Hydrophobicity Distribution Research Articles

New insights on the catalytic center of proteins from peptidylprolyl isomerase group based on the FOD-M model.

Generating the structure of the hydrophobic core is based on the orientation of hydrophobic residues towards the central part of the protein molecule with the simultaneous exposure of polar residues. Such a course of the protein folding process takes place with the active participation of the polar water environment. While the self-assembly process leading to the formation of micelles concerns freely moving bi-polar molecules, bipolar amino acids in polypeptide chain have limited mobility due to the covalent bonds. Therefore, proteins form a more or less perfect micelle-like structure. The criterion is the hydrophobicity distribution, which to a greater or lesser extent reproduces the distribution expressed by the 3D Gaussian function on the protein body. The vast majority of proteins must ensure solubility, so a certain part of it-as it is expected-should reproduce the structuring of micelles. The biological activity of proteins is encoded in the part that does not reproduce the micelle-like system. The location and quantitative assessment of the contribution of orderliness to disorder is of critical importance for the determination of biological activity. The form of maladjustment to the 3D Gauss function may be varied-hence the obtained high diversity of specific interactions with strictly defined molecules: ligands or substrates. The correctness of this interpretation was verified on the basis of the group of enzymes Peptidylprolyl isomerase-E.C.5.2.1.8. In proteins representing this class of enzymes, zones responsible for solubility-micelle-like hydrophobicity system-the location and specificity of the incompatible part in which the specific activity of the enzyme is located and coded were identified. The present study showed that the enzymes of the discussed group show two different schemes of the structure of catalytic center (taking into account the status as defined by the fuzzy oil drop model).

Structural Specificity of Polymorphic Forms of α-Synuclein Amyloid.

The structural transformation producing amyloids is a phenomenon that sheds new light on the protein folding problem. The analysis of the polymorphic structures of the α-synuclein amyloid available in the PDB database allows analysis of the amyloid-oriented structural transformation itself, but also the protein folding process as such. The polymorphic amyloid structures of α-synuclein analyzed employing the hydrophobicity distribution (fuzzy oil drop model) reveal a differentiation with a dominant distribution consistent with the micelle-like system (hydrophobic core with polar shell). This type of ordering of the hydrophobicity distribution covers the entire spectrum from the example with all three structural units (single chain, proto-fibril, super-fibril) exhibiting micelle-like form, through gradually emerging examples of local disorder, to structures with an extremely different structuring pattern. The water environment directing protein structures towards the generation of ribbon micelle-like structures (concentration of hydrophobic residues in the center of the molecule forming a hydrophobic core with the exposure of polar residues on the surface) also plays a role in the amyloid forms of α-synuclein. The polymorphic forms of α-synuclein reveal local structural differentiation with a common tendency to accept the micelle-like structuralization in certain common fragments of the polypeptide chain of this protein.

Sorption Characteristics and Site Energy Distribution Theory of Typical Estrogens on Microplastics

Microplastics (MPs) and estrogens are high-profile emerging contaminants at present, and MPs might become the carrier of estrogens in the environment and induce combined pollution. To study the adsorption behavior of polyethylene (PE) microplastics to typical estrogens, the adsorption isothermal properties of the six estrogens[estrone (E1), 17α-estradiol (17α-E2), 17β-estradiol (17β-E2), estriol (E3), diethylstilbestrol (DES), and ethinylestradiol (17α-EE2)] in single-solute and mixed-solute systems were studied through batch equilibrium adsorption experiments, in which the PE microplastics before and after adsorption were characterized by X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR). Then, the site energy distribution theory of the adsorption of six estrogens on PE microplastics was further analyzed based on the Freundlich model. The results showed that the adsorption process of selected estrogens with two concentrations (100 μg·L-1 and 1000 μg·L-1) on PE were more consistent with the pseudo-second order kinetic model. The increase in initial concentration reduced the equilibrium time of adsorption and increased the adsorbing capacity of estrogens on PE. In the single system (one estrogen) or mixed system (six estrogens) with different concentrations (10 μg·L-1-2000 μg·L-1), the Freundlich model showed the best fitting effect for the adsorption isotherm data (R2>0.94). The results of isothermal adsorption experiments and XPS and FTIR spectra showed that the adsorption of estrogens on PE in the two systems was heterogeneous adsorption, and hydrophobic distribution and van der Waals forces were the principal factors in the process of adsorption. The occurrence of C-O-C (in only the DES and 17α-EE2 systems) and O-C[FY=,1]O (in only the 17α-EE2 system) indicated that the adsorption of synthetic estrogens on PE was affected slightly by chemical bonding function, but no obvious effects were observed for natural estrogens. The results of site energy distribution analysis showed that, compared with the single system, the adsorption site energy of each estrogen shifted to the high-energy region in its entirety in the mixed system, and the site energy increased by 2.15%-40.98%. The energy change in DES was the most significant among all of the estrogens, indicating its competitive advantage in the mixed system. The above results of this study can provide some reference for the study of adsorption behavior, mechanism of action, and environmental risks under the coexisting condition of organic pollutants and MPs.

Programming Aggregate States of DNA Nanorods with Sub-10 nm Hydrophobic Patterns for Tunable Cell Entry.

The intracellular application of DNA nanodevices is challenged by their inadequate cellular entry efficiency, which may be addressed by the development of amphiphilic DNA nanostructures. However, the impact of the spatial distribution of hydrophobicity in cell entry has not been fully explored. Here, we program a spectrum of amphiphilic DNA nanostructures displaying diverse sub-10 nm patterns of cholesterol, which result in distinct aggregate states in the aqueous solution and thus varied cell entry efficiencies. We find that the hydrophobic patterns can lead to discrete aggregate states, from monomers to low-number oligomers (n = 1-6). We demonstrate that the monomers or oligomers with moderate hydrophobic density are preferred for cell entry, with up to ∼174-fold improvement relative to unmodified ones. Our study provides a new clue for the rational design of amphiphilic DNA nanostructures for intracellular applications.

Insights into adsorption mechanisms of nitro polycyclic aromatic hydrocarbons on common microplastic particles: Experimental studies and modeling

Nitro polycyclic aromatic hydrocarbons (NPAHs) and microplastics (MPs) are emerging contaminants that pose a threat to the aquatic ecosystem. Knowledge of the NPAHs and MPs interaction will help the understanding of their fate and risks in natural environment. Here, the adsorption behavior and mechanism of typical NPAHs on microplastics were investigated. The adsorption kinetic and isotherm data showed that the adsorption of NPAHs was controlled by chemical adsorption and hydrophobic partition, because of excellent fit of kinetic and isothermal equations (R2 > 0.9). The adsorption capacity (587–744 μg g−1) was largely dependent on the hydrophobicity of NPAHs. The experiment of environmental factors confirmed the important role of pollutant hydrophobicity, with 1-Npyr of the highest hydrophobicity having the greatest adsorption on MPs (adsorption rate >90%) and less affected by solution pH and ionic strength (changer <5%). In the mixture system, MPs displayed high adsorption capacity for each compound; Interestingly, because compounds with smaller size were easy to occupy the adsorption sites in the pores of MPs, the adsorption of 2-Nflu (724 μg g−1) was even greater than that of 9-Nant (713 μg g−1) and 1-Npyr (703 μg g−1). The model calculation of adsorption also shows that there is surface adsorption and hydrophobic distribution in the adsorption process. The findings provide new insights into the interactions of MPs with organic pollutants in complex environments.

The Contribution of Hydrophobic Interactions to Conformational Changes of Inward/Outward Transmembrane Transport Proteins.

Proteins transporting ions or other molecules across the membrane, whose proper concentration is required to maintain homeostasis, perform very sophisticated biological functions. The symport and antiport active transport can be performed only by the structures specially prepared for this purpose. In the present work, such structures in both In and Out conformations have been analyzed with respect to the hydrophobicity distribution using the FOD-M model. This allowed for identifying the role of individual protein chain fragments in the stabilization of the specific cell membrane environment as well as the contribution of hydrophobic interactions to the conformational changes between In/Out conformations.

Computational and comparative investigation of hydrophobic profile of spike protein of SARS-CoV-2 and SARS-CoV.

The hydrophobic force is one of the most dominant factorsin protein folding. A protein becomes functional only when it achieves its three-dimensional structure and stability upon folding. For a better understanding of the hydrophobic effects and their function in protein folding, quantitative measurement of the hydrophobicity of amino acid side chains is crucial. Spike protein is the primary structural protein in SARS-CoV-2 and SARS-CoV. This study explores how protein sequences in SARS-CoV-2 and SARS-CoV spike proteins encode hydrophobic interactions. Computational tools/techniques have been utilized to investigate the protein sequences of the spike proteins of SARS-CoV-2 and SARS-CoV. Investigations provided an estimate of hydrophobic distribution and its relative strength, indicating a hydrophobic pattern. Analysis of the spike protein's hydrophobic profile may help identify and treat the virus-caused disease; additionally, it can give an insight into the transmissibility and pathogenicity of the virus.

Disordered regions endow structural flexibility to shell proteins and function towards shell–enzyme interactions in 1,2-propanediol utilization microcompartment

Intrinsically disordered regions in proteins have been functionally linked to the protein–protein interactions and genesis of several membraneless organelles. Depending on their residual makeup, hydrophobicity or charge distribution they may remain in extended form or may assume certain conformations upon biding to a partner protein or peptide. The present work investigates the distribution and potential roles of disordered regions in the integral proteins of 1,2-propanediol utilization microcompartments. We use bioinformatics tools to identify the probable disordered regions in the shell proteins and enzyme of the 1,2-propanediol utilization microcompartment. Using a combination of computational modelling and biochemical techniques we elucidate the role of disordered terminal regions of a major shell protein and enzyme. Our findings throw light on the importance of disordered regions in the self-assembly, providing flexibility to shell protein and mediating its interaction with a native enzyme. Communicated by Ramaswamy H. Sarma

Effect of Aging on Adsorption of Tetracycline by Microplastics and the Mechanisms

As new pollutants, microplastics (MPs) can adsorb antibiotics in the water environment and migrate together as carriers. However, microplastics will age continuously in the environment, and their adsorption capacity and adsorption mechanism will change accordingly. With polyethylene (PE) and polystyrene (PS) as the target MPs, which were irradiated by ultraviolet (UV-254), the changes in the physical and chemical properties of MPs before and after aging, such as the color, surface morphology, and functional groups, were compared, and their effects on the adsorption of tetracycline (TC) as well as the related mechanism were explored. The results showed that the pseudo-second-order model could better fit the adsorption process, the adsorption equilibrium was reached within 24 hours, the adsorption capacity of aged MPs for TC was significantly higher than that of original MPs, and the adsorption capacity of PS was higher than that of PE. Langmuir and Freundlich isothermal adsorption equations could both describe the adsorption isothermal test data, and the adsorption of TC on MPs was a spontaneous and endothermic physical adsorption process, whereas aging had no obvious effect on the adsorption thermodynamic characteristics of MPs. With the increase in pH value, the adsorption capacity first increased and then decreased. The maximum adsorption capacity of MPs before and after aging was reached at pH=5. UV aging increased the specific surface area of MPs, generating oxygen-containing functional groups such as -C＝O, -OH, and O＝C＝O, changing the physical and chemical properties of MPs, and thus changing the adsorption mechanism of MPs for TC. Compared with the original PE MPs, in addition to hydrophobic distribution, van der Waals forces, and electrostatic interactions, pore filling was also an important adsorption mechanism of aged PE. The main adsorption mechanisms of original PS microplastics were hydrophobic distribution, van der Waals forces, electrostatic interaction, and π-π interaction, whereas there was hydrogen bonding for aged PS.

Influence of AC corona discharge on the hydrophobicity of silicone rubber surface in high-speed airflow environment

Corona discharge is one of the key factors that lead to the hydrophobicity loss of silicone rubber insulators used on the roof of high-speed trains. Based on the artificial experimental wind-tunnel platform, influences of AC corona intensity and airflow velocity on the hydrophobicity distribution of the silicone rubber surface were studied. According to the corona discharge phenomena and measured discharge current, influences of airflow velocity and voltage on the characteristics of corona discharge in a high-speed airflow environment were discussed. Results reveal that the hydrophobicity distribution on the silicone rubber surface shifts along the airflow direction in the high-speed airflow environment when the voltage is relatively high. When ionization zone develops to the needle-plate gap, the discharge path is deflected to the direction of airflow, which is responsible for the change of the hydrophobicity distribution. It is notable that the deflection distance decreases with the increase of airflow velocity. This is attributed to the fact that the electrons with variable horizontal distance from the electron to the plate electrode center are subjected to different electric field forces, resulting in different influences of high-speed airflow on them. These results are of engineering and theoretical significance for insulators used in high-speed railways.

Study on moisture migration mechanism of dough during subfreezing storage

AbstractBackground and ObjectivesThe objective of this study was to investigate the effects of subfreezing storage on gluten protein denaturation and water retention. On this basis, the surface hydrophobicity, secondary structure, thermal stability, microstructure, and moisture distribution of gluten protein were measured.FindingsThe results showed that at the end of storage, the hydrophobicity indexes of wheat gluten proteins (−9°C and −12°C) stored under subfreezing conditions were significantly lower than those stored at 4°C and slightly lower than those stored at −18°C. The secondary structure stability of wheat gluten stored at −18°C was similar. P21 stored at −18°C was significantly higher than those stored at 4°C and showed an upward trend. The quality of the dough was similar to those stored at −18°C.ConclusionsThe deformation and water retention of gluten during subfreezing storage are similar to those stored at −18°C.Significance and NoveltyThe changes in dough moisture and gluten protein structure during frozen storage at different freezing temperatures were explored to provide a theoretical basis for the application of subfrozen storage in the frozen flour products industry.

Transmembrane peptide effects on bacterial membrane integrity and organization

As the bacterial multidrug resistance crisis continues, membrane-active antimicrobial peptides are being explored as an alternate treatment to conventional antibiotics. In contrast to antimicrobial peptides, which function by a nonspecific membrane disruption mechanism, here we describe a series of transmembrane (TM) peptides that are designed to act as drug efflux inhibitors by aligning with and out-competing a conserved TM4-TM4 homodimerization motif within bacterial small multidrug resistance proteins. The peptides contain two terminal tags: a C-terminal lysine tag to direct the peptides toward the negatively charged bacterial membrane, and an uncharged N-terminal sarcosine (N-methyl-glycine) tag to promote membrane insertion. While effective at inhibiting efflux activity, ostensibly through their designed mechanism of action, the impact of the peptides on the bacterial inner membrane remains undetermined. To evaluate the extant peptide-membrane interactions, we performed a series of biophysical measurements. Circular dichroism spectroscopy and Trp fluorescence showed that the peptides insert into the membrane generally in helical form. Interestingly, differential scanning calorimetry of the peptides added to bacterial-like membranes (POPE:POPG 3:1) revealed the peptides’ ability to demix the POPE and POPG lipids, creating two pools, one of which is likely a peptide-POPG conglomerate, and the other a POPE-rich component where the native POPG content has been depleted. However, dye leakage assays confirmed that these events occur without causing significant membrane disruption both in vitro and in vivo, indicating that the peptides can target the small multidrug resistance TM4-TM4 motif without nonspecific membrane disruption. In related studies, DiOC2(3) fluorescence indicated moderate peptide-mediated reduction of the proton motive force for all peptides, including control peptides that did not display inhibitory activity. The overall findings suggest that peptides designed with suitable tags, sequence hydrophobicity, and charge distribution can be directed more generally to impact proteins whose function involves membrane-embedded protein-protein interactions.

Prediction of polarity-dependent environmental behaviors of humic substances (HS) using a HS hydrophobicity index based on hydrophilic interaction chromatography

A variety of analytical methods have been applied to describe the properties of aquatic humic substances (HS). However, there are only a few methods available to probe HS hydrophobicity because of the heterogeneous character of HS. In this study, hydrophilic interaction chromatography (HILIC) equipped with a UV detector was employed to describe the heterogeneous distribution of HS with respect to its hydrophobicity and to suggest a representative HS hydrophobicity index. To this end, various mobile phases were explored to achieve the optimal separation capability of HILIC. The highest resolution was obtained with a mobile phase comprising acetonitrile and water at a ratio of 70:30 (v:v). A calibration curve was successfully constructed using eight different HS precursor compounds, which allowed for the successful conversion of the retention time (RT) into the octanol-water partition coefficient (Kow) (log Kow = −2.83 × (RT) + 17.44, R2 = 0.950). Several possible HS hydrophobicity indices were derived from the HILIC chromatogram. Among those, the weight-average log KOW value exhibited the strongest negative correlation with the well-known polarity index, (O + N)/C ratios, of seven reference HS samples. This new HILIC-based index (i.e., average log KOW) also presented a good relationship with the HS binding coefficients with pyrene as well as the extent of HS adsorption onto kaolinite at a given solution chemistry (i.e., at a high ionic strength and a neutral pH), both of which are known to be largely governed by the hydrophobic nature of HS. This study demonstrated that the average KOW value based on HILIC is an intuitive and robust HS hydrophobicity index to fully represent the heterogeneous distribution of hydrophobicity within a bulk HS and could be applied to predict many environmental behaviors related to HS hydrophobicity or HS polarity.

Connexins and Pannexins-Similarities and Differences According to the FOD-M Model.

Connexins and pannexins are the transmembrane proteins of highly distinguished biological activity in the form of transport of molecules and electrical signals. Their common role is to connect the external environment with the cytoplasm of the cell, while connexin is also able to link two cells together allowing the transport from one to another. The analysis presented here aims to identify the similarities and differences between connexin and pannexin. As a comparative criterion, the hydrophobicity distribution in the structure of the discussed proteins was used. The comparative analysis is carried out with the use of a mathematical model, the FOD-M model (fuzzy oil drop model in its Modified version) expressing the specificity of the membrane’s external field, which in the case of the discussed proteins is significantly different from the external field for globular proteins in the polar environment of water. The characteristics of the external force field influence the structure of protein allowing the activity in a different environment.

Characterization and Analysis of Acetaldehyde Wastewater by Molecular Weight Distribution, Hydrophilicity, and Chemical Composition

Acetaldehyde is a typical toxic substance of the petrochemical industry. Dissolved organic carbon (DOC) plays an important role in wastewater treatment. Therefore, the molecular weight, hydrophilicity, and chemical composition of DOC in acetaldehyde wastewater were evaluated. First, the molecular weight (MW) distribution was investigated; the results showed that acetaldehyde wastewater was mainly composed of components with a MW less than 1 kDa, and possessed higher proportion of protein-like substances that were dominant contributors to membrane fouling. Then, the distribution of hydrophobicity was evaluated; hydrophobic bases were reported to be slowly biodegradable fractions due to the high humic content. Finally, gas chromatography–mass spectrometry (GC-MS) was utilized to determine chemical composition, and 30 pollutants were detected. Aldehydes, hydrocarbons, ketones, alcohols, furans, phenols, and organic acids were the dominant pollutants. Most of them were moderately toxic compounds. The comprehensive characterization of acetaldehyde wastewater will contribute to control strategies and sustainable development.

Changes in Biochemical Properties and Activity of Trypsin-like Protease (Litopenaeus vannamei) Treated by Atmospheric Cold Plasma (ACP).

The changes in the functional properties of trypsin from shrimps (Litopenaeus vannamei) after, Atmospheric Cold Plasma (ACP) treatments, have been evaluated in terms of enzyme inactivation, surface hydrophobicity, secondary structure, fluorescence intensity, and particle size distribution. Different exposure voltages of 10, 20, 30, 40, and 50 kV at various treatment times (1, 2, 3, and 4 min) have been employed, in a separate assay. The results showed that trypsin-like protease activity decreased (by about 50%), and the kinetic constants Km value increased, while the kcat value decreased. Surface hydrophobicity and fluorescence intensity revealed a significant increase compared to the control sample. A high degree of protein degradation has been noticed by SDS-PAGE analysis. In addition, circular dichroism indicated that random coil and α-helix contents declined while β-turn and β-sheet contents have raised. A sharp drop in the particle size was observed with increasing the treatment voltage from 0 to 40 kV for 4 min, and the corresponding peak reached the minimum of 531.2 nm. Summing up the results, it can be concluded that the ACP technique effectively affects the activity of trypsin-like protease, which in terms enhances the quality of dietary protein.

CICLOP: a robust and accurate computational framework for protein inner cavity detection

Abstract Motivation Internal cavities in proteins are of critical functional importance. They can serve as substrate/ligand-binding sites, pave path for movement of biomolecules and even mediate structural conformations occurring between domain interfaces during structural transitions. Yet, there is a paucity of computational tools that can accurately and reliably characterize the inner cavities of the proteins, a prerequisite for elucidating their functions. Results We have developed a novel method, CICLOP, that can accurately identify these regions at an atomistic resolution. The method is able to accurately detect residues lining the inner cavity, the diameter and volume occupied by the cavity, as well as physico-chemical properties of residues lining the cavity, such as their hydrophobicity and secondary structure distribution in detail. Additionally, our method also provides an option for computing conservation scores for the residues detected on the inside, allowing for a thorough functional characterization of the cavity. Availability and implementation CICLOP is available at http://ciclop.raylab.iiitd.edu.in/. A compiled Linux executable can be downloaded from https://ciclop.raylab.iiitd.edu.in/standalone/. Supplementary information Supplementary data are available at Bioinformatics online.

Modification of magnetite-doped NH2-MIL-100(Fe) with aliphatic C8 carbon chain for feasible protein purification in reversed-phase mode

NH2-MIL-100(Fe) is a stable Metal-Organic Frameworks (MOFs) possessing numerous tunable properties. In this study, we have successfully modified NH2-MIL-100(Fe) with aliphatic C8 carbon chain to create a hydrophobic surface distribution. The detailed characterizations of NH2-MIL-100(Fe)-C8 were performed to demonstrate its attractive properties, such as unique MOF architecture, sufficient surface area, and surface hydrophobicity. In addition, the NH2-MIL-100(Fe)-C8 exhibited the distinctive hydrophobic interaction with an individual protein under a specific concentration of acetonitrile, and was able to separate the protein from a mixture with a good resolution. It has a binding capacity of 6.25 μg of BSA/mg particle. Since we have introduced Fe3O4 to NH2-MIL-100(Fe)-C8 to provide with excellent magnetization, the target protein could be easily collected by a magnet and the NH2-MIL-100(Fe)-C8 could be regenerated over 15 times without significant loss of its capacity. Therefore, NH2-MIL-100(Fe)-C8 provides researchers with a convenient and affordable tool for protein separation and purification in reversed-phase mode.

Hydrophilic and Hydrophobic Bionic Distribution of Flow Channel Wall on Water Flooding Suppression in Proton Exchange Membrane Fuel Cell

Hydrophilic and Hydrophobic Bionic Distribution of Flow Channel Wall on Water Flooding Suppression in Proton Exchange Membrane Fuel Cell

On the Dependence of Prion and Amyloid Structure on the Folding Environment.

Currently available analyses of amyloid proteins reveal the necessity of the existence of radical structural changes in amyloid transformation processes. The analysis carried out in this paper based on the model called fuzzy oil drop (FOD) and its modified form (FOD-M) allows quantifying the role of the environment, particularly including the aquatic environment. The starting point and basis for the present presentation is the statement about the presence of two fundamentally different methods of organizing polypeptides into ordered conformations—globular proteins and amyloids. The present study shows the source of the differences between these two paths resulting from the specificity of the external force field coming from the environment, including the aquatic and hydrophobic one. The water environment expressed in the fuzzy oil drop model using the 3D Gauss function directs the folding process towards the construction of a micelle-like system with a hydrophobic core in the central part and the exposure of polarity on the surface. The hydrophobicity distribution of membrane proteins has the opposite characteristic: Exposure of hydrophobicity at the surface of the membrane protein with an often polar center (as in the case of ion channels) is expected. The structure of most proteins is influenced by a more or less modified force field generated by water through the appropriate presence of a non-polar (membrane-like) environment. The determination of the proportion of a factor different from polar water enables the assessment of the protein status by indicating factors favoring the structure it represents.