Spin Labeling Electron Paramagnetic Resonance Research Articles

Study of Protein Dynamics under Nanoconfinement by Spin-Label ESR: A Case of T4 Lysozyme Protein.

The electron spin resonance (ESR) spectra of spin-labeled proteins are sensitive to dynamics, but discrimination between the various dynamics is often difficult. Here, we report an improvement in ESR spectral sensitivity to local backbone dynamics of a protein by a methodology that performs ESR measurement when the protein is confined in the nanochannels of a mesoporous material. An extensive set of ESR data, which includes the spectra of a nitroxide-based side chain from buried and solvent-exposed sites of a T4 lysozyme (T4L) protein, were obtained over a range of temperatures, 200-300 K, to explore the dynamics of T4L under nanoconfinement. Spectra were simulated by performing theoretical fits to the data using the microscopic ordering with macroscopic disordering model. Two principle dynamic modes, which differ in mobility and ordering, are required to account for the spectra at temperatures >240 K. We show that the mobile one correlates only with the local backbone dynamics of buried sites, whereas the other reflects the difference in local hydration dynamics between the labeling sites in T4L. The assignment of the mobile component is supported by the X-ray crystallography data of T4L. Collectively, this study has demonstrated the validity of such a methodology for improving ESR sensitivity to buried sites in a protein.

Effect of Solution Ionic Strength on the pKa of the Nitroxide pH EPR Probe 2,2,3,4,5,5-Hexamethylimidazolidin-1-oxyl.

Spin probe and spin labeling Electron Paramagnetic Resonance methods are indispensable research tools for solving a wide range of bioanalytical problems-from measuring microviscosity and polarity of phase-separated liquids to oxygen concentrations in tissues. One of the emerging uses of spin probes are the studies of proton transfer-related and surface electrostatic phenomena. The latter Electron Paramagnetic Resonance methods rely on molecular probes containing an additional functionality capable of reversible ionization (protonation, in particular) in the immediate proximity to an Electron Paramagnetic Resonance-active reporter group, such as (N-O•) for nitroxides. The consequent formation of protonated and nonprotonated nitroxide species with different magnetic parameters (A iso, g iso) could be readily distinguished by Electron Paramagnetic Resonance. Bioanalytical Electron Paramagnetic Resonance studies employing pH-sensitive paramagnetic probes typically involve determination of the equilibrium constant (pK a) between the protonated and nonprotonated forms of the nitroxide. However, any chemical equilibrium involving charged species, such as ionization of acids and bases, and so the reversible protonation of the nitroxide, is known to be affected by an ionic strength of the solution. Currently, only scarce data for the effect of the solution ionic strength on the experimental pK a's of the ionizable nitroxides can be found in the literature. Here we have carried out a series of Electron Paramagnetic Resonance titration experiments for aqueous solutions of 2,2,3,4,5,5-hexamethylimidazolidin-1-oxyl (HMI) nitroxide known for one of the largest differences in the isotropic nitrogen hyperfine coupling constant A iso between the protonated and nonprotonated forms. Electrolyte concentration was varied over an exceptionally large range (i.e., from 0.05 to 5.0 M) to elucidate the effect of ionic strength on the ionization constant of this pH-sensitive Electron Paramagnetic Resonance probe and the data were compared to the Debye-Hückel limiting law. Effects of the ionic strength on the magnetic parameters of the ionizable nitroxides are also discussed.

Structural Dynamics of the MSCL C-Terminal Domain

The large conductance mechanosensitive channel (MscL), acts as an osmoprotective emergency valve in bacteria by opening a large, water-filled pore in response to changes in membrane tension. In its closed configuration, the last 36 residues at the C-terminus form a bundle of five α-helices co-linear with the five-fold axis of symmetry. Here, we examined the structural dynamics of the C-terminus of EcMscL using site-directed spin labelling electron paramagnetic resonance (SDSL EPR) spectroscopy. These experiments were complemented with computational modelling including molecular dynamics (MD) simulations and finite element (FE) modelling. Our results show that under physiological conditions, the C-terminus is indeed an α-helical bundle, located near the five-fold symmetry axis of the molecule. Both experiments and computational modelling demonstrate that only the top part of the C-terminal domain (from the residue A110 to E118) dissociates during the channel gating, while the rest of the C-terminus stays assembled. This result is consistent with the view that the C-terminus functions as a molecular sieve and stabilizer of the oligomeric MscL structure as previously suggested.

LPS Binding to LptA

Gram-negative bacteria, such as Escherichia coli, have an asymmetric outer membrane (OM) with an outer leaflet rich in lipopolysaccharide (LPS). LPS is a large lipid essential for survival in Gram-negative bacteria and a major factor in the protection of bacteria from adverse environmental stresses. LPS is transported across the inner membrane by MsbA and through the periplasm to the outer leaflet of the OM by the LPS transport (Lpt) proteins LptA, LptC, LptDE, and LptFGB2, the majority of which are essential to Gram-negative bacterial survival. LptA is a periplasmic protein that has been shown to form concentration dependent oligomers that stack end-to-end. The LptA protein fold is speculated to bind the LPS acyl chains in the central pocket of the protein, to protect the hydrophobic region as the molecule crosses the soluble periplasm. In the studies presented here, the binding of LPS at individual sites throughout the LptA protein is characterized using site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy. To determine the location of LPS binding on LptA, fifteen positions located in and around the hypothesized LPS binding pocket on LptA were mutated to cysteine, purified, spin labeled at the unique introduced cysteine, and tested for mobility changes due to the presence of excess exogenous LPS. Our data suggest a 1:1 ratio for the LPS:LptA complex and an affinity gradient from one end of the protein to the other based on Bmax and Kd values quantitatively determined by EPR spectroscopy.

Cooperative Substrate-Cofactor Interactions and Membrane Localization of the Bacterial Phospholipase A2 (PLA2) Enzyme, ExoU

The ExoU type III secretion enzyme is a potent phospholipase A2 secreted by the Gram-negative opportunistic pathogen, Pseudomonas aeruginosa Activation of phospholipase activity is induced by protein-protein interactions with ubiquitin in the cytosol of a targeted eukaryotic cell, leading to destruction of host cell membranes. Previous work in our laboratory suggested that conformational changes within a C-terminal domain of the toxin might be involved in the activation mechanism. In this study, we use site-directed spin-labeling electron paramagnetic resonance spectroscopy to investigate conformational changes in a C-terminal four-helical bundle region of ExoU as it interacts with lipid substrates and ubiquitin, and to examine the localization of this domain with respect to the lipid bilayer. In the absence of ubiquitin or substrate liposomes, the overall structure of the C-terminal domain is in good agreement with crystallographic models derived from ExoU in complex with its chaperone, SpcU. Significant conformational changes are observed throughout the domain in the presence of ubiquitin and liposomes combined that are not observed with either liposomes or ubiquitin alone. In the presence of ubiquitin, two interhelical loops of the C-terminal four-helix bundle appear to penetrate the membrane bilayer, stabilizing ExoU-membrane association. Thus, ubiquitin and the substrate lipid bilayer act synergistically to induce a conformational rearrangement in the C-terminal domain of ExoU.

Site-Directed Spin-Label EPR Spectroscopy of M2 Protein in Lipid Bilayers of Different Curvature Generation Propensity

M2 is a homotetrameric membrane protein critical to generation of membrane curvature in the budding stage of the influenza A virus life cycle. We have designed and interpreted site-directed spin-label electron paramagnetic resonance spectroscopy (SDSL-EPR) experiments on the conformation and dynamics of M2 in lipid bilayers of different propensities for membrane curvature generation. We have obtained data for full length M2 protein spin labelled at multiple sites in the C-terminal juxtamembrane region, which forms a membrane associated amphipathic helix. Continuous wave (CW) and pulsed EPR spectra provide evidence that M2 adopts two conformational states in bilayers, and that the propensity of lipids to form membranes of differing curvature dictates the relative population of these states. Multicomponent simulation of CW-EPR spectra further show lipid bilayers of the highly curved cubic phases stabilize an immobilized conformation of M2, hypothesized to be relevant for curvature generation. We have also characterized the size distribution of large unilamellar vesicles of lipids of different curvature generation propensities alone and in the presence of full-length M2 using dynamic light scattering (DLS).

Saturation-Recovery EPR Spin-Labeling Method for Quantification of Lipids in Domains of Biological Membranes

The presence of integral membrane proteins in biological membranes induces the formation of distinct domains in the lipid bilayer portion of these membranes. We were able to discriminate the existence of three lipid environments in intact fiber cell plasma membranes of the eye lens, namely bulk, boundary, and trapped lipids. However, our qualitative approach did not allow quantification of lipids in each domain. Recently, based on the continuous wave (CW) electron paramagnetic resonance (EPR) spectra of phospholipid analog and cholesterol analog spin labels, we developed a method that allows evaluation of the relative amount of phospholipids and cholesterol in the bulk lipid domain and in the boundary plus trapped lipid domain [M. Raguz, L. Mainali,W. J. O’Brien and W. K. Subczynski, (2015), Exp. Eye Res., 140:179-186]. Here, we will present a new approach that, based on saturation-recovery (SR) EPR, allows evaluation of the relative amount of phospholipids and cholesterol in the bulk plus boundary lipid domain and in the trapped lipid domain. Spectrometer conditions for the successful application of this method to quantify lipids in membrane domains are described. These two methods clearly demonstrate that the method's time window allows the separation of results from the different domains. CW EPR mixes results from the boundary and trapped lipids, while SR EPR mixes results from the bulk and boundary lipids. These two methods complement each other, providing a more complete picture of lipid lateral organization in intact membranes. The abilities of these methods are illustrated in the intact fiber cell plasma membranes from porcine eye lenses.Acknowledgments: This work was supported by grants EY015526, EB001980, and EY001931 from the National Institutes of Health.

Effects of Spin-Labels on Membrane Burial Depth of MARCKS-ED Residues

Site-directed spin-labeling electron paramagnetic resonance spectroscopy is a useful tool to obtain information about the environment of specific residues. One of its applications is to investigate membrane protein topology based on the accessibility of the spin label, with the assumption that the position of the spin label in the membrane is close to that of the native residue. This assumption is valid in proteins with well-ordered structures, but could be problematic in small peptides because the labeling may cause a perturbation that is large enough to change local interactions between the peptide and the membrane. To quantitatively characterize such effects, we have simulated the association of a 25-amino-acid peptide, MARCKS-ED, to membranes with and without spin labels. Our simulations show that the depths of spin labels are ∼6–17 Å deeper than the unlabeled charged and polar residues in the wild-type. When the hydrophobic residue Phe is labeled, however, the spin-label depth is close to that of the native residue as well as the experimental value. Our study suggests that one should be cautious in interpretation of spin label data when charged and polar residues in small peptides are labeled.

Conformational Flexibility and Dynamics of the Internal Loop and Helical Regions of the Kink-Turn Motif in the Glycine Riboswitch by Site-Directed Spin-Labeling.

Site-directed spin-labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy provides a means for a solution state description of site-specific dynamics and flexibility of large RNAs, facilitating our understanding of the effects of environmental conditions such as ligands and ions on RNA structure and dynamics. Here, the utility and capability of EPR line shape analysis and distance measurements to monitor and describe site-specific changes in the conformational dynamics of internal loop nucleobases as well as helix-helix interactions of the kink-turn motif in the Vibrio cholerae (VC) glycine riboswitch that occur upon sequential K(+)-, Mg(2+)-, and glycine-induced folding were explored. Spin-labels were incorporated into the 232-nucleotide sequence via splinted ligation strategies. Thiouridine nucleobase labeling within the internal loop reveals unambiguous differential dynamics for two successive sites labeled, with varied rates of motion reflective of base flipping and base stacking. EPR-based distance measurements for nitroxide spin-labels incorporated within the RNA backbone in the helical regions of the kink-turn motif are reflective of helical formation and tertiary interaction induced by ion stabilization. In both instances, results indicate that the structural formation of the kink-turn motif in the VC glycine riboswitch can be stabilized by 100 mM K(+) where the conformational flexibility of the kink-turn motif is not further tightened by subsequent addition of divalent ions. Although glycine binding is likely to induce structural and dynamic changes in other regions, SDSL indicates no impact of glycine binding on the local dynamics or structure of the kink-turn motif as investigated here. Overall, these results demonstrate the ability of SDSL to interrogate site-specific base dynamics and packing of helices in large RNAs and demonstrate ion-induced stability of the kink-turn fold of the VC riboswitch.

Retraction Note: Changes in the electron paramagnetic resonance spectra of albumin-associated spin-labeled stearic acid as a diagnostic parameter of colorectal cancer.

With more than 940,000 new colorectal cancer cases worldwide each year, there is no better way for colorectal cancer routine screening. The aim of this study was to investigate whether the fatty acid binding to albumin is detectably and significantly altered in colorectal cancer patients when compared with healthy people, in order to find a better way for colorectal cancer diagnosis. One hundred and forty-one patients operatively treated for colorectal cancer were included in the examination, and 180 healthy people were also enrolled as controls. Commercial 16-doxyl stearic acid was used as spin probe. Serum albumin was analyzed by electron paramagnetic resonance (EPR) with spin probe. Discriminant analysis was carried out using the measured EPR spectra by SPSS 20.0. Of the original grouped cases, 89.4% were correctly classified. Of the cross-validated grouped cases, 86.9% were correctly classified. Using Fisher linear discriminant analysis we were able to develop a mathematical model allowing for identification of colorectal cancer patients based on five values (both relative intensity and peak width) which are obtained from the EPR spectrum. Cancer-associated alterations to albumin can be assessed by spin-label EPR. The potential applications for this diagnostic technique are significant and represent a cost-effective means for screening patients with cancer. Spin probe for diagnosis of colorectal cancer might be a useful tool and further studies should take place in order to investigate all stages of colorectal cancer patients.

Investigation of the binding of cis/trans-[MCl4(1H-indazole)(NO)]− (M = Ru, Os) complexes to human serum albumin

Overall binding affinity of sodium or indazolium cis/trans-[MCl4(1H-indazole)(NO)] (M = Ru, Os) complexes towards human serum albumin (HSA) and high molecular mass components of the blood serum was monitored by ultrafiltration. HSA was found to be mainly responsible for the binding of the studied ruthenium and osmium complexes. In other words, this protein can provide a depot for the compounds and can affect their biodistribution and transport processes. In order to elucidate the HSA binding sites tryptophan fluorescence quenching studies and displacement reactions with the established site markers warfarin and dansylglycine were performed. Conditional stability constants for the binding to sites I and II on HSA were computed showing that the studied ruthenium and osmium complexes are able to bind into both sites with moderately strong affinity (logK’ = 4.4–5.1). Site I is slightly more favored over site II for all complexes. No significant differences in the HSA binding properties were found for these metal complexes demonstrating negligible influence of the type of counterion (sodium vs indazolium), the metal ion center identity (Ru vs. Os) or the position of the nitrosyl group on the binding event. Electron paramagnetic resonance spin labeling of HSA revealed that indazolium trans-[RuCl4(1H-indazole)(NO)] and long-chain fatty acids show competitive binding to HSA. Moreover, this complex has a higher affinity for site I, but when present in excess, it is able to bind to site II as well, and displace fatty acids.

Radial Tilting of the Extracellular Domain of GLIC Revealed by EPR Spectroscopy

Signaling in the brain depends on rapid opening and closing of pentameric ligand-gated ion channels (pLGICs). Defects in these proteins are linked to a variety of diseases including myasthenia, epilepsy and sleep-disorders. In addition, these proteins are therapeutic targets for various drugs including anti-convulsants, anxiolytics, anesthetics and sedatives. While recent crystal structures of prokaryotic and eukaryotic pLGICs solved in detergent micelles have shed light on the molecular architecture of these proteins, describing their conformational dynamics in physiological lipids is essential for understanding their function. Crystal structures of GLIC and the glutamate-activated chloride channel predict that agonist-mediated channel opening is associated with a quaternary twisting and a radial un-blooming (inward tilting) of the extracellular binding domain (ECD). Using site directed spin labeling electron paramagnetic resonance (SDSL EPR) spectroscopy and functional GLIC channels reconstituted in liposomes, we are testing these gating predictions. Residues located at the top of β-strands (β1, 2, 5, 6, 8) were mutated to cysteine, labeled with the spin probe MTSL and proton-induced gating motions were measured using continuous wave (CW) and double electron-electron resonance (DEER) spectroscopy. CW EPR spectroscopy data showed the spin label attached to I92C, S93C, V94C (β5), T99C and Q101C (β6) moved into a slightly more constrained/immobile environment at pH 3.0 as compared to pH 7.6. DEER distance distributions for K48 (β2), S93 (β5), T99 and Q101 (β6) revealed the probes moved closer together at pH 3.0, suggesting that the inner β-sheet of the extracellular domain of GLIC tilt inwards upon agonist activation.

Cholesterol-Dependent Conformational Exchange of the C-Terminal Domain of the Influenza A M2 Protein.

The C-terminal amphipathic helix of the influenza A M2 protein plays a critical cholesterol-dependent role in viral budding. To provide atomic-level detail on the impact cholesterol has on the conformation of M2 protein, we spin-labeled sites right before and within the C-terminal amphipathic helix of the M2 protein. We studied the spin-labeled M2 proteins in membranes both with and without cholesterol. We used a multipronged site-directed spin-label electron paramagnetic resonance (SDSL-EPR) approach and collected data on line shapes, relaxation rates, accessibility of sites to the membrane, and distances between symmetry-related sites within the tetrameric protein. We demonstrate that the C-terminal amphipathic helix of M2 populates at least two conformations in POPC/POPG 4:1 bilayers. Furthermore, we show that the conformational state that becomes more populated in the presence of cholesterol is less dynamic, less membrane buried, and more tightly packed than the other state. Cholesterol-dependent changes in M2 could be attributed to the changes cholesterol induces in bilayer properties and/or direct binding of cholesterol to the protein. We propose a model consistent with all of our experimental data that suggests that the predominant conformation we observe in the presence of cholesterol is relevant for the understanding of viral budding.

Dimerization interface and dynamic properties of yeast IF1 revealed by Site-Directed Spin Labeling EPR spectroscopy

The mitochondrial ATPase inhibitor, IF1, regulates the activity of the mitochondrial ATP synthase. The oligomeric state of IF1 related to pH is crucial for its inhibitory activity. Although extensive structural studies have been performed to characterize the oligomeric states of bovine IF1, only little is known concerning those of yeast IF1. While bovine IF1 can be found as an inhibitory dimer at low pH and a non-inhibitory tetramer at high pH, a monomer/dimer equilibrium has been described for yeast IF1, high pH values favoring the monomeric state. Combining different strategies involving the grafting of nitroxide spin labels combined with Electron Paramagnetic Resonance (EPR) spectroscopy, the present study brings the first structural characterization, at the residue level, of yeast IF1 in its dimeric form. The results show that the dimerization interface involves the central region of the peptide revealing that the dimer corresponds to a non-inhibitory state. Moreover, we demonstrate that the C-terminal region of the peptide is highly dynamic and that this segment is probably folded back onto the central region. Finally, the pH-dependence of the inter-label distance distribution has been observed indicating a conformational change between two structural states in the dimer.

In Vitro Demonstration of Dual Light-Driven Na+/H+ Pumping by a Microbial Rhodopsin

A subfamily of rhodopsin pigments was recently discovered in bacteria and proposed to function as dual-function light-driven H+/Na+ pumps, ejecting sodium ions from cells in the presence of sodium and protons in its absence. This proposal was based primarily on light-induced proton flux measurements in suspensions of Escherichia coli cells expressing the pigments. However, because E. coli cells contain numerous proteins that mediate proton fluxes, indirect effects on proton movements involving endogenous bioenergetics components could not be excluded. Therefore, an in vitro system consisting of the purified pigment in the absence of other proteins was needed to assign the putative Na+ and H+ transport definitively. We expressed IAR, an uncharacterized member from Indibacter alkaliphilus in E. coli cell suspensions, and observed similar ion fluxes as reported for KR2 from Dokdonia eikasta. We purified and reconstituted IAR into large unilamellar vesicles (LUVs), and demonstrated the proton flux criteria of light-dependent electrogenic Na+ pumping activity in vitro, namely, light-induced passive proton flux enhanced by protonophore. The proton flux was out of the LUV lumen, increasing lumenal pH. In contrast, illumination of the LUVs in a Na+-free suspension medium caused a decrease of lumenal pH, eliminated by protonophore. These results meet the criteria for electrogenic Na+ transport and electrogenic H+ transport, respectively, in the presence and absence of Na+. The direction of proton fluxes indicated that IAR was inserted inside-out into our sealed LUV system, which we confirmed by site-directed spin-label electron paramagnetic resonance spectroscopy. We further demonstrate that Na+ transport by IAR requires Na+ only on the cytoplasmic side of the protein. The in vitro LUV system proves that the dual light-driven H+/Na+ pumping function of IAR is intrinsic to the single rhodopsin protein and enables study of the transport activities without perturbation by bioenergetics ion fluxes encountered in vivo.

Elucidating the design principles of photosynthetic electron-transfer proteins by site-directed spin labeling EPR spectroscopy

Site-directed spin labeling electron paramagnetic resonance (SDSL EPR) spectroscopy is a powerful tool to determine solvent accessibility, side-chain dynamics, and inter-spin distances at specific sites in biological macromolecules. This information provides important insights into the structure and dynamics of both natural and designed proteins and protein complexes. Here, we discuss the application of SDSL EPR spectroscopy in probing the charge-transfer cofactors in photosynthetic reaction centers (RC) such as photosystem I (PSI) and the bacterial reaction center (bRC). Photosynthetic RCs are large multi-subunit proteins (molecular weight≥300kDa) that perform light-driven charge transfer reactions in photosynthesis. These reactions are carried out by cofactors that are paramagnetic in one of their oxidation states. This renders the RCs unsuitable for conventional nuclear magnetic resonance spectroscopy investigations. However, the presence of native paramagnetic centers and the ability to covalently attach site-directed spin labels in RCs makes them ideally suited for the application of SDSL EPR spectroscopy. The paramagnetic centers serve as probes of conformational changes, dynamics of subunit assembly, and the relative motion of cofactors and peptide subunits. In this review, we describe novel applications of SDSL EPR spectroscopy for elucidating the effects of local structure and dynamics on the electron-transfer cofactors of photosynthetic RCs. Because SDSL EPR Spectroscopy is uniquely suited to provide dynamic information on protein motion, it is a particularly useful method in the engineering and analysis of designed electron transfer proteins and protein networks. This article is part of a Special Issue entitled Biodesign for Bioenergetics — the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.

A new insight into a problem of mediating effects of humic acids on binding and biological effects of organic pollutants in natural soil

A major focus of this manuscript is to investigate the molecular environment of soil where organic pollutants including an active functional group, such as amine, are bound to humic acids (HA). Close consideration has been taken to binding and biological effects of organic pollutants in natural soil mediated by HA in dependence on the amine base. The investigation is carried out using a method of spin labeling electron paramagnetic resonance (SL EPR). Spin labels (SL) 2,5,5-trimethyl-2-(3-aminophenyl)pyrrolidin-1-yloxy (Anilino-SL) and 4-Amino-2,2,6,6-tetramethylpiperidine-1-oxyl (4-Amino-TEMPO), as well as extracellular fungal laccase from Trametes versicolor, are applied to samples of chernozem, its HA and standard HA, such as Elliott Soil HA, Pahokee Peat HA, leonardite. It is shown that HA mediate the interaction of amines with soil through the partitioning of them among the different compartments of soil in dependence on the amine base. Both aliphatic and aromatic amines become immediately bound to soil organic matter but via different mechanisms. HA bind only the aromatic amines. Their binding sites are located in the hydrophobic and anaerobic compartments of soil. Moreover, spectroscopic analysis evidenced that a number of binding sites are limited, and aromatic amines attracted to hydrophobic compartments in the soil environment form here the ordered structure. Kinetic analysis of a temporal change in the concentration of bound and non-bound aromatic amines points at a pronounced diamagnetic effect of compartments where aromatic amines become bound. In contrast to amine with a weak base, the aliphatic amines are not influenced by HA and remain in an active soil part. Manuscript concludes that mediating effects of HA are first realized through their electrochemical property. They define and isolate pollutants with a definitive base that can be described using the Octanol-Water Partition Coefficient. This binding in turn defines a biological effect of organic pollutants including amine with a weak base via the oxygen factor that results in a decrease in the magnitude of aerobic soil biota and disbalance of the soil microorganism community.

Shaping the water crevice to accommodate the voltage sensor in a down conformation: a molecular dynamics simulation study.

Voltage sensor domains (VSD) of voltage-dependent ion channels share a basic molecular structure with a voltage-sensing phosphatase and a voltage-gated proton channel. The VSD senses and responds to changes in the membrane potential by undergoing conformational changes associated with the movement of the charged arginines located on the S4 segment. Although several functional and structural studies have provided useful information about the conformational changes in many ion channels, a detailed and unambiguous explanation has not been published. Therefore, understanding the principle of voltage-dependent gating at an atomic level is required. In this study, we took advantage of the available spin labeling electron paramagnetic resonance spectrometry data and computational methods to investigate the structure and dynamic properties of the Up-state (activated) and Down-state (resting) conformations of the VSD by means of all-atom molecular dynamics (MD) simulations. The MD results of the Down conformation determined in bilayers with and without lipid phosphates both revealed a different shape of the aqueous crevice, in which more water molecules surround and fill the intracellular crevice in its Down state than in its Up state. The solvent accessible surface within the crevice has a complementary shape that can account for water-mediated interactions between the voltage sensor and the lipid bilayer. The results support the previously reported experimental data.

CW-EPR studies revealed different motional properties and oligomeric states of the integrin β1a transmembrane domain in detergent micelles or liposomes.

Integrins are heterodimeric membrane proteins that regulate essential processes: cell migration, cell growth, extracellular matrix assembly and tumor metastasis. Each integrin α or β subunit contains a large extracellular domain, a single transmembrane (TM) domain, and a short cytoplasmic tail. The integrin TM domains are important for heterodimeric association and dissociation during the conversion from inactive to active states. Moreover, integrin clustering occurs by homo-oligomeric interactions between the TM helices. Here, the transmembrane and cytoplasmic (TMC) domains of integrin β1a were overexpressed, and the protein was purified in detergent micelles and/or reconstituted in liposomes. To investigate the TM domain conformational properties of integrin β1a, 26 consecutive single cysteine mutants were generated for site-directed spin labeling and continuous-wave electron paramagnetic resonance (CW-EPR) mobility and accessibility analyses. The mobility analysis identified two integrin β1a-TM regions with different motional properties in micelles and a non-continuous integrin β1a-TM helix with high immobility in liposomes. The accessibility analysis verified the TM range (Val737-Lys752) of the integrin β1a-TMC in micelles. Further mobility and accessibility comparisons of the integrin β1a-TMC domains in micelles or liposomes identified distinctively different oligomeric states of integrin β1a-TM, namely a monomer embedded in detergent micelles and leucine-zipper-like homo-oligomeric clusters in liposomes.

C-terminal juxtamembrane region of full-length M2 protein forms a membrane surface associated amphipathic helix.

The influenza A M2 protein is a 97-residue integral membrane protein involved in viral budding and proton conductance. Although crystal and NMR structures exist of truncated constructs of the protein, there is disagreement between models and only limited structural data are available for the full-length protein. Here, the structure of the C-terminal juxtamembrane region (sites 50-60) is investigated in the full-length M2 protein using site-directed spin-labeling electron paramagnetic resonance (EPR) spectroscopy in lipid bilayers. Sites 50-60 were chosen for study because this region has been shown to be critical to the role the M2 protein plays in viral budding. Continuous wave EPR spectra and power saturation data in the presence of paramagnetic membrane soluble oxygen are consistent with a membrane surface associated amphipathic helix. Comparison between data from the C-terminal juxtamembrane region in full-length M2 protein with data from a truncated M2 construct demonstrates that the line shapes and oxygen accessibilities are remarkably similar between the full-length and truncated form of the protein.