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Shultz KD, Al Anbari YF, Wright NT. I told you to stop: obscurin's role in epithelial cell migration. Biochem Soc Trans 2024; 52:1947-1956. [PMID: 39051125 DOI: 10.1042/bst20240564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/02/2024] [Accepted: 07/11/2024] [Indexed: 07/27/2024]
Abstract
The giant cytoskeletal protein obscurin contains multiple cell signaling domains that influence cell migration. Here, we follow each of these pathways, examine how these pathways modulate epithelial cell migration, and discuss the cross-talk between these pathways. Specifically, obscurin uses its PH domain to inhibit phosphoinositide-3-kinase (PI3K)-dependent migration and its RhoGEF domain to activate RhoA and slow cell migration. While obscurin's effect on the PI3K pathway agrees with the literature, obscurin's effect on the RhoA pathway runs counter to most other RhoA effectors, whose activation tends to lead to enhanced motility. Obscurin also phosphorylates cadherins, and this may also influence cell motility. When taken together, obscurin's ability to modulate three independent cell migration pathways is likely why obscurin knockout cells experience enhanced epithelial to mesenchymal transition, and why obscurin is a frequently mutated gene in several types of cancer.
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Affiliation(s)
- Kamrin D Shultz
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Dr., Harrisonburg, VA 22807, U.S.A
| | - Yasmin F Al Anbari
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Dr., Harrisonburg, VA 22807, U.S.A
| | - Nathan T Wright
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Dr., Harrisonburg, VA 22807, U.S.A
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Mauriello GE, Moncure GE, Nowzari RA, Miller CJ, Wright NT. The N-terminus of obscurin is flexible in solution. Proteins 2023; 91:485-496. [PMID: 36306263 DOI: 10.1002/prot.26442] [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: 07/05/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
The N-terminal half of the giant cytoskeletal protein obscurin is comprised of more than 50 Ig-like domains, arranged in tandem. Domains 18-51 are connected to each other through short 5-residue linkers, and this arrangement has been previously shown to form a semi-flexible rod in solution. Domains 1-18 generally have slightly longer ~7 residue interdomain linkers, and the multidomain structure and motion conferred by this kind of linker is understudied. Here, we use NMR, SAXS, and MD to show that these longer linkers are associated with significantly more domain/domain flexibility, with the resulting multidomain structure being moderately compact. Further examination of the relationship between interdomain flexibility and linker length shows there is a 5 residue "sweet spot" linker length that results in dual-domain systems being extended, and conversely that both longer or shorter linkers result in a less extended structure. This detailed knowledge of the obscurin N terminus structure and flexibility allowed for mathematical modeling of domains 1-18, which suggests that this region likely forms tangles if left alone in solution. Given how infrequently protein tangles occur in nature, and given the pathological outcomes that occur when tangles do arise, our data suggest that obscurin is likely either significantly scaffolded or else externally extended in the cell.
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Affiliation(s)
- Gianna E Mauriello
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, USA
| | - Grace E Moncure
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, USA
| | - Roujon A Nowzari
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, USA
| | - Callie J Miller
- Department of Engineering, James Madison University, Harrisonburg, Virginia, USA
| | - Nathan T Wright
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, USA
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Sun B, Kekenes-Huskey PM. Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling. Q Rev Biophys 2023; 56:e2. [PMID: 36628457 PMCID: PMC11070111 DOI: 10.1017/s003358352300001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cardiac sarcomere is a cellular structure in the heart that enables muscle cells to contract. Dozens of proteins belong to the cardiac sarcomere, which work in tandem to generate force and adapt to demands on cardiac output. Intriguingly, the majority of these proteins have significant intrinsic disorder that contributes to their functions, yet the biophysics of these intrinsically disordered regions (IDRs) have been characterized in limited detail. In this review, we first enumerate these myofilament-associated proteins with intrinsic disorder (MAPIDs) and recent biophysical studies to characterize their IDRs. We secondly summarize the biophysics governing IDR properties and the state-of-the-art in computational tools toward MAPID identification and characterization of their conformation ensembles. We conclude with an overview of future computational approaches toward broadening the understanding of intrinsic disorder in the cardiac sarcomere.
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Affiliation(s)
- Bin Sun
- Research Center for Pharmacoinformatics (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China
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Marzolf DR, Seffernick JT, Lindert S. Protein Structure Prediction from NMR Hydrogen-Deuterium Exchange Data. J Chem Theory Comput 2021; 17:2619-2629. [PMID: 33780620 DOI: 10.1021/acs.jctc.1c00077] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Amide hydrogen-deuterium exchange (HDX) has long been used to determine regional flexibility and binding sites in proteins; however, the data are too sparse for full structural characterization. Experiments that measure HDX rates, such as HDX-NMR, have far higher throughput compared to structure determination via X-ray crystallography, cryo-EM, or a full suite of NMR experiments. Data from HDX-NMR experiments encode information on the protein structure, making HDX a prime candidate to be supplemented by computational algorithms for protein structure prediction. We have developed a methodology to incorporate HDX-NMR data into ab initio protein structure prediction using the Rosetta software framework to predict structures based on experimental agreement. To demonstrate the efficacy of our algorithm, we examined 38 proteins with HDX-NMR data available, comparing the predicted model with and without the incorporation of HDX data into scoring. The root-mean-square deviation (rmsd, a measure of the average atomic distance between superimposed models) of the predicted model improved by 1.42 Å on average after incorporating the HDX-NMR data into scoring. The average rmsd improvement for the proteins where the selected model rmsd changed after incorporating HDX data was 3.63 Å, including one improvement of more than 11 Å and seven proteins improving by greater than 4 Å, with 12/15 proteins improving overall. Additionally, for independent verification, two proteins that were not part of the original benchmark were scored including HDX data, with a dramatic improvement of the selected model rmsd of nearly 9 Å for one of the proteins. Moreover, we have developed a confidence metric allowing us to successfully identify near-native models in the absence of a native structure. Improvement in model selection with a strong confidence measure demonstrates that protein structure prediction with HDX-NMR is a powerful tool which can be performed with minimal additional computational strain and expense.
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Affiliation(s)
- Daniel R Marzolf
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Justin T Seffernick
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
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Shashi V, Geist J, Lee Y, Yoo Y, Shin U, Schoch K, Sullivan J, Stong N, Smith E, Jasien J, Kranz P, Lee Y, Shin YB, Wright NT, Choi M, Kontrogianni-Konstantopoulos A. Heterozygous variants in MYBPC1 are associated with an expanded neuromuscular phenotype beyond arthrogryposis. Hum Mutat 2019; 40:1115-1126. [PMID: 31264822 PMCID: PMC6688907 DOI: 10.1002/humu.23760] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/27/2019] [Accepted: 04/02/2019] [Indexed: 01/22/2023]
Abstract
Encoding the slow skeletal muscle isoform of myosin binding protein-C, MYBPC1 is associated with autosomal dominant and recessive forms of arthrogryposis. The authors describe a novel association for MYBPC1 in four patients from three independent families with skeletal muscle weakness, myogenic tremors, and hypotonia with gradual clinical improvement. The patients carried one of two de novo heterozygous variants in MYBPC1, with the p.Leu263Arg variant seen in three individuals and the p.Leu259Pro variant in one individual. Both variants are absent from controls, well conserved across vertebrate species, predicted to be damaging, and located in the M-motif. Protein modeling studies suggested that the p.Leu263Arg variant affects the stability of the M-motif, whereas the p.Leu259Pro variant alters its structure. In vitro biochemical and kinetic studies demonstrated that the p.Leu263Arg variant results in decreased binding of the M-motif to myosin, which likely impairs the formation of actomyosin cross-bridges during muscle contraction. Collectively, our data substantiate that damaging variants in MYBPC1 are associated with a new form of an early-onset myopathy with tremor, which is a defining and consistent characteristic in all affected individuals, with no contractures. Recognition of this expanded myopathic phenotype can enable identification of individuals with MYBPC1 variants without arthrogryposis.
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Affiliation(s)
- Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, North Carolina
| | - Janelle Geist
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Youngha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yongjin Yoo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Unbeom Shin
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, North Carolina
| | - Jennifer Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, North Carolina
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York
| | - Edward Smith
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, North Carolina
| | - Joan Jasien
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, North Carolina
| | - Peter Kranz
- Division of Neuroradiology, Department of Radiology, Duke Health, Durham, North Carolina
| | - Yoonsung Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - Yong Beom Shin
- Department of Rehabilitation Medicine, Pusan National University College of Medicine, Pusan, Republic of Korea
| | - Nathan T Wright
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
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