Conformational Changes In Membrane Proteins Research Articles

Neurotransmitter uptake of synaptic vesicles studied by X-ray diffraction

The size, polydispersity, and electron density profile of synaptic vesicles (SVs) can be studied by small-angle X-ray scattering (SAXS), i.e. by X-ray diffraction from purified SV suspensions in solution. Here we show that size and shape transformations, as they appear in the functional context of these important synaptic organelles, can also be monitored by SAXS. In particular, we have investigated the active uptake of neurotransmitters, and find a mean vesicle radius increase of about 12% after the uptake of glutamate, which indicates an unusually large extensibility of the vesicle surface, likely to be accompanied by conformational changes of membrane proteins and rearrangements of the bilayer. Changes in the electron density profile (EDP) give first indications for such a rearrangement. Details of the protein structure are screened, however, by SVs polydispersity. To overcome the limitations of large ensemble averages and heterogeneous structures, we therefore propose serial X-ray diffraction by single free electron laser pulses. Using simulated data for realistic parameters, we show that this is in principle feasible, and that even spatial distances between vesicle proteins could be assessed by this approach.

PK a Calculations in Membrane Proteins from Molecular Dynamics Simulations.

The conformational changes of membrane proteins are crucial to their function and usually lead to fluctuations in the electrostatic environment of the protein surface. A very effective way to quantify these changes is by calculating the pK a values of the protein's titratable residues, which can be regarded as electrostatic probes. To achieve this, we need to take advantage of the fast and reliable pK a calculators developed for globular proteins and adapt them to include the explicit effects of membranes. Here, we provide a detailed linear response approximation protocol that uses our own software (PypKa) to calculate reliable pK a values from short MD simulations of membrane proteins.

Membrane Protein Dynamics Revealed by X-Ray Scattering with a Femtosecond Free-Electron Laser

The recent development of ultrafast X-ray free-election lasers (XFELs) gives a new avenue to experimentally investigate protein dynamics in the picosecond and femtosecond time regimes. The XFEL beam of the Linac Coherent Light Source (LCLS) has a very high peak X-ray brightness, which is key for probing elusive ultra-fast structural changes during the biological function of protein molecules. With XFEL probes, femtosecond time-resolved small- and wide-angle X-ray scattering (TR-SWAXS) experiments afford unprecedented opportunities in membrane biophysics. Here we describe the application of XFEL technology in pump-probe, TR-SWAXS experiments to structurally interrogate the conformational changes of membrane proteins, with an emphasis on G-protein-coupled receptors. Rhodopsin in detergent micelles was delivered to the X-ray beam using micro-jet technology. Time-resolved data were generated by recording X-ray scattering following the pump-laser illumination (light) as well as X-ray scattering without pump-laser illumination (dark). The 2D X-ray scattering patterns were radially integrated to generate 1D scattering profiles versus momentum transfer vector (Q). On-the-fly data analysis using the OnDA software package revealed the light-triggered “protein quake” of rhodopsin during early stages of its activation (within 10 ps). Double-difference profiles of rhodopsin-opsin solution scattering from −200 fs to 100 ps emphasized the structural effects of photoactivation. The signal from retinal after light excitation propagates as a shock wave throughout the protein and into the solvent. Theoretical molecular dynamics (MD) simulations provide a molecular interpretation and show that the calculated radius of gyration (Rg) of rhodopsin increases upon light excitation. Pump-probe experiments of photoactive proteins using an XFEL bring structural biology to a new level that will enable high-resolution structural movies of biomolecules in action. Establishing whether there is a single activation step or an energy landscape will be significant to understanding the functional GPCR activation mechanisms.

Integrating hydrogen-deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins.

Biological membranes define the boundaries of cells and are composed primarily of phospholipids and membrane proteins. It has become increasingly evident that direct interactions of membrane proteins with their surrounding lipids play key roles in regulating both protein conformations and function. However, the exact nature and structural consequences of these interactions remain difficult to track at the molecular level. Here, we present a protocol that specifically addresses this challenge. First, hydrogen-deuterium exchange mass spectrometry (HDX-MS) of membrane proteins incorporated into nanodiscs of controlled lipid composition is used to obtain information on the lipid species that are involved in modulating the conformational changes in the membrane protein. Then molecular dynamics (MD) simulations in lipid bilayers are used to pinpoint likely lipid-protein interactions, which can be tested experimentally using HDX-MS. By bringing together the MD predictions with the conformational readouts from HDX-MS, we have uncovered key lipid-protein interactions implicated in stabilizing important functional conformations. This protocol can be applied to virtually any integral membrane protein amenable to classic biophysical studies and for which a near-atomic-resolution structure or homology model is available. This protocol takes ~4 d to complete, excluding the time for data analysis and MD simulations, which depends on the size of the protein under investigation.

Microfabricated silicon chip as lipid membrane sample holder for serial protein crystallography

Abstract Rapid progress in protein crystallography techniques at X-ray free electron lasers (X-FELs) requires the development of new methods for sample delivery. Recording dynamic changes in protein structures is one of the aims. To assess protein dynamics, sample holders for crystallography need to become active devices, providing possibilities to induce in situ changes of the protein conformation during the experiments. We propose an integrated device for crystallographic studies on 2D crystals of membrane proteins. The conceptual device can support physiological conditions and provide a platform for electrophysiological measurements, as well as for electrical stimulation during the diffraction experiments at X-FELs. This allows for triggering conformational changes in membrane proteins, ultimately permitting to take series of crystallographic snapshots of the dynamic behavior of proteins. The device integrates a microfabricated silicon chip between two microfluidic transport layers. We demonstrate the fabrication of the device, describe its key components and show the method of sample loading and lipid bilayer formation with the use of the microfluidic delivery system. Electrochemical impedance spectroscopy (EIS) has been used to characterize the properties of lipid bilayers formed in the microfabricated silicon nitride support. Minimizing the sample consumption, mimicking physiological conditions during crystallographic data collection and an interface for electrochemical characterization and addressing protein 2D crystals are the key properties of the proposed device.

Using X-ray Footprinting and Mass Spectrometry to Study the Structure and Function of Membrane Proteins.

Membrane proteins are crucial for cellular sensory cascades and metabolite transport, and hence are key pharmacological targets. Structural studies by traditional highresolution techniques are limited by the requirements for high purity and stability when handled in high concentration and nonnative buffers. Hence, there is a growing requirement for the use of alternate methods in a complementary but orthogonal approach to study the dynamic and functional aspects of membrane proteins in physiologically relevant conditions. In recent years, significant progress has been made in the field of X-ray radiolytic labeling in combination with mass spectroscopy, commonly known as X-ray Footprinting and Mass Spectrometry (XFMS), which provide residue-specific information on the solvent accessibility of proteins. In combination with both lowresolution biophysical methods and high-resolution structural data, XFMS is capable of providing valuable insights into structure and dynamics of membrane proteins, which have been difficult to obtain by standalone high-resolution structural techniques. The XFMS method has also demonstrated a unique capability for identification of structural waters and their dynamics in protein cavities at both a high degree of spatial and temporal resolution, and thus capable of identifying conformational hot-spots in transmembrane proteins. We provide a perspective on the place of XFMS amongst other structural biology methods and showcase some of the latest developments in its usage for studying conformational changes in membrane proteins.

Interplay between the electrostatic membrane potential and conformational changes in membrane proteins.

Transmembrane electrostatic membrane potential is a major energy source of the cell. Importantly, it determines the structure as well as function of charge-carrying membrane proteins. Here, we discuss the relationship between membrane potential and membrane proteins, in particular whether the conformation of these proteins is integrally connected to the membrane potential. Together, these concepts provide a framework for rationalizing the types of conformational changes that have been observed in membrane proteins and for better understanding the electrostatic effects of the membrane potential on both reversible as well as unidirectional dynamic processes of membrane proteins.

Polar Interactions Play an Important Role in the Energetics of the Main Phase Transition of Phosphatidylcholine Membranes.

Conformational changes of membrane proteins are accompanied by deformation in the surrounding lipid bilayer. To gain insight into the energetics of membrane deformation, the phase behavior of dimyristoylphosphatidylcholine (DMPC) membranes in the presence of the dipole potential, ψd, modifiers was investigated by differential scanning calorimetry. 7-Ketocholesterol, which weakens ψd and reduces membrane-perpendicular dipole–dipole repulsion, causes a discrete second peak on the high-temperature side of the main transition, whereas 6-ketocholestanol, which strengthens ψd and increases membrane-perpendicular dipole–dipole repulsion, merely produces a shoulder. Measurements on pure DMPC vesicles showed that the observed temperature profile could not be explained by a single endothermic process, that is, breaking of van der Waals forces between hydrocarbon chains alone. Removal of NaCl from the buffer caused an increase in the main transition temperature and the appearance of an obvious shoulder, implicating polar interactions. Consideration of the phosphatidylcholine (PC) head group dipole moment indicates direct interactions between PC dipoles that are unlikely to account for the additional process. It seems more likely that the breaking of an in-plane hydrogen-bonded network consisting of hydrating water dipoles together with zwitterionic lipid head groups is responsible. The evidence presented supports the idea that the breaking of van der Waals forces between lipid tails required for the main phase transition of PC membranes is coupled to partial breaking of a hydrogen-bonded network at the membrane surface.

Doubly spin-labeled nanodiscs to improve structural determination of membrane proteins by ESR.

Pulsed dipolar spectroscopy (PDS) is a powerful tool to explore conformational changes of membrane proteins (MPs). However, the MPs suffer from relatively weak dipolar signals due to their complex nature in membrane environments, which consequently reduces the interspin distance resolution obtainable by PDS. Here we report the use of nanodiscs (NDs) to improve the distance resolution. Two genetically engineered membrane scaffold protein mutants are introduced, each of which is shown to form double-labeled ND efficiently and with high homogeneity. The resultant interspin distance distribution is featured by a small distribution width, suggesting high resolution. When PDS is performed on a binary mixture of the double-labeled ND devoid of MPs and the un-labeled ND with incorporated double-labeled MPs, the overall amplitude of dipolar signals is increased, leading to a critical enhancement of the distance resolution. A theoretical foundation is provided to validate the analysis. With this approach, the determination of MP structures can be studied at high resolution in NDs.

Fullerenol C60(OH)36 protects human erythrocyte membrane against high-energy electrons

Fullerenols (polyhydroxylated fullerene C60) are nanomaterial with potentially broad applicability in biomedical sciences with high antioxidant ability, thus, we investigated the radioprotecting potential of fullerenol C60(OH)36 on human erythrocytes irradiated by high-energy electrons of 6 MeV. The results demonstrate that C60(OH)36 at concentration of 150 μg/mL protects the erythrocytes against the radiation-induced hemolysis (comparing to non-protected cells, we observed 30% and 39% protection for 0.65 and 1.3 kGy irradiation doses, respectively). The protecting effect was confirmed by 32% decreased release of potassium cations comparing to the cells irradiated without C60(OH)36. Measurements of the amount of lactate dehydrogenase (LDH) released from the irradiated erythrocytes showed that the size of the pores formed by irradiation was not sufficient to release LDH across the erythrocyte membranes. We also report a significant decrease of the affinity of acetylcholinesterase (AChE) for the substrate in the presence of fullerenol, indicating the relatively strong adsorption of C60(OH)36 to components of plasma membrane. Changes in membrane fluidity detected by fluorescence spectroscopy and conformational changes in membrane proteins detected by spin labeling suggest the dose-dependent formation of disulfide groups as an effect of oxidation and this process was inhibited by C60(OH)36. We suppose that scavenging the ROS as well as adsorption of fullerenol to membrane proteins and steric protection of -SH groups against oxidation are responsible for the observed effects.

Effect of Cyanide on Mitochondrial Membrane Depolarization Induced by Uncouplers.

In this work, it was found that the ability of common uncouplers - carbonyl cyanide p-trifluoromethoxyphenylhydrazone (FCCP) and 2,4-dinitrophenol (DNP) - to reduce membrane potential of isolated rat liver mitochondria was diminished in the presence of millimolar concentrations of the known cytochrome c oxidase inhibitor - cyanide. In the experiments, mitochondria were energized by addition of ATP in the presence of rotenone, inhibiting oxidation of endogenous substrates via respiratory complex I. Cyanide also reduced the uncoupling effect of FCCP and DNP on mitochondria energized by succinate in the presence of ferricyanide. Importantly, cyanide did not alter the protonophoric activity of FCCP and DNP in artificial bilayer lipid membranes. The causes of the effect of cyanide on the efficiency of protonophoric uncouplers in mitochondria are considered in the framework of the suggestion that conformational changes of membrane proteins could affect the state of lipids in their vicinity. In particular, changes in local microviscosity and vacuum permittivity could change the efficiency of protonophore-mediated translocation.

The dipole potential correlates with lipid raft markers in the plasma membrane of living cells

The dipole potential generating an electric field much stronger than any other type of membrane potential influences a wide array of phenomena, ranging from passive permeation to voltage-dependent conformational changes of membrane proteins. It is generated by the ordered orientation of lipid carbonyl and membrane-attached water dipole moments. Theoretical considerations and indirect experimental evidence obtained in model membranes suggest that the dipole potential is larger in liquid-ordered domains believed to correspond to lipid rafts in cell membranes. Using three different dipole potential-sensitive fluorophores and four different labeling approaches of raft and nonraft domains, we showed that the dipole potential is indeed stronger in lipid rafts than in the rest of the membrane. The magnitude of this difference is similar to that observed between the dipole potential in control and sphingolipid-enriched cells characteristic of Gaucher's disease. The results established that the heterogeneity of the dipole potential in living cell membranes is correlated with lipid rafts and imply that alterations in the lipid composition of the cell membrane in human diseases can lead to substantial changes in the dipole potential.

Erythrocytes properties in varicose veins patients

Varicose veins (VV) are enlarged veins of the subcutaneous tissue, usually caused by faulty or damaged venous valves leading to impaired blood flow. Blood stasis, excessive clotting disorder and alterations in the vein walls are symptoms of Virchow's triad which may affect the morphotic elements of blood, including erythrocytes.The aim of this study was to investigate alterations in the properties of the erythrocytes taken from varicose veins in comparison to those from antecubital vein of patients with chronic venous disease. The investigation was conducted on whole erythrocytes using spin labeling method in EPR spectroscopy and flow cytometry.The internal viscosity of cells was determined by Tempamine. The conformation state of internal proteins, mainly hemoglobin and membrane proteins was determined by maleimide spin label (MSL, 4-maleimido-2,2,6,6-tetramethylpiperidine-1-oxyl). The plasma membrane fluidity was measured using two spin labeled fatty acids (5- and 16-doxylstearic acid), while conformational state of membrane protein was measured using two covalently bound spin labels MSL and ISL [4-(2-iodoacetamido)-2,2,6,6-tetramethylpiperidine-1-oxyl]. The osmotic fragility and the shape and size of the erythrocytes were also determined.A decrease in internal viscosity of the erythrocytes from varicose vein was observed. A significant decrease in lipid membrane fluidity indicated by 5-DS, which is located at the polar region of lipid layer was found in the erythrocytes from varicose vein in comparison to normal vein. A significant decrease in the motion of MSL and ISL attached to erythrocyte membrane proteins from varicose vein was found. Changes in the plasma membrane of the erythrocytes from varicose vein were also confirmed by measuring osmotic fragility. These cells were more sensitive to hemolysis than red blood cells from the peripheral blood vein. Meanwhile, no significant differences in size and shape were observed between the erythrocytes taken from varicose veins and those from peripheral veins.In conclusion, the erythrocytes from varicose veins exhibited decreased intracellular viscosity and decreased plasma membrane fluidity. At the same time, conformational changes of membrane proteins and higher osmotic fragility of these cells were found in comparison to the erythrocytes obtained from peripheral veins in the same patients with chronic venous disease. Our findings strongly suggest that presented abnormalities in the erythrocyte plasma membrane may have significant pathophysiological implications, including shortened cell survival and alterations in the hemorheology of the varicose vein blood.

Antibacterial Activity and Membrane-Disruptive Mechanism of 3-p-trans-Coumaroyl-2-hydroxyquinic Acid, a Novel Phenolic Compound from Pine Needles of Cedrus deodara, against Staphylococcus aureus.

Recently, we reported that a novel phenolic compound isolated from Cedrus deodara, 3-p-trans-coumaroyl-2-hydroxyquinic acid (CHQA), exhibits a potent antioxidant activity. The present study aimed to evaluate the antibacterial activity of CHQA against eleven food-borne pathogens and to elucidate its mechanism of action against Staphylococcus aureus. The results from minimum inhibitory concentration (MIC) determinations showed that CHQA exhibited moderate inhibitory effects on all of the tested pathogens with MIC values ranging from 2.5–10 mg/mL. Membrane potential measurements and flow cytometric analysis demonstrated that CHQA damaged the cytoplasmic membrane of S. aureus, causing a significant membrane hyperpolarization with a loss of membrane integrity. Moreover, CHQA induced an increase in membrane fluidity and conformational changes in membrane protein of S. aureus, suggesting that CHQA probably acts on the cell membrane by interactions with membrane lipid and protein. Transmission electron microscopic observations further confirmed that CHQA disrupted the cell membrane of S. aureus and caused severe morphological changes, which even led to leakage of intracellular constituents. These findings indicated that CHQA could have the potential to serve as a natural antibacterial agent to control and prevent the growth of pathogens in food and in food-processing environments.

Transient Conformational Changes of Sensory Rhodopsin II Investigated by Vibrational Stark Effect Probes.

Sensory rhodopsin II (SRII) is the primary light sensor in the photophobic reaction of the halobacterium Natronomonas pharaonis. Photoactivation of SRII results in a movement of helices F and G of this seven-helical transmembrane protein. This conformational change is conveyed to the transducer protein (HtrII). Global changes in the protein backbone have been monitored by IR difference spectroscopy by recording frequency shifts in the amide bands. Here we investigate local structural changes by judiciously inserting thiocyanides at different locations of SRII. These vibrational Stark probes absorb in a frequency range devoid of any protein vibrations and respond to local changes in the dielectric, electrostatics, and hydrogen bonding. As a proof of principle, we demonstrate the use of Stark probes to test the conformational changes occurring in SRII 12 ms after photoexcitation and later. Thus, a methodology is provided to trace local conformational changes in membrane proteins by a minimal invasive probe at the high temporal resolution inherent to IR spectroscopy.

Mobility Measurements Probe Conformational Changes in Membrane Proteins due to Tension.

The function of membrane-embedded proteins such as ion channels depends crucially on their conformation. We demonstrate how conformational changes in asymmetric membrane proteins may be inferred from measurements of their diffusion. Such proteins cause local deformations in the membrane, which induce an extra hydrodynamic drag on the protein. Using membrane tension to control the magnitude of the deformations, and hence the drag, measurements of diffusivity can be used to infer-via an elastic model of the protein-how conformation is changed by tension. Motivated by recent experimental results [Quemeneur et al., Proc. Natl. Acad. Sci. U.S.A. 111, 5083 (2014)], we focus on KvAP, a voltage-gated potassium channel from Aeropyrum pernix. The conformation of KvAP is found to change considerably due to tension, with its "walls," where the protein meets the membrane, undergoing significant angular strains. The torsional stiffness is determined to be 26.8k(B)T per radian at room temperature. This has implications for both the structure and the function of such proteins in the environment of a tension-bearing membrane.

Oxidative footprinting in the study of structure and function of membrane proteins: current state and perspectives.

Membrane proteins, such as receptors, transporters and ion channels, control the vast majority of cellular signalling and metabolite exchange processes and thus are becoming key pharmacological targets. Obtaining structural information by usage of traditional structural biology techniques is limited by the requirements for the protein samples to be highly pure and stable when handled in high concentrations and in non-native buffer systems, which is often difficult to achieve for membrane targets. Hence, there is a growing requirement for the use of hybrid, integrative approaches to study the dynamic and functional aspects of membrane proteins in physiologically relevant conditions. In recent years, significant progress has been made in the field of oxidative labelling techniques and in particular the X-ray radiolytic footprinting in combination with mass spectrometry (MS) (XF-MS), which provide residue-specific information on the solvent accessibility of proteins. In combination with both low- and high-resolution data from other structural biology approaches, it is capable of providing valuable insights into dynamics of membrane proteins, which have been difficult to obtain by other structural techniques, proving a highly complementary technique to address structure and function of membrane targets. XF-MS has demonstrated a unique capability for identification of structural waters and conformational changes in proteins at both a high degree of spatial and a high degree of temporal resolution. Here, we provide a perspective on the place of XF-MS among other structural biology methods and showcase some of the latest developments in its usage for studying water-mediated transmembrane (TM) signalling, ion transport and ligand-induced allosteric conformational changes in membrane proteins.

Time-resolved structural studies with serial crystallography: A new light on retinal proteins.

Structural information of the different conformational states of the two prototypical light-sensitive membrane proteins, bacteriorhodopsin and rhodopsin, has been obtained in the past by X-ray cryo-crystallography and cryo-electron microscopy. However, these methods do not allow for the structure determination of most intermediate conformations. Recently, the potential of X-Ray Free Electron Lasers (X-FELs) for tracking the dynamics of light-triggered processes by pump-probe serial femtosecond crystallography has been demonstrated using 3D-micron-sized crystals. In addition, X-FELs provide new opportunities for protein 2D-crystal diffraction, which would allow to observe the course of conformational changes of membrane proteins in a close-to-physiological lipid bilayer environment. Here, we describe the strategies towards structural dynamic studies of retinal proteins at room temperature, using injector or fixed-target based serial femtosecond crystallography at X-FELs. Thanks to recent progress especially in sample delivery methods, serial crystallography is now also feasible at synchrotron X-ray sources, thus expanding the possibilities for time-resolved structure determination.

Controlled Modulation of Lipid Bilayer State by a Photosensitive Membrane Effector

The lipid membrane matrix represents a 2-D liquid-crystal, the properties of which, at fixed other conditions, are locally modulated by the presence of effectors as e.g. cholesterol (passive) or proteins (passive and active). Not only does the incorporation of effectors into the host matrix locally or even globally modify the initial state of the host per se, most probably the state of the matrix in turn serves as a control tool for regulating the work of functional units (e.g. proteins).Results are presented on a membrane model system that was inoculated with a photosensitive and thus active variety of cholesterol. Azobenzene-cholesterol (azo-chol) exhibits a reversible trans-cis transition (365nm: trans- to cis-; 455nm: cis- to trans-). In a membrane, the azobenzene group, covalently connected to the cholesterol by an ester bond, is confined into the headgroup region. The system was explored by a combination of spectroscopic (UV-vis, NMR, mass spectroscopy), thermodynamic (Langmuir compression, calorimetry) and structural studies (X-ray/neutron reflectometry, grazing incidence X-ray diffraction). The conformational change of the guest upon illumination is coupled into the host system, inducing a transition of the whole membrane. The increased demand of headgroup area for the cis-azo-group pushes the membrane into a more compressed state, and vice versa for trans-azo-chol. The switching process between the two final states exhibits first-order kinetics. The state of the host bilayer is modulated as a response to the conformational switching of the guest effector via external light illumination. In a more general context, similar behavior may be found upon the conformational changes of membrane proteins during work.

The Effect of Highly Hydroxylated Fullerenol C60(OH)36on Human Erythrocyte Membrane Organization

The mechanism of the interaction of highly hydroxylated fullerenol C60(OH)36with erythrocyte membranes was studied by electron spin resonance spectroscopy (ESR) of stearic acid derivatives labeled with a nitroxyl radical at C-12 or C-16 and with a nitroxyl derivative of maleimide covalently attached to sulfhydryl groups of membrane proteins. A significant increase in membrane fluidity in the hydrophobic region of the lipid bilayer was observed for 12-doxylstearic acid at fullerenol concentrations of 100 mg/L or 150 mg/L, while for 16-doxylstearic acid significant increase in fluidity was only observed at 150 mg/L. Fullerenol at 100 mg/L or 150 mg/L caused conformational changes in membrane proteins, expressed as an increase in thehw/hsparameter, when fullerenol was added before the maleimide spin label (MSL) to the membrane suspension. The increase of thehw/hsparameter may be caused by changes in lipid-protein or protein-protein interactions which increase the mobility of the MSL label and as a result increase the membrane fluidity. Incubation of the membranes with the MSL before the addition of fullerenol blocked the available membrane protein –SH groups and minimized the interaction of fullerenol with them. This confirms that fullerenol interacts with erythrocyte membrane proteins via available protein –SH groups.