Efficiently Differentiating Agonists and Competitive Antagonists for Weak Allosteric Protein-Ligand Interactions with Linear Response Theory.

What makes an agonist and a competitive antagonist? In this work, we aim to answer this question by performing parallel tempering Monte Carlo simulations on the serotonin type 3A (5-HT3A) receptor. We use linear response theory to predict conformational changes in the 5-HT3A receptor active site after weak perturbations are applied to its allosteric binding sites. A covariance tensor is built from conformational sampling of its apo state, and a harmonic approximation allows us to substitute the calculation of ligand-induced forces with the binding site's displacement vector. Remarkably, our study demonstrates the feasibility of effectively discerning between agonists and competitive antagonists for multiple ligands, requiring computationally expensive calculations only once per protein.

Investigating the Role of GABA in Neural Development and Disease Using Mice Lacking GAD67 or VGAT Genes.

Normal development and function of the central nervous system involves a balance between excitatory and inhibitory neurotransmission. Activity of both excitatory and inhibitory neurons is modulated by inhibitory signalling of the GABAergic and glycinergic systems. Mechanisms that regulate formation, maturation, refinement, and maintenance of inhibitory synapses are established in early life. Deviations from ideal excitatory and inhibitory balance, such as down-regulated inhibition, are linked with many neurological diseases, including epilepsy, schizophrenia, anxiety, and autism spectrum disorders. In the mammalian forebrain, GABA is the primary inhibitory neurotransmitter, binding to GABA receptors, opening chloride channels and hyperpolarizing the cell. We review the involvement of down-regulated inhibitory signalling in neurological disorders, possible mechanisms for disease progression, and targets for therapeutic intervention. We conclude that transgenic models of disrupted inhibitory signalling-in GAD67+/- and VGAT-/- mice-are useful for investigating the effects of down-regulated inhibitory signalling in a range of neurological diseases.

Functional divergence of the two Elongator subcomplexes during neurodevelopment.

The highly conserved Elongator complex is a translational regulator that plays a critical role in neurodevelopment, neurological diseases, and brain tumors. Numerous clinically relevant variants have been reported in the catalytic Elp123 subcomplex, while no missense mutations in the accessory subcomplex Elp456 have been described. Here, we identify ELP4 and ELP6 variants in patients with developmental delay, epilepsy, intellectual disability, and motor dysfunction. We determine the structures of human and murine Elp456 subcomplexes and locate the mutated residues. We show that patient-derived mutations in Elp456 affect the tRNA modification activity of Elongator in vitro as well as in human and murine cells. Modeling the pathogenic variants in mice recapitulates the clinical features of the patients and reveals neuropathology that differs from the one caused by previously characterized Elp123 mutations. Our study demonstrates a direct correlation between Elp4 and Elp6 mutations, reduced Elongator activity, and neurological defects. Foremost, our data indicate previously unrecognized differences of the Elp123 and Elp456 subcomplexes for individual tRNA species, in different cell types and in different key steps during the neurodevelopment of higher organisms.

The True Amphipathic Nature of Graphene Flakes: A Versatile 2D Stabilizer.

The fundamental colloidal properties of pristine graphene flakes remain incompletely understood, with conflicting reports about their chemical character, hindering potential applications that could exploit the extraordinary electronic, thermal, and mechanical properties of graphene. Here, the true amphipathic nature of pristine graphene flakes is demonstrated through wet-chemistry testing, optical microscopy, electron microscopy, and density functional theory, molecular dynamics, and Monte Carlo calculations, and it is shown how this fact paves the way for the formation of ultrastable water/oil emulsions. In contrast to commonly used graphene oxide flakes, pristine graphene flakes possess well-defined hydrophobic and hydrophilic regions: the basal plane and edges, respectively, the interplay of which allows small flakes to be utilized as stabilizers with an amphipathic strength that depends on the edge-to-surface ratio. The interactions between flakes can be also controlled by varying the oil-to-water ratio. In addition, it is predicted that graphene flakes can be efficiently used as a new-generation stabilizer that is active under high pressure, high temperature, and in saline solutions, greatly enhancing the efficiency and functionality of applications based on this material.

Measuring the quality of life of the families of children with eczema in Hong Kong.

BACKGROUND: Eczema is the most common skin problem among children in Hong Kong. Previous studies have highlighted that the quality of life of the families of children with eczema influences the effects of eczema interventions. However, the Chinese version of the Family Dermatology Life Quality Index (C-FDLQI), a tool for measuring the quality of life of the families of children with eczema, has not yet been validated. OBJECTIVE: This study examined the psychometric properties of the C-FDLQI among parents and caregivers of children with eczema in Hong Kong. METHODS: This study evaluated the internal consistency, test-retest reliability and structural validity of the C-FDLQI and its convergent validity by examining its correlations with the SCORing Atopic Dermatitis (SCORAD) and the Cantonese version of the Children's Dermatology Life Quality Index (C-CDLQI) among 147 Chinese parents/caregivers of children with varying degrees of eczema. RESULTS: Based on the ratings by an expert panel, both the content validity index and semantic equivalence of the C-FDLQI were satisfactory (>0.90). The C-FDLQI showed high internal consistency, with a Cronbach α of 0.95. Its test-retest reliability was good, with weighted kappa values for the items ranging from 0.70 to 1.00. The total scores of the C-FDLQI showed positive correlations with those of the C-CDLQI (Pearson r = 0.75, p < 0.001) and SCORAD (Pearson r = 0.62, p < 0.001). Known-group comparisons of the C-FDLQI between the parents/caregivers of children with mild eczema and those of children with moderate to severe eczema showed a significant difference (t = -7.343, p < 0.001), indicating that the C-FDLQI had acceptable convergent validity. Confirmatory factor analysis supported the one-factor structure of the C-FDLQI. CONCLUSION: The results suggest that the C-FDLQI is a reliable and valid tool for evaluating the quality of life of parents or caregivers of children with eczema in Hong Kong.

Hypermethylation of the p16 gene promoter in pterygia and its association with the expression of DNA methyltransferase 3b.

PURPOSE: A pterygium has long been considered as a degenerative condition. After p53 protein was found to be abnormally expressed in the epithelium, researchers suggested that a pterygium may be a tumor, but additional evidence is required to support this hypothesis. Aberrant methylation of the p16 gene (CDKN2A) promoter and resultant gene silencing play important roles in the pathogenesis of many types of human cancers. The purpose of this study was to investigate hypermethylation of the p16 promoter in pterygia and the relationship between this hypermethylation and the expression of p16 and DNA methyltransferase 3b (DNMT3b) proteins. METHODS: We studied the methylation status of p16 and the expression of p16 and DNMT3b proteins by performing methylation-specific polymerase chain reaction and immunohistochemistry, respectively, in specimens of 129 pterygia and 16 normal conjunctiva. The results were statistically analyzed. RESULTS: Hypermethylation of the p16 gene promoter was detected in 21 (16.3%) of 129 pterygial specimens. Among them, 46 (35.7%) were positive for p16 protein expression, and 83 (64.3%) were negative. Staining for p16 was limited to the nuclei of the epithelial layer. We observed a significant reverse correlation between hypermethylation of the p16 promoter and the expression of p16 protein (p=0.006). Thirty-eight (29.5%) pterygial specimens were positive for DNMT3b protein expression, and 91 (70.5%) were negative. DNMT3b staining was limited to the nuclei of the epithelial layer. A significant correlation was found between hypermethylation of the p16 promoter and the expression of DNMT3b protein (p<0.001). CONCLUSIONS: The p16 gene promoter was hypermethylated in pterygia, and this hypermethylation was strongly linked to expression of the positive expression of DNMT3b protein and to the suppression of p16 protein. These data provided molecular evidence that methylation occurs in pterygia and that it may play a role in the their development.

Effect of p53 codon 72 polymorphism on p53 protein expression in pterygium.

BACKGROUND: The p53 protein is expressed in pterygial epithelium, but the reported prevalence of its expression varies widely. Although the cause of this variation is unknown, several factors that may play a role have been investigated, but without conclusive findings. In the present study, the role of p53 codon 72 polymorphism, and that of both age and gender, on p53 expression in pterygium was investigated. METHODS: Pterygium and blood samples were harvested from 55 patients undergoing pterygium surgery. The pterygial specimens were studied immunohistochemically using antibodies against p53 protein. Polymerase chain reaction based analysis was used to resolve the p53 codon 72 polymorphism. RESULTS: Thirty-one (56.4%) of the 55 pterygial specimens were positive for p53 staining. The distributions of the three genotypes of the p53 codon 72 polymorphism in the p53-positive and -negative staining groups were not statistically different. The allelic frequency in the two groups was also not statistically different, nor was there any significant difference between both groups with respect to age or gender. CONCLUSIONS: A correlation between p53 codon 72 polymorphism, sex and gender and p53 protein expression was not found.

Prediction of 5-HT3 receptor agonist-binding residues using homology modeling.

5-HT(3) receptors demonstrate significant structural and functional homology to other members of the Cys-loop ligand-gated ion channel superfamily. The extracellular domains of these receptors share similar sequence homology (approximately 20%) with Limnaea acetylcholine binding protein, for which an x-ray crystal structure is available. We used this structure as a template for computer-based homology modeling of the 5-HT(3) receptor extracellular domain. AutoDock software was used to dock 5-HT into the putative 5-HT(3) receptor ligand-binding site, resulting in seven alternative energetically favorable models. Residues located no more than 5 A from the docked 5-HT were identified for each model; of these, 12 were found to be common to all seven models with five others present in only certain models. Some docking models reflected the cation-pi interaction previously demonstrated for W183, and data from these and other studies were used to define our preferred models.