Effect of Urea on the Organization and Dynamics of Triton X-100 Micelles: A Fluorescence Approach

Cost-effective Purification of Membrane Proteins using a Dual-detergent Strategy

Understanding the mechanisms of membrane protein function is critical for biomedical research and drug discovery as membrane proteins constitute ∼30% of the proteins encoded by the genomes of both lower and higher organisms and are targets for two-thirds of approved drugs worldwide. Significant progress has been made in engineering host expression systems for large-scale production of membrane proteins and in determining their three-dimensional high-resolution structures. Despite these efforts, the study of membrane proteins at the atomic level is challenging due to poor expression and extraction, low yields of functional protein, and the complexity and heterogeneity of source membranes. Structural and spectroscopic studies of any membrane protein require that the protein be extracted from its native membranes into a membrane-mimetic stable environment, which is often achieved by the use of detergents. Unfortunately, there is no magic detergent that can extract all membrane proteins and successful extraction often requires a thorough screen of detergents. Furthermore, membrane protein purification in general and the detergents used are very expensive, which puts a financial constraint on sophisticated membrane protein studies. To overcome this hurdle, a dual-detergent strategy has recently been developed and successfully applied to purify various classes of pure, stable, and functionally relevant membrane proteins in a cost-effective manner. This strategy uses an inexpensive detergent for solubilization of the desired protein from membranes and a second detergent during protein purification. In the Basic Protocol, we describe the dual-detergent strategy to significantly reduce the overall purification cost of a bacterial membrane protein using the magnesium ion channel MgtE as an example. Support Protocols are also provided for selecting a suitable E. coli strain for protein expression and the optimal detergent(s) for membrane protein solubilization. © 2022 Wiley Periodicals LLC. Basic Protocol: Expression, membrane solubilization, and cost-effective purification of MgtE Support Protocol 1: Selecting a suitable E. coli strain for optimal protein expression Support Protocol 2: Identification of suitable detergents for membrane protein solubilization.

Site-directed fluorescence approaches to monitor the structural dynamics of proteins using intrinsic Trp and labeled with extrinsic fluorophores

Comprehensive understanding of a protein’s function depends on having reliable, sophisticated tools to study protein structural dynamics in physiologically-relevant conditions. Here, we present an effective, robust step-by-step protocol to monitor the structural dynamics (including hydration dynamics) of a protein utilizing various site-directed fluorescence (SDFL) approaches. This protocol should be widely applicable for studying soluble proteins, intrinsically-disordered proteins, and membrane proteins.

For complete details on the use and execution of this protocol, please refer to Das et al. (2020), Das and Raghuraman (2021), and Chatterjee et al. (2021).

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A step-by-step protocol to monitor the structural dynamics of proteins using SDFL

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Applicable to proteins with intrinsic Trp and labeled with extrinsic fluorophores

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This protocol should be widely applicable for soluble and membrane proteins

Effectiveness of dual-detergent strategy using Triton X-100 in membrane protein purification

Membrane solubilization by detergents is a critical step for successful membrane protein purification. Alkyl maltoside detergents such as DDM and DM are very expensive and are commonly used to produce most of the high-quality proteins in stable and functional form. Recently, dual-detergent strategy using inexpensive detergents for membrane solubilization step has been shown to be highly effective in purifying different classes of membrane proteins in a cost-effective manner. In this work, we have monitored the effectiveness of 'dual-detergent strategy' towards successful purification of the isolated voltage sensing domain (VSD) of KvAP and the inward rectifying K⁺ channel, KirBac1.1. We demonstrate that the inexpensive detergent Triton X-100 extracts the activated conformation of the KvAP-VSD well without compromising the structural integrity of the sensor, and also retains its proper structural dynamics. Importantly, the cost associated with solubilizing the KvAP sensor can be reduced by ∼2000 fold. To the best of our knowledge, our results constitute the first report characterizing the purification of KvAP voltage sensor using an inexpensive detergent. However, the dual-detergent strategy using Triton X-100 for membrane solubilization is not effective for the purification of inward rectifying K⁺ channel, KirBac1.1 even in presence of high salt concentration during solubilization. We propose that the dual-detergent strategy will be useful for extracting stable and functional proteins that are both DDM- and DM-extractable, but will be ineffective if the protein is only DM-extractable. The relevance of the effectiveness of dual-detergent strategy with respect to the hydrophobic thickness of proteins is discussed.

Site-Directed Fluorescence Approaches for Dynamic Structural Biology of Membrane Peptides and Proteins

Membrane proteins mediate a number of cellular functions and are associated with several diseases and also play a crucial role in pathogenicity. Due to their importance in cellular structure and function, they are important drug targets for ~60% of drugs available in the market. Despite the technological advancement and recent successful outcomes in determining the high-resolution structural snapshot of membrane proteins, the mechanistic details underlining the complex functionalities of membrane proteins is least understood. This is largely due to lack of structural dynamics information pertaining to different functional states of membrane proteins in a membrane environment. Fluorescence spectroscopy is a widely used technique in the analysis of functionally-relevant structure and dynamics of membrane protein. This review is focused on various site-directed fluorescence (SDFL) approaches and their applications to explore structural information, conformational changes, hydration dynamics, and lipid-protein interactions of important classes of membrane proteins that include the pore-forming peptides/proteins, ion channels/transporters and G-protein coupled receptors.

Discerning the Structure Factor of Charged Micelles in Water and Supercooled Solvent by Contrast Variation X-ray Scattering

Sodium dodecyl sulfate (SDS) is a well-known anionic surfactant that forms micelles in various solvents including supercooled sugar-urea melt. Here, we explore the application of contrast variation small-angle X-ray scattering (SAXS) in discerning the structure and interactions of SDS micelles in aqueous solution and in a room-temperature supercooled solvent. The SAXS patterns can be analyzed in terms of a core-shell ellipsoid model. For aqueous SDS micelles, at low volume fractions, the features due to intermicellar interaction, S(q), in the SAXS pattern are poorly resolved because of the prominent contribution from shell scattering. Increasing the electron density of the solvent by the addition of the urea or fructose-urea mixture (at a weight ratio of 6:4) permits the systematic variation of shell scattering without influencing the structure drastically. For a 10% solution of SDS in water, the contribution from the shell can be completely masked by the addition of 40% urea or fructose-urea mixture. The fructose-urea mixture is a preferred additive as it can vary the scattering length density over a wide range and serves as a matrix to form supercooled micelles. The structural parameters of micelles in supercooled fructose-urea melt are obtained from contrast variation SAXS, small-angle neutron scattering, and high-resolution transmission electron microscopy.

Biochemical and biophysical characterization of a prokaryotic Mg2+ ion channel: Implications for cost-effective purification of membrane proteins

Although magnesium is the second most abundant cation present in the cell, the transport mechanism of Mg²⁺ across membranes is poorly understood. Importantly, the prokaryotic MgtE Mg²⁺ channel is related to mammalian SLC41A1 transporters and, therefore, biochemical and biophysical characterization of MgtE and its orthologs assumes significance. To date, the purification and structure determination of MgtE from Thermus thermophilus has been carried out using the widely used nonionic detergent, n-dodecyl-β-d-maltopyranoside (DDM). However, DDM is an expensive detergent and alternative methods to produce high-quality proteins in stable and functional form will be practically advantageous to carry out structural studies in a cost-effective manner. In this work, we have utilized 'dual-detergent strategy' to successfully purify MgtE channel in a stable and functional form by employing relatively inexpensive detergents (Triton X-100 and Anzergent 3-14) for membrane solubilization and subsequently changed to DDM during purification. Our results show that Triton X-100 and Anzergent 3-14 extract MgtE well and the quality of purified protein is comparable to DDM-extracted MgtE. Interestingly, addition of high concentration of salt and glycerol during solubilization does not significantly affect the quantity and quality of MgtE. Importantly, limited proteolysis assay, circular dichroism spectroscopy and ensemble tryptophan fluorescence strongly support the use of Triton X-100, in particular, as an inexpensive, alternative detergent for the purification of MgtE without compromising the structural integrity of the channel and Mg²⁺-induced gating-related conformational dynamics. Overall, these results are relevant for the cost-effective purification of stable and functional membrane proteins in general, and magnesium channels, in particular.

Influence of additives on thermoresponsive polymers in aqueous media: a case study of poly(N-isopropylacrylamide)

Thermoresponsive polymers (TRPs) in different solvent media have been studied over a long period and are important from both scientific and technical points of view.

Analysing the microenvironment of 2-p-toluidinylnaphthalene-6-sulfonate (TNS) in solvents and in different conformational states of proteins in relation to its fluorescence properties: a computational study

Characterization of different conformational states of proteins is essential to understand their stability and activity. Biophysical techniques aid in analysing these conformational states and molecular fluorescence is one of the most reliable and quickly accessible methods. Apart from the intrinsic fluorescence of proteins, external fluorescence dyes such as TNS, ANS, nile red and thioflavin are also used to characterize partially unfolded, aggregated and fibrillar states of proteins, though their exact molecular-level interactions with proteins are yet to be completely unravelled. The present study attempts to investigate the binding of TNS molecules on different conformational states of proteins. Unconstrained molecular dynamics simulation of 50 molecules of TNS with the native state of BSA, native and two partially unfolded states of RNase A and α-lactalbumin in water was carried out. Dynamics simulation of TNS alone in different solvents such as water, ethanol, DMF and DMSO was also performed. Binding environments in all the proteins and the solvents were analysed in terms of H-bonding interactions, order of contacts, amino acid specificity and conformational changes of TNS, and correlated with experimentally observed fluorescence changes of the dye. The results suggest that TNS forms aggregates in water whereas in non-aqueous solvents the order of aggregates is lower which might result in an enhancement of its fluorescence intensity. Further, TNS preferably interacts with basic and aromatic amino acid residues of the proteins. In RNase A and α-lactalbumin, most of the TNS molecules tend to form aggregates even with the unfolded conformations of the proteins. However in BSA, the number of aggregated TNS molecules is less and TNS molecules in monomeric form are found in the hydrophobic crevices of the protein. This might result in an enhancement of the fluorescence in BSA compared to the other proteins. The distributions of angles and dihedrals of TNS in different environments suggest that the bending movement between the naphthyl and tolyl rings is constrained whereas significant planar rotations could be observed both in solvents and in protein-bound states.

Cloud point phenomena in aqueous solutions of an anionic gemini surfactant with a dibenzene spacer in the presence of tetra-n-propyl-ammonium bromide

The cloud point behaviour of a carboxylate gemini surfactant,O,O′-bis(sodium 2-dodecylcarboxylate)-p-dibenzenediol was observed in the presence of tetra-propyl-ammonium bromide.

Dansyl-labeled anionic amphiphile with a hexadecanoic carbon chain: synthesis and detection for shape transitions in organized molecular assemblies

The probing properties of a new fluorophore-labeled anionic surfactant, sodium 16-(N-dansyl)aminocetylate (16-DAN-ACA) were investigated systematically in molecular assemblies, especially in the transitions between micelles and vesicles. 16-DAN-ACA can efficiently differentiate the two different aggregate types in mixed cationic and anionic surfactant systems. The fluorescence anisotropy of 16-DAN-ACA was found to be sensitive for directly detecting the micellar growth in micelles containing oppositely charged surfactants; both cationic cetyltrimethylammonium bromide (CTAB) systems and anionic sodium dodecyl sulfate (SDS) systems were studied. The results indicated that the 16-DAN-ACA is a good fluorescent probe for differentiating the different aggregates, and even more can be used to detect the micellar growth.

Miltefosine and BODIPY-labeled alkylphosphocholine with leishmanicidal activity: Aggregation properties and interaction with model membranes

Miltefosine (hexadecylphosphocholine, MT) afforded successful oral treatment against human visceral and cutaneous leishmaniasis. Knowledge of MT aggregation in aqueous solutions and of its interaction with lipid membranes is important to understand pharmacokinetics, bioavailability and antiparasitic effects. Methods based on surface tension and fluorescence spectroscopy gave the value of 50μM for critical micelle concentration (CMC) in buffered water solution, and the value is influenced by salt content. Interaction between MT and lipid vesicles was monitored by fluorescence and the drug promotes only minor changes in the surface of the vesicles. At MT concentration below CMC, modifications in probe fluorescence are due to disordering effects promoted by the drug in the bilayer. Above the CMC, MT promoted large modifications in the vesicles as a whole, resulting in mixed aggregates containing lipids, drug and probe. Effects are less evident above thermal phase transition when the bilayer is in less ordered state.

Impact of urea on detergent micelle properties

Co-solvents, such as urea, can entail drastic changes in the micellization behavior of detergents. We present a systematic quantification of the impact of urea on the critical micellar concentration, the micellization thermodynamics, and the micelle size in three homologous series of commonly used non-ionic alkyl detergents. To this end, we performed demicellization experiments by isothermal titration calorimetry and hydrodynamic size measurements by dynamic light scattering on alkyl maltopyranosides, cyclohexyl alkyl maltopyranosides, and alkyl glucopyranosides at urea concentrations of 0-8 M. For all detergents studied, we found that the critical micellar concentration increases exponentially because the absolute Gibbs free energy of micellization decreases linearly over the entire urea concentration range, as does the micelle size. In contrast, the enthalpic and entropic contributions to micellization reveal more complex, nonlinear dependences on urea concentration. Both free energy and size changes are more pronounced for long-chain detergents, which bury more apolar surface area upon micelle formation. The Gibbs free energy increments per methylene group within each detergent series depend on urea concentration in a linear fashion, although they result from the entropic term for alkyl maltosides but are of enthalpic origin for cyclohexyl alkyl maltosides. We compare our results to transfer free energies of amino acid side chains, relate them to protein-folding data, and discuss how urea-induced changes in detergent micelle properties affect in vitro investigations on membrane proteins.

Effects of arginine and other solution additives on the self-association of different surfactants: an investigation at single-molecule resolution

Fluorescence correlation spectroscopy is used to monitor the self-association of SDS and DTAB monomers at single-molecule resolution. Tetramethylrhodamine-5-maleimide (TMR) has been chosen as a probe because rhodamine dyes have been shown to bind surfactant micelles. Correlation functions obtained by FCS experiments have been fit using conventional discrete diffusional component analysis as well as the more recent maximum entropy method (MEM). Hydrodynamic radii calculated from the diffusion time values increase with surfactant concentration as the monomers self-associate. Effects of several solution additives on the self-association property of the surfactants have been studied. Urea and glycerol inhibit self-association, and arginine shows a dual nature. With SDS, arginine favors self-association, and with DTAB, it inhibits micelle formation. We propose surfactant self-association to be a "supersimplified" model of protein aggregation.

A new semi-empirical kinetic method for the determination of ion exchange constants for the counterions of cationic micelles

A new method, based upon semi-empirical kinetic approach, for the determination of ion exchange constant for ion exchange processes occurring between counterions at the cationic micellar surface is described in this review article. Basically, the method involves a reaction kinetic probe which gives observed pseudo-first-order rate constants (k(obs)) for a nucleophilic substitution reaction between the nonionic and anionic reactants (R and S) in the presence of a constant concentration of both reactants as well as cationic micelles and varying concentrations of an inert inorganic or organic salt (MX). The observed data (k(obs), versus [MX]) fit satisfactorily (in terms of residual errors) to an empirical equation which could be derived from an equation explaining the mechanism of the reaction of the kinetic probe in terms of pseudophase micellar (PM) model coupled with another empirical equation. This (another) empirical equation explains the effect of [MX] on cationic micellar binding constant (K(S)) of the anionic reactant (say S) and gives an empirical constant, K(X/S). The magnitude of K(X/S) is the measure of the ability of X(-) to expel S(-) from a cationic micellar pseudophase to the bulk aqueous phase through ion exchange X(-)/S(-). The values of K(X/S) and K(Y/S) (where Y(-) is another inert counterion) give the ion exchange constant, K(X)(Y) (=K(X)/K(Y) where K(X) and K(Y) represent cationic micellar binding constants of X(-) and Y(-), respectively). The suitability of this method is demonstrated by the use of three different reaction kinetic probes and various MX.

Kinetic Coupled with UV Spectral Evidence for Near-Irreversible Nonionic Micellar Binding ofN-Benzylphthalimide under the Typical Reaction Conditions: An Observation Against a Major Assumption of the Pseudophase Micellar Model

Pseudo-first-order rate constants (k(obs)) for alkaline hydrolysis of N-benzylphthalimide (1) show a nonlinear decrease with the increase in [C(m)E(n)]T (total concentration of Brij 58, m = 16, n = 20 and Brij 56, m = 16, n = 10) at constant [CH(3)CN] and [NaOH]. These nonionic micellar effects, within the certain typical reaction conditions, have been explained in terms of the pseudophase micellar (PM) model. The values of micellar binding constants (KS) of 1 are 1.04 x 10(3) M(-1) (at 1.0 x 10(-3) M NaOH) and 1.08 x 10(3) M(-1) (at 2.0 x 10(-3) M NaOH) for C(16)E(20) as well as 600 M(-1) (at 7.6 x 10(-4) M NaOH) and 670 M(-1) (at 1.0 x 10(-3) M NaOH) for C(16)E(10) micelles. The pseudo-first-order rate constants (kM) for hydrolysis of 1 in C(16)E(20) micellar pseudophase are approximately 90-fold smaller than those (kW) in water phase. The values of kM for hydrolysis of 1 in C(16)E(10) micelles are almost zero. Kinetic coupled with UV spectral data reveals significant irreversible nonionic micellar binding of 1 molecules in the micellar environment of nearly zero hydroxide ion concentration at >or=0.14 M C(16)E(20) and 1.0 x 10(-3) M NaOH while such observations could not be detected at <or=0.17 M C(16)E(20) and 2.0 x 10(-3) M NaOH. Significantly, such irreversible C(16)E(10) micellar binding of 1 molecules could be detected at 8.8 x 10(-2) M C(16)E(10) and 1.0 x 10(-3) M NaOH as well as at >or=3 x 10(-3) M C(16)E(10) and 7.6 x 10(-4) M NaOH, while the rate of hydrolysis of 1 is completely ceased at >or=0.05 M C(16)E(10) and 7.6 x 10(-4) M NaOH. The rate of hydrolysis of 1 at 5.0 x 10(-2) and 8.8 x 10(-2) M C(16)E(10) and 1.0 x 10(-3) M NaOH reveals the formation of presumably phthalic anhydride, whereas such observation was not observed in the C(16)E(20) micellar system under similar experimental conditions.

Monitoring the looping up of acyl chain labeled NBD lipids in membranes as a function of membrane phase state

Lipids that are labeled with the NBD (7-nitrobenz-2-oxa-1,3-diazol-4-yl) group are widely used as fluorescent analogues of native lipids in biological and model membranes to monitor a variety of processes. The NBD group of acyl chain labeled NBD lipids is known to loop up to the membrane interface in fluid phase membranes. However, the organization of these lipids in gel phase membranes is not resolved. In this paper, we monitored the influence of the membrane phase state on the looping up behavior of acyl chain labeled NBD lipids utilizing red edge excitation shift (REES) and other sensitive fluorescence approaches. Interestingly, our REES results indicate that NBD group of lipids, which are labeled at the fatty acyl region, resides in the more hydrophobic region in gel phase membranes, and complete looping of the NBD group occurs only in the fluid phase. This is supported by other fluorescence parameters such as polarization and lifetime. Taken together, our results demonstrate that membrane packing, which depends on temperature and the phase state of the membrane, significantly affects the localization of acyl chain labeled NBD lipids. In view of the wide ranging use of NBD-labeled lipids in cell and membrane biology, these results could have potentially important implications in future studies involving these lipids as tracers.

Orientation and dynamics of melittin in membranes of varying composition utilizing NBD fluorescence

Melittin is a cationic hemolytic peptide isolated from the European honey bee, Apis mellifera. The organization of membrane-bound melittin has earlier been shown to be dependent on the physical state and composition of membranes. In this study, we covalently labeled the N-terminal (Gly-1) and Lys-7 of melittin with an environment-sensitive fluorescent probe, the NBD group, to monitor the influence of negatively charged lipids and cholesterol on the organization and dynamics of membrane-bound melittin. Our results show that the NBD group of melittin labeled at its N-terminal end does not exhibit red edge excitation shift in DOPC and DOPC/DOPG membranes, whereas the NBD group of melittin labeled at Lys-7 exhibits REES of approximately 8 nm. This could be attributed to difference in membrane microenvironment experienced by the NBD groups in these analogs. Interestingly, the membrane environment of the NBD groups is sensitive to the presence of cholesterol, which is supported by time-resolved fluorescence measurements. Importantly, the orientation of melittin is found to be parallel to the membrane surface as determined by membrane penetration depth analysis using the parallax method in all cases. Our results constitute the first report to our knowledge describing the orientation of melittin in cholesterol-containing membranes. These results assume significance in the overall context of the role of membrane lipids in the orientation and function of membrane proteins and peptides.

Effect of ionic strength on the organization and dynamics of membrane-bound melittin

Melittin, a cationic hemolytic peptide, is intrinsically fluorescent due to the presence of a single functionally important tryptophan residue. We have previously shown that the sole tryptophan of melittin is localized in a motionally restricted environment in the membrane interface. We have monitored the effect of ionic strength on the organization and dynamics of membrane-bound melittin utilizing fluorescence and circular dichroism (CD) spectroscopic approaches. Our results show that red edge excitation shift (REES) of melittin bound to membranes is sensitive to the change in ionic strength of the medium. This could be attributed to a change in the immediate environment around melittin tryptophan with increasing ionic strength due to differential solvation of ions. Interestingly, the rotational mobility of melittin does not appear to be affected with change in ionic strength. In addition, fluorescence parameters such as lifetime and acrylamide quenching of melittin indicate an increase in water penetration in the membrane interface upon increasing ionic strength. Our results suggest that the solvent dynamics and water penetration in the interfacial region of the membranes are significantly affected at physiologically relevant ionic strength. These results assume significance in the overall context of the influence of ionic strength in the organization and dynamics of membrane proteins and membrane-active peptides.

Effect of urea on self-organization of sodium N-(11-acrylamidoundecanoyl)-l-valinate in water

In this paper, the hypotheses proposed for the action of urea on the perturbation of molecular assemblies have been tested through studies of the effects of urea on the aggregation properties of a chiral surfactant, sodium N-(11-acrylamidoundecanoyl)-L-valinate in water. Surface tension, fluorescence, and circular dichroism were used to characterize the solution behavior of the amphiphile in the presence of urea. Surface tension measurement indicated decrease of critical aggregation concentration (cac) with the addition of urea in the low concentration range. Fluorescence probe studies using pyrene and 1-anilinonaphthalene indicated solubilization of urea molecules near the aggregate-water interface. Fluorescence anisotropy measurements using 1,6-diphenylhexatriene as probe molecule suggested increase of packing of the hydrocarbon chains of the amphiphiles upon addition of low concentration of urea. Dynamic light scattering measurements showed an increase of the hydrodynamic radius (R(h)) in the presence of increased concentration of urea. At higher concentrations of urea, the R(h) value decreased. Circular dichroism spectra showed the presence of chiral aggregates even in the presence of high concentration of urea.

Photophysical Study of 3-Acetyl-4-oxo-6,7-dihydro-12H-indolo[2,3-a]quinolizine in Biomimetic Reverse Micellar Nanocavities: A Spectroscopic Approach

Photophysical properties of 3-acetyl-4-oxo-6,7-dihydro-12H-indolo[2,3-a]quinolizine (AODIQ), a bioactive molecule, has been investigated in well-characterized, monodispersed biomimicking nanocavities formed by sodium bis(2-ethylhexyl)sulfosuccinate (AOT) in heptane using steady-state and picosecond time resolved fluorescence and fluorescence anisotropy. The emission behavior of AODIQ is very much dependent upon the water/surfactant mole ratio (W), i.e., on the water pool size of the reverse micellar core. AODIQ exhibits a sharp decrease in fluorescence anisotropy with increasing W, implying that the overall motional restriction experienced by the molecule is decreased with increased hydration. Some of the depth-dependent relevant fluorescence parameters, namely, fluorescence maxima and fluorescence anisotropy (r), have been monitored for exploiting the distribution and microenvironment around the probe in the reverse micelles. Fluorescence spectral position and fluorescence quenching studies suggest that the probe does not penetrate into the reverse micellar core; rather it binds at the interfacial region. Quantitaive estimates of the micropolarity and microviscosity at the binding sites of the probe molecule have been determined as a function of W.