Faculty Opinions recommendation of Detailed computational study of p53 and p16: using evolutionary sequence analysis and disease-associated mutations to predict the functional consequences of allelic variants.

Author(s):  
Janet Thornton
2016 ◽  
Author(s):  
Duccio Malinverni ◽  
Alfredo Jost Lopez ◽  
Paolo De Los Rios ◽  
Gerhard Hummer ◽  
Alessandro Barducci

AbstractThe interaction between the Heat Shock Proteins 70 and 40 is at the core of the ATPase regulation of the chaperone machinery that maintains protein homeostasis. However, the structural details of this fundamental interaction are still elusive and contrasting models have been proposed for the transient Hsp70/Hsp40 complexes. Here we combine molecular simulations based on both coarsegrained and atomistic models with co-evolutionary sequence analysis to shed light on this problem by focusing on the bacterial DnaK/DnaJ system. The integration of these complementary approaches resulted into a novel structural model that rationalizes previous experimental observations. We identify an evolutionary-conserved interaction surface formed by helix II of the DnaJ J-domain and a groove on lobe IIA of the DnaK nucleotide binding domain, involving the inter-domain linker.


2014 ◽  
Vol 99 (11) ◽  
pp. E2429-E2436 ◽  
Author(s):  
Chantal Zevenbergen ◽  
Wim Klootwijk ◽  
Robin P. Peeters ◽  
Marco Medici ◽  
Yolanda B. de Rijke ◽  
...  

Context: Thyroid hormones (TH) are important for normal brain development and abnormal TH regulation in the brain results in neurocognitive impairments. The type 2 deiodinase (D2) is important for local TH control in the brain by generating the active hormone T3 from its precursor T4. Dysfunction of D2 likely results in a neurocognitive phenotype. No mutations in D2 have been reported yet. Objective: The objective of the study was to identify D2 mutations in patients with intellectual disability and to test their functional consequences. Design, Setting, and Patients: The patients were selected from the multicenter Thyroid Origin of Psychomotor Retardation study, which is a cohort of 946 subjects with unexplained intellectual disability. Based on characteristic serum TH values, the coding region of the DIO2 gene was sequenced in 387 patients. Functional consequences were assessed by in vitro D2 assays or intact cell metabolism studies using cells transfected with wild-type or mutant D2. Results: Sequence analysis revealed two heterozygous mutations: c.11T>A (p.L4H) in three subjects and c.305C>T (p.T102I) in one subject. Sequence analysis of family members revealed several carriers, but no segregation was observed with thyroid parameters or neurocognitive phenotype. Extensive tests with different in vitro D2 assays did not show differences between wild-type and mutant D2. Conclusion: This study describes the identification and functional consequences of novel genetic variation in TH activating enzyme D2. Family studies and functional tests suggest that these variants do not underlie the neurocognitive impairment. Altogether our data provide evidence of the existence of rare but apparently harmless genetic variants of D2.


2017 ◽  
Vol 14 (2) ◽  
Author(s):  
Eudes Barbosa ◽  
Richard Röttger ◽  
Anne-Christin Hauschild ◽  
Siomar de Castro Soares ◽  
Sebastian Böcker ◽  
...  

AbstractDistinct bacteria are able to cope with highly diverse lifestyles; for instance, they can be free living or host-associated. Thus, these organisms must possess a large and varied genomic arsenal to withstand different environmental conditions. To facilitate the identification of genomic features that might influence bacterial adaptation to a specific niche, we introduce LifeStyle-Specific-Islands (LiSSI). LiSSI combines evolutionary sequence analysis with statistical learning (Random Forest with feature selection, model tuning and robustness analysis). In summary, our strategy aims to identify conserved consecutive homology sequences (islands) in genomes and to identify the most discriminant islands for each lifestyle.


1999 ◽  
Vol 37 (2) ◽  
pp. 105-114 ◽  
Author(s):  
Y. GRAser ◽  
M. EL Fari ◽  
R. Vilgalys ◽  
A. F. A. Kuijpers ◽  
G. S. DE Hoog ◽  
...  

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