1
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Pei J, Andreeva A, Chuguransky S, Lázaro Pinto B, Paysan-Lafosse T, Dustin Schaeffer R, Bateman A, Cong Q, Grishin NV. Bridging the Gap between Sequence and Structure Classifications of Proteins with AlphaFold Models. J Mol Biol 2024:168764. [PMID: 39197652 DOI: 10.1016/j.jmb.2024.168764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 08/13/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024]
Abstract
Classification of protein domains based on homology and structural similarity serves as a fundamental tool to gain biological insights into protein function. Recent advancements in protein structure prediction, exemplified by AlphaFold, have revolutionized the availability of protein structural data. We focus on classifying about 9000 Pfam families into ECOD (Evolutionary Classification of Domains) by using predicted AlphaFold models and the DPAM (Domain Parser for AlphaFold Models) tool. Our results offer insights into their homologous relationships and domain boundaries. More than half of these Pfam families contain DPAM domains that can be confidently assigned to the ECOD hierarchy. Most assigned domains belong to highly populated folds such as Immunoglobulin-like (IgL), Armadillo (ARM), helix-turn-helix (HTH), and Src homology 3 (SH3). A large fraction of DPAM domains, however, cannot be confidently assigned to ECOD homologous groups. These unassigned domains exhibit statistically different characteristics, including shorter average length, fewer secondary structure elements, and more abundant transmembrane segments. They could potentially define novel families remotely related to domains with known structures or novel superfamilies and folds. Manual scrutiny of a subset of these domains revealed an abundance of internal duplications and recurring structural motifs. Exploring sequence and structural features such as disulfide bond patterns, metal-binding sites, and enzyme active sites helped uncover novel structural folds as well as remote evolutionary relationships. By bridging the gap between sequence-based Pfam and structure-based ECOD domain classifications, our study contributes to a more comprehensive understanding of the protein universe by providing structural and functional insights into previously uncharacterized proteins.
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Affiliation(s)
- Jimin Pei
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Antonina Andreeva
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Sara Chuguransky
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Beatriz Lázaro Pinto
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Typhaine Paysan-Lafosse
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - R Dustin Schaeffer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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2
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Fleming JR, Müller I, Zacharchenko T, Diederichs K, Mayans O. Molecular insights into titin's A-band. J Muscle Res Cell Motil 2023; 44:255-270. [PMID: 37258982 PMCID: PMC10665226 DOI: 10.1007/s10974-023-09649-1] [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: 03/06/2023] [Accepted: 04/11/2023] [Indexed: 06/02/2023]
Abstract
The thick filament-associated A-band region of titin is a highly repetitive component of the titin chain with important scaffolding properties that support thick filament assembly. It also has a demonstrated link to human disease. Despite its functional significance, it remains a largely uncharacterized part of the titin protein. Here, we have performed an analysis of sequence and structure conservation of A-band titin, with emphasis on poly-FnIII tandem components. Specifically, we have applied multi-dimensional sequence pairwise similarity analysis to FnIII domains and complemented this with the crystallographic elucidation of the 3D-structure of the FnIII-triplet A84-A86 from the fourth long super-repeat in the C-zone (C4). Structural models serve here as templates to map sequence conservation onto super-repeat C4, which we show is a prototypical representative of titin's C-zone. This templating identifies positionally conserved residue clusters in C super-repeats with the potential of mediating interactions to thick-filament components. Conservation localizes to two super-repeat positions: Ig domains in position 1 and FnIII domains in position 7. The analysis also allows conclusions to be drawn on the conserved architecture of titin's A-band, as well as revisiting and expanding the evolutionary model of titin's A-band.
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Affiliation(s)
| | - Iljas Müller
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Thomas Zacharchenko
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- Wellcome Centre for Cell-Matrix Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Kay Diederichs
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Olga Mayans
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
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3
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Riguene E, Theodoridou M, Barrak L, Elrayess MA, Nomikos M. The Relationship between Changes in MYBPC3 Single-Nucleotide Polymorphism-Associated Metabolites and Elite Athletes' Adaptive Cardiac Function. J Cardiovasc Dev Dis 2023; 10:400. [PMID: 37754829 PMCID: PMC10531821 DOI: 10.3390/jcdd10090400] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/01/2023] [Accepted: 09/16/2023] [Indexed: 09/28/2023] Open
Abstract
Athletic performance is a multifactorial trait influenced by a complex interaction of environmental and genetic factors. Over the last decades, understanding and improving elite athletes' endurance and performance has become a real challenge for scientists. Significant tools include but are not limited to the development of molecular methods for talent identification, personalized exercise training, dietary requirements, prevention of exercise-related diseases, as well as the recognition of the structure and function of the genome in elite athletes. Investigating the genetic markers and phenotypes has become critical for elite endurance surveillance. The identification of genetic variants contributing to a predisposition for excellence in certain types of athletic activities has been difficult despite the relatively high genetic inheritance of athlete status. Metabolomics can potentially represent a useful approach for gaining a thorough understanding of various physiological states and for clarifying disorders caused by strength-endurance physical exercise. Based on a previous GWAS study, this manuscript aims to discuss the association of specific single-nucleotide polymorphisms (SNPs) located in the MYBPC3 gene encoding for cardiac MyBP-C protein with endurance athlete status. MYBPC3 is linked to elite athlete heart remodeling during or after exercise, but it could also be linked to the phenotype of cardiac hypertrophy (HCM). To make the distinction between both phenotypes, specific metabolites that are influenced by variants in the MYBPC3 gene are analyzed in relation to elite athletic performance and HCM. These include theophylline, ursodeoxycholate, quinate, and decanoyl-carnitine. According to the analysis of effect size, theophylline, quinate, and decanoyl carnitine increase with endurance while decreasing with cardiovascular disease, whereas ursodeoxycholate increases with cardiovascular disease. In conclusion, and based on our metabolomics data, the specific effects on athletic performance for each MYBPC3 SNP-associated metabolite are discussed.
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Affiliation(s)
- Emna Riguene
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (E.R.); (L.B.); (M.A.E.)
| | - Maria Theodoridou
- Biomedical Research Center (BRC), Qatar University, Doha P.O. Box 2713, Qatar;
| | - Laila Barrak
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (E.R.); (L.B.); (M.A.E.)
| | - Mohamed A. Elrayess
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (E.R.); (L.B.); (M.A.E.)
- Biomedical Research Center (BRC), Qatar University, Doha P.O. Box 2713, Qatar;
| | - Michail Nomikos
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (E.R.); (L.B.); (M.A.E.)
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4
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Stergiou C, Williams R, Fleming JR, Zouvelou V, Ninou E, Andreetta F, Rinaldi E, Simoncini O, Mantegazza R, Bogomolovas J, Tzartos J, Labeit S, Mayans O, Tzartos S. Immunological and Structural Characterization of Titin Main Immunogenic Region; I110 Domain Is the Target of Titin Antibodies in Myasthenia Gravis. Biomedicines 2023; 11:biomedicines11020449. [PMID: 36830985 PMCID: PMC9952892 DOI: 10.3390/biomedicines11020449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Myasthenia gravis (MG) is an autoimmune disease caused by antibodies targeting the neuromuscular junction (NJ) of skeletal muscles. The major MG autoantigen is nicotinic acetylcholine receptor. Other autoantigens at the NJ include MuSK, LRP4 and agrin. Autoantibodies to the intra-sarcomeric striated muscle-specific gigantic protein titin, although not directed to the NJ, are invaluable biomarkers for thymoma and MG disease severity. Thymus and thymoma are critical in MG mechanisms and management. Titin autoantibodies bind to a 30 KDa titin segment, the main immunogenic region (MIR), consisting of an Ig-FnIII-FnIII 3-domain tandem, termed I109-I111. In this work, we further resolved the localization of titin epitope(s) to facilitate the development of more specific anti-titin diagnostics. For this, we expressed protein samples corresponding to 8 MIR and non-MIR titin fragments and tested 77 anti-titin sera for antibody binding using ELISA, competition experiments and Western blots. All anti-MIR antibodies were bound exclusively to the central MIR domain, I110, and to its containing titin segments. Most antibodies were bound also to SDS-denatured I110 on Western blots, suggesting that their epitope(s) are non-conformational. No significant difference was observed between thymoma and non-thymoma patients or between early- and late-onset MG. In addition, atomic 3D-structures of the MIR and its subcomponents were elucidated using X-ray crystallography. These immunological and structural data will allow further studies into the atomic determinants underlying titin-based autoimmunity, improved diagnostics and how to eventually treat titin autoimmunity associated co-morbidities.
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Affiliation(s)
| | - Rhys Williams
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | | | - Vasiliki Zouvelou
- 1st Neurology Department, Eginition Hospital, National and Kapodistrian University of Athens, 157 72 Athens, Greece
| | | | - Francesca Andreetta
- Fondazione I.R.C.C.S., Istituto Neurologico Carlo Besta, 20133 Milano, Italy
| | - Elena Rinaldi
- Fondazione I.R.C.C.S., Istituto Neurologico Carlo Besta, 20133 Milano, Italy
| | - Ornella Simoncini
- Fondazione I.R.C.C.S., Istituto Neurologico Carlo Besta, 20133 Milano, Italy
| | - Renato Mantegazza
- Fondazione I.R.C.C.S., Istituto Neurologico Carlo Besta, 20133 Milano, Italy
| | - Julius Bogomolovas
- School of Medicine, University of California, La Jolla, San Diego, CA 92093, USA
| | - John Tzartos
- School of Medicine, Attikon University Hospital, National and Kapodistrian University of Athens, 124 62 Athens, Greece
| | - Siegfried Labeit
- DZHK Partner Site Mannheim-Heidelberg, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
- Myomedix GmbH, 69151 Neckargemuend, Germany
| | - Olga Mayans
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Socrates Tzartos
- Tzartos NeuroDiagnostics, 115 23 Athens, Greece
- Hellenic Pasteur Institute, 115 21 Athens, Greece
- Department of Pharmacy, University of Patras, 265 00 Patras, Greece
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5
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Interdomain Linker Effect on the Mechanical Stability of Ig Domains in Titin. Int J Mol Sci 2022; 23:ijms23179836. [PMID: 36077234 PMCID: PMC9456048 DOI: 10.3390/ijms23179836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
Titin is the largest protein in humans, composed of more than one hundred immunoglobulin (Ig) domains, and plays a critical role in muscle’s passive elasticity. Thus, the molecular design of this giant polyprotein is responsible for its mechanical function. Interestingly, most of these Ig domains are connected directly with very few interdomain residues/linker, which suggests such a design is necessary for its mechanical stability. To understand this design, we chose six representative Ig domains in titin and added nine glycine residues (9G) as an artificial interdomain linker between these Ig domains. We measured their mechanical stabilities using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) and compared them to the natural sequence. The AFM results showed that the linker affected the mechanical stability of Ig domains. The linker mostly reduces its mechanical stability to a moderate extent, but the opposite situation can happen. Thus, this effect is very complex and may depend on each particular domain’s property.
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6
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Su K, Mayans O, Diederichs K, Fleming JR. Pairwise sequence similarity mapping with PaSiMap: Reclassification of immunoglobulin domains from titin as case study. Comput Struct Biotechnol J 2022; 20:5409-5419. [PMID: 36212532 PMCID: PMC9529554 DOI: 10.1016/j.csbj.2022.09.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/22/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
A novel multidimensional scaling pipeline for sequence analysis. A simple way to distinguish between unique and shared sequence features. Titin domains were reclassified, improving upon earlier analysis.
Sequence comparison is critical for the functional assignment of newly identified protein genes. As uncharacterized protein sequences accumulate, there is an increasing need for sensitive tools for their classification. Here, we present a novel multidimensional scaling pipeline, PaSiMap, which creates a map of pairwise sequence similarities. Uniquely, PaSiMap distinguishes between unique and shared features, allowing for a distinct view of protein-sequence relationships. We demonstrate PaSiMap’s efficiency in detecting sequence groups and outliers using titin’s 169 immunoglobulin (Ig) domains. We show that Ig domain similarity is hierarchical, being firstly determined by chain location, then by the loop features of the Ig fold and, finally, by super-repeat position. The existence of a previously unidentified domain repeat in the distal, constitutive I-band is revealed. Prototypic Igs, plus notable outliers, are identified and thereby domain classification improved. This re-classification can now guide future molecular research. In summary, we demonstrate that PaSiMap is a sensitive tool for the classification of protein sequences, which adds a new perspective in the understanding of inter-protein relationships. PaSiMap is applicable to any biological system defined by a linear sequence, including polynucleotide chains.
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7
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Zhou T, Fleming JR, Lange S, Hessel AL, Bogomolovas J, Stronczek C, Grundei D, Ghassemian M, Biju A, Börgeson E, Bullard B, Linke WA, Chen J, Kovermann M, Mayans O. Molecular Characterisation of Titin N2A and Its Binding of CARP Reveals a Titin/Actin Cross-linking Mechanism. J Mol Biol 2021; 433:166901. [PMID: 33647290 PMCID: PMC8052292 DOI: 10.1016/j.jmb.2021.166901] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/14/2021] [Accepted: 02/22/2021] [Indexed: 12/16/2022]
Abstract
Striated muscle responds to mechanical overload by rapidly up-regulating the expression of the cardiac ankyrin repeat protein, CARP, which then targets the sarcomere by binding to titin N2A in the I-band region. To date, the role of this interaction in the stress response of muscle remains poorly understood. Here, we characterise the molecular structure of the CARP-receptor site in titin (UN2A) and its binding of CARP. We find that titin UN2A contains a central three-helix bundle fold (ca 45 residues in length) that is joined to N- and C-terminal flanking immunoglobulin domains by long, flexible linkers with partial helical content. CARP binds titin by engaging an α-hairpin in the three-helix fold of UN2A, the C-terminal linker sequence, and the BC loop in Ig81, which jointly form a broad binding interface. Mutagenesis showed that the CARP/N2A association withstands sequence variations in titin N2A and we use this information to evaluate 85 human single nucleotide variants. In addition, actin co-sedimentation, co-transfection in C2C12 cells, proteomics on heart lysates, and the mechanical response of CARP-soaked myofibrils imply that CARP induces the cross-linking of titin and actin myofilaments, thereby increasing myofibril stiffness. We conclude that CARP acts as a regulator of force output in the sarcomere that preserves muscle mechanical performance upon overload stress.
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Affiliation(s)
- Tiankun Zhou
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | | | - Stephan Lange
- Division of Cardiology, School of Medicine, University of California, San Diego 92093, CA, USA; Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg 413 45, Sweden
| | - Anthony L Hessel
- Institute of Physiology II, University Hospital Münster, Münster, Germany
| | - Julius Bogomolovas
- School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159 Mannheim, Germany
| | - Chiara Stronczek
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - David Grundei
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Majid Ghassemian
- Department of Chemistry and Biochemistry, University of California, San Diego 92093, CA, USA
| | - Andrea Biju
- Division of Cardiology, School of Medicine, University of California, San Diego 92093, CA, USA
| | - Emma Börgeson
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg 413 45, Sweden
| | - Belinda Bullard
- Department of Biology, University of York, York YO10 5DD, UK
| | - Wolfgang A Linke
- Institute of Physiology II, University Hospital Münster, Münster, Germany
| | - Ju Chen
- School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany.
| | - Olga Mayans
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.
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8
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Stronczek C, Lange S, Bullard B, Wolniak S, Börgeson E, Mayans O, Fleming JR. The N2A region of titin has a unique structural configuration. J Gen Physiol 2021; 153:211969. [PMID: 33836065 PMCID: PMC8042602 DOI: 10.1085/jgp.202012766] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/09/2021] [Indexed: 01/04/2023] Open
Abstract
The N2A segment of titin is a main signaling hub in the sarcomeric I-band that recruits various signaling factors and processing enzymes. It has also been proposed to play a role in force production through its Ca2+-regulated association with actin. However, the molecular basis by which N2A performs these functions selectively within the repetitive and extensive titin chain remains poorly understood. Here, we analyze the structure of N2A components and their association with F-actin. Specifically, we characterized the structure of its Ig domains by elucidating the atomic structure of the I81-I83 tandem using x-ray crystallography and computing a homology model for I80. Structural data revealed these domains to present heterogeneous and divergent Ig folds, where I81 and I83 have unique loop structures. Notably, the I81-I83 tandem has a distinct rotational chain arrangement that confers it a unique multi-domain topography. However, we could not identify specific Ca2+-binding sites in these Ig domains, nor evidence of the association of titin N2A components with F-actin in transfected C2C12 myoblasts or C2C12-derived myotubes. In addition, F-actin cosedimentation assays failed to reveal binding to N2A. We conclude that N2A has a unique architecture that predictably supports its selective recruitment of binding partners in signaling, but that its mechanical role through interaction with F-actin awaits validation.
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Affiliation(s)
- Chiara Stronczek
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Stephan Lange
- Division of Cardiology, School of Medicine, University of California, San Diego, San Diego, CA.,Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | | | | | - Emma Börgeson
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Olga Mayans
- Department of Biology, University of Konstanz, Konstanz, Germany
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9
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Abstract
Muscle stiffness, muscle elasticity and explosive strength are the main components of athletes' performance and they show a sex-based as well as ethnicity variation. Muscle stiffness is thought to be one of the risk factors associated with sports injuries and is less common in females than in males. These observations may be explained by circulating levels of sex hormones and their specific receptors. It has been shown that higher levels of estrogen are associated with lower muscle stiffness responsible for suppression of collagen synthesis. It is thought that these properties, at least in part, depend on genetic factors. Particularly, the gene encoding estrogen receptor 1 (ESR1) is one of the candidates that may be associated with muscle stiffness. Muscle elasticity increases with aging and there is evidence suggesting that titin (encoded by the TTN gene), a protein that is expressed in cardiac and skeletal muscles, is one of the factors responsible for elastic properties of the muscles. Mutations in the TTN gene result in some types of muscular dystrophy or cardiomyopathy. In this context, TTN may be regarded as a promising candidate for studying the elastic properties of muscles in athletes. The physiological background of explosive strength depends not only on the muscle architecture and muscle fiber composition, but also on the central nervous system and functionality of neuromuscular units. These properties are, at least partly, genetically determined. In this context, the ACTN3 gene code for α-actinin 3 has been widely researched.
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10
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Uapinyoying P, Goecks J, Knoblach SM, Panchapakesan K, Bonnemann CG, Partridge TA, Jaiswal JK, Hoffman EP. A long-read RNA-seq approach to identify novel transcripts of very large genes. Genome Res 2020; 30:885-897. [PMID: 32660935 PMCID: PMC7370890 DOI: 10.1101/gr.259903.119] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/22/2020] [Indexed: 12/15/2022]
Abstract
RNA-seq is widely used for studying gene expression, but commonly used sequencing platforms produce short reads that only span up to two exon junctions per read. This makes it difficult to accurately determine the composition and phasing of exons within transcripts. Although long-read sequencing improves this issue, it is not amenable to precise quantitation, which limits its utility for differential expression studies. We used long-read isoform sequencing combined with a novel analysis approach to compare alternative splicing of large, repetitive structural genes in muscles. Analysis of muscle structural genes that produce medium (Nrap: 5 kb), large (Neb: 22 kb), and very large (Ttn: 106 kb) transcripts in cardiac muscle, and fast and slow skeletal muscles identified unannotated exons for each of these ubiquitous muscle genes. This also identified differential exon usage and phasing for these genes between the different muscle types. By mapping the in-phase transcript structures to known annotations, we also identified and quantified previously unannotated transcripts. Results were confirmed by endpoint PCR and Sanger sequencing, which revealed muscle-type-specific differential expression of these novel transcripts. The improved transcript identification and quantification shown by our approach removes previous impediments to studies aimed at quantitative differential expression of ultralong transcripts.
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Affiliation(s)
- Prech Uapinyoying
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, D.C. 20010, USA.,Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Sciences, Washington, D.C. 20052, USA.,Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jeremy Goecks
- Computational Biology Program, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Susan M Knoblach
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, D.C. 20010, USA.,Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Sciences, Washington, D.C. 20052, USA
| | - Karuna Panchapakesan
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, D.C. 20010, USA
| | - Carsten G Bonnemann
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, D.C. 20010, USA.,Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Terence A Partridge
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, D.C. 20010, USA.,Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Sciences, Washington, D.C. 20052, USA
| | - Jyoti K Jaiswal
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, D.C. 20010, USA.,Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Sciences, Washington, D.C. 20052, USA
| | - Eric P Hoffman
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, D.C. 20010, USA.,Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, New York 13902, USA
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11
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Fleming JR, Rigden DJ, Mayans O. The importance of chain context in assessing small nucleotide variants in titin: in silico case study of the I10-I11 tandem and its arrhythmic right ventricular cardiomyopathy linked position T2580. J Biomol Struct Dyn 2020; 39:3480-3490. [PMID: 32396765 DOI: 10.1080/07391102.2020.1768148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Non-synonymous small nucleotide variations (nsSNVs) in the giant muscle protein, titin, have key roles in the development of several myopathologies. Although there is considerable motive to screen at-risk individuals for nsSNVs, to identify patients in early disease stages while therapeutic intervention is still possible, the clinical significance of most titin variations remains unclear. Therefore, there is a growing need to establish methods to classify nsSNVs in a simple, economic and rapid manner. Due to its strong correlation to arrhythmogenic right ventricular cardiomyopathy (ARVC), one particular mutation in titin-T2580I, located in the I10 immunoglobulin domain-has received considerable attention. Here, we use the I10-I11 tandem as a case study to explore the possible benefits of considering the titin chain context-i.e. domain interfaces-in the assessment of titin nsSNVs. Specifically, we investigate which exchanges mimic the conformational molecular phenotype of the T2580I mutation at the I10-I11 domain interface. Then, we computed a residue stability landscape for domains alone and in tandem to define a Domain Interface Score (DIS) which identifies several hotspot residues. Our findings suggest that the T2580 position is highly sensitive to exchange and that any variant found in this position should be considered with care. Furthermore, we conclude that the consideration of the higher order structure of the titin chain is important to gain accurate insights into the vulnerability of positions in linker regions and that titin nsSNV prediction benefits from a contextual analysis. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- J R Fleming
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - D J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - O Mayans
- Department of Biology, University of Konstanz, Konstanz, Germany
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12
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Scalable, Non-denaturing Purification of Phosphoproteins Using Ga 3+-IMAC: N2A and M1M2 Titin Components as Study case. Protein J 2019; 38:181-189. [PMID: 30719619 DOI: 10.1007/s10930-019-09815-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The purification of phosphorylated proteins in a folded state and in large enough quantity for biochemical or biophysical analysis remains a challenging task. Here, we develop a new implementation of the method of gallium immobilized metal chromatography (Ga3+-IMAC) as to permit the selective enrichment of phosphoproteins in the milligram scale and under native conditions using automated FPLC instrumentation. We apply this method to the purification of the UN2A and M1M2 components of the muscle protein titin upon being monophosphorylated in vitro by cAMP-dependent protein kinase (PKA). We found that UN2A is phosphorylated by PKA at its C-terminus in residue S9578 and M1M2 is phosphorylated in its interdomain linker sequence at position T32607. We demonstrate that the Ga3+-IMAC method is efficient, economical and suitable for implementation in automated purification pipelines for recombinant proteins. The procedure can be applied both to the selective enrichment and to the removal of phosphoproteins from biochemical samples.
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13
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Nesterenko Y, Hill CJ, Fleming JR, Murray P, Mayans O. The ZT Biopolymer: A Self-Assembling Protein Scaffold for Stem Cell Applications. Int J Mol Sci 2019; 20:E4299. [PMID: 31484291 PMCID: PMC6747707 DOI: 10.3390/ijms20174299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/14/2022] Open
Abstract
The development of cell culture systems for the naturalistic propagation, self-renewal and differentiation of cells ex vivo is a high goal of molecular engineering. Despite significant success in recent years, the high cost of up-scaling cultures, the need for xeno-free culture conditions, and the degree of mimicry of the natural extracellular matrix attainable in vitro using designer substrates continue to pose obstacles to the translation of cell-based technologies. In this regard, the ZT biopolymer is a protein-based, stable, scalable, and economical cell substrate of high promise. ZT is based on the naturally occurring assembly of two human proteins: titin-Z1Z2 and telethonin. These protein building blocks are robust scaffolds that can be conveniently functionalized with full-length proteins and bioactive peptidic motifs by genetic manipulation, prior to self-assembly. The polymer is, thereby, fully encodable. Functionalized versions of the ZT polymer have been shown to successfully sustain the long-term culturing of human embryonic stem cells (hESCs), human induced pluripotent stem cells (hiPSCs), and murine mesenchymal stromal cells (mMSCs). Pluripotency of hESCs and hiPSCs was retained for the longest period assayed (4 months). Results point to the large potential of the ZT system for the creation of a modular, pluri-functional biomaterial for cell-based applications.
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Affiliation(s)
| | - Christopher J Hill
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | | | - Patricia Murray
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Olga Mayans
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.
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14
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Monitoring Unfolding of Titin I27 Single and Bi Domain with High-Pressure NMR Spectroscopy. Biophys J 2019; 115:341-352. [PMID: 30021109 DOI: 10.1016/j.bpj.2018.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/26/2018] [Accepted: 06/05/2018] [Indexed: 11/23/2022] Open
Abstract
A complete description of the pathways and mechanisms of protein folding requires a detailed structural and energetic characterization of the folding energy landscape. Simulations, when corroborated by experimental data yielding global information on the folding process, can provide this level of insight. Molecular dynamics (MD) has often been combined with force spectroscopy experiments to decipher the unfolding mechanism of titin immunoglobulin-like single or multidomain, the giant multimodular protein from sarcomeres, yielding information on the sequential events during titin unfolding under stretching. Here, we used high-pressure NMR to monitor the unfolding of titin I27 Ig-like single domain and tandem. Because this method brings residue-specific information on the folding process, it can provide quasiatomic details on this process without the help of MD simulations. Globally, the results of our high-pressure analysis are in agreement with previous results obtained by the combination of experimental measurements and MD simulation and/or protein engineering, although the intermediate folding state caused by the early detachment of the AB β-sheet, often reported in previous works based on MD or force spectroscopy, cannot be detected. On the other hand, the A'G parallel β-sheet of the β-sandwich has been confirmed as the Achilles heel of the three-dimensional scaffold: its disruption yields complete unfolding with very similar characteristics (free energy, unfolding volume, kinetics rate constants) for the two constructs.
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15
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Azad A, Poloni G, Sontayananon N, Jiang H, Gehmlich K. The giant titin: how to evaluate its role in cardiomyopathies. J Muscle Res Cell Motil 2019; 40:159-167. [PMID: 31147888 PMCID: PMC6726704 DOI: 10.1007/s10974-019-09518-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 05/28/2019] [Indexed: 01/02/2023]
Abstract
Titin, the largest protein known, has attracted a lot of interest in the cardiovascular field in recent years, since the discovery that truncating variants in titin are commonly found in patients with dilated cardiomyopathy. This review will discuss the contribution of variants in titin to inherited cardiac conditions (cardiomyopathies) and how model systems, such as animals and cellular systems, can help to provide insights into underlying disease mechanisms. It will also give an outlook onto exciting technological developments, such as in the field of CRISPR, which may facilitate future research on titin variants and their contributions to cardiomyopathies.
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Affiliation(s)
- Amar Azad
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence, University of Oxford, Oxford, OX3 9DU, UK
- Swansea University Medical School, Swansea, SA2 8PP, UK
| | - Giulia Poloni
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence, University of Oxford, Oxford, OX3 9DU, UK
| | - Naeramit Sontayananon
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence, University of Oxford, Oxford, OX3 9DU, UK
| | - He Jiang
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence, University of Oxford, Oxford, OX3 9DU, UK
| | - Katja Gehmlich
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence, University of Oxford, Oxford, OX3 9DU, UK.
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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16
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Affiliation(s)
- Wolfgang A. Linke
- Institute of Physiology II, University of Münster, 48149 Münster, Germany
- Deutsches Zentrum für Herz-Kreislaufforschung, Partner Site Göttingen, 37073 Göttingen, Germany
- Cardiac Mechanotransduction Group, Clinic for Cardiology and Pneumology, University Medical Center, 37073 Göttingen, Germany
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17
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Simkovic F, Ovchinnikov S, Baker D, Rigden DJ. Applications of contact predictions to structural biology. IUCRJ 2017; 4:291-300. [PMID: 28512576 PMCID: PMC5414403 DOI: 10.1107/s2052252517005115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/03/2017] [Indexed: 06/07/2023]
Abstract
Evolutionary pressure on residue interactions, intramolecular or intermolecular, that are important for protein structure or function can lead to covariance between the two positions. Recent methodological advances allow much more accurate contact predictions to be derived from this evolutionary covariance signal. The practical application of contact predictions has largely been confined to structural bioinformatics, yet, as this work seeks to demonstrate, the data can be of enormous value to the structural biologist working in X-ray crystallo-graphy, cryo-EM or NMR. Integrative structural bioinformatics packages such as Rosetta can already exploit contact predictions in a variety of ways. The contribution of contact predictions begins at construct design, where structural domains may need to be expressed separately and contact predictions can help to predict domain limits. Structure solution by molecular replacement (MR) benefits from contact predictions in diverse ways: in difficult cases, more accurate search models can be constructed using ab initio modelling when predictions are available, while intermolecular contact predictions can allow the construction of larger, oligomeric search models. Furthermore, MR using supersecondary motifs or large-scale screens against the PDB can exploit information, such as the parallel or antiparallel nature of any β-strand pairing in the target, that can be inferred from contact predictions. Contact information will be particularly valuable in the determination of lower resolution structures by helping to assign sequence register. In large complexes, contact information may allow the identity of a protein responsible for a certain region of density to be determined and then assist in the orientation of an available model within that density. In NMR, predicted contacts can provide long-range information to extend the upper size limit of the technique in a manner analogous but complementary to experimental methods. Finally, predicted contacts can distinguish between biologically relevant interfaces and mere lattice contacts in a final crystal structure, and have potential in the identification of functionally important regions and in foreseeing the consequences of mutations.
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Affiliation(s)
- Felix Simkovic
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Sergey Ovchinnikov
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Box 357370, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Box 357370, Seattle, WA 98195, USA
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
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18
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Zhou T, Fleming JR, Franke B, Bogomolovas J, Barsukov I, Rigden DJ, Labeit S, Mayans O. CARP interacts with titin at a unique helical N2A sequence and at the domain Ig81 to form a structured complex. FEBS Lett 2016; 590:3098-110. [PMID: 27531639 DOI: 10.1002/1873-3468.12362] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/29/2016] [Accepted: 08/09/2016] [Indexed: 11/07/2022]
Abstract
The cardiac ankyrin repeat protein (CARP) is up-regulated in the myocardium during cardiovascular disease and in response to mechanical or toxic stress. Stress-induced CARP interacts with the N2A spring region of the titin filament to modulate muscle compliance. We characterize the interaction between CARP and titin-N2A and show that the binding site in titin spans the dual domain UN2A-Ig81. We find that the unique sequence UN2A is not structurally disordered, but that it has a stable, elongated α-helical fold that possibly acts as a constant force spring. Our findings portray CARP/titin-N2A as a structured node and help to rationalize the molecular basis of CARP mechanosensing in the sarcomeric I-band.
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Affiliation(s)
- Tiankun Zhou
- Department of Biology, University of Konstanz, Germany.,Institute of Integrative Biology, University of Liverpool, UK
| | - Jennifer R Fleming
- Department of Biology, University of Konstanz, Germany.,Institute of Integrative Biology, University of Liverpool, UK
| | | | - Julius Bogomolovas
- Department of Integrative Pathophysiology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Igor Barsukov
- Institute of Integrative Biology, University of Liverpool, UK
| | - Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, UK
| | - Siegfried Labeit
- Department of Integrative Pathophysiology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Olga Mayans
- Department of Biology, University of Konstanz, Germany. .,Institute of Integrative Biology, University of Liverpool, UK.
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19
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Bogomolovas J, Fleming JR, Anderson BR, Williams R, Lange S, Simon B, Khan MM, Rudolf R, Franke B, Bullard B, Rigden DJ, Granzier H, Labeit S, Mayans O. Exploration of pathomechanisms triggered by a single-nucleotide polymorphism in titin's I-band: the cardiomyopathy-linked mutation T2580I. Open Biol 2016; 6:160114. [PMID: 27683155 PMCID: PMC5043576 DOI: 10.1098/rsob.160114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/01/2016] [Indexed: 02/06/2023] Open
Abstract
Missense single-nucleotide polymorphisms (mSNPs) in titin are emerging as a main causative factor of heart failure. However, distinguishing between benign and disease-causing mSNPs is a substantial challenge. Here, we research the question of whether a single mSNP in a generic domain of titin can affect heart function as a whole and, if so, how. For this, we studied the mSNP T2850I, seemingly linked to arrhythmogenic right ventricular cardiomyopathy (ARVC). We used structural biology, computational simulations and transgenic muscle in vivo methods to track the effect of the mutation from the molecular to the organismal level. The data show that the T2850I exchange is compatible with the domain three-dimensional fold, but that it strongly destabilizes it. Further, it induces a change in the conformational dynamics of the titin chain that alters its reactivity, causing the formation of aberrant interactions in the sarcomere. Echocardiography of knock-in mice indicated a mild diastolic dysfunction arising from increased myocardial stiffness. In conclusion, our data provide evidence that single mSNPs in titin's I-band can alter overall muscle behaviour. Our suggested mechanisms of disease are the development of non-native sarcomeric interactions and titin instability leading to a reduced I-band compliance. However, understanding the T2850I-induced ARVC pathology mechanistically remains a complex problem and will require a deeper understanding of the sarcomeric context of the titin region affected.
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Affiliation(s)
- Julius Bogomolovas
- Department of Integrative Pathophysiology, Medical Faculty Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Jennifer R Fleming
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Brian R Anderson
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ 85724, USA
| | - Rhys Williams
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Stephan Lange
- School of Medicine, University of California San Diego, 9500 Gilman Drive, MC-0613C, La Jolla, CA 92093, USA
| | - Bernd Simon
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Muzamil M Khan
- Institute of Molecular and Cell Biology, Mannheim University of Applied Sciences, Paul-Wittsackstraße 110, 68163 Mannheim, Germany Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Rüdiger Rudolf
- Institute of Molecular and Cell Biology, Mannheim University of Applied Sciences, Paul-Wittsackstraße 110, 68163 Mannheim, Germany Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Barbara Franke
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Belinda Bullard
- Department of Biology, University of York, York YO10 5DD, UK
| | - Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Henk Granzier
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ 85724, USA
| | - Siegfried Labeit
- Department of Integrative Pathophysiology, Medical Faculty Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Olga Mayans
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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