1
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Wang J, Chen S, Yuan Q, Chen J, Li D, Wang L, Yang Y. Predicting the effects of mutations on protein solubility using graph convolution network and protein language model representation. J Comput Chem 2024; 45:436-445. [PMID: 37933773 DOI: 10.1002/jcc.27249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/11/2023] [Accepted: 10/21/2023] [Indexed: 11/08/2023]
Abstract
Solubility is one of the most important properties of protein. Protein solubility can be greatly changed by single amino acid mutations and the reduced protein solubility could lead to diseases. Since experimental methods to determine solubility are time-consuming and expensive, in-silico methods have been developed to predict the protein solubility changes caused by mutations mostly through protein evolution information. However, these methods are slow since it takes long time to obtain evolution information through multiple sequence alignment. In addition, these methods are of low performance because they do not fully utilize protein 3D structures due to a lack of experimental structures for most proteins. Here, we proposed a sequence-based method DeepMutSol to predict solubility change from residual mutations based on the Graph Convolutional Neural Network (GCN), where the protein graph was initiated according to predicted protein structure from Alphafold2, and the nodes (residues) were represented by protein language embeddings. To circumvent the small data of solubility changes, we further pretrained the model over absolute protein solubility. DeepMutSol was shown to outperform state-of-the-art methods in benchmark tests. In addition, we applied the method to clinically relevant genes from the ClinVar database and the predicted solubility changes were shown able to separate pathogenic mutations. All of the data sets and the source code are available at https://github.com/biomed-AI/DeepMutSol.
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Affiliation(s)
- Jing Wang
- Guangzhou institute of technology, Xidian University, Guangzhou, China
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Sheng Chen
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Qianmu Yuan
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Jianwen Chen
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Danping Li
- School of Telecommunications Engineering, Xidian University, Xi'an, China
| | - Lei Wang
- School of Electronic Engineering, Xidian University, Xi'an, China
| | - Yuedong Yang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
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2
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Chen Y, Zeng W, Yu S, Chen J, Zhou J. Gene co-expression network analysis reveals the positive impact of endocytosis and mitochondria-related genes over nitrogen metabolism in Saccharomyces cerevisiae. Gene 2022; 821:146267. [PMID: 35150821 DOI: 10.1016/j.gene.2022.146267] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/06/2021] [Accepted: 01/27/2022] [Indexed: 12/24/2022]
Abstract
Nitrogen metabolism is essential for most cellular activities. Therefore, a deep understanding of its regulatory mechanisms is necessary for the efficient utilization of nitrogen sources for Saccharomyces cerevisiae. In this study, a gene co-expression network was constructed for S. cerevisiae S288C with different nitrogen sources. From this, a key gene co-expression module related to nitrogen source preference utilization was obtained, and 10 hub genes centrally located in the co-expression network were identified. Functional studies verified that the endocytosis-related genes CAP1 and END3 significantly increased the utilization of multiple non-preferred amino acids and reduced the accumulation of the harmful nitrogen metabolite precursor urea by regulating amino acid transporters and TOR pathway. The mitochondria-related gene ATP12, MRPL22, MRP1 and NAM9 significantly increased the utilization of multiple non-preferred amino acids and reduced accumulation of the urea by coordinately regulating nitrogen catabolism repression, Ssy1p-Ptr3p-Ssy5p signaling sensor system, amino acid transporters, TOR pathway and urea metabolism-related pathways. Furthermore, these data revealed the potential positive effects of endocytosis and mitochondrial ribosomes protein translation on nitrogen source preference. This study provides new analytical perspectives for complex regulatory networks involving nitrogen metabolism in S. cerevisiae.
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Affiliation(s)
- Yu Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shiqin Yu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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3
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Yang Y, Zeng L, Vihinen M. PON-Sol2: Prediction of Effects of Variants on Protein Solubility. Int J Mol Sci 2021; 22:8027. [PMID: 34360790 PMCID: PMC8348231 DOI: 10.3390/ijms22158027] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 01/13/2023] Open
Abstract
Genetic variations have a multitude of effects on proteins. A substantial number of variations affect protein-solvent interactions, either aggregation or solubility. Aggregation is often related to structural alterations, whereas solubilizable proteins in the solid phase can be made again soluble by dilution. Solubility is a central protein property and when reduced can lead to diseases. We developed a prediction method, PON-Sol2, to identify amino acid substitutions that increase, decrease, or have no effect on the protein solubility. The method is a machine learning tool utilizing gradient boosting algorithm and was trained on a large dataset of variants with different outcomes after the selection of features among a large number of tested properties. The method is fast and has high performance. The normalized correct prediction rate for three states is 0.656, and the normalized GC2 score is 0.312 in 10-fold cross-validation. The corresponding numbers in the blind test were 0.545 and 0.157. The performance was superior in comparison to previous methods. The PON-Sol2 predictor is freely available. It can be used to predict the solubility effects of variants for any organism, even in large-scale projects.
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Affiliation(s)
- Yang Yang
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China; (Y.Y.); (L.Z.)
| | - Lianjie Zeng
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China; (Y.Y.); (L.Z.)
- Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, BMC B13, SE-221 84 Lund, Sweden
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4
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Galber C, Carissimi S, Baracca A, Giorgio V. The ATP Synthase Deficiency in Human Diseases. Life (Basel) 2021; 11:life11040325. [PMID: 33917760 PMCID: PMC8068106 DOI: 10.3390/life11040325] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/01/2021] [Accepted: 04/03/2021] [Indexed: 11/29/2022] Open
Abstract
Human diseases range from gene-associated to gene-non-associated disorders, including age-related diseases, neurodegenerative, neuromuscular, cardiovascular, diabetic diseases, neurocognitive disorders and cancer. Mitochondria participate to the cascades of pathogenic events leading to the onset and progression of these diseases independently of their association to mutations of genes encoding mitochondrial protein. Under physiological conditions, the mitochondrial ATP synthase provides the most energy of the cell via the oxidative phosphorylation. Alterations of oxidative phosphorylation mainly affect the tissues characterized by a high-energy metabolism, such as nervous, cardiac and skeletal muscle tissues. In this review, we focus on human diseases caused by altered expressions of ATP synthase genes of both mitochondrial and nuclear origin. Moreover, we describe the contribution of ATP synthase to the pathophysiological mechanisms of other human diseases such as cardiovascular, neurodegenerative diseases or neurocognitive disorders.
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Affiliation(s)
- Chiara Galber
- Consiglio Nazionale delle Ricerche, Institute of Neuroscience, I-35121 Padova, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, I-40126 Bologna, Italy
| | - Stefania Carissimi
- Consiglio Nazionale delle Ricerche, Institute of Neuroscience, I-35121 Padova, Italy
| | - Alessandra Baracca
- Department of Biomedical and Neuromotor Sciences, University of Bologna, I-40126 Bologna, Italy
| | - Valentina Giorgio
- Consiglio Nazionale delle Ricerche, Institute of Neuroscience, I-35121 Padova, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, I-40126 Bologna, Italy
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5
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Ceccatelli Berti C, di Punzio G, Dallabona C, Baruffini E, Goffrini P, Lodi T, Donnini C. The Power of Yeast in Modelling Human Nuclear Mutations Associated with Mitochondrial Diseases. Genes (Basel) 2021; 12:300. [PMID: 33672627 PMCID: PMC7924180 DOI: 10.3390/genes12020300] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/17/2022] Open
Abstract
The increasing application of next generation sequencing approaches to the analysis of human exome and whole genome data has enabled the identification of novel variants and new genes involved in mitochondrial diseases. The ability of surviving in the absence of oxidative phosphorylation (OXPHOS) and mitochondrial genome makes the yeast Saccharomyces cerevisiae an excellent model system for investigating the role of these new variants in mitochondrial-related conditions and dissecting the molecular mechanisms associated with these diseases. The aim of this review was to highlight the main advantages offered by this model for the study of mitochondrial diseases, from the validation and characterisation of novel mutations to the dissection of the role played by genes in mitochondrial functionality and the discovery of potential therapeutic molecules. The review also provides a summary of the main contributions to the understanding of mitochondrial diseases emerged from the study of this simple eukaryotic organism.
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Affiliation(s)
| | | | | | | | | | | | - Claudia Donnini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy; (C.C.B.); (G.d.P.); (C.D.); (E.B.); (P.G.); (T.L.)
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6
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Human Mitochondrial Pathologies of the Respiratory Chain and ATP Synthase: Contributions from Studies of Saccharomyces cerevisiae. Life (Basel) 2020; 10:life10110304. [PMID: 33238568 PMCID: PMC7700678 DOI: 10.3390/life10110304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022] Open
Abstract
The ease with which the unicellular yeast Saccharomyces cerevisiae can be manipulated genetically and biochemically has established this organism as a good model for the study of human mitochondrial diseases. The combined use of biochemical and molecular genetic tools has been instrumental in elucidating the functions of numerous yeast nuclear gene products with human homologs that affect a large number of metabolic and biological processes, including those housed in mitochondria. These include structural and catalytic subunits of enzymes and protein factors that impinge on the biogenesis of the respiratory chain. This article will review what is currently known about the genetics and clinical phenotypes of mitochondrial diseases of the respiratory chain and ATP synthase, with special emphasis on the contribution of information gained from pet mutants with mutations in nuclear genes that impair mitochondrial respiration. Our intent is to provide the yeast mitochondrial specialist with basic knowledge of human mitochondrial pathologies and the human specialist with information on how genes that directly and indirectly affect respiration were identified and characterized in yeast.
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7
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Mazurenko S. Predicting protein stability and solubility changes upon mutations: data perspective. ChemCatChem 2020. [DOI: 10.1002/cctc.202000933] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Stanislav Mazurenko
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of Science Masaryk University Zerotinovo nam. 617/9 601 77 Brno Czech Republic
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8
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Homoplasmic deleterious MT-ATP6/8 mutations in adult patients. Mitochondrion 2020; 55:64-77. [PMID: 32858252 DOI: 10.1016/j.mito.2020.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/13/2020] [Accepted: 08/14/2020] [Indexed: 01/10/2023]
Abstract
To address the frequency of complex V defects, we systematically sequenced MT-ATP6/8 genes in 512 consecutive patients. We performed functional analysis in muscle or fibroblasts for 12 out of 27 putative homoplasmic mutations and in cybrids for four. Fibroblasts, muscle and cybrids with known deleterious mutations underwent parallel analysis. It included oxidative phosphorylation spectrophotometric assays, western blots, structural analysis, ATP production, glycolysis and cell proliferation evaluation. We demonstrated the deleterious nature of three original mutations. Striking gradation in severity of the mutations consequences and differences between muscle, fibroblasts and cybrids implied a likely under-diagnosis of human complex V defects.
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9
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Barros MH, McStay GP. Modular biogenesis of mitochondrial respiratory complexes. Mitochondrion 2019; 50:94-114. [PMID: 31669617 DOI: 10.1016/j.mito.2019.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/04/2019] [Accepted: 10/10/2019] [Indexed: 11/29/2022]
Abstract
Mitochondrial function relies on the activity of oxidative phosphorylation to synthesise ATP and generate an electrochemical gradient across the inner mitochondrial membrane. These coupled processes are mediated by five multi-subunit complexes that reside in this inner membrane. These complexes are the product of both nuclear and mitochondrial gene products. Defects in the function or assembly of these complexes can lead to mitochondrial diseases due to deficits in energy production and mitochondrial functions. Appropriate biogenesis and function are mediated by a complex number of assembly factors that promote maturation of specific complex subunits to form the active oxidative phosphorylation complex. The understanding of the biogenesis of each complex has been informed by studies in both simple eukaryotes such as Saccharomyces cerevisiae and human patients with mitochondrial diseases. These studies reveal each complex assembles through a pathway using specific subunits and assembly factors to form kinetically distinct but related assembly modules. The current understanding of these complexes has embraced the revolutions in genomics and proteomics to further our knowledge on the impact of mitochondrial biology in genetics, medicine, and evolution.
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Affiliation(s)
- Mario H Barros
- Departamento de Microbiologia - Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil.
| | - Gavin P McStay
- Department of Biological Sciences, Staffordshire University, Stoke-on-Trent, United Kingdom.
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10
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Paladin L, Piovesan D, Tosatto SCE. SODA: prediction of protein solubility from disorder and aggregation propensity. Nucleic Acids Res 2019; 45:W236-W240. [PMID: 28505312 PMCID: PMC7059794 DOI: 10.1093/nar/gkx412] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/09/2017] [Indexed: 01/08/2023] Open
Abstract
Solubility is an important, albeit not well understood, feature determining protein behavior. It is of paramount importance in protein engineering, where similar folded proteins may behave in very different ways in solution. Here we present SODA, a novel method to predict the changes of protein solubility based on several physico-chemical properties of the protein. SODA uses the propensity of the protein sequence to aggregate as well as intrinsic disorder, plus hydrophobicity and secondary structure preferences to estimate changes in solubility. It has been trained and benchmarked on two different datasets. The comparison to other recently published methods shows that SODA has state-of-the-art performance and is particularly well suited to predict mutations decreasing solubility. The method is fast, returning results for single mutations in seconds. A usage example estimating the full repertoire of mutations for a human germline antibody highlights several solubility hotspots on the surface. The web server, complete with RESTful interface and extensive help, can be accessed from URL: http://protein.bio.unipd.it/soda.
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Affiliation(s)
- Lisanna Paladin
- Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35121 Padova, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35121 Padova, Italy
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35121 Padova, Italy.,CNR Institute of Neuroscience, Viale G. Colombo 3, 35121 Padova, Italy
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11
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Oláhová M, Yoon WH, Thompson K, Jangam S, Fernandez L, Davidson JM, Kyle JE, Grove ME, Fisk DG, Kohler JN, Holmes M, Dries AM, Huang Y, Zhao C, Contrepois K, Zappala Z, Frésard L, Waggott D, Zink EM, Kim YM, Heyman HM, Stratton KG, Webb-Robertson BJM, Snyder M, Merker JD, Montgomery SB, Fisher PG, Feichtinger RG, Mayr JA, Hall J, Barbosa IA, Simpson MA, Deshpande C, Waters KM, Koeller DM, Metz TO, Morris AA, Schelley S, Cowan T, Friederich MW, McFarland R, Van Hove JLK, Enns GM, Yamamoto S, Ashley EA, Wangler MF, Taylor RW, Bellen HJ, Bernstein JA, Wheeler MT. Biallelic Mutations in ATP5F1D, which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder. Am J Hum Genet 2018; 102:494-504. [PMID: 29478781 PMCID: PMC6117612 DOI: 10.1016/j.ajhg.2018.01.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/26/2018] [Indexed: 01/07/2023] Open
Abstract
ATP synthase, H+ transporting, mitochondrial F1 complex, δ subunit (ATP5F1D; formerly ATP5D) is a subunit of mitochondrial ATP synthase and plays an important role in coupling proton translocation and ATP production. Here, we describe two individuals, each with homozygous missense variants in ATP5F1D, who presented with episodic lethargy, metabolic acidosis, 3-methylglutaconic aciduria, and hyperammonemia. Subject 1, homozygous for c.245C>T (p.Pro82Leu), presented with recurrent metabolic decompensation starting in the neonatal period, and subject 2, homozygous for c.317T>G (p.Val106Gly), presented with acute encephalopathy in childhood. Cultured skin fibroblasts from these individuals exhibited impaired assembly of F1FO ATP synthase and subsequent reduced complex V activity. Cells from subject 1 also exhibited a significant decrease in mitochondrial cristae. Knockdown of Drosophila ATPsynδ, the ATP5F1D homolog, in developing eyes and brains caused a near complete loss of the fly head, a phenotype that was fully rescued by wild-type human ATP5F1D. In contrast, expression of the ATP5F1D c.245C>T and c.317T>G variants rescued the head-size phenotype but recapitulated the eye and antennae defects seen in other genetic models of mitochondrial oxidative phosphorylation deficiency. Our data establish c.245C>T (p.Pro82Leu) and c.317T>G (p.Val106Gly) in ATP5F1D as pathogenic variants leading to a Mendelian mitochondrial disease featuring episodic metabolic decompensation.
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Affiliation(s)
- Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Wan Hee Yoon
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Sharayu Jangam
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liliana Fernandez
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - Jean M Davidson
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Megan E Grove
- Clinical Genomics Program, Stanford Health Care, Stanford, CA 94305, USA
| | - Dianna G Fisk
- Clinical Genomics Program, Stanford Health Care, Stanford, CA 94305, USA
| | - Jennefer N Kohler
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - Matthew Holmes
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Annika M Dries
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - Yong Huang
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - Chunli Zhao
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zachary Zappala
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laure Frésard
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Daryl Waggott
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - Erika M Zink
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Young-Mo Kim
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Heino M Heyman
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Kelly G Stratton
- Computing & Analytics Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Bobbie-Jo M Webb-Robertson
- Computing & Analytics Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jason D Merker
- Clinical Genomics Program, Stanford Health Care, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Stephen B Montgomery
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Paul G Fisher
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - René G Feichtinger
- Department of Pediatrics, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Johannes A Mayr
- Department of Pediatrics, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Julie Hall
- Department of Neuroradiology, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK
| | - Ines A Barbosa
- Department of Medical and Molecular Genetics, King's College London School of Basic and Medical Biosciences, London SE1 9RT, UK
| | - Michael A Simpson
- Department of Medical and Molecular Genetics, King's College London School of Basic and Medical Biosciences, London SE1 9RT, UK
| | - Charu Deshpande
- Clinical Genetics Unit, Guys and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Katrina M Waters
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - David M Koeller
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Thomas O Metz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Andrew A Morris
- Institute of Human Development, University of Manchester, Manchester M13 9PL, UK; Willink Metabolic Unit, Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK
| | - Susan Schelley
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tina Cowan
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Marisa W Friederich
- Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado at Denver, Aurora, CO 80045, USA
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Johan L K Van Hove
- Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado at Denver, Aurora, CO 80045, USA
| | - Gregory M Enns
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Euan A Ashley
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA; Clinical Genomics Program, Stanford Health Care, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Hugo J Bellen
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan A Bernstein
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew T Wheeler
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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12
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Boonamnaj P, Sompornpisut P. Insight into the Role of the Hv1 C-Terminal Domain in Dimer Stabilization. J Phys Chem B 2018; 122:1037-1048. [PMID: 29290112 DOI: 10.1021/acs.jpcb.7b08669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The voltage-gated proton-selective channel (Hv1) conducts protons in response to changes in membrane potential. The Hv1 protein forms dimers in the membrane. Crystal structures of Hv1 channels have revealed that the primary contacts between the two monomers are in the C-terminal domain (CTD), which forms a coiled-coil structure. The role of Hv1-CTD in channel assembly and activity is not fully understood. Here, molecular dynamics (MD) simulations of full-length and truncated CTD models of human and mouse Hv1 channels reveal a strong contribution of the CTD to the packing of the transmembrane domains. Simulations of the CTD models highlight four fundamental interactions of the key residues contributing to dimer stability. These include salt bridges, hydrophobic interactions, hydrogen bonds, and a disulfide bond across the dimer interface. At neutral pH, salt-bridge interactions increase dimer stability and the dimer becomes less stable at acidic pH. Hydrophobic core packing of the heptad pattern is important for stability, as shown by favorable nonpolar binding free energies rather than by electrostatic components. Moreover, free-energy calculations indicate that a more uniform hydrophobic core in the coiled-coil structure of the Hv1-NIN, a channel carrying the triple mutation M234N-N235I-V236N, leads to an increase in dimer stability with respect to the wild-type. A Cys disulfide bond has a strong impact on dimer stability by holding the dimer together and facilitating the interactions described above. These results are consistent with dissociative temperatures and energy barriers of dimer dissociation obtained from the temperature-accelerated MD.
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Affiliation(s)
- Panisak Boonamnaj
- Department of Chemistry, Faculty of Science, Chulalongkorn University , Bangkok 10330, Thailand
| | - Pornthep Sompornpisut
- Department of Chemistry, Faculty of Science, Chulalongkorn University , Bangkok 10330, Thailand
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Yang Y, Niroula A, Shen B, Vihinen M. PON-Sol: prediction of effects of amino acid substitutions on protein solubility. Bioinformatics 2016; 32:2032-4. [PMID: 27153720 DOI: 10.1093/bioinformatics/btw066] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/30/2016] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Solubility is one of the fundamental protein properties. It is of great interest because of its relevance to protein expression. Reduced solubility and protein aggregation are also associated with many diseases. RESULTS We collected from literature the largest experimentally verified solubility affecting amino acid substitution (AAS) dataset and used it to train a predictor called PON-Sol. The predictor can distinguish both solubility decreasing and increasing variants from those not affecting solubility. PON-Sol has normalized correct prediction ratio of 0.491 on cross-validation and 0.432 for independent test set. The performance of the method was compared both to solubility and aggregation predictors and found to be superior. PON-Sol can be used for the prediction of effects of disease-related substitutions, effects on heterologous recombinant protein expression and enhanced crystallizability. One application is to investigate effects of all possible AASs in a protein to aid protein engineering. AVAILABILITY AND IMPLEMENTATION PON-Sol is freely available at http://structure.bmc.lu.se/PON-Sol The training and test data are available at http://structure.bmc.lu.se/VariBench/ponsol.php CONTACT mauno.vihinen@med.lu.se SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yang Yang
- Center for Systems Biology, School of Computer Science and Technology, Soochow University, Suzhou 215006, China and Department of Experimental Medical Science, Lund University, Lund SE 221 84, Sweden
| | - Abhishek Niroula
- Department of Experimental Medical Science, Lund University, Lund SE 221 84, Sweden
| | | | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, Lund SE 221 84, Sweden
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14
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Rutter J, Hughes AL. Power(2): the power of yeast genetics applied to the powerhouse of the cell. Trends Endocrinol Metab 2015; 26:59-68. [PMID: 25591985 PMCID: PMC4315768 DOI: 10.1016/j.tem.2014.12.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 12/09/2014] [Accepted: 12/09/2014] [Indexed: 11/18/2022]
Abstract
The budding yeast Saccharomyces cerevisiae has served as a remarkable model organism for numerous seminal discoveries in biology. This paradigm extends to the mitochondria, a central hub for cellular metabolism, where studies in yeast have helped to reinvigorate the field and launch an exciting new era in mitochondrial biology. Here we discuss a few recent examples in which yeast research has laid a foundation for our understanding of evolutionarily conserved mitochondrial processes and functions, from key factors and pathways involved in the assembly of oxidative phosphorylation (OXPHOS) complexes to metabolite transport, lipid metabolism, and interorganelle communication. We also highlight new areas of yeast mitochondrial biology that are likely to aid in our understanding of the mitochondrial etiology of disease in the future.
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Affiliation(s)
- Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Adam L Hughes
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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15
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HEJZLAROVÁ K, MRÁČEK T, VRBACKÝ M, KAPLANOVÁ V, KARBANOVÁ V, NŮSKOVÁ H, PECINA P, HOUŠTĚK J. Nuclear Genetic Defects of Mitochondrial ATP Synthase. Physiol Res 2014; 63:S57-71. [DOI: 10.33549/physiolres.932643] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Disorders of ATP synthase, the key enzyme of mitochondrial energy provision belong to the most severe metabolic diseases presenting as early-onset mitochondrial encephalo-cardiomyopathies. Up to now, mutations in four nuclear genes were associated with isolated deficiency of ATP synthase. Two of them, ATP5A1 and ATP5E encode enzyme’s structural subunits α and ε, respectively, while the other two ATPAF2 and TMEM70 encode specific ancillary factors that facilitate the biogenesis of ATP synthase. All these defects share a similar biochemical phenotype with pronounced decrease in the content of fully assembled and functional ATP synthase complex. However, substantial differences can be found in their frequency, molecular mechanism of pathogenesis, clinical manifestation as well as the course of the disease progression. While for TMEM70 the number of reported patients as well as spectrum of the mutations is steadily increasing, mutations in ATP5A1, ATP5E and ATPAF2 genes are very rare. Apparently, TMEM70 gene is highly prone to mutagenesis and this type of a rare mitochondrial disease has a rather frequent incidence. Here we present overview of individual reported cases of nuclear mutations in ATP synthase and discuss, how their analysis can improve our understanding of the enzyme biogenesis.
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Affiliation(s)
| | | | | | | | | | | | | | - J. HOUŠTĚK
- Department of Bioenergetics, Institute of Physiology Academy of Sciences of the Czech Republic, Prague, Czech Republic
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Jonckheere AI, Smeitink JAM, Rodenburg RJT. Mitochondrial ATP synthase: architecture, function and pathology. J Inherit Metab Dis 2012; 35:211-25. [PMID: 21874297 PMCID: PMC3278611 DOI: 10.1007/s10545-011-9382-9] [Citation(s) in RCA: 383] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/22/2011] [Accepted: 07/27/2011] [Indexed: 12/16/2022]
Abstract
Human mitochondrial (mt) ATP synthase, or complex V consists of two functional domains: F(1), situated in the mitochondrial matrix, and F(o), located in the inner mitochondrial membrane. Complex V uses the energy created by the proton electrochemical gradient to phosphorylate ADP to ATP. This review covers the architecture, function and assembly of complex V. The role of complex V di-and oligomerization and its relation with mitochondrial morphology is discussed. Finally, pathology related to complex V deficiency and current therapeutic strategies are highlighted. Despite the huge progress in this research field over the past decades, questions remain to be answered regarding the structure of subunits, the function of the rotary nanomotor at a molecular level, and the human complex V assembly process. The elucidation of more nuclear genetic defects will guide physio(patho)logical studies, paving the way for future therapeutic interventions.
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Affiliation(s)
- An I. Jonckheere
- Department of Pediatrics, Nijmegen Center for Mitochondrial Disorders, 656 Laboratory for Genetic, Endocrine, and Metabolic Disorders, Radboud University Nijmegen Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Jan A. M. Smeitink
- Department of Pediatrics, Nijmegen Center for Mitochondrial Disorders, 656 Laboratory for Genetic, Endocrine, and Metabolic Disorders, Radboud University Nijmegen Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Richard J. T. Rodenburg
- Department of Pediatrics, Nijmegen Center for Mitochondrial Disorders, 656 Laboratory for Genetic, Endocrine, and Metabolic Disorders, Radboud University Nijmegen Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands
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