Development of novel computational biology pipeline for the efficient classification of titin SNPs for clinical use - TTNPred

Institutions
  • WG Mayans (Biophysik und Strukturbiologie)
Publications
    Fleming, Jennifer R.; Rigden, Daniel J.; Mayans, Olga (2021): 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 Journal of Biomolecular Structure and Dynamics. Taylor & Francis. 2021, 39(10), pp. 3480-3490. ISSN 0739-1102. eISSN 1538-0254. Available under: doi: 10.1080/07391102.2020.1768148

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

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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.

Origin (projects)

    Nesterenko, Yevheniia; Hill, Christopher J.; Fleming, Jennifer R.; Murray, Patricia; Mayans, Olga (2019): The ZT Biopolymer : A Self-Assembling Protein Scaffold for Stem Cell Applications International Journal of Molecular Sciences. 2019, 20(17), 4299. eISSN 1422-0067. Available under: doi: 10.3390/ijms20174299

The ZT Biopolymer : A Self-Assembling Protein Scaffold for Stem Cell Applications

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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.

Origin (projects)

    Hill, Christopher J.; Fleming, Jennifer R.; Mousavinejad, Masoumeh; Nicholson, Rachael; Tzokov, Svetomir B.; Bullough, Per A.; Bogomolovas, Julius; Morgan, Mark R.; Mayans, Olga; Murray, Patricia (2019): Self‐Assembling Proteins as High‐Performance Substrates for Embryonic Stem Cell Self‐Renewal Advanced Materials. 2019, 31(17), 1807521. ISSN 0935-9648. eISSN 1521-4095. Available under: doi: 10.1002/adma.201807521

Self‐Assembling Proteins as High‐Performance Substrates for Embryonic Stem Cell Self‐Renewal

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The development of extracellular matrix mimetics that imitate niche stem cell microenvironments and support cell growth for technological applications is intensely pursued. Specifically, mimetics are sought that can enact control over the self-renewal and directed differentiation of human pluripotent stem cells (hPSCs) for clinical use. Despite considerable progress in the field, a major impediment to the clinical translation of hPSCs is the difficulty and high cost of large-scale cell production under xeno-free culture conditions using current matrices. Here, a bioactive, recombinant, protein-based polymer, termed ZTFn , is presented that closely mimics human plasma fibronectin and serves as an economical, xeno-free, biodegradable, and functionally adaptable cell substrate. The ZTFn substrate supports with high performance the propagation and long-term self-renewal of human embryonic stem cells while preserving their pluripotency. The ZTFn polymer can, therefore, be proposed as an efficient and affordable replacement for fibronectin in clinical grade cell culturing. Further, it can be postulated that the ZT polymer has significant engineering potential for further orthogonal functionalization in complex cell applications.

Origin (projects)

    Adams, Michael; Fleming, Jennifer R.; Riehle, Eva; Zhou, Tiankun; Zacharchenko, Thomas; Markovic, Marija; Mayans, Olga (2019): Scalable, Non-denaturing Purification of Phosphoproteins Using Ga3+-IMAC : N2A and M1M2 Titin Components as Study case The Protein Journal. 2019, 38(2), pp. 181-189. ISSN 1572-3887. eISSN 1875-8355. Available under: doi: 10.1007/s10930-019-09815-w

Scalable, Non-denaturing Purification of Phosphoproteins Using Ga3+-IMAC : N2A and M1M2 Titin Components as Study case

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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.

Origin (projects)

Funding sources
Name Finanzierungstyp Kategorie Project no.
Europäische Union third-party funds research funding program 479/18
Further information
Period: 01.01.2018 – 31.12.2019