Evolution favors protein mutational robustness in sufficiently large populations

BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar proteins can differ substantially in their robustness to mutations and capacity to evolve new functions, but it has remained unclear whether any of these differences might be due to evolutionary selection for these properties. RESULTS: Here we use laboratory experiments to demonstrate that evolution favors protein mutational robustness if the evolving population is sufficiently large. We neutrally evolve cytochrome P450 proteins under identical selection pressures and mutation rates in populations of different sizes, and show that proteins from the larger and thus more polymorphic population tend towards higher mutational robustness. Proteins from the larger population also evolve greater stability, a biophysical property that is known to enhance both mutational robustness and evolvability. The excess mutational robustness and stability is well described by existing mathematical theories, and can be quantitatively related to the way that the proteins occupy their neutral network. CONCLUSIONS: Our work is the first experimental demonstration of the general tendency of evolution to favor mutational robustness and protein stability in highly polymorphic populations. We suggest that this phenomenon may contribute to the mutational robustness and evolvability of viruses and bacteria that exist in large populations

Inferring stabilizing mutations from protein phylogenies : application to influenza hemagglutinin

One selection pressure shaping sequence evolution is the requirement that a protein fold with sufficient stability to perform its biological functions. We present a conceptual framework that explains how this requirement causes the probability that a particular amino acid mutation is fixed during evolution to depend on its effect on protein stability. We mathematically formalize this framework to develop a Bayesian approach for inferring the stability effects of individual mutations from homologous protein sequences of known phylogeny. This approach is able to predict published experimentally measured mutational stability effects (ΔΔG values) with an accuracy that exceeds both a state-of-the-art physicochemical modeling program and the sequence-based consensus approach. As a further test, we use our phylogenetic inference approach to predict stabilizing mutations to influenza hemagglutinin. We introduce these mutations into a temperature-sensitive influenza virus with a defect in its hemagglutinin gene and experimentally demonstrate that some of the mutations allow the virus to grow at higher temperatures. Our work therefore describes a powerful new approach for predicting stabilizing mutations that can be successfully applied even to large, complex proteins such as hemagglutinin. This approach also makes a mathematical link between phylogenetics and experimentally measurable protein properties, potentially paving the way for more accurate analyses of molecular evolution

To retain or remove the syndesmotic screw: a review of literature

Introduction: Syndesmotic positioning screws are frequently placed in unstable ankle fractures. Many facets of adequate placement techniques have been the subject of various studies. Whether or not the syndesmosis screw should be removed prior to weight-bearing is still debated. In this study, the recent literature is reviewed concerning the need for removal of the syndesmotic screw. Materials and methods: A comprehensive literature search was conducted in the electronic databases of the Cochrane Library, Pubmed Medline and EMbase from January 2000 to October 2010. Results: A total of seven studies were identified in the literature. Most studies found no difference in outcome between retained or removed screws. Patients with screws that were broken, or showed loosening, had similar or improved outcome compared to patients with removed screws. Removal of the syndesmotic screws, when deemed necessary, is usually not performed before 8-12 weeks. Conclusion: There is paucity in randomized controlled trials on the absolute need for removal of the syndesmotic screw. However, current literature suggests that it might be reserved for intact screws that cause hardware irritation or reduced range of motion after 4-6 months

Changes in the Brain Microstructure of Children with Primary Monosymptomatic Nocturnal Enuresis: A Diffusion Tensor Imaging Study

Background: Primary monosymptomatic nocturnal enuresis (PMNE) is a common disorder in school-aged children. Previous studies have suggested that a developmental delay might play a role in the pathology of children with PMNE. However, microstructural abnormalities in the brains of these children have not been thoroughly investigated. Methodology/Principal Findings: In this work, we evaluated structural changes in the brains of children with PMNE using diffusion tensor imaging (DTI). Two groups consisting of 26 children with PMNE and 26 healthy controls were scanned using magnetic resonance DTI. The diffusion parameters of fractional anisotropy (FA) and mean diffusivity (MD) were subjected to whole-brain, voxel-wise group comparisons using statistical parametric mapping (SPM). When compared to healthy subjects, children with PMNE showed both a decrease in FA and an increase in MD in the thalamus. MD also increased in the frontal lobe, the anterior cingulate cortex and the insula; these areas are all involved in controlling micturition. The significant changes seen in the thalamus could affect both urine storage and arousal from sleep. Conclusions/Significance: The microstructure abnormalities were observed in the thalamus, the medial frontal gyrus, the anterior cingulate cortex and the insula, which are involved in micturition control network. This indicates developmenta

Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces

<p>Abstract</p> <p>Background</p> <p>Empirical binding models have previously been investigated for the energetics of protein complexation (ΔG models) and for the influence of mutations on complexation (i.e. differences between wild-type and mutant complexes, ΔΔG models). We construct binding models to directly compare these processes, which have generally been studied separately.</p> <p>Results</p> <p>Although reasonable fit models were found for both ΔG and ΔΔG cases, they differ substantially. In a dataset curated for the absence of mainchain rearrangement upon binding, non-polar area burial is a major determinant of ΔG models. However this ΔG model does not fit well to the data for binding differences upon mutation. Burial of non-polar area is weighted down in fitting of ΔΔG models. These calculations were made with no repacking of sidechains upon complexation, and only minimal packing upon mutation. We investigated the consequences of more extensive packing changes with a modified mean-field packing scheme. Rather than emphasising solvent exposure with relatively extended sidechains, rotamers are selected that exhibit maximal packing with protein. This provides solvent accessible areas for proteins that are much closer to those of experimental structures than the more extended sidechain regime. The new packing scheme increases changes in non-polar burial for mutants compared to wild-type proteins, but does not substantially improve agreement between ΔG and ΔΔG binding models.</p> <p>Conclusion</p> <p>We conclude that solvent accessible area, based on modelled mutant structures, is a poor correlate for ΔΔG upon mutation. A simple volume-based, rather than solvent accessibility-based, model is constructed for ΔG and ΔΔG systems. This shows a more consistent behaviour. We discuss the efficacy of volume, as opposed to area, approaches to describe the energetic consequences of mutations at interfaces. This knowledge can be used to develop simple computational screens for binding in comparative modelled interfaces.</p

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

ABSTRACT:Journal ArticleSCOPUS: ar.jinfo:eu-repo/semantics/publishe

Path to Facilitate the Prediction of Functional Amino Acid Substitutions in Red Blood Cell Disorders – A Computational Approach

A major area of effort in current genomics is to distinguish mutations that are functionally neutral from those that contribute to disease. Single Nucleotide Polymorphisms (SNPs) are amino acid substitutions that currently account for approximately half of the known gene lesions responsible for human inherited diseases. As a result, the prediction of non-synonymous SNPs (nsSNPs) that affect protein functions and relate to disease is an important task.In this study, we performed a comprehensive analysis of deleterious SNPs at both functional and structural level in the respective genes associated with red blood cell metabolism disorders using bioinformatics tools. We analyzed the variants in Glucose-6-phosphate dehydrogenase (G6PD) and isoforms of Pyruvate Kinase (PKLR & PKM2) genes responsible for major red blood cell disorders. Deleterious nsSNPs were categorized based on empirical rule and support vector machine based methods to predict the impact on protein functions. Furthermore, we modeled mutant proteins and compared them with the native protein for evaluation of protein structure stability.We argue here that bioinformatics tools can play an important role in addressing the complexity of the underlying genetic basis of Red Blood Cell disorders. Based on our investigation, we report here the potential candidate SNPs, for future studies in human Red Blood Cell disorders. Current study also demonstrates the presence of other deleterious mutations and also endorses with in vivo experimental studies. Our approach will present the application of computational tools in understanding functional variation from the perspective of structure, expression, evolution and phenotype

The effectiveness of a web-based brief alcohol intervention in reducing heavy drinking among adolescents aged 15 to 20 years with a low educational background: Study protocol for a randomized controlled trial

Contains fulltext : 102984.pdf (publisher's version ) (Open Access)Background: The serious negative health consequences of heavy drinking among adolescents is cause for concern, especially among adolescents aged 15 to 20 years with a low educational background. In the Netherlands, there is a lack of alcohol prevention programs directed to the drinking patterns of this specific target group. The study described in this protocol will test the effectiveness of a web-based brief alcohol intervention that aims to reduce alcohol use among heavy drinking adolescents aged 15 to 20 years with a low educational background. Methods/design: The effectiveness of the What Do You Drink (WDYD) web-based brief alcohol intervention will be tested among 750 low-educated, heavy drinking adolescents. It will use a two-arm parallel group cluster randomized controlled trial. Classes of adolescents from educational institutions will be randomly assigned to either the experimental (n = 375: web-based brief alcohol intervention) or control condition (n = 375: no intervention). Primary outcomes measures will be: 1) the percentage of participants who drink within the normative limits of the Dutch National Health Council for low-risk drinking, 2) reductions in mean weekly alcohol consumption, and 3) frequency of binge drinking. The secondary outcome measures include the alcohol-related cognitions, attitudes, self-efficacy, and subjective norms, which will be measured at baseline and at one and six months after the intervention. Discussion: This study protocol presents the study design of a two-arm parallel-group randomized controlled trial to evaluate the effectiveness of the WDYD web-based brief alcohol intervention. We hypothesized a reduction in mean weekly alcohol consumption and in the frequency of binge drinking in the experimental condition, resulting from the web-based brief alcohol intervention, compared to the control condition.7 p