scholarly journals Determinants of trafficking, conduction, and disease within a K+ channel revealed through multiparametric deep mutational scanning

2022 ◽  
Author(s):  
Willow Coyote-Maestas ◽  
David Nedrud ◽  
Yungui He ◽  
Daniel Schmidt

A longstanding goal in protein science and clinical genetics is to develop quantitative models of sequence, structure, and function relationships and delineate the mechanisms by which mutations cause disease. Deep Mutational Scanning (DMS) is a promising strategy to map how amino acids contribute to protein structure and function and to advance clinical variant interpretation. Here, we introduce 7,429 single residue missense mutation into the Inward Rectifier K+ channel Kir2.1 and determine how this affects folding, assembly, and trafficking, as well as regulation by allosteric ligands and ion conduction. Our data provide high-resolution information on a cotranslationally-folded biogenic unit, trafficking and quality control signals, and segregated roles of different structural elements in fold-stability and function. We show that Kir2.1 trafficking mutants are underrepresented in variant effect databases, which has implications for clinical practice. By comparing fitness scores with expert-reviewed variant effects, we can predict the pathogenicity of variants of unknown significance and disease mechanisms of know pathogenic mutations. Our study in Kir2.1 provides a blueprint for how multiparametric DMS can help us understand the mechanistic basis of genetic disorders and the structure-function relationships of proteins.

BMJ ◽  
1989 ◽  
Vol 298 (6688) ◽  
pp. 1629-1631 ◽  
Author(s):  
H. M. Kingston

1992 ◽  
Vol 62 (1) ◽  
pp. 34-36 ◽  
Author(s):  
M. Taglialatela ◽  
G.E. Kirsch ◽  
A.M. VanDongen ◽  
J.A. Drewe ◽  
H.A. Hartmann ◽  
...  

Circulation ◽  
2015 ◽  
Vol 132 (suppl_3) ◽  
Author(s):  
Elisa Mastantuono ◽  
Thomas Wieland ◽  
Riccardo Berutti ◽  
Peter Lichtner ◽  
Tim Strom ◽  
...  

Background: Whole-exome-sequencing (WES) is becoming a common molecular diagnostic test for patients with genetic disorders. However, this technique allows the identification not only of mutations responsible for the disease under investigation, but also of variants potentially causing other diseases, the so called “incidental findings” (IFs). The American College of Medical Genetics and Genomics (ACMG) stated that IFs should be reported based on clinical validity and utility and indicated a list of 56 actionable genes. Among these, nearly half (20/56) are major genes associated with channelopathies and cardiomyopathies. Despite these recommendations, most of the studies so far published, reported also mutations in minor genes among the actionable findings. Methods: WES was performed in 5891 individuals without known channelopathies or cardiomyopathies. Exome data were first filtered based on genotype quality. Subsequently, a frequency filter was applied, considering 1000 Genomes, ExAC and our internal exome database. Variants reported as pathogenic in ClinVar or novel but expected to be pathogenic (nonsense, frameshift and splice) were further investigated, following the ACMG guidelines. Major (20) and minor (73) genes associated with channelopathies and cardiomyopathies were evaluated. Results: We identified 3514 variants in the 93 genes under investigation, after applying the quality and frequency filters. Eight variants were classified as pathogenic and 52 as likely pathogenic and they were detected in around 1% of the individuals. The vast majority (85%) of pathogenic or likely pathogenic variants were located in the 20 actionable genes indicated by ACMG. The inclusion of minor genes increased the number of variants of unknown significance (VUS), from 865 to 3454. Conclusion: Our data support the ACMG recommendations in reporting only IFs identified in the 20 major cardiac actionable genes. Indeed, the inclusion of minor genes is mainly increasing the number of VUS, without significantly impacting the number of pathogenic and likely pathogenic variants. The percentage of individuals with potentially clinical relevant variants in these genes is too high in relation to the disease-prevalence: a cardiologic evaluation is warranted.


2016 ◽  
Vol 44 (6) ◽  
pp. 1561-1569 ◽  
Author(s):  
David C. Grainger

The histone-like nucleoid structuring (H-NS) protein is a major component of the folded chromosome in Escherichia coli and related bacteria. Functions attributed to H-NS include management of genome evolution, DNA condensation, and transcription. The wide-ranging influence of H-NS is remarkable given the simplicity of the protein, a small peptide, possessing rudimentary determinants for self-association, hetero-oligomerisation and DNA binding. In this review, I will discuss our understanding of H-NS with a focus on these structural elements. In particular, I will consider how these interaction surfaces allow H-NS to exert its different effects.


2018 ◽  
Author(s):  
Jonathan B. Leano ◽  
Kevin C. Slep

AbstractTubulin-binding TOG domains are found arrayed in a number of proteins that regulate microtubule dynamics. While much is known about the structure and function of TOG domains in the XMAP215 microtubule polymerase family, less in known about the TOG domain array found in the CLASP family. The CLASP TOG array promotes microtubule pause, potentiates rescue, and limits catastrophe. How distinct the TOG domains of CLASP are from one another, from XMAP215 TOG domains, and whether they are positionally conserved across CLASP family members is poorly understood. We present the x-ray crystal structures of human CLASP1 TOG1 and TOG2. The structures of CLASP1 TOG1 and TOG2 are distinct from each other, from CLASP TOG3, and are positionally conserved across species. While studies have failed to detect CLASP TOG1 tubulin-binding activity, TOG1 is structurally similar to the free-tubulin binding TOG domains of XMAP215. In contrast, though CLASP TOG2 and TOG3 have tubulin binding activity, they are structurally distinct from the free-tubulin binding TOG domains of XMAP215. CLASP TOG2 has a convex architecture, predicted to engage a hyper-curved tubulin state. CLASP TOG3 has unique structural elements in the C-terminal half of its α-solenoid domain that modeling studies implicate in binding to laterally-associated tubulin subunits in the microtubule lattice in a mode similar to, yet distinct from XMAP215 TOG4. These findings highlight the structural diversity of TOG domains within the CLASP TOG array and provide a molecular foundation for understanding CLASP-dependent effects on microtubule dynamics.


2012 ◽  
Vol 42 (1) ◽  
pp. 71-79 ◽  
Author(s):  
Chai Ann Ng ◽  
Allan M. Torres ◽  
Guilhem Pagès ◽  
Philip W. Kuchel ◽  
Jamie I. Vandenberg

2022 ◽  
pp. practneurol-2021-002989
Author(s):  
Thanuja Dharmadasa ◽  
Jakub Scaber ◽  
Evan Edmond ◽  
Rachael Marsden ◽  
Alexander Thompson ◽  
...  

A minority (10%–15%) of cases of amyotrophic lateral sclerosis (ALS), the most common form of motor neurone disease (MND), are currently attributable to pathological variants in a single identifiable gene. With the emergence of new therapies targeting specific genetic subtypes of ALS, there is an increasing role for routine genetic testing for all those with a definite diagnosis. However, potential harm to both affected individuals and particularly to asymptomatic relatives can arise from the indiscriminate use of genetic screening, not least because of uncertainties around incomplete penetrance and variants of unknown significance. The most common hereditary cause of ALS, an intronic hexanucleotide repeat expansion in C9ORF72, may be associated with frontotemporal dementia independently within the same pedigree. The boundary of what constitutes a possible family history of MND has therefore extended to include dementia and associated psychiatric presentations. Notwithstanding the important role of clinical genetics specialists, all neurologists need a basic understanding of the current place of genetic testing in MND, which holds lessons for other neurological disorders.


2011 ◽  
Vol 108 (43) ◽  
pp. 17684-17689 ◽  
Author(s):  
V. P. T. Pau ◽  
F. J. Smith ◽  
A. B. Taylor ◽  
L. V. Parfenova ◽  
E. Samakai ◽  
...  

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