a decrease in enzymatic activity in apo-SOD1 was observed compared to holo-SOD1. Comparative intrinsic and ANS fluorescence results of holo/apo-WT-hSOD1 and mutants indicated structural alterations in the local environment of tryptophan residue and hydrophobic patches, respectively. Experimental and MD data supported that substitution effect and metal deficiency of mutants (apo forms) in the dimer interface may promote the tendency to protein mis-folding and aggregation, consequently disrupting the dimer-monomer equilibrium and increased propensity to dissociation dimer into SOD-monomer ultimately leading to loss of stability and function. Overall, data analysis of apo/holo SOD1 forms on protein structure and function using computational and experimental studies will contribute to a better understanding of ALS pathogenicity.
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Affiliation(s)
- Hamza Dakhil Zaji
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Bagher Seyedalipour
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Haider Munzer Hanun
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Payam Baziyar
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mona Akhlaghi
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
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Pan Q, Nguyen TB, Ascher DB, Pires DEV. Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures. Brief Bioinform 2022; 23:bbac025. [PMID: 35189634 PMCID: PMC9155634 DOI: 10.1093/bib/bbac025] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 01/13/2022] [Accepted: 01/30/2022] [Indexed: 12/26/2022] Open
Abstract
Changes in protein sequence can have dramatic effects on how proteins fold, their stability and dynamics. Over the last 20 years, pioneering methods have been developed to try to estimate the effects of missense mutations on protein stability, leveraging growing availability of protein 3D structures. These, however, have been developed and validated using experimentally derived structures and biophysical measurements. A large proportion of protein structures remain to be experimentally elucidated and, while many studies have based their conclusions on predictions made using homology models, there has been no systematic evaluation of the reliability of these tools in the absence of experimental structural data. We have, therefore, systematically investigated the performance and robustness of ten widely used structural methods when presented with homology models built using templates at a range of sequence identity levels (from 15% to 95%) and contrasted performance with sequence-based tools, as a baseline. We found there is indeed performance deterioration on homology models built using templates with sequence identity below 40%, where sequence-based tools might become preferable. This was most marked for mutations in solvent exposed residues and stabilizing mutations. As structure prediction tools improve, the reliability of these predictors is expected to follow, however we strongly suggest that these factors should be taken into consideration when interpreting results from structure-based predictors of mutation effects on protein stability.
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Affiliation(s)
- Qisheng Pan
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, Queensland 4072, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3052, Australia
| | - Thanh Binh Nguyen
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, Queensland 4072, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3052, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, Queensland 4072, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3052, Australia
- Department of Biochemistry, University of Cambridge, 80 Tennis Ct Rd, Cambridge CB2 1GA, UK
| | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, Queensland 4072, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3052, Australia
- School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria 3053, Australia
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Sanavia T, Birolo G, Montanucci L, Turina P, Capriotti E, Fariselli P. Limitations and challenges in protein stability prediction upon genome variations: towards future applications in precision medicine. Comput Struct Biotechnol J 2020; 18:1968-1979. [PMID: 32774791 PMCID: PMC7397395 DOI: 10.1016/j.csbj.2020.07.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 12/13/2022] Open
Abstract
Protein stability predictions are becoming essential in medicine to develop novel immunotherapeutic agents and for drug discovery. Despite the large number of computational approaches for predicting the protein stability upon mutation, there are still critical unsolved problems: 1) the limited number of thermodynamic measurements for proteins provided by current databases; 2) the large intrinsic variability of ΔΔG values due to different experimental conditions; 3) biases in the development of predictive methods caused by ignoring the anti-symmetry of ΔΔG values between mutant and native protein forms; 4) over-optimistic prediction performance, due to sequence similarity between proteins used in training and test datasets. Here, we review these issues, highlighting new challenges required to improve current tools and to achieve more reliable predictions. In addition, we provide a perspective of how these methods will be beneficial for designing novel precision medicine approaches for several genetic disorders caused by mutations, such as cancer and neurodegenerative diseases.
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Affiliation(s)
- Tiziana Sanavia
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126 Torino, Italy
| | - Giovanni Birolo
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126 Torino, Italy
| | - Ludovica Montanucci
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Paola Turina
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via F. Selmi 3, 40126 Bologna, Italy
| | - Emidio Capriotti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via F. Selmi 3, 40126 Bologna, Italy
| | - Piero Fariselli
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126 Torino, Italy
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Wang Y, Mao Y, Zhang X, Liu H, Peng W, Liang L, Shi M, Xiao Y, Zhang Y, Zhang F, Yan R, Guo B. TAK1 may promote the development of diabetic nephropathy by reducing the stability of SnoN protein. Life Sci 2019; 228:1-10. [PMID: 31028803 DOI: 10.1016/j.lfs.2019.04.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/08/2019] [Accepted: 04/23/2019] [Indexed: 10/26/2022]
Abstract
AIMS This study aimed to investigate the role of transforming growth factor-β-activated protein kinase 1(TAK1) in the development of diabetic nephropathy (DN) by regulating the protein stability of Ski-related novel protein N(SnoN). MAIN METHODS A combination of in vivo and in vitro model systems was used to investigate how TAK1 regulated the expression of SnoN protein in DN. The study determined the effects of modulating the expression or activity of TAK1 on the SnoN protein level and its influence on the epithelial-mesenchymal transition (EMT) and extracellular matrix (ECM) deposition. KEY FINDINGS Under the high-glucose condition, the activation of TGF-β1/TAK1-induced phosphorylation and ubiquitination of SnoN protein resulted in reduced SnoN protein level as a consequence of enhanced SnoN degradation, which promoted EMT and ECM deposition in renal tubular epithelial cells. The study showed that TAK1 impaired SnoN protein level by decreasing the protein stability of SnoN. SIGNIFICANCE TAK1 mediated the phosphorylation of SnoN, resulting in SnoN ubiquitination and eventual degradation, which enhanced EMT and ECM deposition to promote renal fibrosis during DN.
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Affiliation(s)
- Yuanyuan Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Pathophysiology, Guizhou Medical University, Guiyang, Guizhou 550025, China; Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Yanwen Mao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Pathophysiology, Guizhou Medical University, Guiyang, Guizhou 550025, China; Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Xiaohuan Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Pathophysiology, Guizhou Medical University, Guiyang, Guizhou 550025, China; Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Huiming Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Pathophysiology, Guizhou Medical University, Guiyang, Guizhou 550025, China; Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Wei Peng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Pathophysiology, Guizhou Medical University, Guiyang, Guizhou 550025, China; Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Luqun Liang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Pathophysiology, Guizhou Medical University, Guiyang, Guizhou 550025, China; Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Mingjun Shi
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Pathophysiology, Guizhou Medical University, Guiyang, Guizhou 550025, China; Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Ying Xiao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Pathophysiology, Guizhou Medical University, Guiyang, Guizhou 550025, China; Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Yingying Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Pathophysiology, Guizhou Medical University, Guiyang, Guizhou 550025, China; Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Fan Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Pathophysiology, Guizhou Medical University, Guiyang, Guizhou 550025, China; Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Rui Yan
- Department of Nephrology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, China.
| | - Bing Guo
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Pathophysiology, Guizhou Medical University, Guiyang, Guizhou 550025, China; Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, Guizhou 550025, China.
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