C13–C13 and N15–C13 correlation spectroscopy of membrane-associated and uniformly labeled human immunodeficiency virus and influenza fusion peptides: Amino acid-type assignments and evidence for multiple conformations

Computational methods to study enveloped viral entry

The protein-membrane interactions that mediate viral infection occur via loosely ordered, transient assemblies, creating challenges for high-resolution structure determination. Computational methods and in particular molecular dynamics simulation have thus become important adjuncts for integrating experimental data, developing mechanistic models, and suggesting testable hypotheses regarding viral function. However, the large molecular scales of virus-host interaction also create challenges for detailed molecular simulation. For this reason, continuum membrane models have played a large historical role, although they have become less favored for high-resolution models of protein assemblies and lipid organization. Here, we review recent progress in the field, with an emphasis on the insight that has been gained using a mixture of coarse-grained and atomic-resolution molecular dynamics simulations. Based on successes and challenges to date, we suggest a multiresolution strategy that should yield the best mixture of computational efficiency and physical fidelity. This strategy may facilitate further simulations of viral entry by a broader range of viruses, helping illuminate the diversity of viral entry strategies and the essential common elements that can be targeted for antiviral therapies.

A small-angle neutron scattering study of the physical mechanism that drives the action of a viral fusion peptide

Viruses have evolved a variety of ways for delivering their genetic cargo to a target cell. One mechanism relies on a short sequence from a protein of the virus that is referred to as a fusion peptide. In some cases, the isolated fusion peptide is also capable of causing membranes to fuse. Infection by HIV-1 involves the 23 amino acid N-terminal sequence of its gp41 envelope protein, which is capable of causing membranes to fuse by itself, but the mechanism by which it does so is not fully understood. Here, a variant of the gp41 fusion peptide that does not strongly promote fusion was studied in the presence of vesicles composed of a mixture of unsaturated lipids and cholesterol by small-angle neutron scattering and circular dichroism spectroscopy to improve the understanding of the mechanism that drives vesicle fusion. The peptide concentration and cholesterol content govern both the peptide conformation and its impact on the bilayer structure. The results indicate that the mechanism that drives vesicle fusion by the peptide is a strong distortion of the bilayer structure by the peptide when it adopts the β-sheet conformation.

Solid-State NMR for Studying the Structure and Dynamics of Viral Assemblies

Structural virology reveals the architecture underlying infection. While notably electron microscopy images have provided an atomic view on viruses which profoundly changed our understanding of these assemblies incapable of independent life, spectroscopic techniques like NMR enter the field with their strengths in detailed conformational analysis and investigation of dynamic behavior. Typically, the large assemblies represented by viral particles fall in the regime of biological high-resolution solid-state NMR, able to follow with high sensitivity the path of the viral proteins through their interactions and maturation steps during the viral life cycle. We here trace the way from first solid-state NMR investigations to the state-of-the-art approaches currently developing, including applications focused on HIV, HBV, HCV and influenza, and an outlook to the possibilities opening in the coming years.

REDOR solid-state NMR as a probe of the membrane locations of membrane-associated peptides and proteins

Rotational-echo double-resonance (REDOR) solid-state NMR is applied to probe the membrane locations of specific residues of membrane proteins. Couplings are measured between protein (13)CO nuclei and membrane lipid or cholesterol (2)H and (31)P nuclei. Specific (13)CO labeling is used to enable unambiguous assignment and (2)H labeling covers a small region of the lipid or cholesterol molecule. The (13)CO-(31)P and (13)CO-(2)H REDOR respectively probe proximity to the membrane headgroup region and proximity to specific insertion depths within the membrane hydrocarbon core. One strength of the REDOR approach is use of chemically-native proteins and membrane components. The conventional REDOR pulse sequence with 100 kHz (2)H π pulses is robust with respect to the (2)H quadrupolar anisotropy. The (2)H T1's are comparable to the longer dephasing times (τ's) and this leads to exponential rather than sigmoidal REDOR buildups. The (13)CO-(2)H buildups are well-fitted to A×(1-e(-γτ)) where A and γ are fitting parameters that are correlated as the fraction of molecules (A) with effective (13)CO-(2)H coupling d=3γ/2. The REDOR approach is applied to probe the membrane locations of the "fusion peptide" regions of the HIV gp41 and influenza virus hemagglutinin proteins which both catalyze joining of the viral and host cell membranes during initial infection of the cell. The HIV fusion peptide forms an intermolecular antiparallel β sheet and the REDOR data support major deeply-inserted and minor shallowly-inserted molecular populations. A significant fraction of the influenza fusion peptide molecules form a tight hairpin with antiparallel N- and C-α helices and the REDOR data support a single peptide population with a deeply-inserted N-helix. The shared feature of deep insertion of the β and α fusion peptide structures may be relevant for fusion catalysis via the resultant local perturbation of the membrane bilayer. Future applications of the REDOR approach may include samples that contain cell membrane extracts and use of lower temperatures and dynamic nuclear polarization to reduce data acquisition times.

Solid-state NMR spectroscopy of the HIV gp41 membrane fusion protein supports intermolecular antiparallel β sheet fusion peptide structure in the final six-helix bundle state

The HIV gp41 protein catalyzes fusion between viral and target cell membranes. Although the ~20-residue N-terminal fusion peptide (FP) region is critical for fusion, the structure of this region is not well characterized in large gp41 constructs that model the gp41 state at different times during fusion. This paper describes solid-state NMR (SSNMR) studies of FP structure in a membrane-associated construct (FP-Hairpin), which likely models the final fusion state thought to be thermostable trimers with six-helix bundle structure in the region C-terminal of the FP. The SSNMR data show that there are populations of FP-Hairpin with either α helical or β sheet FP conformation. For the β sheet population, measurements of intermolecular (13)C-(13)C proximities in the FP are consistent with a significant fraction of intermolecular antiparallel β sheet FP structure with adjacent strand crossing near L7 and F8. There appears to be negligible in-register parallel structure. These findings support assembly of membrane-associated gp41 trimers through interleaving of N-terminal FPs from different trimers. Similar SSNMR data are obtained for FP-Hairpin and a construct containing the 70 N-terminal residues of gp41 (N70), which is a model for part of the putative pre-hairpin intermediate state of gp41. FP assembly may therefore occur at an early fusion stage. On a more fundamental level, similar SSNMR data are obtained for FP-Hairpin and a construct containing the 34 N-terminal gp41 residues (FP34) and support the hypothesis that the FP is an autonomous folding domain.

Drug-induced conformational and dynamical changes of the S31N mutant of the influenza M2 proton channel investigated by solid-state NMR

The M2 protein of influenza A viruses forms a tetrameric proton channel that is targeted by the amantadine class of antiviral drugs. A S31N mutation in the transmembrane (TM) domain of the protein has caused widespread amantadine resistance in most of the currently circulating flu viruses. Recently, a new family of compounds based on amantadine- and aryl-substituted isoxazole were discovered to inhibit the S31N channel activity and reduce replication of S31N-harboring viruses. We now use solid-state NMR spectroscopy to investigate the effects of one of these isoxazole compounds, WJ352, on the conformation of the S31N TM segment and the dynamics of the proton-selective residue, His37. Chemical shift perturbations show that WJ352 changes the conformational equilibrium of multiple TM residues, with the maximal perturbation occurring at the crucial Asn31. (13)C-(2)H distance measurements and (1)H-(1)H NOE cross peaks indicate that the adamantane moiety of the drug is bound in the spacious pore between Asn31 and Gly34 while the phenyl tail is located near Val27. Thus, the polar amine points to the channel exterior rather than to His37, in contrast to amantadine and rimantadine in the wild-type channel, suggesting that the drug is significantly stabilized by hydrophobic interactions between the adamantane and the TM peptide. (15)N and (13)C chemical shifts indicate that at low pH, His37 undergoes fast exchange among the τ tautomer, the π tautomer, and the cationic state due to proton transfer with water. The exchange rate is higher than the wild-type channel, consistent with the larger single-channel conductance of the mutant. Drug binding at acidic pH largely suppresses this exchange, reverting the histidines to a similar charge distribution as that of the high-pH closed state.

Detection of closed influenza virus hemagglutinin fusion peptide structures in membranes by backbone (13)CO- (15)N rotational-echo double-resonance solid-state NMR

The influenza virus fusion peptide is the N-terminal ~20 residues of the HA2 subunit of the hemagglutinin protein and this peptide plays a key role in the fusion of the viral and endosomal membranes during initial infection of a cell. The fusion peptide adopts N-helix/turn/C-helix structure in both detergent and membranes with reports of both open and closed interhelical topologies. In the present study, backbone (13)CO-(15)N REDOR solid-state NMR was applied to the membrane-associated fusion peptide to detect the distribution of interhelical distances. The data clearly showed a large fraction of closed and semi-closed topologies and were best-fitted to a mixture of two structures that do not exchange. One of the earlier open structural models may have incorrect G13 dihedral angles derived from TALOS analysis of experimentally correct (13)C shifts.

The influenza fusion peptide adopts a flexible flat V conformation in membranes

Knowledge about the influenza fusion peptide (FP) membrane insertion mode is crucial for understanding its fusogenic mechanism. NMR and electron paramagnetic resonance experiments showed that in micelles, the FP inserted as a fixed-angle inverted V. In membranes, however, it was shown to insert as a straight α-helix (by molecular-dynamics simulations) and to adopt multiple kinked conformations (by solid-state NMR). In this work we performed explicit-solvent molecular-dynamics simulations of the influenza FP, and its F9A and W14A mutants, in POPC membranes. The Hα1 chemical shifts predicted from the molecular-dynamics structures are in excellent agreement with the experimental values obtained for the three peptides. The peptide orientation and conformations observed from the simulations lead to a flexible flat-V model in which the peptide lies almost flat on the membrane surface and alternates between kinked and straight-helix conformations.

Molecular dynamics simulations and conductance studies of the interaction of VP1 N-terminus from Polio virus and gp41 fusion peptide from HIV-1 with lipid membranes

The icosahedral Polio virus capsid consists of 60 copies of each of the coat proteins VP1, VP2, VP3 and myristolyated VP4 (myrVP4). Catalyzed by the host cell receptor the Polio virus enters the host cell via externalization of myrVP4 and the N terminal part of VP1. There are several assumptions about the individual role of both of the proteins in the mechanism of membrane attachment and genome injection. We use the first 32 N terminal amino acids of VP1 and applied molecular dynamics simulations to assess its mechanism of function when attached and inserted into hydrated lipid membranes (POPC). Helical models are placed in various positions in regard to the lipid membrane to start with. As a comparison, the first 33 amino acids of the fusion peptide of gp41 of HIV-1 are simulated under identical conditions. Computational data support the idea that VP1 is not penetrating into the membrane to form a pore; it rather lays on the membrane surface and only perturbs the membrane. Furthermore, this idea is strengthened by channel recordings of both peptides showing irregular openings.

Irregular structure of the HIV fusion peptide in membranes demonstrated by solid-state NMR and MD simulations

To better understand peptide-induced membrane fusion at a molecular level, we set out to determine the structure of the fusogenic peptide FP23 from the HIV-1 protein gp41 when bound to a lipid bilayer. An established solid-state (19)F nuclear magnetic resonance (NMR) approach was used to collect local orientational constraints from a series of CF(3)-phenylglycine-labeled peptide analogues in macroscopically aligned membranes. Fusion assays showed that these (19)F-labels did not significantly affect peptide function. The NMR spectra were characteristic of well-behaved samples, without any signs of heterogeneity or peptide aggregation at 1:300 in 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC). We can conclude from these NMR data that FP23 has a well-defined (time-averaged) conformation and undergoes lateral diffusion in the bilayer plane, presumably as a monomer or small oligomer. Attempts to evaluate its conformation in terms of various secondary structures, however, showed that FP23 does not form any type of regular helix or β-strand. Therefore, all-atom molecular dynamics (MD) simulations were carried out using the orientational NMR constraints as pseudo-forces to drive the peptide into a stable alignment and structure. The resulting picture suggests that FP23 can adopt multiple β-turns and insert obliquely into the membrane. Such irregular conformation explains why the structure of the fusion peptide could not be reliably determined by any biophysical method so far.

13C-13C correlation spectroscopy of membrane-associated influenza virus fusion peptide strongly supports a helix-turn-helix motif and two turn conformations

The influenza virus fusion peptide (IFP) is the N-terminal domain of the viral hemagglutinin protein, binds to the endosomal membrane, and plays a critical role in fusion between the viral and endosomal membranes which is a primary step in infection. The IFP is also an important system for testing simulation methods for membrane-associated peptides. In detergent, the IFP forms helix-turn-helix and helix-turn-strand structures at pH 5.0 and 7.4, respectively, while simulations in membranes by different groups have yielded conflicting results with some reports of a continuous helix without a turn. In this study, (13)C-(13)C NMR correlation spectra were obtained for the membrane-associated IFP and the (13)C chemical shifts supported a helix-turn-helix motif at both pH 5.0 and 7.4 with an alternate turn conformation at pH 5.0 that was absent at pH 7.4. The alternate conformation was correlated with protonation of the side chain of Glu-11 in the turn and with greater fusion at pH 5.0. The structures are overall consistent with the hypothesis of "inverted V" membrane location of the IFP with insertion of the N-terminal region into the membrane and contact of the turn with the lipid/water interface. The positions of hydrophobic residues in the pH 5.0 structure may favor membrane insertion with resultant increased membrane perturbation and fusion rate. In addition to their functional relevance, these IFP structures are important reference data for simulations of the membrane-associated IFP which can in principle detect the full conformational distribution of the IFP.

Solid-state NMR spectroscopy of human immunodeficiency virus fusion peptides associated with host-cell-like membranes: 2D correlation spectra and distance measurements support a fully extended conformation and models for specific antiparallel strand registries

The human immunodeficiency virus (HIV) is "enveloped" by a membrane, and infection of a host cell begins with fusion between viral and target cell membranes. Fusion is catalyzed by the HIV gp41 protein which contains a functionally critical approximately 20-residue apolar "fusion peptide" (HFP) that associates with target cell membranes. In this study, chemically synthesized HFPs were associated with host-cell-like membranes and had "scatter-uniform" labeling (SUL), that is, only one residue of each amino acid type was U-(13)C, (15)N labeled. For the first sixteen HFP residues, an unambiguous (13)C chemical shift assignment was derived from 2D (13)C/(13)C correlation spectra with short mixing times, and the shifts were consistent with continuous beta-strand conformation. (13)C-(13)C contacts between residues on adjacent strands were derived from correlation spectra with long mixing times and suggested close proximity of the following residues: Ala-6/Gly-10, Ala-6/Phe-11, and Ile-4/Gly-13. Specific antiparallel beta-strand registries were further tested using a set of HFPs that were (13)CO-labeled at Ala-14 and (15)N-labeled at either Val-2, Gly-3, Ile-4, or Gly-5. The solid-state NMR data were fit with 50-60% population of antiparallel HFP with either Ala-14/Gly-3 or Ala-14/Ile-4 registries and 40-50% population of structures not specified by the NMR experiments. The first two registries correlated with intermolecular hydrogen bonding of 15-16 apolar N-terminal residues and this hydrogen-bonding pattern would be consistent with a predominant location of these residues in the hydrophobic membrane interior. To our knowledge, these results provide the first residue-specific structural models for membrane-associated HFP in its beta-strand conformation.