Conformationally flexible core-bearing detergents with a hydrophobic or hydrophilic pendant: Effect of pendant polarity on detergent conformation and membrane protein stability

Rational Approach to Improve Detergent Efficacy for Membrane Protein Stabilization

Membrane protein structures are essential for the molecular understanding of diverse cellular processes and drug discovery. Detergents are not only widely used to extract membrane proteins from membranes but also utilized to preserve native protein structures in aqueous solution. However, micelles formed by conventional detergents are suboptimal for membrane protein stabilization, necessitating the development of novel amphiphilic molecules with enhanced protein stabilization efficacy. In this study, we prepared two sets of tandem malonate-derived glucoside (TMG) variants, both of which were designed to increase the alkyl chain density in micelle interiors. The alkyl chain density was modulated either by reducing the spacer length (TMG-Ms) or by introducing an additional alkyl chain between the two alkyl chains of the original TMGs (TMG-Ps). When evaluated with a few membrane proteins including a G protein-coupled receptor, TMG-P10,8 was found to be substantially more efficient at extracting membrane proteins and also effective at preserving protein integrity in the long term compared to the previously described TMG-A13. This result reveals that inserting an additional alkyl chain between the two existing alkyl chains is an effective way to optimize detergent properties for membrane protein study. This new biochemical tool and the design principle described have the potential to facilitate membrane protein structure determination.

Trends in the Diversification of the Detergentome

Detergents are amphiphilic molecules that serve as enabling steps for today's world applications. The increasing diversity of the detergentome is key to applications enabled by detergent science. Regardless of the application, the optimal design of detergents is determined empirically, which leads to failed preparations, and raising costs. To facilitate project planning, here we review synthesis strategies that drive the diversification of the detergentome. Synthesis strategies relevant for industrial and academic applications include linear, modular, combinatorial, bio-based, and metric-assisted detergent synthesis. Scopes and limitations of individual synthesis strategies in context with industrial product development and academic research are discussed. Furthermore, when designing detergents, the selection of molecular building blocks, i. e., head, linker, tail, is as important as the employed synthesis strategy. To facilitate the design of safe-to-use and tailor-made detergents, we provide an overview of established head, linker, and tail groups and highlight selected scopes and limitations for applications. It becomes apparent that most recent contributions to the increasing chemical diversity of detergent building blocks originate from the development of detergents for membrane protein studies. The overview of synthesis strategies and molecular blocks will bring us closer to the ability to predictably design and synthesize optimal detergents for challenging future applications.

Melamine-cored glucosides for membrane protein solubilization and stabilization: importance of water-mediated intermolecular hydrogen bonding in detergent performance

Membrane proteins play essential roles in a number of biological processes, and their structures are important in elucidating such processes at the molecular level and also for rational drug design and development. Membrane protein structure determination is notoriously challenging compared to that of soluble proteins, due largely to the inherent instability of their structures in non-lipid environments. Micelles formed by conventional detergents have been widely used for membrane protein manipulation, but they are suboptimal for long-term stability of membrane proteins, making downstream characterization difficult. Hence, there is an unmet need for the development of new amphipathic agents with enhanced efficacy for membrane protein stabilization. In this study, we designed and synthesized a set of glucoside amphiphiles with a melamine core, denoted melamine-cored glucosides (MGs). When evaluated with four membrane proteins (two transporters and two G protein-coupled receptors), MG-C11 conferred notably enhanced stability compared to the commonly used detergents, DDM and LMNG. These promising findings are mainly attributed to a unique feature of the MGs, i.e., the ability to form dynamic water-mediated hydrogen-bond networks between detergent molecules, as supported by molecular dynamics simulations. Thus, MG-C11 is the first example of a non-peptide amphiphile capable of forming intermolecular hydrogen bonds within a protein-detergent complex environment. Detergent micelles formed via a hydrogen-bond network could represent the next generation of highly effective membrane-mimetic systems useful for membrane protein structural studies.

Amphiphilic dendrons as supramolecular holdase chaperones

The aggregation of incompletely or incorrectly folded proteins is implicated in diseases including Alzheimer's, cataracts, and other maladies. Natural systems express protein chaperones to prevent or even reverse harmful protein aggregation. Synthetic chaperone-like systems have sought to mimic the action of their biological counterparts but typically require substantial optimization and high concentrations to be functional, or lack programmability that would enable the targeting of specific protein substrates. Here we report a series of amphiphilic dendrons that undergo assembly and inhibit the aggregation of fragment 16-22 amyloid β protein (Aβ16-22). We show that monodisperse dendrons with hydrophilic tetraethylene glycol chains and a hydrophobic core based on naphthyl and benzyl ethers undergo supramolecular assembly in aqueous solutions to form sphere-like particles. The solubility of these dendrons and their assemblies is tuned by varying the relative sizes of their hydrophilic and hydrophobic regions. Two water-soluble dendrons are discovered and shown, via fluorescence experiments with rhodamine 6G, to generate a hydrophobic environment. Furthermore, we demonstrate that sub-stoichiometric concentrations of these amphiphilic dendrons stabilize Aβ16-22 peptide with respect to aggregation, mimicking the activity of holdase chaperones. Our results highlight the potential of these amphiphilic molecules as the basis for a novel approach to artificial chaperones that may address many of the challenges associated with existing synthetic chaperone mimics.

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drug-binding and dynamics, protein-lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.

Tris(hydroxymethyl)aminomethane Linker-Bearing Triazine-Based Triglucosides for Solubilization and Stabilization of Membrane Proteins

High-resolution membrane protein structures are essential for a fundamental understanding of the molecular basis of diverse cellular processes and for drug discovery. Detergents are widely used to extract membrane-spanning proteins from membranes and maintain them in a functional state for downstream characterization. Due to limited long-term stability of membrane proteins encapsulated in conventional detergents, development of novel agents is required to facilitate membrane protein structural study. In the current study, we designed and synthesized tris(hydroxymethyl)aminomethane linker-bearing triazine-based triglucosides (TTGs) for solubilization and stabilization of membrane proteins. When these glucoside detergents were evaluated for four membrane proteins including two G protein-coupled receptors, a few TTGs including TTG-C10 and TTG-C11 displayed markedly enhanced behaviors toward membrane protein stability relative to two maltoside detergents [DDM (n-dodecyl-β-d-maltoside) and LMNG (lauryl maltose neopentyl glycol)]. This is a notable feature of the TTGs as glucoside detergents tend to be inferior to maltoside detergents at stabilizing membrane proteins. The favorable behavior of the TTGs for membrane protein stability is likely due to the high hydrophobicity of the lipophilic groups, an optimal range of hydrophilic-lipophilic balance, and the absence of cis-trans isomerism.

Micelle Formation in Aqueous Solutions of the Cholesterol-Based Detergent Chobimalt Studied by Small-Angle Scattering

The structure and interaction parameters of the water-soluble cholesterol-based surfactant, Chobimalt, are investigated by small-angle neutron and X-ray scattering techniques. The obtained data are analyzed by a model-independent approach applying the inverse Fourier transformation procedure as well as considering a model fitting procedure, using a core-shell form factor and hard-sphere structure factor. The analysis reveals the formation of the polydisperse spherical or moderately elongated ellipsoidal shapes of the Chobimalt micelles with the hard sphere interaction in the studied concentration range 0.17-6.88 mM. The aggregation numbers are estimated from the micelle geometry observed by small-angle scattering and are found to be in the range of 200-300. The low pH of the solution does not have a noticeable effect on the structure of the Chobimalt micelles. The critical micelle concentrations of the synthetic surfactant Chobimalt in water and in H2O-HCl solutions were obtained according to fluorescence measurements as ~3 μM and ~2.5 μM, respectively. In-depth knowledge of the basic structural properties of the detergent micelles is necessary for further applications in bioscience and biotechnology.

Travel light: Essential packing for membrane proteins with an active lifestyle

We review the considerable progress during the recent decade in the endeavours of designing, optimising, and utilising carrier particle systems for structural and functional studies of membrane proteins in near-native environments. New and improved systems are constantly emerging, novel studies push the perceived limits of a given carrier system, and specific carrier systems consolidate and entrench themselves as the system of choice for particular classes of target membrane protein systems. This review covers the most frequently used carrier systems for such studies and emphasises similarities and differences between these systems as well as current trends and future directions for the field. Particular interest is devoted to the biophysical properties and membrane mimicking ability of each system and the manner in which this may impact an embedded membrane protein and an eventual structural or functional study.

Surface Properties of Alkyldi(oxyethylene) β-D-Maltoside

A series of nonionic disaccharide-based surfactants alkyldi(oxyethylene) β-d-maltosides (4a-4h, n = 6-16) were synthesized, and their physicochemical properties were further investigated. Six β-D-maltosides (4c-4h, n = 8-16) exhibited a fan-shaped texture feature, whereas hexyldi(oxyethylene) β-D-maltoside (4a) had the strongest hygroscopicity. Owing to the incorporation of the hydrophilic dioxyethyl spacer (-(OCH₂CH₂)₂-), the related water solubility improved significantly. Tetradecyldi(oxyethylene) β-D-maltoside (4g) had good water solubility, whereas hexadecyldi(oxyethylene) β-D-maltoside (4h) had weak water solubility. Meanwhile, the surface tension of β-D-maltosides (4a-4g, n = 6-14) had a decreasing tendency with increasing the alkyl chain length, whereas 4g had the best surface activity. Furthermore, decyldi(oxyethylene) β-D-maltoside (4e) had the best foaming ability and foam stability. Dodecyldi(oxyethylene) β-D-maltoside (4f) had the best emulsifying property in the rapeseed oil/water system. In contrast, both ammonium dodecyl sulfate (NH₄DS)/4f and cetyltrimethylammonium chloride (CTAC)/4f binary surfactant systems showed a synergistic effect in surface activity because the C_CMC/CMC^id_mix was <1. NaCl impacted the surface activity of the aqueous 4f solution through salt-surfactant synergistic effects. The results showed that such surfactants should have potential applications in the related field in the future.

Antibacterial and cytotoxic properties of star-shaped quaternary ammonium-functionalized polymers with different pendant groups

The correlation between the structure and biological activity of polymers is critically important for rationally designing effective antibacterial polymers. Here, the antibacterial activity, cytotoxicity, and selectivity of structurally well-defined, star-shaped...

Malachite Green, the hazardous materials that can bind to Apo-transferrin and change the iron transfer

Different groups of synthetic dyes might lead to environmental pollution. The binding affinity among hazardous materials with biomolecules necessitates a detailed understanding of their binding properties. Malachite Green might induce a change in the iron transfer by Apo-transferrin. Spectroscopic studies showed malachite green oxalate (MGO) could form the apo-transferrin-MGO complex and change the Accessible Surface Area (ASA) of the key amino acids for iron transfer. According to the ASA results the accessible surface area of Tyrosine, Aspartate, and Histidine of apo-transferrin significantly were changed, which can be considered as a convincing reason for changing the iron transfer. Moreover, based on the fluorescence data MGO could quench the fluorescence intensity of apo-transferrin in a static quenching mechanism. The experimental and Molecular Dynamic simulation results represented that the binding process led to micro environmental changes, around tryptophan residues and altered the tertiary structure of apo-transferrin. The Circular Dichroism (CD) spectra result represented a decrease in the amount of the α-Helix, as well as, increase in the β-sheet volumes of the apo-transferrin structure. Moreover, FTIR spectroscopy results showed a hypochromic shift in the peaks of amide I and II. Molecular docking and MD simulation confirmed all the computational findings.

Surface Properties and Liquid Crystal Properties of Alkyltetra(oxyethyl) β-d-Glucopyranoside

Hydrophilic alkyl polyglycosides (APGs) and alkyl glycosides (AGs) with anomeric pure are a class of important substitutes for petroleum-based surfactants. Improving their water solubility should make such hydrophilic glycosurfactants have more excellent potential application value. To solve the inherent problem of poor water solubility of traditional alkyl β-d-glucopyranoside (5), a series of alkyltetra(oxyethyl) β-d-glucopyranosides (4a-4g, n = 7-18) were successfully synthesized by introducing tetra(oxyethylene) fragments to carry out the structural modification. The relationship between the related structure and the physicochemical properties was further investigated, including their hydrophilic-lipophilic balance (HLB), water-solubility, foaming performance, emulsification, hygroscopicity, surface activity, and thermotropic/lyotropic liquid crystal phase behavior. The results showed that the water solubility gradually decreased as the alkyl chain length increased due to the gradual decrease of their HLB number. Octadecyltetra(oxyethyl) β-d-glucopyranoside (4g, n = 18) was found to be insoluble in water at 25 °C. Taken together, long-chain alkyl glycosides had good foaming properties and excellent emulsifying properties. Among them, dodecyltetra(oxyethyl) β-d-glucopyranoside (4d, n = 12) had the best foaming performance. In the rapeseed oil/water system, cetyltetra(oxyethyl) β-d-glucopyranoside (4f, n = 16) had the best emulsifying ability. With the increase of the alkyl chain length, the critical micelle concentration (C_cmc), γ_cmc, Γ_max, and hygroscopicity of this series of glycosides showed a downward trend. Differential scanning calorimetry (DSC) and polarizing optical microscopy (POM) showed that the thermal stability increased with the increase of the alkyl chain length, and alkyltetra(oxyethyl) β-d-glucopyranosides (4d-4g, n = 12-18) had the corresponding melting points and clearing points. Alkyltetra(oxyethyl) β-d-glucopyranosides (4b-4g, n = 8-18) formed a smectic phase with a typical fan-shaped and focal conic texture during the cooling process. In the water contact experiments, it was found that glycosides (4b-4g, n = 8-18) at high concentrations transformed into various lyotropic liquid crystal including hexagonal phase, bicontinuous cubic phase, and lamellar phase phases. Therefore, such green nonionic glycosurfactants alkyltetra(oxyethyl) β-d-glucopyranosides should have potential practical application prospects.