Lipid-protein interactions in membranes: effect of lipid composition on mobility of spin-labeled cysteine residues in yeast plasma membrane.

In order to gain direct evidence for lipid-dependent protein conformation in membrane, effects of modification of lipid composition on mobility of spin-labeled cysteine residues were investigated in the plasma membrane of the yeast Saccharomyces cerevisiae. Conversion of the bulk of phospholipids to diglycerides by treatment of the membrane with phospholipase C substantially enhanced spectral anisotropy. However, alterations of the viscosity of the lipid-bilayer by enriching the membrane with palmitelaidic or oleic acid had no effect on mobility of spin-labeled cysteine residues. These observations indicate that while the spin-labeled residues are not in direct contact with the lipid core of the membrane, there are lipid-protein interactions to the extent that removal of the polar portion of the bulk of phospholipids induces conformational changes in proteins, which in turn restrict mobility of these residues. It is concluded that conformation of membrane proteins on lipid structure and that phospholipids have a role in preserving the native conformation of proteins.     

19F NMR Spectroscopy as a Probe of Cytoplasmic Viscosity and Weak Protein Interactions in Living Cells

Protein mobility in living cells is vital for cell function. Both cytosolic viscosity and weak protein–protein interactions affect mobility, but examining viscosity and weak interaction effects is challenging. Herein, we demonstrate the use of ¹⁹F NMR spectroscopy to measure cytoplasmic viscosity and to characterize nonspecific protein–protein interactions in living Escherichia coli cells. The origins of resonance broadening in Escherichia coli cells were also investigated. We found that sample inhomogeneity has a negligible effect on resonance broadening, the cytoplasmic viscosity is only about 2–3 times that of water, and ubiquitous transient weak protein–protein interactions in the cytosol play a significant role in governing the detection of proteins by using in‐cell NMR spectroscopy.     

Translational Dynamics of Lipidated Ras Proteins in the Presence of Crowding Agents and Compatible Osmolytes

Ras proteins are small GTPases and are involved in transmitting signals that control cell growth, differentiation, and proliferation. Since the cell cytoplasm is crowded with different macromolecules, understanding the translational dynamics of Ras proteins in crowded environments is crucial to yielding deeper insight into their reactivity and function. Herein, the translational dynamics of lipidated N‐Ras and K‐Ras4B is studied in the bulk and in the presence of a macromolecular crowder (Ficoll) and the compatible osmolyte and microcrowder sucrose by fluorescence correlation spectroscopy. The results reveal that N‐Ras forms dimers due to the presence of its lipid moiety in the hypervariable region, whereas K‐Ras4B remains in its monomeric form in the bulk. Addition of a macromolecular crowding agent gradually favors clustering of the Ras proteins. In 20 wt % Ficoll N‐Ras forms trimers and K‐Ras4B dimers. Concentrations of sucrose up to 10 wt % foster formation of N‐Ras trimers and K‐Ras dimers as well. The results can be rationalized in terms of the excluded‐volume effect, which enhances the association of the proteins, and, for the higher concentrations, by limited‐hydration conditions. The results of this study shed new light on the association state of these proteins in a crowded environment. This is of particular interest for the Ras proteins, because their solution state—monomeric or clustered—influences their membrane‐partitioning behavior and their interplay with cytosolic interaction partners.     

Fluorescence recovery after photobleaching measurements of polymers in a surface forces apparatus

The surface forces apparatus has been combined with fluorescence recovery after photobleaching to measure translational diffusion of polymer confined between mica sheets. This article presents findings using polydimethylsiloxane with number‐average molecular weight M_n = 2200 g mol^?1, the chains end‐labeled with soluble fluorescent dye. Melts with thickness 10 nm display a translational diffusion coefficient (D) with a bulk component and a slower component assigned to surface diffusion. Reduction of thickness to 1.8 nm causes mobility to split into two populations—an immobile fraction (immobile on the time scale of 30–60 min) and a mobile fraction who's D slow only weakly with diminishing film thickness. However, when load causes the confining mica sheets to flatten, D of the mobile fraction drops by up to an additional order of magnitude, depending on the local pressure that squeezes on the polymer. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2010     

Electric migration of α‐hemolysin in supported n‐bilayers: A model for transmembrane protein microelectrophoresis

Proteome analysis involves separating proteins as a preliminary step toward their characterization. This paper reports on the translational migration of a model transmembrane protein (α‐hemolysin) in supported n‐bilayers (n, the number of bilayers, varies from 1 to around 500 bilayers) when an electric field parallel to the membrane plane is applied. The migration changes in direction as the charge on the protein changes its sign. Its electrophoretic mobility is shown to depend on size and charge. The electrophoretic mobility varies as 1/R², with R the equivalent geometric radius of the embedded part of the protein. Measuring mobilities at differing pH in our system enables us to determine the pI and the charge of the protein. Establishing all these variations points to the feasibility of electrophoretic transport of a charged object in this medium and is a first step toward electrophoretic separation of membrane proteins in n‐bilayer systems.     

Computer simulation study of bulk atactic polystyrene in the vicinity of the glass transition

Molecular dynamics (MD) simulations of bulk atactic polystyrene have been performed in a temperature range from 100 K to 650 K at atmospheric pressure. Local translational mobility has been investigated by measuring the mean square translational displacements of monomers. The long-time asymptotic slope of these dependencies is 0.54 at T>T_g, showing Rouse behavior. Cross-over from motion in the cage to Rouse like dynamics has been studied at T>T_g with a characteristic crossover time follows a power law behavior as a function of T, as predicted by mode-coupling theory (MCT). Local orientational mobility has been studied via the orientational autocorrelation functions, ACFs, (Legendre polynomials of the first and second, order) of both the main-chain and side-group bonds. The relaxation times of the orientational α-relaxation follow the same power law (γ∼2.9) as the characteristic translational diffusion time. Below T>T_g both types of dynamics are described by the same activated law. The ACFs time-distribution functions reveal the existence of activated local rearrangements already above T>T_g.     

Dipolar Relaxation Dynamics at the Active Site of an ATPase Regulated by Membrane Lateral Pressure

The active transport of ions across biological membranes requires their hydration shell to interact with the interior of membrane proteins. However, the influence of the external lipid phase on internal dielectric dynamics is hard to access by experiment. Using the octahelical transmembrane architecture of the copper‐transporting P_1B‐type ATPase from Legionella pneumophila as a model structure, we have established the site‐specific labeling of internal cysteines with a polarity‐sensitive fluorophore. This enabled dipolar relaxation studies in a solubilized form of the protein and in its lipid‐embedded state in nanodiscs. Time‐dependent fluorescence shifts revealed the site‐specific hydration and dipole mobility around the conserved ion‐binding motif. The spatial distribution of both features is shaped significantly and independently of each other by membrane lateral pressure.     

Temperature dependence of molecular motions in bulk polystyrene

Time-resolved optical spectroscopy is used to investigate the reorientation of three rigid probes and one labeled chain in bulk polystyrene. Orientational correlation times for these probes and labels are found to be in the range of 10^?8–10^?10 s at temperatures of 180–300°C. Consistent with previous studies, the attachment of a chromophore into the chain backbone slows its dynamics by about an order of magnitude. The temperature dependences of the correlation times are similar to the temperature dependence of the viscosity. When combined with probe reorientation times near and below T_g, these results indicate that probe reorientation tracks the temperature dependence of the viscosity quite well over twelve decades in time. In contrast, literature results for the translational diffusion of similarly sized probes indicates a substantially weaker temperature dependence near T_g. Thus it appears that a fundamental change in the mechanism of probe motion occurs near T_g. © 1994 John Wiley & Sons, Inc.     

Curvature sorting of peripheral proteins on solid-supported wavy membranes

Cellular membrane deformation and the associated redistribution of membrane-bound proteins are important aspects of membrane function. Current model membrane approaches for studying curvature sensing are limited to positive curvatures and often require complex and delicate experimental setups. To overcome these challenges, we fabricated a wavy substrate by imposing a range of curvatures onto an adhering lipid bilayer membrane. We examined the curvature sorting of several peripheral proteins binding to the wavy membrane and observed them to partition into distinct regions of curvature. Furthermore, single-molecule imaging experiments suggested that the curvature sensing of proteins on low-curvature substrates requires cooperative interactions.     

Self-assembly of solid-supported membranes using a triggered fusion of phospholipid-enriched proteoliposomes prepared from the inner mitochondrial membrane

A general procedure for the formation ofsolid-supported artificial membranes containing transmembrane proteins is reported. The main objective was to directly use the pool of proteins of the native biomembrane (here the inner membrane from mitochondria of human carcinogenic hepatic cells) and to avoid purification steps with detergent. Proteoliposomes of phospholipid-enriched inner membranes from mitochondria were tethered and fused onto a tailored surface via a streptavidin link. The failure of some preliminary experiments on membrane formation was attributed to strong nonspecific interactions between the solid surface and the protuberant hydrophilic parts of the transmembrane complexes. The correct loading of uniform membranes was performed after optimization of a tailored surface, covered with a grafted short-chain poly(ethylene glycol), so that nonspecific interactions are reduced. Step-by-step assembly of the structure and triggered fusion of the immobilized proteoliposomes were monitored by surface plasmon resonance and fluorescence photobleaching recovery, respectively. The long-range lateral diffusion coefficient (at 22 degrees C) for a fluorescent lipid varies from 2.5 x 10(-8) cm2 s(-1) for a tethered lipid bilayer without protein to 10(-9) cm2 s(-1) for a tethered membrane containing the transmembrane proteins of the respiratory chain at a protein area fraction of about 15%. The decrease in the diffusion coefficient in the tethered membrane with increase in protein area fraction was too pronounced to be fully explained by the theoretical models of obstructed lateral diffusion. Covalent tethering links with the solid are certainly involved in the decrease of the overall lateral mobility of the components in the supported membrane at the highest protein-to-lipid ratios.     

Molecular probe techniques for studying diffusion and relaxation in thin and ultrathin polymer films

Two optically based, molecular probe techniques are employed to study relaxation and small-molecule translational diffusion in thin and ultrathin (thicknesses < ∼200 nm) polymer films. Second harmonic generation (SHG) is used to study the reorientational dynamics of a nonlinear optical chromophore, Disperse Red 1 (DR1) (previously shown to be an effective probe of α-relaxation dynamics) either covalently attached or freely doped in polymer films. Our studies on films ranging in thickness from 7 nm to 1 μm show little change in T_g with film thickness; however, a substantial broadening of the relaxation distribution is observed as film thickness decreases below approximately 150 nm. Experimental guidelines are given for using fluorescence nonradiative energy transfer (NRET) to study translational diffusion in ultrathin polymer films. Appropriate choice of a fluorescence donor species is important along with ensuring that diffusion is slow enough to be measured appropriately. Initial results on the diffusion of a small-molecule probe, lophine, in poly(isobutyl methacrylate) indicates that there is little change in probe diffusion coefficients in films as thin as 90 nm as compared to bulk films. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35: 2795–2802, 1997     

Effects of diffusion on the self-termination kinetics of isopropylol radicals in solution

Rate constants for the bimolecular self-reaction of isopropylol radicals [(CH₃)₂?OH] in various solvents are determined as functions of temperature by kinetic electron spin resonance. For hydrocarbon solvents they are well described by theoretical equations for reactions controlled by translational diffusion if diffusion coefficients of 2-propanol, a constant reaction distance, and a spin statistical factor of 1/4 are applied. Deviations from 2k_t ～ D at high diffusion constants agree with trends expected from recent theoretical models. For hydrogen-bonding solvents large negative deviations are observed. They are attributed to steric constraints and slower rotational diffusion of radical–solvent aggregates. The disproportionation-to-combination ratio of isopropylol increases with solvent viscosity. As previously for tert-butyl, this is explained by anisotropic reorientation during encounters. Further, rate data are given for the decarbonylation of the 2-hydroxy-2-methylpropanoyl radical and for several hydrogen abstraction reactions of isopropylol.     

Effect of chain length on rates of diffusion-limited small molecule-polymer and polymer-polymer reactions: Phosphorescence quenching studies

Model interactions have been studied by phosphorescence quenching to obtain a better understanding of the chain length dependence of interpolymeric chain end-chain end reactions such as those involved in the termination step of free radical polymerization. For small molecule-polymer interactions in dilute cyclohexane solution, quenching rate constant (k_q) data agree with the Smoluchowski equation prediction that k_q scales as polymer molecular weight (MW) to the -½ power, confirming self-diffusion control. For polymer-polymer interactions in dilute solution, the chain length dependence is weaker than that predicted by translational diffusion control, as described by the Smoluchowski equation, but is stronger than that predicted by renormalization group theory. For interactions between 70000 MW benzil-end-labeled polystyrene and varying MWs of anthracene-end-labeled polystyrene at 300 g/L polymer, k_q decreases by a factor of 10 in going from MWs of 100 to 1000 g/mol; beyond 1000 g/mol, k_q is nearly independent of chain length. Such effects indicate that the importance of oligomeric radical self-diffusion and polymer radical chain-end segmental mobility must be carefully considered in understanding the termination process in free radical polymerization. © 1996 John Wiley & Sons, Inc.     

NMR and Molecular Genetics as Tools for Investigating Protein Interactions in Membrane Systems

In our laboratory, we have applied the tools of nuclear magnetic resonance (NMR) spectroscopy and molecular genetics to investigate the structural and dynamic properties of membrane-associated proteins and their interactions with membrane components. There are two general classes of membrane proteins, i.e., intrinsic and peripheral ones. For the intrinsic membrane proteins, we have chosen the membranebound D-lactate dehydrogenase (D-LDH) of Escherichia coli as a model to study protein-lipid interactions in membranes. D-LDH is a respiratory enzyme of molecularweight 65, 000 containing flavin adenine dinucleotide (FAD) as a cofactor. The activity of purified D-LDH is enhanced up to 100-fold by lipids and detergents. The gene for D-LDH has been sequenced, and production of the enzyme amplified up to 300-times normal levels. We have biosynthetically incorporated 5-fluorotryptophan (5F-Trp) into D-LDH and studied the five Trp residues by ¹⁹F-NMR spectroscopy. In order to gain additional information using ¹⁹F-NMR, site-specific, oligonucleotide-directed mutagenesis has been used to insert a sixth Trp into D-LDH at various positions throughout the 571-amino acid chain. These mutant D-LDHs are being characterized biochemically and through NMR. For peripheral membrane proteins, we have chosen two periplasmic binding proteins, histidine-binding protein J (J protein) of Salmonella Typhimurium and glutamine-binding protein (GlnBP) of E. coli as models to investigate the structure-function relationship in periplasmic binding protein-mediated active transport systems. These two proteins both have molecular weights of approximately 25, 000. By using mutant J proteins and GlnBPs and site-specific, oligonucleotide-directed mutagenesis techniques, we have assigned several resonances to specific amino acid residues. We are investigating the relationship between ligand-induced conformational changes in these two proteins and their roles in the active transport of ligand across the cell membrane. We have found that a combination of isotopic labeling, biochemistry, molecular biology, and NMR is a very useful approach to investigate various interactions of membrane-associated protein systems.     

Accurately describing weak analyte-additive interactions by capillary electrophoresis

When modeling analyte-additive interactions in capillary electrophoresis (CE), it is necessary to correct for all changes in the apparent electrophoretic mobility of an analyte that are not due to specific binding. Current models based on dynamic complexation have corrected for bulk viscosity changes in the background electrolyte (BGE) when additives are used, while assuming negligible changes in the dielectric constant and other physicochemical properties of the solution. In this report, a study of weak interactions between deoxyribonucleotides and hydroxypropyl-beta-cyclodextrin (HP-beta-CD) revealed significant nonideality in binding isotherms. Changes in the dielectric properties of the solution due to the addition of high concentrations of HP-beta-CD to the BGE was observed to alter the electrophoretic mobility of analytes. A relative dielectric correction factor was required to normalize analyte mobilities to a reference state of zero additive concentration. The use of both a relative dielectric factor and a viscosity correction factor was found to increase the accuracy of the model, reflected by a higher degree of correlation between predicted and measured analyte mobilities. This type of correction is particularly relevant when studying weak analyte binding interactions or when using high concentrations of additive in the BGE. This work is vital for accurate determination of weak binding constants and mobility values, as well as providing a deeper understanding of the fundamental parameters influencing a separation in CE.     

Anomalous and Normal Diffusion of Tracers in Crowded Environments: E ect of Size Disparity between Tracer and Crowders

The dynamics of tracers in crowded matrix is of interest in various areas of physics, such as the diffusion of proteins in living cells. By using two-dimensional (2D) Langevin dynamics simulations, we investigate the diffusive properties of a tracer of a diameter in crowded environments caused by randomly distributed crowders of a diameter. Results show that the emergence of subdiffusion of a tracer at intermediate time scales depends on the size ratio of the tracer to crowders δ. If δ falls between a lower critical size ratio and a upper one, the anomalous diffusion occurs purely due to the molecular crowding. Further analysis indicates that the physical origin of subdiffusion is the "cage effect". Moreover, the subdiffusion exponent α decreases with the increasing medium viscosity and the degree of crowding, and gets a minimum αmin=0.75 at δ=1. At long time scales, normal diffusion of a tracer is recovered. For δ≤1, the relative mobility of tracers is independent of the degree of crowding. Meanwhile, it is sensitive to the degree of crowding for δ>1. Our results are helpful in deepening the understanding of the diffusive properties of biomacromolecules that lie within crowded intracellular environments, such as proteins, DNA and ribosomes.     

Gelation mechanism of ionic polysaccharides

Experimental results obtained by membrane equilibria, osmotic pressure, viscosity and circular dichroism measurements on alginate and pectate solutions in the presence of Ca²⁺ ions are presented. From equilibrium dialysis data both electrostatic and cooperative interactions seem to describe the binding process of Ca²⁺ ions onto polymer chains. An increase of the number-average molecular weight M̄_n for both poly-saccharides with calcium ion concentration is observed. An increase of polymer dimensions can well account for the observed increase of the intrinsic viscosity [η] with bound Ca²⁺ ion concentration at several ionic strengths.     

SITE-TO-SITE DIFFUSION IN PROTEINS AS OBSERVED BY ENERGY TRANSFER AND FREQUENCY-DOMAIN FLUOROMETRY *

Abstract We report measurements of the site-to-site diffusion coefficients in proteins and model compounds, which were measured using time-dependent energy transfer and frequency-domain fluorometry. The possibility of measuring these diffusion coefficients were shown from simulations, which demonstrate that donor (D)-to-acceptor (A) diffusion alters the donor frequency response, and that this effect is observable in the presence of a distribution of donor-to-acceptor distances. For decay times typical of tryptophan fluorescence, the simulations indicate that D-A diffusion coefficients can be measured ranging from ^?7 to ^?5 cm²/s. This possibility was verified by studies of a methylenechain linked D-A pair in solutions of varying viscosity. The D-A diffusion was also measured for two labeled peptides and two proteins, melittin and troponin I. In most cases we used global analysis of data sets obtained with varying amounts of collisional quenchers to vary the donor decay time. Unfolding of troponin I results in more rapid D-A diffusion, whereas for melittin more rapid diffusion was observed in the α-helical state but over a limited range of distances.     

The Ras dimer structure

Oncogenic mutated Ras is a key player in cancer, but despite intense and expensive approaches its catalytic center seems undruggable. The Ras dimer interface is a possible alternative drug target. Dimerization at the membrane affects cell growth signal transduction. In vivo studies indicate that preventing dimerization of oncogenic mutated Ras inhibits uncontrolled cell growth. Conventional computational drug-screening approaches require a precise atomic dimer model as input to successfully access drug candidates. However, the proposed dimer structural models are controversial. Here, we provide a clear-cut experimentally validated N-Ras dimer structural model. We incorporated unnatural amino acids into Ras to enable the binding of labels at multiple positions via click chemistry. This labeling allowed the determination of multiple distances of the membrane-bound Ras-dimer measured by fluorescence and electron paramagnetic resonance spectroscopy. In combination with protein–protein docking and biomolecular simulations, we identified key residues for dimerization. Site-directed mutations of these residues prevent dimer formation in our experiments, proving our dimer model to be correct. The presented dimer structure enables computational drug-screening studies exploiting the Ras dimer interface as an alternative drug target.

By combining the incorporation of unnatural amino acids, click chemistry, FRET and EPR distance measurements, protein modeling and biomolecular simulations, we obtained an unambiguous Ras dimer structural model and disrupt the dimer by mutagenesis.