17 research outputs found
Identification of genetic variants associated with Huntington's disease progression: a genome-wide association study
Background Huntington's disease is caused by a CAG repeat expansion in the huntingtin gene, HTT. Age at onset has been used as a quantitative phenotype in genetic analysis looking for Huntington's disease modifiers, but is hard to define and not always available. Therefore, we aimed to generate a novel measure of disease progression and to identify genetic markers associated with this progression measure. Methods We generated a progression score on the basis of principal component analysis of prospectively acquired longitudinal changes in motor, cognitive, and imaging measures in the 218 indivduals in the TRACK-HD cohort of Huntington's disease gene mutation carriers (data collected 2008â11). We generated a parallel progression score using data from 1773 previously genotyped participants from the European Huntington's Disease Network REGISTRY study of Huntington's disease mutation carriers (data collected 2003â13). We did a genome-wide association analyses in terms of progression for 216 TRACK-HD participants and 1773 REGISTRY participants, then a meta-analysis of these results was undertaken. Findings Longitudinal motor, cognitive, and imaging scores were correlated with each other in TRACK-HD participants, justifying use of a single, cross-domain measure of disease progression in both studies. The TRACK-HD and REGISTRY progression measures were correlated with each other (r=0·674), and with age at onset (TRACK-HD, r=0·315; REGISTRY, r=0·234). The meta-analysis of progression in TRACK-HD and REGISTRY gave a genome-wide significant signal (p=1·12 Ă 10â10) on chromosome 5 spanning three genes: MSH3, DHFR, and MTRNR2L2. The genes in this locus were associated with progression in TRACK-HD (MSH3 p=2·94 Ă 10â8 DHFR p=8·37 Ă 10â7 MTRNR2L2 p=2·15 Ă 10â9) and to a lesser extent in REGISTRY (MSH3 p=9·36 Ă 10â4 DHFR p=8·45 Ă 10â4 MTRNR2L2 p=1·20 Ă 10â3). The lead single nucleotide polymorphism (SNP) in TRACK-HD (rs557874766) was genome-wide significant in the meta-analysis (p=1·58 Ă 10â8), and encodes an aminoacid change (Pro67Ala) in MSH3. In TRACK-HD, each copy of the minor allele at this SNP was associated with a 0·4 units per year (95% CI 0·16â0·66) reduction in the rate of change of the Unified Huntington's Disease Rating Scale (UHDRS) Total Motor Score, and a reduction of 0·12 units per year (95% CI 0·06â0·18) in the rate of change of UHDRS Total Functional Capacity score. These associations remained significant after adjusting for age of onset. Interpretation The multidomain progression measure in TRACK-HD was associated with a functional variant that was genome-wide significant in our meta-analysis. The association in only 216 participants implies that the progression measure is a sensitive reflection of disease burden, that the effect size at this locus is large, or both. Knockout of Msh3 reduces somatic expansion in Huntington's disease mouse models, suggesting this mechanism as an area for future therapeutic investigation
Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries
Abstract
Background
Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres.
Methods
This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and lowâmiddle-income countries.
Results
In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of âsingle-useâ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for lowâmiddle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia.
Conclusion
This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both highâ and lowâmiddleâincome countries
Comparative Analysis of Sulfonium-Ï, Ammonium-Ï, and Sulfur-Ï Interactions and Relevance to SAM-Dependent Methyltransferases.
Recommended from our members
Comparative Analysis of SulfoniumâÏ, AmmoniumâÏ, and SulfurâÏ Interactions and Relevance to SAM-Dependent Methyltransferases
We report the measurement and analysis of sulfonium-Ï, thioether-Ï, and ammonium-Ï interactions in a ÎČ-hairpin peptide model system, coupled with computational investigation and PDB analysis. These studies indicated that the sulfonium-Ï interaction is the strongest and that polarizability contributes to the stronger interaction with sulfonium relative to ammonium. Computational studies demonstrate that differences in solvation of the trimethylsulfonium versus the trimethylammonium group also contribute to the stronger sulfonium-Ï interaction. In comparing sulfonium-Ï versus sulfur-Ï interactions in proteins, analysis of SAM- and SAH-bound enzymes in the PDB suggests that aromatic residues are enriched in close proximity to the sulfur of both SAM and SAH, but the populations of aromatic interactions of the two cofactors are not significantly different, with the exception of the Me-Ï interactions in SAM, which are the most prevalent interaction in SAM but are not possible for SAH. This suggests that the weaker interaction energies due to loss of the cation-Ï interaction in going from SAM to SAH may contribute to turnover of the cofactor
From peptides to proteins: coiled-coil tetramers to single-chain 4-helix bundles
The design of completely synthetic proteins from first principlesâde novo protein designâis challenging. This is because, despite recent advances in computational proteinâstructure prediction and design, we do not understand fully the sequence-to-structure relationships for protein folding, assembly, and stabilization. Antiparallel 4-helix bundles are amongst the most studied scaffolds for de novo protein design. We set out to re-examine this target, and to determine clear sequence-to-structure relationships, or design rules, for the structure. Our aim was to determine a common and robust sequence background for designing multiple de novo 4-helix bundles. In turn, this could be used in chemical and synthetic biology to direct proteinâprotein interactions and as scaffolds for functional protein design. Our approach starts by analyzing known antiparallel 4-helix coiled-coil structures to deduce design rules. In terms of the heptad repeat, abcdefgâi.e., the sequence signature of many helical bundlesâthe key features that we identify are: a = Leu, d = Ile, e = Ala, g = Gln, and the use of complementary charged residues at b and c. Next, we implement these rules in the rational design of synthetic peptides to form antiparallel homo- and heterotetramers. Finally, we use the sequence of the homotetramer to derive in one step a single-chain 4-helix-bundle protein for recombinant production in E. coli. All of the assembled designs are confirmed in aqueous solution using biophysical methods, and ultimately by determining high-resolution X-ray crystal structures. Our route from peptides to proteins provides an understanding of the role of each residue in each design
Rationally seeded computational protein design of É-helical barrels
Computational protein design is advancing rapidly. Here we describe efficient routes starting from validated parallel and antiparallel peptide assemblies to design two families of α-helical barrel proteins with central channels that bind small molecules. Computational designs are seeded by the sequences and structures of defined de novo oligomeric barrel-forming peptides, and adjacent helices are connected by loop building. For targets with antiparallel helices, short loops are sufficient. However, targets with parallel helices require longer connectors; namely, an outer layer of helixâturnâhelixâturnâhelix motifs that are packed onto the barrels. Throughout these computational pipelines, residues that define open states of the barrels are maintained. This minimizes sequence sampling, accelerating the design process. For each of six targets, just two to six synthetic genes are made for expression in Escherichia coli. On average, 70% of these genes express to give soluble monomeric proteins that are fully characterized, including high-resolution structures for most targets that match the design models with high accuracy
Thermodynamic consequences of Tyr to Trp mutations in the cation-Ï-mediated binding of trimethyllysine by the HP1 chromodomain.
Evolution has converged on cation-Ï interactions for recognition of quaternary alkyl ammonium groups such as trimethyllysine (Kme3). While computational modelling indicates that Trp provides the strongest cation-Ï interaction of the native aromatic amino acids, there is limited corroborative data from measurements within proteins. Herein we investigate a Tyr to Trp mutation in the binding pocket of the HP1 chromodomain, a reader protein that recognizes Kme3. Binding studies demonstrate that the Trp-mediated cation-Ï interaction is about -5 kcal mol-1 stronger, and the Y24W crystal structure shows that the mutation is not perturbing. Quantum mechanical calculations indicate that greater enthalpic binding is predominantly due to increased cation-Ï interactions. NMR studies indicate that differences in the unbound state of the Y24W mutation lead to enthalpy-entropy compensation. These results provide direct experimental quantification of Trp versus Tyr in a cation-Ï interaction and afford insight into the conservation of aromatic cage residues in Kme3 reader domains
Trimethyllysine Reader Proteins Exhibit Widespread Charge-Agnostic Binding via Different Mechanisms to Cationic and Neutral Ligands
In the last 40 years, cationâÏ interactions
have become
part of the lexicon of noncovalent forces that drive protein binding.
Indeed, tetraalkylammoniums are universally bound by aromatic cages
in proteins, suggesting that cationâÏ interactions are
a privileged mechanism for binding these ligands. A prominent example
is the recognition of histone trimethyllysine (Kme3) by the conserved
aromatic cage of reader proteins, dictating gene expression. However,
two proteins have recently been suggested as possible exceptions to
the
conventional understanding of tetraalkylammonium recognition. To broadly
interrogate the role of cationâÏ interactions in protein
binding interactions, we report the first large-scale comparative
evaluation of reader proteins for a neutral Kme3 isostere, experimental
and computational mechanistic studies, and structural analysis. We
find unexpected widespread binding of readers to a neutral isostere
with the first examples of readers that bind the neutral isostere
more tightly than Kme3. We find that no single factor dictates the
charge selectivity, demonstrating the challenge of predicting such
interactions. Further, readers that bind both cationic and neutral
ligands differ in mechanism: binding Kme3 via cationâÏ
interactions and the neutral isostere through the hydrophobic effect
in the same aromatic cage. This discovery explains apparently contradictory
results in previous studies, challenges traditional understanding
of molecular recognition of tetraalkylammoniums by aromatic cages
in myriad proteinâligand interactions, and establishes a new
framework for selective inhibitor design by exploiting differences
in charge dependence
Recommended from our members
Investigation of Trimethyllysine Binding by the HP1 Chromodomain via Unnatural Amino Acid Mutagenesis
Trimethyllysine
(Kme3) reader proteins are targets for inhibition
due to their role in mediating gene expression. Although all such
reader proteins bind Kme3 in an aromatic cage, the driving force for
binding may differ; some readers exhibit evidence for cationâÏ
interactions whereas others do not. We report a general unnatural
amino acid mutagenesis approach to quantify the contribution of individual
tyrosines to cation binding using the HP1 chromodomain as a model
system. We demonstrate that two tyrosines (Y24 and Y48) bind to a
Kme3-histone tail peptide via cationâÏ interactions,
but linear free energy trends suggest they do not contribute equally
to binding. X-ray structures and computational analysis suggest that
the distance and degree of contact between Tyr residues and Kme3 plays
an important role in tuning cationâÏ-mediated Kme3 recognition.
Although
cationâÏ interactions have been studied in a number of
proteins, this work is the first to utilize direct binding assays,
X-ray crystallography, and modeling, to pinpoint factors that influence
the magnitude of the individual cationâÏ interactions