AllerCatPro 2.0: a web server for predicting protein allergenicity potential.

Proteins in food and personal care products can pose a risk for an immediate immunoglobulin E (IgE)-mediated allergic response. Bioinformatic tools can assist to predict and investigate the allergenic potential of proteins. Here we present AllerCatPro 2.0, a web server that can be used to predict protein allergenicity potential with better accuracy than other computational methods and new features that help assessors making informed decisions. AllerCatPro 2.0 predicts the similarity between input proteins using both their amino acid sequences and predicted 3D structures towards the most comprehensive datasets of reliable proteins associated with allergenicity. These datasets currently include 4979 protein allergens, 162 low allergenic proteins, and 165 autoimmune allergens with manual expert curation from the databases of WHO/International Union of Immunological Societies (IUIS), Comprehensive Protein Allergen Resource (COMPARE), Food Allergy Research and Resource Program (FARRP), UniProtKB and Allergome. Various examples of profilins, autoimmune allergens, low allergenic proteins, very large proteins, and nucleotide input sequences showcase the utility of AllerCatPro 2.0 for predicting protein allergenicity potential. The AllerCatPro 2.0 web server is freely accessible at https://allercatpro.bii.a-star.edu.sg.

Tracking Eye Movements for Diagnosis in Myasthenia Gravis: A Comprehensive Review.

BACKGROUND: Around 60%--75% of myasthenia gravis (MG) patients initially present with nonspecific ocular symptoms. Failed recognition of these symptoms may delay the diagnosis of MG up to 5 years or more, leading to a reduced likelihood of remission and increased morbidity. Current diagnostic tests are either poorly sensitive for patients presenting with ocular symptoms alone or are time consuming, invasive, require a high level of technical expertise, and generally are universally difficult to obtain. This review will explore quantitative eye and pupil tracking as a potential noninvasive, time-effective, and less technically demanding alternative to current diagnostic tests of MG. EVIDENCE ACQUISITION: Comprehensive literature review. RESULTS: Thirty-two publications using oculography for the diagnosis of MG and 6 studies using pupillometry were evaluated. In MG patients, extra ocular muscle fatigue was evident in reports of intersaccadic, intrasaccadic and postsaccadic abnormalities, changes in optokinetic nystagmus, slow eye movements, disconjugate saccades, and pupillary constrictor muscle weakness. CONCLUSIONS: Our review identified several potentially useful variables that derive from oculography and pupillometry studies that could assist with a timely diagnosis of MG. Limitations of this review include heterogeneity in design, sample size, and quality of the studies evaluated. There is a need for larger, well-designed studies evaluating eye-tracking measures in the diagnosis of MG, especially for patients presenting with purely ocular symptoms.

Thermal induced changes of rice straw phytolith in relation to arsenic release: A perspective of rice straw arsenic under open burning.

On-site open burning is a common practice for handling rice straw, but its negative impacts, e.g., biomass loss and air pollution, are largely debated worldwide. To address the negative effects of open burning, many efforts have been made to 'ignite' worldwide bans. However, these bans are likely based on a singular view in which some positive aspects of open burning are overlooked. In this study, we aimed to determine the thermal-induced changes of straw and straw arsenic (As) under open burning and heat-treatments (in the temperature range from 300 to 900 °C). It was found that silica phase in rice straw (so-called phytolith) can encapsulate As in its structure. Open burning or heat-treatment of straw resulted in a tighter association of As and phytolith, thereby reducing dissolution of As. We proposed an opinion that open burning causes air pollution, but it can increase the activity of phytolith in sequestrating As, enabling delayed As cycle in rice ecosystems. The combat of on-site open burning of rice straw to reduce air pollution will alter straw handling routines, thereby changing the cycle of straw phytolith and the route of straw As.

AppA: a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody-antigen structures and models.

The study of contact residues and interfacial waters of antibody-antigen (Ab-Ag) structures could help in understanding the principles of antibody-antigen interactions as well as provide guidance for designing antibodies with improved affinities. Given the rapid pace with which new antibody-antigen structures are deposited in the protein databank (PDB), it is crucial to have computational tools to analyze contact residues and interfacial waters, and investigate them at different levels. In this study, we have developed AppA, a web server that can be used to analyze and compare 3D structures of contact residues and interfacial waters of antibody-antigen complexes. To the best of our knowledge, this is the first web server for antibody-antigen structures equipped with the capability for dissecting the contributions of interfacial water molecules, hydrogen bonds, hydrophobic interactions, van der Waals interactions and ionic interactions at the antibody-antigen interface, and for comparing the structures and conformations of contact residues. Various examples showcase the utility of AppA for such analyses and comparisons that could help in the understanding of antibody-antigen interactions and suggest mutations of contact residues to improve affinities of antibodies. The AppA web server is freely accessible at http://mspc.bii.a-star.edu.sg/minhn/appa.html.

Simulations of mutant p53 DNA binding domains reveal a novel druggable pocket.

The DNA binding domain (DBD) of the tumor suppressor p53 is the site of several oncogenic mutations. A subset of these mutations lowers the unfolding temperature of the DBD. Unfolding leads to the exposure of a hydrophobic ß-strand and nucleates aggregation which results in pathologies through loss of function and dominant negative/gain of function effects. Inspired by the hypothesis that structural changes that are associated with events initiating unfolding in DBD are likely to present opportunities for inhibition, we investigate the dynamics of the wild type (WT) and some aggregating mutants through extensive all atom explicit solvent MD simulations. Simulations reveal differential conformational sampling between the WT and the mutants of a turn region (S6-S7) that is contiguous to a known aggregation-prone region (APR). The conformational properties of the S6-S7 turn appear to be modulated by a network of interacting residues. We speculate that changes that take place in this network as a result of the mutational stress result in the events that destabilize the DBD and initiate unfolding. These perturbations also result in the emergence of a novel pocket that appears to have druggable characteristics. FDA approved drugs are computationally screened against this pocket.

AllerCatPro-prediction of protein allergenicity potential from the protein sequence.

MOTIVATION: Due to the risk of inducing an immediate Type I (IgE-mediated) allergic response, proteins intended for use in consumer products must be investigated for their allergenic potential before introduction into the marketplace. The FAO/WHO guidelines for computational assessment of allergenic potential of proteins based on short peptide hits and linear sequence window identity thresholds misclassify many proteins as allergens. RESULTS: We developed AllerCatPro which predicts the allergenic potential of proteins based on similarity of their 3D protein structure as well as their amino acid sequence compared with a data set of known protein allergens comprising of 4180 unique allergenic protein sequences derived from the union of the major databases Food Allergy Research and Resource Program, Comprehensive Protein Allergen Resource, WHO/International Union of Immunological Societies, UniProtKB and Allergome. We extended the hexamer hit rule by removing peptides with high probability of random occurrence measured by sequence entropy as well as requiring 3 or more hexamer hits consistent with natural linear epitope patterns in known allergens. This is complemented with a Gluten-like repeat pattern detection. We also switched from a linear sequence window similarity to a B-cell epitope-like 3D surface similarity window which became possible through extensive 3D structure modeling covering the majority (74%) of allergens. In case no structure similarity is found, the decision workflow reverts to the old linear sequence window rule. The overall accuracy of AllerCatPro is 84% compared with other current methods which range from 51 to 73%. Both the FAO/WHO rules and AllerCatPro achieve highest sensitivity but AllerCatPro provides a 37-fold increase in specificity. AVAILABILITY AND IMPLEMENTATION: https://allercatpro.bii.a-star.edu.sg/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Accumulation of copper and cadmium in soil-rice systems in terrace and lowland paddies of the Red River basin, Vietnam: the possible regulatory role of silicon.

Rice production in floodplain deltas is currently vulnerable to climate change and contamination from anthropogenic activities. The relocation of rice production to upland regions could be an option for increasing the sustainability of rice production. Our study evaluated the spatial patterning of heavy metals, i.e., copper (Cu) and cadmium (Cd), in rice along a topogradient from terrace to lowland areas in the Red River basin. The dataset obtained from the analysis of 61 farm sites throughout the whole basin indicated a large discrepancy in the Cu and Cd contents in rice grains from terrace and lowland paddies. While Cu and Cd were not found in most of the rice grain samples from the terrace paddies, the median Cu and Cd contents of the lowland paddy rice were 1.895 and 0.033 mg kg-1, respectively. Assessing the relationship of Cu and Cd in the soil-rice system to soil properties revealed possible correlations between soil available silicon (Si) and the Cu and Cd contents in rice grain. The enrichment of Si in rice plants likely reduces the translocation of Cu and Cd from soil to grain. Therefore, management of the Si supply, particularly in lowland paddies, should be highlighted as a way to reduce dietary intake of Cu and Cd.

Characterization of Hydration Properties in Structural Ensembles of Biomolecules.

Solute-solvent interactions are critical for biomolecular stability and recognition. Explicit solvent molecular dynamics (MD) simulations are routinely used to probe such interactions. However, detailed analyses and interpretation of the hydration patterns seen in MD simulations can be both complex and time-consuming. A variety of approaches/tools to compute and interrogate hydration properties in structural ensembles of proteins, nucleic acids, or in general any molecule are available and are complemented here with a new and free software package ("JAL"). Central to "JAL" is an intuitive atom centric approach of computing hydration properties. In addition to the standard metrics commonly used to understand hydration, "JAL" introduces two nonstandard utilities: a program to rapidly compute buried waters in an MD trajectory and a new method to compute multiwater bridges around a solute. We demonstrate the utility of the package by probing the hydration characteristics of the tumor suppressor protein p53 and the translation initiation factor eif4E. "JAL" is hosted online and can be accessed for free at http://mspc.bii.a-star.edu.sg/minhn/jal.html .

Discovering Putative Protein Targets of Small Molecules: A Study of the p53 Activator Nutlin.

Small molecule drugs bind to a pocket in disease causing target proteins based on complementarity in shape and physicochemical properties. There is a likelihood that other proteins could have binding sites that are structurally similar to the target protein. Binding to these other proteins could alter their activities leading to off target effects of the drug. One such small molecule drug Nutlin binds the protein MDM2, which is upregulated in several types of cancer and is a negative regulator of the tumor suppressor protein p53. To investigate the off target effects of Nutlin, we present here a shape-based data mining effort. We extracted the binding pocket of Nutlin from the crystal structure of Nutlin bound MDM2. We next mined the protein structural database (PDB) for putative binding pockets in other human protein structures that were similar in shape to the Nutlin pocket in MDM2 using our topology-independent structural superimposition tool CLICK. We detected 49 proteins which have binding pockets that were structurally similar to the Nutlin binding site of MDM2. All of the potential complexes were evaluated using molecular mechanics and AutoDock Vina docking scores. Further, molecular dynamics simulations were carried out on four of the predicted Nutlin-protein complexes. The binding of Nutlin to one of these proteins, gamma glutamyl hydrolase, was also experimentally validated by a thermal shift assay. These findings provide a platform for identifying potential off-target effects of existing/new drugs and also opens the possibilities for repurposing drugs/ligands.

Women from racial or ethnic minority and low socioeconomic backgrounds receive more prenatal education: Results from the 2012 to 2014 Pregnancy Risk Assessment Monitoring System.

BACKGROUND: Racial or ethnic and socioeconomic disparities in adverse birth outcomes are well known, but few studies have examined disparities in the receipt of prenatal health education. The objectives of this study were to examine racial or ethnic and socioeconomic variations in receiving (1) comprehensive prenatal health education and (2) education about human immunodeficiency virus (HIV) testing, breastfeeding, alcohol, and smoking cessation from health care practitioners. METHODS: Data were drawn from the 2012 to 2014 Pregnancy Risk Assessment Monitoring System (PRAMS). Twenty-seven states were included with an analysis sample size of 68 025 participants. Receiving counseling on all listed health topics during prenatal care visits was denoted as comprehensive prenatal health education. Logistic regression was used to examine the association of racial or ethnic and socioeconomic variables with receiving comprehensive prenatal health education, and HIV testing, breastfeeding, alcohol, and smoking cessation advice separately. RESULTS: Multivariable results showed that racial or ethnic minorities and women with a high school degree or less; receiving Women, Infant, and Children (WIC) assistance; and on Medicaid during pregnancy have higher odds of receiving comprehensive prenatal health education (all P  ≤0 .001). Results were similar for receiving HIV testing, breastfeeding, alcohol, and smoking counseling. Low household income was associated with receiving counseling on HIV testing, alcohol, and smoking (all P ≤ 0.001). CONCLUSION: Despite reporting higher levels of prenatal health education on a variety of health-related topics, disadvantaged women continue to experience disparities in adverse birth outcomes suggesting that education is insufficient in promoting positive behaviors and birth outcomes.

Topology independent comparison of RNA 3D structures using the CLICK algorithm.

RNA molecules are attractive therapeutic targets because non-coding RNA molecules have increasingly been found to play key regulatory roles in the cell. Comparing and classifying RNA 3D structures yields unique insights into RNA evolution and function. With the rapid increase in the number of atomic-resolution RNA structures, it is crucial to have effective tools to classify RNA structures and to investigate them for structural similarities at different resolutions. We previously developed the algorithm CLICK to superimpose a pair of protein 3D structures by clique matching and 3D least squares fitting. In this study, we extend and optimize the CLICK algorithm to superimpose pairs of RNA 3D structures and RNA-protein complexes, independent of the associated topologies. Benchmarking Rclick on four different datasets showed that it is either comparable to or better than other structural alignment methods in terms of the extent of structural overlaps. Rclick also recognizes conformational changes between RNA structures and produces complementary alignments to maximize the extent of detectable similarity. Applying Rclick to study Ribonuclease III protein correctly aligned the RNA binding sites of RNAse III with its substrate. Rclick can be further extended to identify ligand-binding pockets in RNA. A web server is developed at http://mspc.bii.a-star.edu.sg/minhn/rclick.html.

Effect of polyDADMAC on aggregation of clay-size particles in red mud: Implications for immobilization practices.

PolyDADMAC (PD) is a high charge density cationic polymer of diallyldimethylammonium chloride which has been recently developed as a coagulant in water purification. As PD has high affinity to fine negatively-charged colloids, it is worth to ascertain if PD can affect surface properties of clay-size particles in red mud waste and be applied to develop immobilization techniques for red mud storage areas. In the current study, a test tube method in combination with surface charge measurement was used for determination of the colloidal properties of a red mud sample under the variation of PD, soluble Al and Si, and variable pH conditions. Observations for the PD concentration range from 0.25 to 2.0 mM revealed that PD can increase surface charge and enhance aggregation or at least shift the aggregation zone to higher pH. This suggests a possible application of PD for immobilization of red mud in alkaline condition. It was also found that soluble Al and Si acted to modify the effect of PD and aggregation properties of red mud. While soluble Si supported aggregation, Al appeared as an enhancer for dispersion of red mud. It implies that development of PD-based techniques for immobilization of red mud needs to consider the effects of soluble Al and Si.

Ecological model of school engagement and attention-deficit/hyperactivity disorder in school-aged children.

School engagement protects against negative mental health outcomes; however, few studies examined the relationship between school engagement and attention-deficit hyperactivity disorder (ADHD) using an ecological framework. The aims were to examine: (1) whether school engagement has an independent protective association against the risk of ADHD in children, and (2) whether environmental factors have an association with ADHD either directly or indirectly via their association with school engagement. This cross-sectional study used data from the 2011-2012 National Survey of Children's Health, which collected information about children's mental health, family life, school, and community. The sample contained 65,680 children aged 6-17 years. Structural equation modeling was used to estimate the direct association of school engagement and ADHD and indirect associations of latent environmental variables (e.g., family socioeconomic status (SES), adverse childhood experiences (ACEs), environmental safety, and neighborhood amenities) and ADHD. School engagement had a direct and inverse relationship with ADHD (ß = - 0.35, p < 0.001) such that an increase in school engagement corresponds with a decrease in ADHD diagnosis. In addition, family SES (ß = - 0.03, p = 0.002), ACEs (ß = 0.10, p < 0.001), environment safety (ß = - 0.10, p < 0.001), and neighborhood amenities (ß = - 0.01, p = 0.025) all had an indirect association with ADHD via school engagement. In conclusion, school engagement had a direct association with ADHD. Furthermore, environmental correlates showed indirect associations with ADHD via school engagement. School programs targeted at reducing ADHD should consider family and community factors in their interventions.

Copper encapsulated in grass-derived phytoliths: Characterization, dissolution properties and the relation of content to soil properties.

The formation of phytoliths as a result of the precipitation of Si in many Si-rich plant species is known to encapsulate organic matter. This work aims to examine the possible encapsulation of Cu in grass phytoliths in an orange growing area, where Cu-rich fungicides have been excessively applied. Batch experiments, in combination with SEM-EDS and microscopy, were conducted for the grass-derived phytoliths and phytoliths separated from soil, thus revealing their dissolution properties, morphotypes and contents, in relation to soil properties. By measuring the Cu release accompanying the dissolution of phytoliths by different extractants, especially an Na2CO3/HNO3 solution, it was revealed that Cu was encapsulated within the silica body of the phytolith. This sink of Cu in the grass can be cycled to serve as a new Cu source in soils. Phytolith contents in the soil were up to 17.7 g kg-1 and tended to accumulate in soil depths from 0 to 20 cm. A positive correlation was found for soil phytolith and phytCu contents and may be indicative of the role of phytoliths as an enhancer of Cu accumulation in soil. It would be worth developing suitable techniques for the determination of phytCu, because common extraction/digestion methods are not suited for evaluating this Cu pool.

Structural analysis of protein tyrosine phosphatase 1B reveals potentially druggable allosteric binding sites.

Catalytic proteins such as human protein tyrosine phosphatase 1B (PTP1B), with conserved and highly polar active sites, warrant the discovery of druggable nonactive sites, such as allosteric sites, and potentially, therapeutic small molecules that can bind to these sites. Catalyzing the dephosphorylation of numerous substrates, PTP1B is physiologically important in intracellular signal transduction pathways in diverse cell types and tissues. Aberrant PTP1B is associated with obesity, diabetes, cancers, and neurodegenerative disorders. Utilizing clustering methods (based on root mean square deviation, principal component analysis, nonnegative matrix factorization, and independent component analysis), we have examined multiple PTP1B structures. Using the resulting representative structures in different conformational states, we determined consensus clustroids and used them to identify both known and novel binding sites, some of which are potentially allosteric. We report several lead compounds that could potentially bind to the novel PTP1B binding sites and can be further optimized. Considering the possibility for drug repurposing, we discovered homologous binding sites in other proteins, with ligands that could potentially bind to the novel PTP1B binding sites.

The interfacial character of antibody paratopes: analysis of antibody-antigen structures.

SUMMARY: In this study, computational methods are applied to investigate the general properties of antigen engaging residues of a paratope from a non-redundant dataset of 403 antibody-antigen complexes to dissect the contribution of hydrogen bonds, hydrophobic, van der Waals contacts and ionic interactions, as well as role of water molecules in the antigen-antibody interface. Consistent with previous reports using smaller datasets, we found that Tyr, Trp, Ser, Asn, Asp, Thr, Arg, Gly, His contribute substantially to the interactions between antibody and antigen. Furthermore, antibody-antigen interactions can be mediated by interfacial waters. However, there is no reported comprehensive analysis for a large number of structured waters that engage in higher ordered structures at the antibody-antigen interface. From our dataset, we have found the presence of interfacial waters in 242 complexes. We present evidence that suggests a compelling role of these interfacial waters in interactions of antibodies with a range of antigens differing in shape complementarity. Finally, we carry out 296 835 pairwise 3D structure comparisons of 771 structures of contact residues of antibodies with their interfacial water molecules from our dataset using CLICK method. A heuristic clustering algorithm is used to obtain unique structural similarities, and found to separate into 368 different clusters. These clusters are used to identify structural motifs of contact residues of antibodies for epitope binding. AVAILABILITY AND IMPLEMENTATION: This clustering database of contact residues is freely accessible at http://mspc.bii.a-star.edu.sg/minhn/pclick.html. CONTACT: minhn@bii.a-star.edu.sg, chandra@bii.a-star.edu.sg or zhong_pingyu@immunol.a-star.edu.sg. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Discovery of Rab1 binding sites using an ensemble of clustering methods.

Targeting non-native-ligand binding sites for potential investigative and therapeutic applications is an attractive strategy in proteins that share common native ligands, as in Rab1 protein. Rab1 is a subfamily member of Rab proteins, which are members of Ras GTPase superfamily. All Ras GTPase superfamily members bind to native ligands GTP and GDP, that switch on and off the proteins, respectively. Rab1 is physiologically essential for autophagy and transport between endoplasmic reticulum and Golgi apparatus. Pathologically, Rab1 is implicated in human cancers, a neurodegenerative disease, cardiomyopathy, and bacteria-caused infectious diseases. We have performed structural analyses on Rab1 protein using a unique ensemble of clustering methods, including multi-step principal component analysis, non-negative matrix factorization, and independent component analysis, to better identify representative Rab1 proteins than the application of a single clustering method alone does. We then used the identified representative Rab1 structures, resolved in multiple ligand states, to map their known and novel binding sites. We report here at least a novel binding site on Rab1, involving Rab1-specific residues that could be further explored for the rational design and development of investigative probes and/or therapeutic small molecules against the Rab1 protein. Proteins 2017; 85:859-871. © 2016 Wiley Periodicals, Inc.

Rclick: a web server for comparison of RNA 3D structures.

RNA molecules play important roles in key biological processes in the cell and are becoming attractive for developing therapeutic applications. Since the function of RNA depends on its structure and dynamics, comparing and classifying the RNA 3D structures is of crucial importance to molecular biology. In this study, we have developed Rclick, a web server that is capable of superimposing RNA 3D structures by using clique matching and 3D least-squares fitting. Our server Rclick has been benchmarked and compared with other popular servers and methods for RNA structural alignments. In most cases, Rclick alignments were better in terms of structure overlap. Our server also recognizes conformational changes between structures. For this purpose, the server produces complementary alignments to maximize the extent of detectable similarity. Various examples showcase the utility of our web server for comparison of RNA, RNA-protein complexes and RNA-ligand structures.