Single-particle tracking for DNA tether length monitoring

We describe a simple single-particle tracking approach for monitoring the length of DNA molecules in tethered particle motion experiments. In this method, the trajectory of a submicroscopic bead tethered by a DNA molecule to a glass surface is determined by videomicroscopy coupled to image analysis. The amplitude of motion of the bead is measured by the standard deviation of the distribution of successive positions of the bead in a given time interval. We were able to describe theoretically the variation of the equilibrium value of the amplitude of the bead motion with the DNA tether length for the entire applicable DNA length range (up to ~3500 bp). The sensitivity of the approach was illustrated by the evidence obtained for conformational changes introduced into a Holliday junction by the binding of the Escherichia coli RuvA protein. An advantage of this method is that the trajectory of the tethered bead, rather than its averaged motion, is measured, allowing analysis of the conformational dynamics of DNA chains at the single-molecule level.     

Tag–probe labeling methods for live-cell imaging of membrane proteins

Instead of using reconstituted proteoliposomes, in situ investigations of membrane proteins in living cell membranes are important because the heterogeneous and dynamic nature of biomembranes significantly affects their behavior. Protein-specific labeling is a key technique for the detection of a target protein by fluorescence measurements, particularly fluorescence microscopy. However, conventional genetic fusion with fluorescent proteins has several shortcomings. Post-translational labeling methods using a genetically encodable tag and synthetic probes targeting to the tag can overcome these limitations. This review summarizes emerging tag–probe techniques for labeling specific membrane proteins and their applications, including endocytotic internalization, partitioning to specific membrane domains, interprotein interactions, and conformational changes.     

On the mechanism of the reconstitution of F1-depleted ATPase complex with purified F1: Possible conformational effects

The membrane sector (F₀) of H⁺-ATPase was prepared by trypsin and urea treatment of F₁-F₀ and reconstituted with purified F₁. The oligomycin sensitivity of the reconstituted F₁-F₀ complex obtained by treating F₁ or F₀ with Mg²⁺ before binding is much higher than that obtained without Mg²⁺ treatment. The greater change in the intrinsic fluorescence of the reconstituted F₁-F₀ complex obtained by Mg²⁺ treatment suggests that conformational changes may occur during the reconstitution. We deduce that Mg²⁺ binds to membrane lipids, thus decreasing membrane fluidity and changing the physical state of the lipids to provide a suitable microenvironment for conformational changes in F₀. The data also suggest that the conformational change in the F₀ portion of the F₁-F₀ complex can be transmitted to the F₁ portion, the conformation of which is in turn altered, resulting in the formation of an F₁-F₀ complex with high oligomycin sensitivity. On the other hand, Mg²⁺ may act on F₁ directly to induce a suitable conformational change which is then trnsmitted to F₀, resulting in the formation of an H⁺-ATPase with greater sensitivity to oligomycin.Abbreviations STED 0.25 M sucrose, 10 mM Tris-SO₄, 0.2 mM EDTA, and 1 mM dithiothreitol, pH 8.0 - NADH nicotinamide adenine dinucleotide, reduced form - olig. oligomycin - OSCP oligomycin sensitivity conferring protein - F₆ coupling factor 6 - F₁ coupling factor one (or F₁-ATPase) - F₁ ^{+Mg 2+} and F₁ ^{–Mg 2+} the F₁ treated and untreated with 1 mM Mg²⁺ respectively - F₀ the membrane sector proteins of the H⁺-ATPase - TUF₀ trypsin-urea – F₀ - EUF₀ EDTA-urea – F₀ - F₀ ^{+Mg 2+} and F₀ ^{–Mg 2+} the F₀ treated and untreated with 1 mM Mg²⁺ respectively - (F₁ · F₀)^{+Mg 2+} and (F₁ · F₀)^{–Mg 2+} the reconstituted F₁ · F₀ complex containing Mg²⁺-treated F₁ and F₀ and untreated F₁ and F₀ respectively - F₁ · F₀ ^{+Mg 2+} and F₁ · F₀ ^{–Mg 2+} the reconstituted H⁺-ATPase complex derived from the binding of purified F₁ to the F₀ treated and untreated with Mg²⁺ respectively - F₁ ^{+Mg 2+} · F₀ and F₁ ^{–Mg 2+} · F₀ the reconstituted H⁺-ATPase derived from the binding of F₀ to the purified F₁ treated and untreated with Mg²⁺ respectively     

Elastic network normal mode dynamics reveal the GPCR activation mechanism

G‐protein‐coupled receptors (GPCR) are a family of membrane‐embedded metabotropic receptors which translate extracellular ligand binding into an intracellular response. Here, we calculate the motion of several GPCR family members such as the M2 and M3 muscarinic acetylcholine receptors, the A_2A adenosine receptor, the β₂‐adrenergic receptor, and the CXCR4 chemokine receptor using elastic network normal modes. The normal modes reveal a dilation and a contraction of the GPCR vestibule associated with ligand passage, and activation, respectively. Contraction of the vestibule on the extracellular side is correlated with cavity formation of the G‐protein binding pocket on the intracellular side, which initiates intracellular signaling. Interestingly, the normal modes of rhodopsin do not correlate well with the motion of other GPCR family members. Electrostatic potential calculation of the GPCRs reveal a negatively charged field around the ligand binding site acting as a siphon to draw‐in positively charged ligands on the membrane surface. Altogether, these results expose the GPCR activation mechanism and show how conformational changes on the cell surface side of the receptor are allosterically translated into structural changes on the inside. Proteins 2014; 82:579–586. © 2013 Wiley Periodicals, Inc.     

A Remote Controlled Valve in Liposomes for Triggered Liposomal Release

In order to reduce the toxicity and increase the efficacy of drugs, there is a need for smart drug delivery systems. Liposomes are one of the promising tools for this purpose. An ideal liposomal delivery system should be stable, long-circulating, accumulate at the target site and release its drug in a controlled manner. Even though there have been many developments to this end, the dilemma of having a stable liposome during circulation but converting it into a leaky structure at the target site is still a major challenge. So far, most attempts have focused on destabilizing the liposome in response to a specific stimulus at a target site, but with limited success. Our approach is to keep the stable liposome but build in a remote-controlled valve as a new release mechanism, instead. The valve is a pore-forming bacterial membrane protein. It has been engineered such that, after being reconstituted into the liposomes, its opening and closing can be controlled on command by the ambient pH, light or a combination of both. In addition, a much higher degree of flexibility for fine-tuning of the liposome's response to its environment is achieved.     

Rotational mobility and domain flexibility of membrane-bound bacterial coupling factor as detected with the triplet probe eosin-isothiocyanate

The membrane-bound coupling factor (BF₁) of chromatophores from the photosynthetic bacerium Rhodopseudomonas sphaeroides was covalently labeled with the triplet probe eosin-isothiocyanate. The labeled enzyme was isolated and functionally reconstituted into depleted chromatophores from the same bacterium. ATPase and ATP synthase activities of the reconstituted vesicles were strongly dependent on the labeling conditions, decreasing at increasing load of eosin molecules per BF₁. When labeling was carried out in the dark and in the presence of ATP, one molecule of eosin isothiocyanate was bound per BF₁ and the activities catalyzed by the reconstituted and labeled enzyme were as high as in untreated chromatophores. Upon light energization of the chromatophore membrane, a large conformational change of BF₁ could be detected by using the triplet probe as a spectroscopic tool. The domain flexibility and rotational mobility of the reconstituted coupling enzyme were directly related to the enhancement of the ATPase activity induced by light. Both the light-stimulated ATPase activity and conformational changes could be prevented by addition of ADP or oligomycin and affected to the same extent by uncouplers and inhibitors of electron transport. Moreover, the detected conformational changes were reversible in time, appearing with a half-time of 10 ms upon illumination of the chromatophores, and disappearing with a half-time of 70 ms in the dark. The results obtained prove the feasibility of the spectroscopic technique in detecting conformational changes of the membrane-bound BF₁, similarly to what already has been observed for chloroplast coupling factor (Wagner, R. and Junge, W. (1980) FEBS Lett. 114, 327–333), and add to the possibility of characterizing, by this method, energy transduction at a molecular level.     

In vitro Investigation of the MexAB Efflux Pump From Pseudomonas aeruginosa

There is an emerging scientific need for reliable tools for monitoring membrane protein transport. We present a methodology leading to the reconstitution of efflux pumps from the Gram-negative bacteria Pseudomonas aeruginosa in a biomimetic environment that allows for an accurate investigation of their activity of transport. Three prerequisites are fulfilled: compartmentation in a lipidic environment, use of a relevant index for transport, and generation of a proton gradient. The membrane protein transporter is reconstituted into liposomes together with bacteriorhodopsin, a light-activated proton pump that generates a proton gradient that is robust as well as reversible and tunable. The activity of the protein is deduced from the pH variations occurring within the liposome, using pyranin, a pH-dependent fluorescent probe. We describe a step-by-step procedure where membrane protein purification, liposome formation, protein reconstitution, and transport analysis are addressed. Although they were specifically designed for an RND transporter, the described methods could potentially be adapted for use with any other membrane protein transporter energized by a proton gradient.     

A remote controlled valve in liposomes for triggered liposomal release

In order to reduce the toxicity and increase the efficacy of drugs, there is a need for smart drug delivery systems. Liposomes are one of the promising tools for this purpose. An ideal liposomal delivery system should be stable, long-circulating, accumulate at the target site and release its drug in a controlled manner. Even though there have been many developments to this end, the dilemma of having a stable liposome during circulation but converting it into a leaky structure at the target site is still a major challenge. So far, most attempts have focused on destabilizing the liposome in response to a specific stimulus at a target site, but with limited success. Our approach is to keep the stable liposome but build in a remote-controlled valve as a new release mechanism, instead. The valve is a pore-forming bacterial membrane protein. It has been engineered such that, after being reconstituted into the liposomes, its opening and closing can be controlled on command by the ambient pH, light or a combination of both. In addition, a much higher degree of flexibility for fine-tuning of the liposome's response to its environment is achieved.     

High-level expression of soluble subunit b of F1F0 ATP synthase in Escherichia coli cell-free system

The overexpression of subunit b of F₁F₀ adenosine triphosphate (ATP) synthase from Escherichia coli is so toxic that it even prevents the transformation of plasmids encoding this protein into E. coli BL21 (DE3). In the present work, E. coli cell-free system was chosen as an alternative to express this highly toxic membrane protein. This protein was either produced as precipitates followed by detergent resolubilization or expressed as a soluble form with detergent addition. Among several types of tested detergents, Brij 58 could effectively solubilize approximately 85% of the target membrane protein within a wide range of concentration (48 to 178 times critical micelle concentration [CMC]) with little effect on the expression level. With the presence of Brij 58 at the final concentration of 96 times CMC in the E. coli cell-free system, 789 μg/mL of soluble subunit b was achieved after 4 h biosynthesis, which is the highest level for the expression of membrane proteins in a batch-mode cell-free expression system. The present work provides a rapid and efficient procedure of expressing one membrane protein with high cytotoxicity in the cell-free system and will be helpful to further exploration of reconstituting F₁F₀ ATP synthase into liposome or polymer vesicle to design a nanoelectromechanical system device.     

Fold-Unfold Transitions in the Selectivity and Mechanism of Action of the N-Terminal Fragment of the Bactericidal/Permeability-Increasing Protein (rBPI21)

Septic or endotoxic shock is a common cause of death in hospital intensive care units. In the last decade numerous antimicrobial peptides and proteins have been tested in the search for an efficient drug to treat this lethal disease. Now in phase III clinical trials, rBPI₂₁, a recombinant N-terminal fragment of the bactericidal/permeability-increasing protein (BPI), is a promising drug to reduce lesions caused by meningococcal sepsis. We correlated structural and stability data with functional information of rBPI₂₁ bound to both model systems of eukaryotic and bacterial membranes. On interaction with membranes, rBPI₂₁ loses its conformational stability, as studied by circular dichroism. This interaction of rBPI₂₁ at membrane level was higher in the presence of negatively charged phospholipid relatively to neutral ones, with higher partition coefficients (K_p), suggesting a preference for bacterial membranes over mammalian membranes. rBPI₂₁ binding to membranes is reinforced when its disulfide bond is broken due to conformational changes of the protein. This interaction is followed by liposome aggregation due to unfolding, which ensures protein aggregation, and interfacial localization of rBPI₂₁ in membranes, as studied by extensive quenching by acrylamide and 5-deoxylstearic acid and not by 16-deoxylstearic acid. An uncommon model of the selectivity and mechanism of action is proposed, where membrane induces unfolding of the antimicrobial protein, rBPI₂₁. The unfolding ensures protein aggregation, established by protein-protein interaction at membrane surface or between adjacent membranes covered by the unfolded protein. This protein aggregation step may lead to membrane perturbation.     

Structural Changes during ATP Hydrolysis Activity of the ATP Synthase from Escherichia coli as Revealed by Fluorescent Probes

F₁F₀-ATPase complexes undergo several changes in their tertiary and quaternary structureduring their functioning. As a possible way to detect some of these different conformationsduring their activity, an environment-sensitive fluorescence probe was bound to cysteineresidues, introduced by site-directed mutagenesis, in the subunit of the Escherichia colienzyme. Fluorescence changes and ATP hydrolysis rates were compared under variousconditions in F₁ and in reconstituted F₁F₀. The results are discussed in terms of possible modes ofoperation of the ATP synthases.     

Assessing the Conformational Changes of pb5, the Receptor-binding Protein of Phage T5, upon Binding to Its Escherichia coli Receptor FhuA

Within tailed bacteriophages, interaction of the receptor-binding protein (RBP) with the target cell triggers viral DNA ejection into the host cytoplasm. In the case of phage T5, the RBP pb5 and the receptor FhuA, an outer membrane protein of Escherichia coli, have been identified. Here, we use small angle neutron scattering and electron microscopy to investigate the FhuA-pb5 complex. Specific deuteration of one of the partners allows the complete masking in small angle neutron scattering of the surfactant and unlabeled proteins when the complex is solubilized in the fluorinated surfactant F₆-DigluM. Thus, individual structures within a membrane protein complex can be described. The solution structure of FhuA agrees with its crystal structure; that of pb5 shows an elongated shape. Neither displays significant conformational changes upon interaction. The mechanism of signal transduction within phage T5 thus appears different from that of phages binding cell wall saccharides, for which structural information is available.     

Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model

The decryption of sequence of structural events during protein conformational transitions is essential to a detailed understanding of molecular functions ofvarious biological nanomachines. Coarse‐grained models have proven useful by allowing highly efficient simulations of protein conformational dynamics. By combining two coarse‐grained elastic network models constructed based on the beginning and end conformations of a transition, we have developed an interpolated elastic network model to generate a transition pathway between the two protein conformations. For validation, we have predicted the order of local and global conformational changes during key ATP‐driven transitions in three important biological nanomachines (myosin, F₁ ATPase and chaperonin GroEL). We have found that the local conformational change associated with the closing of active site precedes the global conformational change leading to mechanical motions. Our finding is in good agreement with the distribution of intermediate experimental structures, and it supports the importance of local motions at active site to drive or gate various conformational transitions underlying the workings of a diverse range of biological nanomachines. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

NMR Structures of α-Proteobacterial ATPase-Regulating ζ-Subunits

NMR structures of ζ-subunits, which are recently discovered α-proteobacterial F₁F₀-ATPase-regulatory proteins representing a Pfam protein family of 246 sequences from 219 species (PF07345), exhibit a four-helix bundle, which is different from all other known F₁F₀-ATPase inhibitors. Chemical shift mapping reveals a conserved ADP/ATP binding site in ζ-subunit, which mediates long-range conformational changes related to function, as revealed by the structure of the Paracoccus denitrificans ζ-subunit in complex with ADP. These structural data suggest a new mechanism of F₁F₀-ATPase regulation in α-proteobacteria.     

Investigating the interactions of the 18 kDa translocator protein and its ligand PK11195 in planar lipid bilayers

The functional effects of a drug ligand may be due not only to an interaction with its membrane protein target, but also with the surrounding lipid membrane. We have investigated the interaction of a drug ligand, PK11195, with its primary protein target, the integral membrane 18 kDa translocator protein (TSPO), and model membranes using Langmuir monolayers, quartz crystal microbalance with dissipation monitoring (QCM-D) and neutron reflectometry (NR). We found that PK11195 is incorporated into lipid monolayers and lipid bilayers, causing a decrease in lipid area/molecule and an increase in lipid bilayer rigidity. NR revealed that PK11195 is incorporated into the lipid chain region at a volume fraction of ~ 10%. We reconstituted isolated mouse TSPO into a lipid bilayer and studied its interaction with PK11195 using QCM-D, which revealed a larger than expected frequency response and indicated a possible conformational change of the protein. NR measurements revealed a TSPO surface coverage of 23% when immobilised to a modified surface via its polyhistidine tag, and a thickness of 51 Å for the TSPO layer. These techniques allowed us to probe both the interaction of TSPO with PK11195, and PK11195 with model membranes. It is possible that previously reported TSPO-independent effects of PK11195 are due to incorporation into the lipid bilayer and alteration of its physical properties. There are also implications for the variable binding profiles observed for TSPO ligands, as drug–membrane interactions may contribute to the apparent affinity of TSPO ligands.     

Isolation and properties of OSCP and an F1-ATPase binding protein from rat liver mitochondria - evidence against OSCP as the linking "stalk" between F1 and the membrane.

Oligomycin Sensitivity Conferral Protein (OSCP) and an F₁-ATPase Binding Protein were isolated from F₁-depleted rat liver mitochondrial membrane. Their molecular weights on polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate and urea were 22,500 and 8,500 respectively. When incubated with liver TUA (trypsin, urea and ammonia-treated) submitochondrial particles, the binding protein was effective in the binding of F₁ to the particles with the resultant particle-bound ATPase activity not oligomycin sensitive. When OSCP was then incubated with the reconstituted membrane-bound ATPase, its activity became oligomycin sensitive. These results suggest that, first; the binding protein, but not OSCP, connects F₁-ATPase to the membrane of rat liver mitochondria and maybe to the “stalk”, if indeed there is a stalk in mitochondrial membrane ATPase complex; and second; the function of OSCP is solely to render the ATPase activity sensitive to oligomycin and other similar inhibitors.     

On the mechanism of activation of protein kinase FA (an activating factor of ATP.Mg-dependent protein phosphatase) in brain myelin

Protein kinase F_A (an activating factor of ATP·Mg-dependent protein phosphatase) has been characterized to exist in two forms in the purified brain myelin. One form of kinase F_A is spontaneously active and trypsin-labile, whereas the other form of kinase F_A is inactive and trypsin-resistant, suggesting a different membrane topography with active F_A exposed on the outer face of the myelin membrane and inactivu F_Q buried within the myelin membrane. When myelin was solubilized in 1% Triton X-100, all kinase F_A became active and trypsin-labile. Phospholipid reconstitution studies further indicated that when kinase F_A was reconstituted in acidic phospholipids, such as phosphatidylinositol and phosphatidylserine, the enzyme activity was inhibited in a dose-dependent manner, suggesting that kinase F_A interacts with acidic phospholipids which inhibit its activity. Furthermore, when myelin was incubated with exogenous phospholipase C, the inactive/trypsin-resistant F_A could be converted to the active/trypsin-labile F_A in a time- and dose-dependent manner. Taken together, it is concluded that membrane phospholipids play an important role in modulating the activity of kinase F_A in the brain myelin. It is suggested that phospholipase C may mediate the activation-sequestration of inactive/trypsin-resistant kinase F_A in the brain myelin through the phospholipase C-katalyzed degradation of acidic membrane phospholipids. The activation-sequestration of protein Kinase F_A may represent one mode of control modulating the activity of kinase F_A in the central nervous system myelin.     

On the mechanism of activation of protein kinase FA (an activating factor of ATP·Mg-dependent protein phosphatase) in brain myelin

Protein kinase F_A (an activating factor of ATP·Mg-dependent protein phosphatase) has been characterized to exist in two forms in the purified brain myelin. One form of kinase F_A is spontaneously active and trypsin-labile, whereas the other form of kinase F_A is inactive and trypsin-resistant, suggesting a different membrane topography with active F_A exposed on the outer face of the myelin membrane and inactivu F_Q buried within the myelin membrane. When myelin was solubilized in 1% Triton X-100, all kinase F_A became active and trypsin-labile. Phospholipid reconstitution studies further indicated that when kinase F_A was reconstituted in acidic phospholipids, such as phosphatidylinositol and phosphatidylserine, the enzyme activity was inhibited in a dose-dependent manner, suggesting that kinase F_A interacts with acidic phospholipids which inhibit its activity. Furthermore, when myelin was incubated with exogenous phospholipase C, the inactive/trypsin-resistant F_A could be converted to the active/trypsin-labile F_A in a time- and dose-dependent manner. Taken together, it is concluded that membrane phospholipids play an important role in modulating the activity of kinase F_A in the brain myelin. It is suggested that phospholipase C may mediate the activation-sequestration of inactive/trypsin-resistant kinase F_A in the brain myelin through the phospholipase C-katalyzed degradation of acidic membrane phospholipids. The activation-sequestration of protein Kinase F_A may represent one mode of control modulating the activity of kinase F_A in the central nervous system myelin.     

Modelling the influence of thermal effects induced by radio frequency electric field on the dynamics of the ATPase nano-biomolecular motors

We model the dynamics of the F₀ component of the F₀F₁-ATPase mitochondrion-based nano-motor operating in a stochastically-fluctuating medium that represents the intracellular environment. The stochastic dynamics are modeled via Langevin equation of motion wherein fluctuations are treated as white noise. We have investigated the influence of an applied alternating electric field on the rotary motion of the F₀ rotor in such an environment. The exposure to the field induces a temperature rise in the mitochondrion’s membrane, within which the F₀ is embedded. The external field also induces an electric potential that promotes a change in the mitochondrion’s transmembrane potential (TMP). Both the induced temperature and the change in TMP contribute to a change in the dynamics of the F₀. We have found that for external fields in the radio frequency (RF) range, normally present in the environment and encountered by biological systems, the contribution of the induced thermal effects, relative to that of the induced TMP, to the dynamics of the F₀ is more significant. The changes in the dynamics of the F₀ part affect the frequency of the rotary motion of the F₀F₁-ATPase protein motor which, in turn, affects the production rate of the ATP molecules.     

Does PGE1 induce modifications at the membrane level of bone marrow macrophages ?: A fluorescence study

The effect of prostaglandin E₁ (PGE₁), and F_2α (PGF_2α) on the surface membrane configuration of bone marrow macrophages was studied. We measured the fluorescence intensity of membrane bound ANS in prostaglandin pretreated cells. The effect on fluorescence intensity of a blocker of the prostaglandin binding site (SC19220) and inhibitors of prostaglandin synthesis (aspirin, indomethacin, diclophenate, Eicosa 5,8,11,14 tetraynoic acid) also were studied. Enhancement of the fluorescence intensity of bound ANS in cells pretreated with PGE₁ indicates a conformational change localized at the membrane surface. That those changes are confined to the cell surface was shown by the failure of PGE₁ or PGF_2α to alter the fluorescence polarization of bound DPH used as indicator of membrane core viscosity. Our data indicate that PGE₁ could act at the surface of the membrane and that its action causes rapid structural perturbation at strategic points in the molecular organization of the membrane of bone marrow macrophages