Amide Exchange Rates Research Articles

Solution NMR studies reveal novel CLIC4 chaperone activity with respect to profilin-1.

Despite its name, chloride intracellular channel 4 (CLIC4) is a soluble enzyme that can catalyze glutathione-dependent thiol transfers. It is unclear how this enzymatic activity relates to its biological role in remodeling the actin cytoskeleton. Previous studies have shown that CLIC4 interacts with profilin-1, a critical regulator of actin polymerization. We confirmed a direct interaction, 170 ± 20 μM by microscale thermophoresis. However, using solution nuclear magnetic resonance (NMR) spectroscopy, we demonstrate that CLIC4 has a higher affinity for profilin when it is unfolded. Amide hydrogen exchange studies demonstrate that the N- and C-terminal helices of profilin readily unfold, whereas the central β-beta sheet core remains relatively intact. Interaction with CLIC4 increases amide exchange rates throughout profilin, indicating preferential stabilization of partially unfolded intermediates. We note that profilin is glutathionylated in proteomic studies of cells exposed to oxidative stress. Profilin is unfolded by glutathionylation of buried cysteine residues in its N- or C-terminal helices, and this disrupts its ability to bind actin, as measured by pyrene-actin polymerization assay. We are currently attempting to demonstrate that CLIC4 can reverse glutathionylation of profilin-1 and promote its refolding in cells and in vitro.

Structural dynamics of pentapeptide repeat proteins.

Pentapeptide repeat proteins (PRPs) represent a large superfamily with more than 38 000 sequences in nearly 3500 species, the majority belonging to cyanobacteria but represented among all branches of life. PRPs contain at least eight consecutive pentapeptide repeats with the consensus (A/C/S/V/T/L/I)(D/N/S/K/E/I/R)(L/F)(S/T/R/E/Q/K/V/D)(G/D/E/N/R/Q/K). PRPs fold into right-handed quadrilateral β helices, also known as repeat-five-residue (Rfr)-folds, with four consecutive pentapeptide repeats comprising a single coil, the ~90° change in polypeptide direction in square-shaped coils achieved by type I, II and IV β turns, and hydrogen bonds between coils establishing β ladders on each Rfr-fold face. PRPs are broadly categorized into group 1 and 2 involved in antibiotic resistance and group 3 currently having unknown functions. Motivated by their intriguing structures, we are investigating PRP biophysical characteristics, including Rfr-fold thermal stability, β turn and β ladder hydrogen bond amide exchange rates and backbone dynamics. Here, we present analysis of 20 ns molecular dynamics (MD) simulations and all atom normal mode analysis (aaNMA) calculations for four group 1 and group 2 and four group 3 PRPs whose structures have been determined by X-ray crystallography. The MD cross-correlation matrices and aaNMA indicated strong correlated motion between adjacent coils and weak coupled motion between coils separated by one or more intervening coils. Slow anticorrelated motions were detected between adjacent coils in aaNMA modes that we hypothesize are requisite to access exchange-competent states necessary to permit solvent exchange of amide hydrogens involved in β-ladder and β-turns hydrogen bonds, which can have lifetimes on the order of months.

Mapping Protein-Ligand Interactions with Proteolytic Fragmentation, Hydrogen/Deuterium Exchange-Mass Spectrometry.

Biological processes are the result of noncovalent, protein-ligand interactions, where the ligands range from small organic and inorganic molecules to lipids, nucleic acids, peptides, and proteins. Amide groups within proteins constantly exchange protons with water. When immersed in heavy water (D2O), mass spectrometry (MS) can measure the change of mass associated with the hydrogen to deuterium exchange (HDX). Protein-ligand interactions modify the hydrogen exchange rates of amide protons, and the measurement of the amide exchange rates can provide rich information regarding the dynamical structure of the protein-ligand complex. This chapter describes a protocol for conducting bottom-up, continuous uptake, proteolytic fragmentation HDX-MS experiments that can help identify and map the interacting peptides of a protein-ligand interface. This tutorial outlines the fundamental theory governing hydrogen exchange; provides practical information regarding the preparation of protein samples and solutions; and describes the exchange reaction, reaction quenching, enzymatic digestion, chromatographic separation, and peptide analysis by MS. Tables list representative combinations of fluidic components used by HDX-MS researchers and summarize the available HDX-MS analysis software packages. Additionally, two HDX-MS case studies are used to illustrate protein-ligand interactions involving: (1) a continuous sequence of interacting residues and (2) a set of discontinuously numbered residues, residing spatially near each other.

Using hydrogen-deuterium exchange to monitor protein structure in the presence of gold nanoparticles.

The potential applications of protein-functionalized gold nanoparticles (AuNPs) have motivated many studies characterizing protein-AuNP interactions. However, the lack of detailed structural information has hindered our ability to understand the mechanism of protein adsorption on AuNPs. In order to determine the structural perturbations that occur during adsorption, hydrogen/deuterium exchange (HDX) of amide protons was measured for two proteins by NMR. Specifically, we measured both slow (5-300 min) and fast (10-500 ms) H/D exchange rates for GB3 and ubiquitin, two well-characterized proteins. Overall, amide exchange rates are very similar in the presence and absence of AuNPs, supporting a model where the adsorbed protein remains largely folded on the AuNP surface. Small differences in exchange rates are observed for several loop residues, suggesting that the secondary structure remains relatively rigid while loops and surface residues can experience perturbations upon binding. Strikingly, several of these residues are close to lysines, which supports a model where positive surface residues may interact favorably with AuNP-bound citrate. Because these proteins appear to remain folded on AuNP surfaces, these studies suggest that it may be possible to engineer functional AuNP-based nanoconjugates without the use of chemical linkers.

Quantitative Bayesian model‐based analysis of amide proton transfer MRI

Amide Proton Transfer (APT) reports on contrast derived from the exchange of protons between amide groups and water. Commonly, APT contrast is quantified by asymmetry analysis, providing an ensemble contrast of both amide proton concentration and exchange rate. An alternative is to sample the off-resonant spectrum and fit an exchange model, permitting the APT effect to be quantified, correcting automatically for confounding effects of spillover, field inhomogeneity, and magnetization transfer. Additionally, it should permit amide concentration and exchange rate to be independently quantified. Here, a Bayesian method is applied to this problem allowing pertinent prior information to be specified. A three-pool model was used incorporating water protons, amide protons, and magnetization transfer effect. The method is demonstrated in simulations, creatine phantoms with varying pH and in vivo (n = 7). The Bayesian model-based approach was able to quantify the APT effect accurately (root-mean-square error < 2%) even when subject to confounding field variation and magnetization transfer effect, unlike traditional asymmetry analysis. The in vivo results gave approximate APT concentration (relative to water) and exchange rate values of 3 × 10(-3) and 15 s(-1) . A degree of correlation was observed between these parameter making the latter difficult to quantify with absolute accuracy, suggesting that more optimal sampling strategies might be required.

Measurement of amide hydrogen exchange rates with the use of radiation damping

A simple method for measuring amide hydrogen exchange rates is presented, which is based on the selective inversion of water magnetization with the use of radiation damping. Simulations show that accurate exchange rates can be measured despite the complications of radiation damping and cross relaxation to the exchange process between amide and water protons. This method cannot eliminate the contributions of the exchange-relayed NOE and direct NOE to the measured exchange rates, but minimize the direct NOE contribution. In addition, the amides with a significant amount of such indirect contributions are possible to be identified from the shape of the exchange peak intensity profiles or/and from the apparent relaxation rates of amide protons which are extracted from fitting the intensity profiles to an equation established here for our experiment. The method was tested on ubiquitin and also applied to an acyl carrier protein. The amide exchange rates for the acyl carrier protein at two pHs indicate that the entire protein is highly dynamic on the second timescale. Low protection factors for the residues in the regular secondary structural elements also suggest the presence of invisible unfolded species. The highly dynamic nature of the acyl carrier protein may be crucial for its interactions with its substrate and enzymes.

A Membrane Cell for On-line Hydrogen/Deuterium Exchange to Study Protein Folding and Protein-Protein Interactions by Mass Spectrometry

A membrane cell for hydrogen and deuterium exchange on-line with mass spectrometry has been developed to monitor protein-protein interactions and protein conformations. It consists of two channels separated by a semipermeable membrane, where one channel carries the protein sample and the other deuterium oxide. The membrane allows transfer of deuterium oxide into the sample flow. The labeling time is controlled via the flow rate in the sample channel. This cell was validated against three models commonly used in hydrogen-deuterium exchange mass spectrometry: monitoring of folded and unfolded states in a protein, mapping the protein secondary structure at the peptide level, and detection of protein and antibody interactions. The system avoids the conventionally used sample dilution and handling, allowing for potential automation.

Polarization and Polarizability Assessed by Protein Amide Acidity

Hydroxide-catalyzed exchange rate constants were determined for those amides of FK506-binding protein (FKBP12), ubiquitin, and chymotrypsin inhibitor 2 (CI2) that are solvent-accessible in the high-resolution X-ray structures. When combined with previous hydrogen exchange results for the rubredoxin from Pyrococcus furiosus, the acidity of these amides was calculated by continuum dielectric methods as a function of the nonpolarizable electrostatic parameter set, internal dielectric, and the charge distribution of the peptide anion. The CHARMM22 parameter set with an internal dielectric value of 3 and an ab initio-derived anion charge distribution yielded an rmsd value of 7 for the 56 amide exchange rate constants ranging from 10(0.67) to 10(9.0) M(-1) s(-1). The OPLS-AA parameter set yielded comparably robust predictions, while that of PARSE, AMBER parm99, and AMBER ff03 performed more poorly. The small value for the optimal internal dielectric, combined with the brief lifetime of the peptide anion intermediate and the uniformity of the correlation between predicted and observed amide acidities, is consistent with electronic polarizability providing the dominant contribution to dielectric shielding. By construction, nonpolarizable force fields do not model electric field attenuation by electronic polarizability. Accurate prediction of the total electrostatic energy by such force fields necessitates the hyperpolarization of the atomic charge values in order to match the average electric field energy density (1/2)epsilon(tau)E(2)(tau) when epsilon(tau) is set to the in vacuo dielectric value of 1. The resulting predictions of the experimental hydrogen exchange data demonstrate the substantial systematic errors in the predicted electrostatic potential that can arise when dielectric shielding due to electronic polarizability is neglected.

NMR Resonance Assignments of Sparsely Labeled Proteins: Amide Proton Exchange Correlations in Native and Denatured States

Protein NMR assignments of large proteins using traditional triple resonance techniques depends on double or triple labeling of samples with (15)N, (13)C, and (2)H. This is not always practical with proteins that require expression in nonbacterial hosts. Labeling with isotopically labeled versions of single amino acids (sparse labeling) often is possible; however, resonance assignment then requires a new strategy. Here a procedure for the assignment of cross-peaks in (15)N-(1)H correlation spectra of sparsely labeled proteins is presented. It relies on the correlation of proton-deuterium amide exchange rates in native and denatured spectra of the intact protein, followed by correlation of chemical shifts in the spectra of the denatured protein with chemical shifts of sequenced peptides derived from the protein. The procedure is successfully demonstrated on a sample of a protein, Galectin-3, selectively labeled with (15)N at all alanine residues.

Backbone dynamics measurements on leukemia inhibitory factor, a rigid four-helical bundle cytokine.

The backbone dynamics of the four-helical bundle cytokine leukemia inhibitory factor (LIF) have been investigated using 15N NMR relaxation and amide proton exchange measurements on a murine-human chimera, MH35-LIF. For rapid backbone motions (on a time scale of 10 ps to 100 ns), as probed by 15N relaxation measurements, the dynamics parameters were calculated using the model-free formalism incorporating the model selection approach. The principal components of the inertia tensor of MH35-LIF, as calculated from its NMR structure, were 1:0.98:0.38. The global rotational motion of the molecule was, therefore, assumed to be axially symmetric in the analysis of its relaxation data. This yielded a diffusion anisotropy D(parallel)/D(perpendicular) of 1.31 and an effective correlation time (4D(perpendicular) + 2D(parallel))(-1) of 8.9 ns. The average values of the order parameters (S2) for the four helices, the long interhelical loops, and the N-terminus were 0.91, 0.84, and 0.65, respectively, indicating that LIF is fairly rigid in solution, except at the N-terminus. The S2 values for the long interhelical loops of MH35-LIF were higher than those of their counterparts in short-chain members of the four-helical bundle cytokine family. Residues involved in LIF receptor binding showed no consistent pattern of backbone mobilities, with S2 values ranging from 0.71 to 0.95, but residues contributing to receptor binding site III had relatively lower S2 values, implying higher amplitude motions than for the backbone of sites I and II. In the relatively slow motion regime, backbone amide exchange measurements showed that a number of amides from the helical bundle exchanged extremely slowly, persisting for several months in 2H2O at 37 degrees C. Evidence for local unfolding was considered, and correlations among various structure-related parameters and the backbone amide exchange rates were examined. Both sets of data concur in showing that LIF is one of the most rigid four-helical bundle cytokines.

Impeded Electron Transfer From a Pathogenic FMN Domain Mutant of Methionine Synthase Reductase and Its Responsiveness to Flavin Supplementation

Methionine synthase reductase (MSR) is a diflavin oxidoreductase that transfers electrons from NADPH to oxidized cobalamin and plays a vital role in repairing inactive cobalamin-dependent methionine synthase. MSR deficiency is a recessive genetic disorder affecting folate and methionine metabolism and is characterized by elevated levels of plasma homocysteine. In this study, we have examined the molecular basis of MSR dysfunction associated with a patient mutation, A129T, which is housed in the FMN binding domain and is adjacent to a cluster of conserved acidic residues found in diflavin oxidoreductases. We show that the substitution of alanine with threonine destabilizes FMN binding without affecting the NADPH coenzyme specificity or affinity, indicating that the mutation's effects may be confined to the FMN module. The A129T MSR mutant transfers electrons to ferricyanide as efficiently as wild type MSR but the rate of cytochrome c, 2,6-dichloroindophenol, and menadione reduction is decreased 10-15 fold. The mutant is depleted in FMN and reactivates methionine synthase with 8% of the efficiency of wild type MSR. Reconstitution of A129T MSR with FMN partially restores its ability to reduce cytochrome c and to reactivate methionine synthase. Hydrogen-deuterium exchange mass spectrometric studies localize changes in backbone amide exchange rates to peptides in the FMN-binding domain. Together, our results reveal that the primary biochemical penalty associated with the A129T MSR mutant is its lower FMN content, provide insights into the distinct roles of the FAD and FMN centers in human MSR for delivering electrons to various electron acceptors, and suggest that patients harboring the A129T mutation may be responsive to riboflavin therapy.

Tetrameric β3‐Peptide Bundles

Tetrameric β³‐Peptide Bundles

Structure-based protein NMR assignments using native structural ensembles

An important step in NMR protein structure determination is the assignment of resonances and NOEs to corresponding nuclei. Structure-based assignment (SBA) uses a model structure ("template") for the target protein to expedite this process. Nuclear vector replacement (NVR) is an SBA framework that combines multiple sources of NMR data (chemical shifts, RDCs, sparse NOEs, amide exchange rates, TOCSY) and has high accuracy when the template is close to the target protein's structure (less than 2 A backbone RMSD). However, a close template may not always be available. We extend the circle of convergence of NVR for distant templates by using an ensemble of structures. This ensemble corresponds to the low-frequency perturbations of the given template and is obtained using normal mode analysis (NMA). Our algorithm assigns resonances and sparse NOEs using each of the structures in the ensemble separately, and aggregates the results using a voting scheme based on maximum bipartite matching. Experimental results on human ubiquitin, using four distant template structures show an increase in the assignment accuracy. Our algorithm also improves the robustness of NVR with respect to structural noise. We provide a confidence measure for each assignment using the percentage of the structures that agree on that assignment. We use this measure to assign a subset of the peaks with even higher accuracy. We further validate our algorithm on data for two additional proteins with NVR. We then show the general applicability of our approach by applying our NMA ensemble-based voting scheme to another SBA tool, MARS. For three test proteins with corresponding templates, including the 370-residue maltose binding protein, we increase the number of reliable assignments made by MARS. Finally, we show that our voting scheme is sound and optimal, by proving that it is a maximum likelihood estimator of the correct assignments.

Interactions of cytosolic phospholipase A2 with pyrrophenone, ca2+ and phospholipids studied using deuterium exchange mass spectrometry

Phospholipase A2 (PLA2) catalyzes hydrolysis of the sn‐2 fatty acyl bond of phospholipids (PL), liberating free fatty acid and lysophospholipid. We are studying the)mechanism of activation, and membrane binding of the cytosolic GIVA PLA2. This enzyme liberates arachidonic acid from phospholipids, which is a precursor formany inflammatory mediators.We have used hydrogen‐deuterium exchange mass spectrometry (DXMS) to study this enzyme. The rate of exchange of each amide proton is directly proportional to the accessibility to bulk solvent. Measurements of exchange rates have been used to characterize changes in solvent accessibility that result from protein/lipid binding interactions, and conformational changes.Group IVA cPLA2's interactions with inhibitors and phospholipid were studied using DXMS. We used pyrrophenone, a potent inhibitor of GIVA PLA2, to probe the changes in conformation upon binding in the active site. Large amide exchange rate changes were seen upon inhibitor binding. We propose that these changes can be explained by the opening of the lid region with inhibitor bound. Large changes were also seen upon calcium‐mediated lipid binding, mainly in the C2 domain. We propose the protein inserting into the lipid membrane causes these changes. These studies show that DXMS is an excellent technique for probing enzyme interfacial activation. This work was supported by NIHGM20,501

Amide Exchange Shows Calcium-Induced Conformational Changes Are Transmitted to the Dimer Interface of S100B

S100B is a 21 kDa member of the S100 calcium-binding protein family. This protein comprises a symmetric homodimer with each subunit having two EF-hands arranged from four alpha-helices (I-IV). S100B binds calcium and undergoes a conformation change leading to the exposure of hydrophobic surface residues that enable the protein to interact with biological target molecules. The most significant structural change that occurs during calcium binding results in a change in the orientation of helix III with respect to helices II and IV. In this work, the calcium-sensitive conformational change has been studied by utilizing fast 1H-15N HSQC experiments and water-transfer methods to follow the amide exchange in apo-S100B and Ca-S100B at 35 degrees C. In apo-S100B, the protection factors are 2-3 orders of magnitude lower for helix III than for helix I, II, or IV. In addition, the exchange stability measured here for the dimer interface helices (I, I', IV, and IV'), in the absence of calcium, is similar to the stability obtained from chemical denaturation experiments. When calcium binds, significant decreases in the protection factors for helices I and IV indicate a modification in the stability of the dimer interface has occurred. In contrast, helix II protection factors increase slightly, which is consistent with a decreased level of surface exposure of this helix. These data have been compared with those of the monomeric S100 protein, calbindin D9k, to illustrate that upon calcium binding there is a balance maintained between the amide exchange rates in helices II and III, although largely the rates are dissimilar for each of these proteins. This distinguishing feature may be important for the calcium-induced conformational change in S100B, where calcium binding is transmitted to the dimer-forming helices.

Role of Native-State Structure in Rubredoxin Native-State Hydrogen Exchange

Amide exchange rates were measured for Pyrococcus furiosus (Pf) rubredoxin substituted with either Zn(II), Ga(III), or Ge(IV). Base-catalyzed exchange rate constants increase up to 3000-fold per unit charge for the highly protected amides surrounding the active site metal, yielding apparent residue-specific conformational energy decreases of more than 8 kcal/mol in a comparison of the Zn(II)- and Ge(IV)-substituted proteins. However, the exchange kinetics for many of the other amides of the protein are insensitive to these metal substitutions. These differential rates are inversely correlated with the distance between the amide nitrogen and the metal in the X-ray structure, out to a distance of at least 12 A, consistent with an electrostatic potential-dependent shifting of the amide nitrogen pK. This strongly correlated distance dependence is consistent with a nativelike structure for the exchange-competent conformations. The electric field potential within the interior of the rubredoxin structure gives rise to a change of as much as a million-fold in the rate for the exchange-competent state of the individual amide hydrogens. Nevertheless, the strength of these electrostatic interactions in Pf rubredoxin appears to be comparable to those previously reported within other proteins. As a result, contrary to the conventional analysis of hydrogen exchange data, for exchange processes that occur via nonglobal transitions, the residual conformational structure will often modulate the observed rates. Although this necessarily complicates the estimation of the conformational equilibria of these exchange-competent states, this dependence on residual structure can provide insight into the conformation of these transient states.

Equilibrium Hydrogen Exchange Reveals Extensive Hydrogen Bonded Secondary Structure in the On-pathway Intermediate of Im7

The four-helical immunity protein Im7 folds through an on-pathway intermediate that has a specific, but partially misfolded, hydrophobic core. In order to gain further insight into the structure of this species, we have identified the backbone hydrogen bonds formed in the ensemble by measuring the amide exchange rates (under EX2 conditions) of the wild-type protein and a variant, I72V. In this mutant the intermediate is significantly destabilised relative to the unfolded state (ΔΔGui=4.4kJ/mol), but the native state is only slightly destabilised (ΔΔGnu=1.8kJ/mol) at 10 °C in 2H2O, pH∗ 7.0 containing 0.4 M Na2SO4, consistent with the view that this residue forms significant non-native stabilising interactions in the intermediate state. Comparison of the hydrogen exchange rates of the two proteins, therefore, enables the state from which hydrogen exchange occurs to be identified. The data show that amides in helices I, II and IV in both proteins exchange slowly with a free energy similar to that associated with global unfolding, suggesting that these helices form highly protected hydrogen-bonded helical structure in the intermediate. By contrast, amides in helix III exchange rapidly in both proteins. Importantly, the rate of exchange of amides in helix III are slowed substantially in the Im7∗ variant, I72V, compared with the wild-type protein, whilst other amides exchange more rapidly in the mutant protein, in accord with the kinetics of folding/unfolding measured using chevron analysis. These data demonstrate, therefore, that local fluctuations do not dominate the exchange mechanism and confirm that helix III does not form stable secondary structure in the intermediate. By combining these results with previously obtained Φ-values, we show that the on-pathway folding intermediate of Im7 contains extensive, stable hydrogen-bonded structure in helices I, II and IV, and that this structure is stabilised by both native and non-native interactions involving amino acid side-chains in these helices.

Relaxation compensation in chemical exchange measurements for the quantitation of amide hydrogen exchange in larger proteins

AbstractThe increasingly rapid transverse relaxation of larger macromolecules serves to limit the practical length of various types of mixing periods. When chemical exchange dynamics are used to determine the rates of amide hydrogen exchange with the bulk solvent, the foreshortened mixing period results in lowered sensitivity. Three approaches are examined for increasing the practical length of the mixing period. The transverse relaxation rate of the amide resonances is decreased by perdeuteration of the carbon‐bound hydrogen positions and also by introduction of a TROSY‐based 15N‐separated pulse sequence. Reference experiments are proposed which provide accurate compensation for relaxation effects so that exchange rate data can be obtained over the entire mixing period profile. As a result, more than a 100‐fold range of amide exchange rates can be accurately determined for a moderate‐sized protein. Copyright © 2003 John Wiley &amp; Sons, Ltd.

Temperature-dependence of protein hydrogen bond properties as studied by high-resolution NMR

The temperature-dependence of a large number of NMR parameters describing hydrogen bond properties in the protein ubiquitin was followed over a range from 5 to 65°C. The parameters comprise hydrogen bond (H-bond) scalar couplings, h3JNC′, chemical shifts, amide proton exchange rates, 15N relaxation parameters as well as covalent 1JNC′ and 1JNH couplings. A global weakening of the h3JNC′ coupling with increasing temperature is accompanied by a global upfield shift of the amide protons and a decrease of the sequential 1JNC′ couplings. If interpreted as a linear increase of the N⋯O distance, the change in h3JNC′ corresponds to an average linear thermal expansion coefficient for the NH→O hydrogen bonds of 1.7×10−4/K, which is in good agreement with overall volume expansion coefficients observed for proteins. A residue-specific analysis reveals that not all hydrogen bonds are affected to the same extent by the thermal expansion. The end of β-sheet β1/β5 at hydrogen bond E64→Q2 appears as the most thermolabile, whereas the adjacent hydrogen bond I3→L15 connecting β-strands β1 and β2 is even stabilized slightly at higher temperatures. Additional evidence for the stabilization of the β1/β2 β-hairpin at higher temperatures is found in reduced hydrogen exchange rates for strand end residue V17. This reduction corresponds to a stabilizing change in free energy of 9.7 kJ/mol for the β1/β2 hairpin. The result can be linked to the finding that the β1/β2 hairpin behaves as an autonomously folding unit in the A-state of ubiquitin under changed solvent conditions. For several amide groups the temperature-dependencies of the amide exchange rates and H-bond scalar couplings are uncorrelated. Therefore, amide exchange rates are not a sole function of the hydrogen bond “strength” as given by the electronic overlap of donors and acceptors, but are clearly dependent on other blocking mechanisms.

Solution structure of the eukaryotic pore-forming cytolysin equinatoxin II: implications for pore formation

Sea anemones produce a family of 18–20 kDa proteins, the actinoporins, that lyse cells by forming pores in cell membranes. Sphingomyelin plays an important role in their lytic activity, with membranes lacking this lipid being largely refractory to these toxins. The structure of the actinoporin equinatoxin II in aqueous solution, determined from NMR data, consists of two short helices packed against opposite faces of a β-sandwich structure formed by two five-stranded β-sheets. The protein core has extensive hydrophobic interfaces formed by residues projecting from the internal faces of the two β-sheets. 15N relaxation data show uniform backbone dynamics, implying that equinatoxin II in solution is relatively rigid, except at the N terminus; its inferred rotational correlation time is consistent with values for monomeric proteins of similar mass. Backbone amide exchange rate data also support the view of a stable structure, even though equinatoxin II lacks disulfide bonds. As monitored by NMR, it unfolds at around 70°C at pH 5.5. At 25°C the structure is stable over the pH range 2.5–7.3 but below pH 2.5 it undergoes a slow transition to an incompletely unfolded structure resembling a molten globule. Equinatoxin II has two significant patches of positive electrostatic potential formed by surface-exposed Lys and Arg residues, which may assist its interaction with charged regions of the lipid head groups. Tyr and Trp residues on the surface may also contribute by interacting with the carbonyl groups of the acyl chains of target membranes. Data from mutational studies and truncated analogues identify two regions of the protein involved in membrane interactions, the N-terminal helix and the Trp-rich region. Once the protein is anchored, the N-terminal helix may penetrate the membrane, with up to four helices lining the pore, although other mechanisms of pore formation cannot be ruled out.