Interfacial rheology of protein–surfactant mixtures

The distribution of proteins and surfactants at fluid interfaces (air–water and oil–water) is determined by the competitive adsorption between the two types of emulsifiers and by the nature of the protein–surfactant interactions, both at the interface and in the bulk phase, with a pronounced impact on the interfacial rheological properties of these systems. Therefore, the interfacial rheology is of practical importance for food dispersion (emulsion or foam) formulation, texture, and stability. In this review, the existence of protein–surfactant interactions, the mechanical behaviour and/or the composition of emulsifiers at the interface are indirectly determined by interfacial rheology of the mixed films. The effect on the interfacial rheology of protein–surfactant mixed films of the protein, the surfactant, the interface and bulk compositions, the method of formation of the interfacial film, the interactions between film forming components, and the displacement of protein by surfactant have been analysed. The last section tries to understand the role of interfacial rheology of protein–surfactant mixed films on food dispersion formation and stability. The emphasis of the present review is on the interfacial dilatational rheology.     

Emulsion stabilisation using polysaccharide–protein complexes

There is a great deal of interest in the Food Industry in the use of polysaccharides and proteins to stabilise oil-in-water emulsions and there is a particular interest nowadays in the use of polysaccharide–protein complexes. There are three classes of complexes namely; (a) naturally-occurring complexes in which protein residues are covalently attached to the polysaccharide chains as is the case, for example, with gum Arabic; (b) Maillard conjugates, which are formed by interaction of the reducing end of a polysaccharide with an amine group on a protein forming a covalent bond; and (c) electrostatic complexes formed between a polysaccharide and a protein with opposite net charge. This review sets out our current understanding of the nature of these different polysaccharide–protein complexes and their ability to stabilise oil-in-water emulsions.     

Ionene–surfactant complexes: temperature and humidity sensitive materials

Solid stoichiometric complexes of [3,12]-ionene and dodecyl sulfate form upon reaction of the bromide of the ionene and the silver salt of dodecyl sulfate in methanol. IR, DSC, and TG investigations indicated that the solid complexes are stable between 30 and 120 °C. TG and DSC also showed that the complexes easily take up water at ambient conditions. These samples are optically isotropic. When exposed to an increased humidity they exhibit optical anisotropy, i.e., birefringence, which is caused by the formation of a hexagonal mesogenic phase. Mesogenicity is necessarily accompanied by a further uptake of water (4–5 H₂O molecules per ionic unit), which is dependent on the relative humidity. The phase behavior as a function of temperature and controlled relative humidity was studied using birefringence measurements and polarizing microscopy.     

Prediction of protein–protein complexes using replica exchange with repulsive scaling

The realistic prediction of protein–protein complex structures is import to ultimately model the interaction of all proteins in a cell and for the design of new protein–protein interactions. In principle, molecular dynamics (MD) simulations allow one to follow the association process under realistic conditions including full partner flexibility and surrounding solvent. However, due to the many local binding energy minima at the surface of protein partners, MD simulations are frequently trapped for long times in transient association states. We have designed a replica-exchange based scheme employing different levels of a repulsive biasing between partners in each replica simulation. The bias acts only on intermolecular interactions based on an increase in effective pairwise van der Waals radii (repulsive scaling (RS)-REMD) without affecting interactions within each protein or with the solvent. For a set of five protein test cases (out of six) the RS-REMD technique allowed the sampling of near-native complex structures even when starting from the opposide site with respect to the native binding site for one partner. Using the same start structures and same computational demand regular MD simulations sampled near native complex structures only for one case. The method showed also improved results for the refinement of docked structures in the vicinity of the native binding geometry compared to regular MD refinement.     

Nanocellulose–surfactant interactions

Biomass-derived nanomaterials, such as cellulose nanocrystals and nanofibrils, are attractive building blocks for the formulation of foams, emulsions, suspensions and multiphase systems. Depending on their surface chemistry, aspect ratio and crystallinity, nanocelluloses can control the rheology and stability of dispersions; they can also confer robust mechanical properties to composites. Synthetic modification of fibrillar cellulose is an option to achieve chemical compatibility in related systems, in the formation of composites, etc. However, this can also limit the environmental benefits gained from the use of the cellulosic component. Thus, an attractive mean to compatibilize and to further expand the applications of nanocelluloses is through the use of surfactants. The chemical toolbox of surfactants developed over the last 60 years allows for a large versatility while their environmental impact can also be minimized. Furthermore, relatively small amounts of surfactants are sufficient to significantly impact the interfacial forces, which has implications in material development, from the colloidal scale to the macro-scale. In this review we attempt to cover the literature pertaining to the combined uses of surfactants and nanocelluloses. We summarize reports on the incorporation with nanocellulose of nonionic, anionic, amphoteric and cationic surfactants. With the ever-expanding interest in the use of renewable materials in a vast range of applications, we hope to provide insights into the application of surfactants as a tool to tailor the compatibility and the surface chemistry of nanocelluloses.     

Modeling large protein–glycosaminoglycan complexes using a fragment-based approach

Glycosaminoglycans (GAGs), a major constituent of the extracellular matrix, participate in cell-signaling by binding specific proteins. Structural data on protein–GAG interactions are crucial to understand and modulate these signaling processes, with potential applications in regenerative medicine. However, experimental and theoretical approaches used to study GAG–protein systems are challenged by GAGs high flexibility limiting the conformational sampling above a certain size, and by the scarcity of GAG-specific docking tools compared to protein–protein or protein–drug docking approaches. We present for the first time an automated fragment-based method for docking GAGs on a protein binding site. In this approach, trimeric GAG fragments are flexibly docked to the protein, assembled based on their spacial overlap, and refined by molecular dynamics. The method appeared more successful than the classical full-ligand approach for most of 13 tested complexes with known structure. The approach is particularly promising for docking of long GAG chains, which represents a bottleneck for classical docking approaches applied to these systems. © 2019 Wiley Periodicals, Inc.     

Dimethylditetradecylammonium bromide (2C14DAB) as a self-assembled surfactant coating for detection of protein–dye complexes by CE-LIF

A self-assembled column coating for capillary electrophoresis in conjunction with laser-induced fluorescence detection (CE-LIF) has been evaluated for the separation and quantitation of protein–dye complexes. This semi-permanent coating, composed of dimethylditetradecyl-ammonium bromide (2C₁₄DAB), is inexpensive and easily assembled onto the column and it allows for better peak resolution and greater control over electroosmotic flow. The versatility of long-chained surfactant coatings was determined particularly with respect to their use with fluorescent probes, different pH buffers, and different proteins. Studies were performed to determine the stability of the coating under various pH and buffer conditions. Red-1c, a red luminescent squarylium dye, was used for on-column protein labeling concurrently with the surfactant coating and LIF detection. Protein–Red-1c complexes were excited with a 650-nm diode laser and their emission detected by a photomultiplier tube with a 664-nm filter. A comparison of pre-column labeling and on-column labeling of a two-model protein system (human serum albumin and β-lactoglobulin A) revealed higher efficiencies and greater sensitivities for both proteins using on-column labeling and coated columns. A linear relationship between peak height and protein concentration was obtained by CE-LIF for this on-column labeling method with 2C₁₄DAB-coated columns and the Red-1c probe.     

Weighted edge based clustering to identify protein complexes in protein–protein interaction networks incorporating gene expression profile

Protein complex detection from protein–protein interaction (PPI) network has received a lot of focus in recent years. A number of methods identify protein complexes as dense sub-graphs using network information while several other methods detect protein complexes based on topological information. While the methods based on identifying dense sub-graphs are more effective in identifying protein complexes, not all protein complexes have high density. Moreover, existing methods focus more on static PPI networks and usually overlook the dynamic nature of protein complexes. Here, we propose a new method, Weighted Edge based Clustering (WEC), to identify protein complexes based on the weight of the edge between two interacting proteins, where the weight is defined by the edge clustering coefficient and the gene expression correlation between the interacting proteins. Our WEC method is capable of detecting highly inter-connected and co-expressed protein complexes. The experimental results of WEC on three real life data shows that our method can detect protein complexes effectively in comparison with other highly cited existing methods.Availability: The WEC tool is available at http://agnigarh.tezu.ernet.in/~rosy8/shared.html.     

A shotgun approach for the identification of platinum–protein complexes

A shotgun approach including peptide-based OFFGEL-isoelectric focusing (IEF) fractionation has been developed with the aim of improving the identification of platinum-binding proteins in biological samples. The method is based on a filter-aided sample preparation (FASP) tryptic digestion under denaturing and reducing conditions of cisplatin–, oxaliplatin–, and carboplatin–protein complexes, followed by OFFGEL-IEF separation of the peptides. Any risk of platinum loss is minimized throughout the procedure due to the removal of the reagents used after each stage of the FASP method and the absence of thiol-based reagents in the focusing buffer employed in the IEF separation. The platinum–peptide complexes stability after the FASP digestion and the IEF separation was confirmed by size exclusion chromatography-inductively coupled plasma-mass spectrometry (SEC-ICP-MS). The suitability of peptide-based OFFGEL-IEF fractionation for reducing the sample complexity for further nano-liquid chromatography-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS/MS) analysis has been demonstrated, allowing the detection of platinum-containing peptides, with significantly lower abundance and ionization efficiency than unmodified peptides. nLC-MS/MS analysis of selected OFFGEL-IEF fractions from tryptic digests with different complexity degrees: standard human serum albumin (HSA), a mixture of five proteins (albumin, transferrin, carbonic anhydrase, myoglobin, and cytochrome-c) and human blood serum allowed the identification of several platinum–peptides from cisplatin–HSA. Cisplatin-binding sites in HSA were elucidated from the MS/MS spectra and assessed considering the protein three-dimensional structure. Most of the potential superficial binding sites available on HSA were identified for all the samples, including a biologically relevant cisplatin-cross-link of two protein domains, demonstrating the capabilities of the methodology.

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Graphical Abstract Graphical abstract shows the several steps involved in the identification of platinum-protein complexes: FASP digestion of proteins, peptide fractionation by OFFGEL-IEF and identification of Pt-complexes by nLC-ESIMS/MS

     

Formation of chitosan—surfactant complexes in aqueous-alcohol media

Russian Chemical Bulletin - The complexation of chitosan and anionic surfactant, sodium dodecyl sulfate (DDS), in aqueous-alcohol media with a variable content of an organic cosolvent (methanol,...     

Capillary electrophoresis methods for the determination of covalent polyphenol–protein complexes

The bioactivities and bioavailability of plant polyphenols including proanthocyanidins and other catechin derivatives may be affected by covalent reaction between polyphenol and proteins. Both processing conditions and gastrointestinal conditions may promote formation of covalent complexes for polyphenol-rich foods and beverages such as wine. Little is known about covalent reactions between proteins and tannin, because suitable methods for quantitating covalent complexes have not been developed. We established capillary electrophoresis methods that can be used to distinguish free protein from covalently bound protein–polyphenol complexes and to monitor polyphenol oxidation products. The methods are developed using the model protein bovine serum albumin and the representative polyphenol (−)epigallocatechin gallate. By pairing capillaries with different diameters with appropriate alkaline borate buffers, we are able to optimize resolution of either the protein–polyphenol complexes or the polyphenol oxidation products. This analytical method, coupled with purification of the covalent complexes by diethylaminoethyl cellulose chromatography, should facilitate characterization of covalent complexes in polyphenol-rich foods and beverages such as wine.     

Extending the applicability of the O-ring theory to protein–DNA complexes

Many biological processes depend on protein-based interactions, which are governed by central regions with higher binding affinities, the hot-spots. The O-ring theory or the “Water Exclusion” hypothesis states that the more deeply buried central regions are surrounded by areas, the null-spots, whose role would be to shelter the hot-spots from the bulk solvent. Although this theory is well-established for protein–protein interfaces, its applicability to other protein interfaces remains unclear. Our goal was to verify its applicability to protein–DNA interfaces. We performed Molecular Dynamics simulations in explicit solvent of several protein–DNA complexes and measured a variety of solvent accessible surface area (SASA) features, as well as, radial distribution functions of hot-spots and null-spots. Our aim was to test the influence of water in their coordination sphere. Our results show that hot-spots tend to have fewer water molecules in their neighborhood when compared to null-spots, and higher values of ΔSASA, which confirms their occlusion from solvent. This study provides evidence in support of the O-ring theory with its applicability to a new type of protein-based interface: protein–DNA.     

Capillary electrophoresis methods for the determination of covalent polyphenol–protein complexes

The bioactivities and bioavailability of plant polyphenols including proanthocyanidins and other catechin derivatives may be affected by covalent reaction between polyphenol and proteins. Both processing conditions and gastrointestinal conditions may promote formation of covalent complexes for polyphenol-rich foods and beverages such as wine. Little is known about covalent reactions between proteins and tannin, because suitable methods for quantitating covalent complexes have not been developed. We established capillary electrophoresis methods that can be used to distinguish free protein from covalently bound protein-polyphenol complexes and to monitor polyphenol oxidation products. The methods are developed using the model protein bovine serum albumin and the representative polyphenol (-)epigallocatechin gallate. By pairing capillaries with different diameters with appropriate alkaline borate buffers, we are able to optimize resolution of either the protein-polyphenol complexes or the polyphenol oxidation products. This analytical method, coupled with purification of the covalent complexes by diethylaminoethyl cellulose chromatography, should facilitate characterization of covalent complexes in polyphenol-rich foods and beverages such as wine.     

Fast force field-based optimization of protein–ligand complexes with graphics processor

Usually based on molecular mechanics force fields, the post-optimization of ligand poses is typically the most time-consuming step in protein–ligand docking procedures. In return, it bears the potential to overcome the limitations of discretized conformation models. Because of the parallel nature of the problem, recent graphics processing units (GPUs) can be applied to address this dilemma. We present a novel algorithmic approach for parallelizing and thus massively speeding up protein–ligand complex optimizations with GPUs. The method, customized to pose-optimization, performs at least 100 times faster than widely used CPU-based optimization tools. An improvement in Root-Mean-Square Distance (RMSD) compared to the original docking pose of up to 42% can be achieved. © 2012 Wiley Periodicals, Inc.     

Empirical estimation of the energetic contribution of individual interface residues in structures of protein–protein complexes

We report a simple algorithm to scan interfaces in protein–protein complexes for identifying binding ‘hot spots’. The change in side-chain solvent accessible area (ΔASA) of interface residues has been related to change in binding energy due to mutating interface residues to Ala (ΔΔG _X → ALA) based on two criteria—hydrogen bonding across the interface and location in the interface core—both of which are major determinants in specific, high-affinity binding. These relationships are used to predict the energetic contribution of individual interface residues. The predictions are tested against 462 experimental X → ALA mutations from 28 interfaces with an average unsigned error of 1.04 kcal/mol. More than 80% of interface hot spots (with experimental ΔΔG ≥ 2 kcal/mol) could be identified as being energetically important. From the experimental values, Asp, Lys, Tyr and Trp are found to contribute most of the binding energy, burying >45 Å² on average. The method described here would be useful to understand and interfere with protein interactions by assessing the energetic importance of individual interface residues. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Calculation of hot spots for protein–protein interaction in p53/PMI-MDM2/MDMX complexes

The recently developed MM/GBSA_IE method is applied to computing hot and warm spots in p53/PMI-MDM2/MDMX protein–protein interaction systems. Comparison of the calculated hot (>2 kcal/mol) and warm spots (>1 kcal/mol) in P53 and PMI proteins interacting with MDM2 and MDMX shows a good quantitative agreement with the available experimental data. Further, our calculation predicted hot spots in MDM2 and MDMX proteins in their interactions with P53 and PMI and they help elucidate the interaction mechanism underlying this important PPI system. In agreement with the experimental result, the present calculation shows that PMI has more hot and warm spots and binds stronger to MDM2/MDMX. The analysis of these hot and warm spots helps elucidate the fundamental difference in binding between P53 and PMI to the MDM2/MDMX systems. Specifically, for p53/PMI-MDM2 systems, p53 and PMI use essentially the same residues (L54, I61, Y67, Q72, V93, H96, and I99) of MDM2 for binding. However, PMI enhanced interactions with residues L54, Y67, and Q72 of MDM2. For the p53/PMI-MDMX system, p53 and PMI use similar residues (M53, I60, Y66, Q71, V92, and Y99) of MDMX for binding. However, PMI exploited three extra residues (M61, K93, and L98) of MDMX for enhanced binding. In addition, PMI enhanced interaction with four residues (M53, Y66, Q71, and Y99) of MDMX. These results gave quantitative explanation on why the binding affinities of PMI-MDM2/MDMX interactions are stronger than that of p53-MDM2/MDMX although their binding modes are similar. © 2018 Wiley Periodicals, Inc.     

H-bond refinement for electron transfer membrane-bound protein–protein complexes: Cytochrome c oxidase and cytochrome c552

In this study we propose a protocol to evaluate membrane-bound cytochrome c oxidase–cytochrome c552 docking candidates. An initial rigid docking algorithm generates docking poses of the cytochrome c oxidase–cytochrome c552, candidates are then aggregated into a 512-DPPC membrane model and solvated in explicit solvent. Molecular dynamic simulations are performed to induce conformational changes to membrane-bound protein complexes. Lastly each protein–protein complex is optimized in terms of its hydrogen bond network, evaluated energetically and ranked. The protocol is directly applicable to other membrane-protein complexes, such as protein–ligand systems.     

MOEPGA: A novel method to detect protein complexes in yeast protein–protein interaction networks based on MultiObjective Evolutionary Programming Genetic Algorithm

The identification of protein complexes in protein–protein interaction (PPI) networks has greatly advanced our understanding of biological organisms. Existing computational methods to detect protein complexes are usually based on specific network topological properties of PPI networks. However, due to the inherent complexity of the network structures, the identification of protein complexes may not be fully addressed by using single network topological property. In this study, we propose a novel MultiObjective Evolutionary Programming Genetic Algorithm (MOEPGA) which integrates multiple network topological features to detect biologically meaningful protein complexes. Our approach first systematically analyzes the multiobjective problem in terms of identifying protein complexes from PPI networks, and then constructs the objective function of the iterative algorithm based on three common topological properties of protein complexes from the benchmark dataset, finally we describe our algorithm, which mainly consists of three steps, population initialization, subgraph mutation and subgraph selection operation. To show the utility of our method, we compared MOEPGA with several state-of-the-art algorithms on two yeast PPI datasets. The experiment results demonstrate that the proposed method can not only find more protein complexes but also achieve higher accuracy in terms of fscore. Moreover, our approach can cover a certain number of proteins in the input PPI network in terms of the normalized clustering score. Taken together, our method can serve as a powerful framework to detect protein complexes in yeast PPI networks, thereby facilitating the identification of the underlying biological functions.     

Polymer–surfactant interaction for controlling the rheological properties of aqueous surfactant solutions

Controlling viscosity of aqueous surfactant solutions is very important for practical formulations. This can be done by having polymers interact with surfactants, thereby forming interconnected physical networks, where main ways of interaction are electrostatic and hydrophobic forces. Polymer–surfactant interactions are long established for viscosity control, but there are many ongoing activities. They are driven by wanting more biocompatible systems, which depend intricately on the choice of surfactant and polymer, and general predictions are not simple for such systems. Surfactants form spherical or wormlike micelles or vesicles. By choice of (co)polymers one can construct systems responsive to external parameters, like temperature or pH, for having tailored rheological properties. Here we describe recent developments with a focus on systems of low concentration, being interesting for applications. In summary, rheological control of polymer–surfactant systems is a versatile topic and a field of colloid science with high relevance for practical formulations.