The measurement of immersion depth and topology of membrane proteins by solution state NMR

An important component of the study of membrane proteins involves the determination of details associated with protein topology — for example, the location of transmembrane residues, specifics of immersion depth, orientation of the protein in the membrane, and extent of solvent exposure for each residue. Solution state NMR is well suited to the determination of immersion depth with the use of paramagnetic additives designed to give rise to depth-specific relaxation effects or chemical shift perturbations. Such additives include spin labels designed to be “anchored” within a given region of the membrane or small freely diffusing paramagnetic species, whose partitioning properties across the water membrane interface create a gradient of paramagnetic effects which correlate with depth. This review highlights the use of oxygen and other small paramagnetic additives in studies of immersion depth and topology of membrane proteins in lipid bilayers and micelles.     

Determination of membrane immersion depth with O(2): a high-pressure (19)F NMR study

Oxygen is known to partition with an increasing concentration gradient toward the hydrophobic membrane interior. At partial pressures (P(O2)) of 100 Atm or more, this concentration gradient is sufficient to induce paramagnetic effects that depend sensitively on membrane immersion depth. This effect is demonstrated for the fluorine nucleus by depth-dependent paramagnetic shifts and spin-lattice relaxation rates, using a fluorinated detergent, CF3(CF(2))(5)C(2)H(4)-O-maltose (TFOM), reconstituted into a lipid bilayer model membrane system. To interpret the spin-lattice relaxation rates (R) in terms of a precise immersion depth, two specifically fluorinated cholesterol species (6-fluorocholesterol and 25-fluorocholesterol), whose membrane immersion depths were independently estimated, were studied by (19)F NMR. The paramagnetic relaxation rates, R, of the cholesterol species were then used to parameterize a Gaussian profile that directly relates R to immersion depth z. This same Gaussian curve could then be used to determine the membrane immersion depth of all six fluorinated chain positions of TFOM and of two adjacent residues of specifically fluorinated analogs of the antibacterial peptide indolicidin. The potential of this method for determination of immersion depth and topology of membrane proteins is discussed.     

Topology and immersion depth of an integral membrane protein by paramagnetic rates from dissolved oxygen

In studies of membrane proteins, knowledge of protein topology can provide useful insight into both structure and function. In this work, we present a solution NMR method for the measurement the tilt angle and average immersion depth of alpha helices in membrane proteins, from analysis of the paramagnetic relaxation rate enhancements arising from dissolved oxygen. No modification to the micelle or protein is necessary, and the topology of both transmembrane and amphipathic helices are readily determined. We apply this method to the measure the topology of a monomeric mutant of phospholamban (AFA-PLN), a 52-residue membrane protein containing both an amphipathic and a transmembrane alpha helix. In dodecylphosphocholine micelles, the amphipathic helix of AFA-PLN was found to have a tilt angle of 87° ± 1° and an average immersion depth of 13.2 ?. The transmembrane helix was found to have an average immersion depth of 5.4 ?, indicating residues 41 and 42 are closest to the micelle centre. The resolution of paramagnetic relaxation rate enhancements from dissolved oxygen compares favourably to those from Ni (II), a hydrophilic paramagnetic species.     

Membrane protein structure determination using paramagnetic tags

The combination of paramagnetic tagging strategies with NMR or EPR spectroscopic techniques can revolutionize de novo structure determination of helical membrane proteins. Leveraging the full potential of this approach requires optimal labeling strategies and prediction of membrane protein topology from sparse and low-resolution distance restraints, as addressed by Chen et?al. (2011).     

Identification and removal of nitroxide spin label contaminant: impact on PRE studies of α-helical membrane proteins in detergent

NMR paramagnetic relaxation enhancement (PRE) provides long‐range distance constraints (～15–25 Å) that can be critical to determining overall protein topology, especially where long‐range NOE information is unavailable such as in the case of larger proteins that require deuteration. However, several challenges currently limit the use of NMR PRE for α‐helical membrane proteins. One challenge is the nonspecific association of the nitroxide spin label to the protein‐detergent complex that can result in spurious PRE derived distance restraints. The effect of the nitroxide spin label contaminant is evaluated and quantified and a robust method for the removal of the contaminant is provided to advance the application of PRE restraints to membrane protein NMR structure determination.     

BCL::MP‐fold: Membrane protein structure prediction guided by EPR restraints

For many membrane proteins, the determination of their topology remains a challenge for methods like X‐ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Electron paramagnetic resonance (EPR) spectroscopy has evolved as an alternative technique to study structure and dynamics of membrane proteins. The present study demonstrates the feasibility of membrane protein topology determination using limited EPR distance and accessibility measurements. The BCL::MP‐Fold (BioChemical Library membrane protein fold) algorithm assembles secondary structure elements (SSEs) in the membrane using a Monte Carlo Metropolis (MCM) approach. Sampled models are evaluated using knowledge‐based potential functions and agreement with the EPR data and a knowledge‐based energy function. Twenty‐nine membrane proteins of up to 696 residues are used to test the algorithm. The RMSD100 value of the most accurate model is better than 8 Å for 27, better than 6 Å for 22, and better than 4 Å for 15 of the 29 proteins, demonstrating the algorithms' ability to sample the native topology. The average enrichment could be improved from 1.3 to 2.5, showing the improved discrimination power by using EPR data. Proteins 2015; 83:1947–1962. © 2015 Wiley Periodicals, Inc     

Determining the depth of insertion of dynamically invisible membrane peptides by gel-phase 1H spin diffusion heteronuclear correlation NMR

Solid-state NMR determination of the depth of insertion of membrane peptides and proteins has so far utilized ¹H spin diffusion and paramagnetic relaxation enhancement experiments, which are typically conducted in the liquid-crystalline phase of the lipid bilayer. For membrane proteins or peptide assemblies that undergo intermediate-timescale motion in the liquid-crystalline membrane, these approaches are no longer applicable because the protein signals are broadened beyond detection. Here we show that the rigid-solid HETCOR experiment, with an additional spin diffusion period, can be used to determine the depth of proteins in gel-phase lipid membranes, where the proteins are immobilized to give high-intensity solid-state NMR spectra. Demonstration on two membrane peptides with known insertion depths shows that well-inserted peptides give rise to high lipid cross peak intensities and low water cross peaks within a modest spin diffusion mixing time, while surface-bound peptides have higher water than lipid cross peaks. Furthermore, well-inserted membrane peptides have nearly identical ¹H cross sections as the lipid chains, indicating equilibration of the peptide and lipid magnetization. Using this approach, we measured the membrane topology of the α-helical fusion peptide of the paramyxovirus, PIV5, in the anionic POPC/POPG membrane, in which the peptide undergoes intermediate-timescale motion at physiological temperature. The gel-phase HETCOR spectra indicate that the α-helical fusion peptide is well inserted into the POPC/POPG bilayer, spanning both leaflets. This insertion motif gives insight into the functional role of the α-helical PIV5 fusion peptide in virus-cell membrane fusion.     

Current applications of bicelles in NMR studies of membrane-associated amphiphiles and proteins

This review covers current trends in studies of membrane amphiphiles and membrane proteins using both fast tumbling bicelles and magnetically aligned bicelle media for both solution state and solid state NMR. The fast tumbling bicelles provide a versatile biologically mimetic membrane model, which in many cases is preferable to micelles, both because of the range of lipids and amphiphiles that may be combined and because radius of curvature effects and strain effects common with micelles may be avoided. Drug and small molecule binding and partitioning studies should benefit from their application in fast tumbling bicelles, tailored to mimic specific membranes. A wide range of topology and immersion depth studies have been shown to be effective in fast tumbling bicelles, while residual dipolar couplings add another dimension to structure refinement possibilities, particularly for situations in which the peptide is uniformly labeled with 15N and 13C. Solid state NMR studies of polytopic transmembrane proteins demonstrate that it is possible to express, purify, and reconstitute membrane proteins, ranging in size from single transmembrane domains to seven-transmembrane GPCRs, into bicelles. The line widths and quality of the resulting 15NH dipole-15N chemical shift spectra demonstrate that there are no insurmountable obstacles to the study of large membrane proteins in magnetically aligned media.     

A refinement protocol to determine structure,topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints

To fully describe the fold space and ultimately the biological function of membrane proteins, it is necessary to determine the specific interactions of the protein with the membrane. This property of membrane proteins that we refer to as structural topology cannot be resolved using X-ray crystallography or solution NMR alone. In this article, we incorporate into XPLOR-NIH a hybrid objective function for membrane protein structure determination that utilizes solution and solid-state NMR restraints, simultaneously defining structure, topology, and depth of insertion. Distance and angular restraints obtained from solution NMR of membrane proteins solubilized in detergent micelles are combined with backbone orientational restraints (chemical shift anisotropy and dipolar couplings) derived from solid-state NMR in aligned lipid bilayers. In addition, a supplementary knowledge-based potential, E _z (insertion depth potential), is used to ensure the correct positioning of secondary structural elements with respect to a virtual membrane. The hybrid objective function is minimized using a simulated annealing protocol implemented into XPLOR-NIH software for general use. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The membrane-dipped neuronal SNARE complex: a site-directed spin labeling electron paramagnetic resonance study

The formation of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex is an essential process for membrane fusion and the neurotransmitter release in neurons. As an initial step toward the determination of the membrane topology of the SNARE complex, residues at the membrane-water interface were investigated with site-specific spin labeling electron paramagnetic resonance. EPR analysis revealed that the basic amino acid-rich interfacial region, which is universal for all transmembrane SNARE proteins, inserts into the membrane, eliminating the gap between the core complex and the membrane. The result raises the possibility that core complex formation directly leads to the apposition of two membranes, which could facilitate membrane fusion.     

Membrane localization of small proteins in Escherichia coli

Escherichia coli synthesize over 60 poorly understood small proteins of less than 50 amino acids. A striking feature of these proteins is that 65% contain a predicted α-helical transmembrane (TM) domain. This prompted us to examine the localization, topology, and membrane insertion of the small proteins. Biochemical fractionation showed that, consistent with the predicted TM helix, the small proteins generally are most abundant in the inner membrane fraction. Examples of both N(in)-C(out) and N(out)-C(in) orientations were found in assays of topology-reporter fusions to representative small TM proteins. Interestingly, however, three of nine tested proteins display dual topology. Positive residues close to the transmembrane domains are conserved, and mutational analysis of one small protein, YohP, showed that the positive inside rule applies for single transmembrane domain proteins as has been observed for larger proteins. Finally, fractionation analysis of small protein localization in strains depleted of the Sec or YidC membrane insertion pathways uncovered differential requirements. Some small proteins appear to be affected by both Sec and YidC depletion, others showed more dependence on one or the other insertion pathway, whereas one protein was not affected by depletion of either Sec or YidC. Thus, despite their diminutive size, small proteins display considerable diversity in topology, biochemical features, and insertion pathways.     

Reptilian reovirus utilizes a small type III protein with an external myristylated amino terminus to mediate cell-cell fusion

Reptilian reovirus is one of a limited number of nonenveloped viruses that are capable of inducing cell-cell fusion. A small, hydrophobic, basic, 125-amino-acid fusion protein encoded by the first open reading frame of a bicistronic viral mRNA is responsible for this fusion activity. Sequence comparisons to previously characterized reovirus fusion proteins indicated that p14 represents a new member of the fusion-associated small transmembrane (FAST) protein family. Topological analysis revealed that p14 is a representative of a minor subset of integral membrane proteins, the type III proteins N(exoplasmic)/C(cytoplasmic) (N(exo)/C(cyt)), that lack a cleavable signal sequence and use an internal reverse signal-anchor sequence to direct membrane insertion and protein topology. This topology results in the unexpected, cotranslational translocation of the essential myristylated N-terminal domain of p14 across the cell membrane. The topology and structural motifs present in this novel reovirus membrane fusion protein further accentuate the diversity and unusual properties of the FAST protein family and clearly indicate that the FAST proteins represent a third distinct class of viral membrane fusion proteins.     

Determination of helical membrane protein topology using residual dipolar couplings and exhaustive search algorithm: application to phospholamban

Dipolar waves are distinct hallmarks of both the secondary and tertiary structures of alpha-helical proteins that are immobilized in membrane bilayers or embedded in anisotropic media. We present a simple, semi-empirical approach that exploits the modulation of the amplitude and average of dipolar waves to determine the topology of alpha-helical proteins. Moreover, we describe the application of this method for the structural determination of a detergent solubilized membrane protein, phospholamban (PLB) that is involved in calcium regulation of cardiac muscle. When combined with high-resolution solid-state NMR data, this method can serve as a fast route for determining the topology of helical membrane proteins solubilized in detergent micelles.     

Rapid exploration of the folding topology of helical membrane proteins using paramagnetic perturbation

An understanding of the folding states of α-helical membrane proteins in detergent systems is important for functional and structural studies of these proteins. Here, we present a rapid and simple method for identification of the folding topology and assembly of transmembrane helices using paramagnetic perturbation in nuclear magnetic resonance spectroscopy. By monitoring the perturbation of signals from glycine residues located at specific sites, the folding topology and the assembly of transmembrane helices of membrane proteins were easily identified without time-consuming backbone assignment. This method is validated with Mistic (membrane-integrating sequence for translation of integral membrane protein constructs) of known structure as a reference protein. The folding topologies of two bacterial histidine kinase membrane proteins (SCO3062 and YbdK) were investigated by this method in dodecyl phosphocholine (DPC) micelles. Combing with analytical ultracentrifugation, we identified that the transmembrane domain of YbdK is present as a parallel dimer in DPC micelle. In contrast, the interaction of transmembrane domain of SCO3062 is not maintained in DPC micelle due to disruption of native structure of the periplasmic domain by DPC micelle.     

A combined NMR and molecular dynamics study of the transmembrane solubility and diffusion rate profile of dioxygen in lipid bilayers

The transmembrane profile of oxygen solubility and diffusivity in a lipid bilayer was assessed by (13)C NMR of the resident lipids (sn-2-perdeuterio-1-myristelaidoyl-2-myristoyl-sn-glycero-3-phosphocholine) in combination with molecular dynamics (MD) simulations. At an oxygen partial pressure of 50 atm, distinct chemical shift perturbations of a paramagnetic origin were observed, spanning a factor of 3.2 within the sn-1 chain and an overall factor of 10 from the headgroup to the hydrophobic interior. The distinguishing feature of the (13)C NMR shift perturbation measurements, in comparison to ESR and fluorescence quenching measurements, is that the local accessibility of oxygen is achieved for nearly all carbon atoms in a single experiment with atomic resolution and without the use of a probe molecule. MD simulations of an oxygenated and hydrated lipid bilayer provided an immersion depth distribution of all carbon nuclei, in addition to the distribution of oxygen concentration and diffusivity with immersion depth. All oxygen-induced (13)C NMR chemical shift perturbations could be reasonably approximated by simply accounting for the MD-derived immersion depth distribution of oxygen in the bilayer, appropriately averaged according to the immersion depth distribution of the (13)C nuclei. Second-order effects in the paramagnetic shift are attributed to the collisionally accessible solid angle or to the propensity of the valence electrons in the vicinity of a given nuclear spin to be polarized or delocalized by oxygen. A method is presented to measure such effects. The excellent agreement between MD and NMR provides an important cross-validation of the two techniques.     

Room to move: crystallizing membrane proteins in swollen lipidic mesophases

The cubic phase or in meso crystallization method is responsible for almost 40 solved integral membrane protein structures. Most of these are small and compact proteins. A model for how crystals form by the in meso method has been proposed that invokes a transition between mesophases. In light of this model, we speculated that a more hydrated and open mesophase, of reduced interfacial curvature, would support facile crystallization of bigger and bulkier proteins. The proposal was explored here by performing crystallization in the presence of additives that swell the cubic phase. The additive concentration inducing swelling, as quantified by small-angle X-ray diffraction, coincided with a "crystallization window" in which two, very different transmembranal proteins produced crystals. That the swollen mesophase can grow structure-grade crystals was proven with one of these, the light-harvesting II complex. In most regards, the structural details of the corresponding complex resembled those of crystals grown by the conventional vapour diffusion method, with some important differences. In particular, packing density in the in meso-grown crystals was dramatically higher, more akin to that seen with water-soluble proteins, which accounts for their enhanced diffracting power. The layered and close in-plane packing observed has been rationalized in a model for nucleation and crystal growth by the in meso method that involves swollen mesophases. These results present a rational case for including mesophase-swelling additives in screens for in meso crystallogenesis. Their use will contribute to broadening the range of membrane proteins that yield to structure determination.     

Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP)

The correct topology and orientation of integral membrane proteins are essential for their proper function, yet such information has not been established for many membrane proteins. A simple technique called fluorescence protease protection (FPP) is presented, which permits the determination of membrane protein topology in living cells. This technique has numerous advantages over other methods for determining protein topology, in that it does not require the availability of multiple antibodies against various domains of the membrane protein, does not require large amounts of protein, and can be performed on living cells. The FPP method employs the spatially confined actions of proteases on the degradation of green fluorescent protein (GFP) tagged membrane proteins to determine their membrane topology and orientation. This simple approach is applicable to a wide variety of cell types, and can be used to determine membrane protein orientation in various subcellular organelles such as the mitochondria, Golgi, endoplasmic reticulum and components of the endosomal/recycling system. Membrane proteins, tagged on either the N-termini or C-termini with a GFP fusion, are expressed in a cell of interest, which is subject to selective permeabilization using the detergent digitonin. Digitonin has the ability to permeabilize the plasma membrane, while leaving intracellular organelles intact. GFP moieties exposed to the cytosol can be selectively degraded through the application of protease, whereas GFP moieties present in the lumen of organelles are protected from the protease and remain intact. The FPP assay is straightforward, and results can be obtained rapidly.     

A guideline to proteome-wide α-helical membrane protein topology predictions

For current state-of-the-art methods, the prediction of correct topology of membrane proteins has been reported to be above 80%. However, this performance has only been observed in small and possibly biased data sets obtained from protein structures or biochemical assays. Here, we test a number of topology predictors on an "unseen" set of proteins of known structure and also on four "genome-scale" data sets, including one recent large set of experimentally validated human membrane proteins with glycosylated sites. The set of glycosylated proteins is also used to examine the ability of prediction methods to separate membrane from nonmembrane proteins. The results show that methods utilizing multiple sequence alignments are overall superior to methods that do not. The best performance is obtained by TOPCONS, a consensus method that combines several of the other prediction methods. The best methods to distinguish membrane from nonmembrane proteins belong to the "Phobius" group of predictors. We further observe that the reported high accuracies in the smaller benchmark sets are not quite maintained in larger scale benchmarks. Instead, we estimate the performance of the best prediction methods for eukaryotic membrane proteins to be between 60% and 70%. The low agreement between predictions from different methods questions earlier estimates about the global properties of the membrane proteome. Finally, we suggest a pipeline to estimate these properties using a combination of the best predictors that could be applied in large-scale proteomics studies of membrane proteins.     

An improved tripod amphiphile for membrane protein solubilization

Intrinsic membrane proteins represent a large fraction of the proteins produced by living organisms and perform many crucial functions. Structural and functional characterization of membrane proteins generally requires that they be extracted from the native lipid bilayer and solubilized with a small synthetic amphiphile, for example, a detergent. We describe the development of a small molecule with a distinctive amphiphilic architecture, a "tripod amphiphile," that solubilizes both bacteriorhodopsin (BR) and bovine rhodopsin (Rho). The polar portion of this amphiphile contains an amide and an amine-oxide; small variations in this polar segment are found to have profound effects on protein solubilization properties. The optimal tripod amphiphile extracts both BR and Rho from the native membrane environments and maintains each protein in a monomeric native-like form for several weeks after delipidation. Tripod amphiphiles are designed to display greater conformational rigidity than conventional detergents, with the long-range goal of promoting membrane protein crystallization. The results reported here represent an important step toward that ultimate goal.     

Simultaneous determination of disulphide bridge topology and three-dimensional structure using ambiguous intersulphur distance restraints: Possibilities and limitations

Knowledge of the native disulphide bridge topology allows the introduction of conformational restraints between remote parts of the peptide chain. This information is therefore of great importance for the successful determination of the three-dimensional structure of cysteine-rich proteins by NMR spectroscopy. In this paper we investigate the limitations of using ambiguous intersulphur restraints [Nilges, M. (1995) J. Mol. Biol., 245, 645–660] associated with NMR experimental information to determine the native disulphide bridge pattern. Using these restraints in a simulated annealing protocol we have determined the correct topology of numerous examples, including a protein with seven disulphide bridges (phospholipase A₂) and a protein in which 25% of the total number of residues are cysteines (-conotoxin GIIIB). We have also characterised the behaviour of the method when only limited experimental data is available, and find that the proposed protocol permits disulphide bridge determination even with a small number of restraints (around 5 NOEs – including a long-range restraint – per residue). In addition, we have shown that under these conditions the use of a reduced penalty function allows the identification of misassigned NOE restraints. These results indicate that the use of ambiguous intersulphur distances with the proposed simulated annealing protocol is a general method for the determination of disulphide bridge topology, particularly interesting in the first steps of NMR study of cysteine-rich proteins. Comparison with previously proposed protocols indicates that the presented method is more reliable and the interpretation of results is straightforward.