Investigation of surface properties of amino acids: polarity scale for amino acids as a means to predict surface exposed residues in films of proteins

PseAraUbi: predicting arabidopsis ubiquitination sites by incorporating the physico-chemical and structural features

We makes three kinds of important features from Arabidopsis thaliana: protein secondary structure based on the Chou-Fasman parameter, amino acids hydrophobicity and polarity information, and analyze their properties. Ubiquitination modification is an important post-translational modification of proteins, which participates in the regulation of many important life activities in cells. At present, ubiquitination proteomics research is mostly concentrated in animals and yeasts, while relatively few studies have been carried out in plants. It can be said that the calculation and prediction of Arabidopsis thaliana ubiquitination sites is still in its infancy. Based on this, we describe a calculation method, PseAraUbi (Prediction of Arabidopsis thaliana ubiquitination sites using pseudo amino acid composition), that can effectively detect ubiquitination sites on Arabidopsis thaliana using support vector machine learning classifiers. Based on protein sequence information, extract features from the Chou-Fasman parameter, amino acids hydrophobicity features, polarity information and selected for classification with the Boruta algorithm. PseAraUbi achieves promising performances with an AUC score of 0.953 with fivefold cross-validation on the training dataset, which are significantly better than that of the pioneer Arabidopsis thaliana ubiquitination sites method. We also proved the ability of our proposed method on independent test sets, thus gaining a competitive advantage. In addition, we also in-depth analyzed the physicochemical properties of amino acids in the region adjacent to the ubiquitination site. To facilitate the community, the source code, optimal feature subset, ubiquitination sites dataset in the Arbidopsis proteome are available at GitHub ( https://github.com/HNUBioinformatics/PseAraUbi.git ) for interest users.

Exploring the structure and stability of amino acids and glycine peptides in biocompatible ionic liquids

Amino acids (AAs) are vital components for a variety of biological systems and can be linked through covalent bonds (or peptide bonds) to form a protein structure.

Understanding the mechanism of replacement of citrate from the surface of gold nanoparticles by amino acids: a theoretical and experimental investigation and their biological application

The present study explores the physicochemical aspects needed for the appropriate in vitro synthesis and surface modification behavior of gold nanoparticles (AuNPs) in the presence of amino acids (AA).

Variants of CEP68 gene are associated with acute urticaria/angioedema induced by multiple non-steroidal anti-inflammatory drugs

Non-steroidal anti-inflammatory drugs (NSAIDs) are the most consumed drugs worldwide because of their efficacy and utility in the treatment of pain and inflammatory diseases. However, they are also responsible for an important number of adverse effects including hypersensitivity reactions. The most important group of these reactions is triggered by non-immunological, pharmacological mechanisms catalogued under the denomination of cross-intolerance (CRI), with acute urticaria/angioedema induced by multiple NSAIDs (MNSAID-UA) the most frequently associated clinical entity. A recent genome-wide association study identified the gene encoding the centrosomal protein of 68 KDa (CEP68) as the major locus associated with aspirin intolerance susceptibility in asthmatics. In this study, we aimed to assess the role of this locus in susceptibility to CRI to NSAIDs by examining 53 common gene variants in a total of 635 patients that were classified as MNSAID-UA (n = 399), airway exacerbations (n = 110) or blended pattern (n = 126), and 425 controls. We found in the MNSAID-UA group a number of variants (17) associated (lowest p-value = 1.13×10⁻⁶), including the non-synonymous Gly74Ser variant (rs7572857) previously associated with aspirin intolerance susceptibility in asthmatics. Although not being significant in the context of multiple testing, eight of these variants were also associated with exacerbated respiratory disease or blended reactions. Our results suggest that CEP68 gene variants may play an important role in MNSAID-UA susceptibility and, despite the different regulatory mechanisms involved depending on the specific affected organ, in the development of hypersensitivity reactions to NSAIDs.

Evaluation of hydropathy of amino acids from a comparison of their viscosities inside vesicles and on supported lipid bilayers

The viscosity of amino acids enclosed in giant lipid vesicles (η(out)) subjected to a shear flow near a solid surface has been studied using quartz crystal microbalance (QCM). This viscosity has been compared with shear viscosity for the different amino acids adsorbed on supported bilayers (SLBs) (η(in)) of the lipids on quartz. Using a first approximation of vesicles as model rigid spheres, the measured viscosities and the extent of deformation of vesicles observed using optical microscopy, two non-dimensional parameters: the reduced volume and the ratio of (η(in))/(η(out)) have been analyzed as a function of physical parameters: vesicle substrate distance (vesicle vs. supported lipid bilayers), vesicle size and their variation as a function of the viscosity. The kinematics of the vesicles with the amino acids compared with the shear at supported lipid bilayers seems to describe a reasonable hydropathy scale for the amino acids. The results show that there is a direct correlation between the above parameters and the polarity variations in amino acids suggesting that the viscous force may be an important parameter and should be taken into account in studies on membrane proteins interacting with cells and cell adhesion in flow chambers where cell membrane and the adhesive substrate are in relative motion.

Genome-wide and follow-up studies identify CEP68 gene variants associated with risk of aspirin-intolerant asthma

Aspirin-intolerant asthma (AIA) is a rare condition that is characterized by the development of bronchoconstriction in asthmatic patients after ingestion of non-steroidal anti-inflammatory drugs including aspirin. However, the underlying mechanisms of AIA occurrence are still not fully understood. To identify the genetic variations associated with aspirin intolerance in asthmatics, the first stage of genome-wide association study with 109,365 single nucleotide polymorphisms (SNPs) was undertaken in a Korean AIA (n = 80) cohort and aspirin-tolerant asthma (ATA, n = 100) subjects as controls. For the second stage of follow-up study, 150 common SNPs from 11 candidate genes were genotyped in 163 AIA patients including intermediate AIA (AIA-I) subjects and 429 ATA controls. Among 11 candidate genes, multivariate logistic analyses showed that SNPs of CEP68 gene showed the most significant association with aspirin intolerance (P values of co-dominant for CEP68, 6.0×10⁻⁵ to 4.0×10⁻⁵). All seven SNPs of the CEP68 gene showed linkage disequilibrium (LD), and the haplotype of CEP68_ht4 (T-G-A-A-A-C-G) showed a highly significant association with aspirin intolerance (OR  = 2.63; 95% CI  = 1.64–4.21; P = 6.0×10⁻⁵). Moreover, the nonsynonymous CEP68 rs7572857G>A variant that replaces glycine with serine showed a higher decline of forced expiratory volume in 1s (FEV₁) by aspirin provocation than other variants (P = 3.0×10⁻⁵). Our findings imply that CEP68 could be a susceptible gene for aspirin intolerance in asthmatics, suggesting that the nonsynonymous Gly74Ser could affect the polarity of the protein structure.

Do properties of bovine serum albumin at fluid/electrolyte interface follow the Hofmeister series?—An analysis using Langmuir and Langmuir–Blodgett films

Folding and solubility of proteins are dependent on their state of hydration. How does a protein-bovine serum albumin (BSA) behave in the presence of Hofmeister electrolytes, especially at interfaces? Langmuir films of bovine serum albumin (BSA) in the presence of different Hofmeister electrolytes at air/solution interface and as Langmuir-Blodgett films (LB films) at solid/solution interface have been studied using the surface pressure-molecular area (pi-A) isotherms and surface energy parameters. Changes in secondary structure have been analyzed using circular dichroism (CD) and fluorescence spectroscopy. Hydrodynamically coupled water fraction of BSA in different environments has been estimated using quartz crystal microbalance (QCM) and related to the secondary structural changes. Molecular modeling of BSA in different environments showed that the protein has a compact structure at the interface compared to vacuum. The contact areas estimated using molecular modeling agreed with the experimental results. The results show that the properties of BSA at the interface follow the Hofmeister series with NaF leading to maximum compaction in the protein. Further, in addition to ion specific solvation and different ion size, water structure alteration and the bound water fractions contribute importantly to the Hofmeister effect.

Structural influence of mono and polyhydric alcohols on the stabilization of collagen

In the present study, solvents effects on the structure of collagen have been examined by circular dichroism and their interfacial tension at glass/liquid and Teflon/liquid. Changes in the conformations of the protein have been analyzed after equilibration with aqueous solutions of monohydric and polyhydric alcohols like methanol, ethanol, n-propanol, propane-2-diol and glycerol. The results from viscosity and Circular dichroism (CD) spectra suggest a clear distinction in the structural changes for collagen with monohydric alcohols as against polyhydric ones. The surface tension and interfacial tension at glass (high surface energy, HFSE) and Teflon (Low surface energy, LSFE) reflect similar differences between the monohydric and polyhydric alcohols. Studies on the interfacial energy of the adsorbed protein at glass/solution interface compared to that of Teflon/solution interface show that the water structure near glass gets perturbed leading to an increase in the average free energy of the bulk water phase and a reduction in hydrophobic effect near the glass. The results suggest that the different solvents alter the hydrophobic effect on the hydrated protein to different extent and thus influence folding equilibrium of the protein without directly interacting with it. Polyhydric alcohols seem to favor the native collagen structure while monohydric alcohols enhance it.

Solid–liquid interfacial energy as a tool to estimate shifts in isoelectric points of adsorbed proteins on solid surfaces

This work reports the estimation of isoelectric points (pIs) of adsorbed amino acids and proteins on solid surfaces in the pH range between 3.5-11.0 from a measurement of solid/liquid interfacial energy. The values thus obtained are compared with the pIs determined in solution phase by other methods. Both glass and Teflon have been chosen as model solid surfaces. Close agreement between the reference pI values, obtained by the capillary isoelectric focusing and those obtained at solid/liquid interface is observed within an average difference of 0.04-0.08 pH unit when the pIs are above the pI of glass. For systems whose pIs are far away from that of glass (either in the acidic or highly alkaline range), a large shift in the isoelectric point is observed. In case of Teflon the pIs are closer to the reported values than at glass/liquid interface. This could be due to the fact that Teflon being a hydrophobic surface, its surface is dominated by dispersive forces, which may not be seriously affected by pH changes. The shift in the values at solid/liquid interface compared to that in solution have been examined using an 'image charge approach.'