Lyophilization Process Design and Development: A Single-Step Drying Approach

High-throughput lyophilization process was designed and developed for protein formulations using a single-step drying approach at a shelf temperature (T_s) of ≥40°C. Model proteins were evaluated at different protein concentrations in amorphous-only and amorphous-crystalline formulations. Single-step drying resulted in product temperature (T_p) above the collapse temperature (T_c) and a significant reduction (of at least 40%) in process time compared to the control cycle (wherein T_p < T_c). For the amorphous-only formulation at a protein concentration of ≤25 mg/mL, single-step drying resulted in product shrinkage and partial collapse, whereas a 50 mg/mL concentration showed minor product shrinkage. The presence of a crystallizing bulking agent improved product appearance at ≤25 mg/mL protein concentration for single-step drying. No impact to other product quality attributes was observed for single-step drying. Vial type, fill height, and scale-up considerations (i.e., choked flow, condenser capacity, lyophilizer design and geometry) were the important factors identified for successful implementation of single-step drying. Although single-step drying showed significant reduction in the edge vial effect, the scale-up considerations need to be addressed critically. Finally, the single-step drying approach can indeed make the lyophilization process high throughput compared to traditional freeze-drying process (i.e., 2-step drying).     

The CSD Drug Subset: The Changing Chemistry and Crystallography of Small Molecule Pharmaceuticals

We report the generation and statistical analysis of the CSD drug subset: a subset of the Cambridge Structural Database (CSD) consisting of every published small-molecule crystal structure containing an approved drug molecule. By making use of InChI matching, a CSD Python API workflow to link CSD entries to the online database Drugbank.ca has been produced. This has resulted in a subset of 8632 crystal structures, representing all published solid forms of 785 unique drug molecules. We hope that this new resource will lead to improvements in targeted cheminformatics and statistical model building in a pharmaceutical setting. In addition to this, as part of the Advanced Digital Design of Pharmaceutical Therapeutics collaboration between academia and industry, we have been given the unique opportunity to run comparative analysis on the internal crystal structure databases of AstraZeneca and Pfizer, alongside comparison to the CSD as a whole.     

Quantification of Silicone Oil and Its Degradation Products in Aqueous Pharmaceutical Formulations by 1H-NMR Spectroscopy

During the past years, there has been an increasing focus on the presence of silicone oil as a contaminant in pharmaceutical formulations kept in prefilled syringes (PFSs). As the PFSs are coated on the inner wall with silicone oil (polydimethylsiloxane), there is a potential risk that the oil can migrate from the inner surface of the primary packing material into the aqueous solution. Several studies have demonstrated that presence of silicone oil as droplets in a high-concentrated protein formulation can cause protein aggregation. Hence, because the use of silicone-coated primary packing material for protein formulations are increasing, the call for an easy and quantitative method for determination of silicone oil and its degradation products in pharmaceutical formulations is therefore needed. Several analytical techniques have in the past been developed with the aim of detecting the presence of silicone oil and degradation products hereof. Most of these methods require hydrolyzation, derivatization, and extraction steps followed by, for example, gas chromatography-mass spectrometry analysis. Applying these methods can cause a loss in detection or an overestimation of the hydrolytic degradation products of silicone oil, that is, trimethylsilanol and dimethylsilanediol. The 2 silanols are highly hydrophilic and prefers the aqueous environment. Analysis of an aqueous formulation obtained from a PFS by ¹H-NMR spectroscopy provides data about the content and levels of silicone oil and the 2 silanols even in levels below 10 ppm. The ¹H-NMR method offers an easy and direct, quantitative measurement of samples intended for clinical use and samples kept at elevated temperature for a prolonged time (i.e., stability studies). The result of the study presented here showed dimethylsilanediol to be the main silicone compound present in the aqueous formulation when kept in baked-on PFSs. The degradation product dimethylsilanediol, in full accordance with expected hydrolytic degradation of silicone oil, increased during storage and with elevated temperature. In addition, the method can be applied to aqueous samples where polydimethylsiloxane has been added as, for example, the major constituent of antifoam.     

Higher-Order Structure Characterization of Pharmaceutical Proteins by 2D Nuclear Magnetic Resonance Methyl Fingerprinting

A key challenge in the analytical assessment of therapeutic proteins is the comprehensive characterization of their higher-order structure (HOS). To directly assess HOS, a new type of assay is warranted. The most sensitive and detailed method for characterizing HOS is unquestionably nuclear magnetic resonance (NMR) spectroscopy. NMR spectroscopy provides direct information about the HOS at an atomic level, and with modern NMR spectrometers and improved pulse sequences, this has become feasible even on unlabeled proteins. Hence, NMR spectroscopy could be a very powerful tool for control of HOS following, for example, process changes resulting in structural changes, oxidation, degradation, or chemical modifications. We present a method for characterizing the HOS of therapeutic proteins by monitoring their methyl groups using 2D H, C-correlated NMR. We use a statistical model that compares the NMR spectrum of a given sample to a reference and results in one output value describing how similar the HOS of the samples are. This makes the overall result easy to interpret even for non-NMR experts. We show that the method is applicable to proteins of varying size and complexity (here up to ～30 kDa) and that it is sufficiently sensitive for the detection of small changes in both primary and HOS.     

DEAD-box protein CYT-19 is activated by exposed helices in a group I intron RNA

DEAD-box proteins are nonprocessive RNA helicases and can function as RNA chaperones, but the mechanisms of their chaperone activity remain incompletely understood. The Neurospora crassa DEAD-box protein CYT-19 is a mitochondrial RNA chaperone that promotes group I intron splicing and has been shown to resolve misfolded group I intron structures, allowing them to refold. Building on previous results, here we use a series of tertiary contact mutants of the Tetrahymena group I intron ribozyme to demonstrate that the efficiency of CYT-19–mediated unfolding of the ribozyme is tightly linked to global RNA tertiary stability. Efficient unfolding of destabilized ribozyme variants is accompanied by increased ATPase activity of CYT-19, suggesting that destabilized ribozymes provide more productive interaction opportunities. The strongest ATPase stimulation occurs with a ribozyme that lacks all five tertiary contacts and does not form a compact structure, and small-angle X-ray scattering indicates that ATPase activity tracks with ribozyme compactness. Further, deletion of three helices that are prominently exposed in the folded structure decreases the ATPase stimulation by the folded ribozyme. Together, these results lead to a model in which CYT-19, and likely related DEAD-box proteins, rearranges complex RNA structures by preferentially interacting with and unwinding exposed RNA secondary structure. Importantly, this mechanism could bias DEAD-box proteins to act on misfolded RNAs and ribonucleoproteins, which are likely to be less compact and more dynamic than their native counterparts.DEAD-box proteins constitute the largest family of RNA helicases and function in all stages of RNA metabolism (1, 2). In vivo, many DEAD-box proteins have been implicated in assembly and conformational rearrangements of large structured RNAs and ribonucleoproteins (RNPs), including the ribosome, spliceosome, and self-splicing introns (3). Thus, it is important to establish how these proteins use their basic mechanisms of RNA binding and helix unwinding to interact with and remodel higher-order RNA structures.Structural and mechanistic studies have elucidated the basic steps of the ATPase cycle of DEAD-box proteins and have provided an understanding of the coupling between ATPase and duplex unwinding activities (4–11). The conserved helicase core consists of two flexibly linked RecA-like domains that contain at least 12 conserved motifs, including the D-E-A-D sequence in the ATP-binding motif II (3, 12). Binding of ATP and double-stranded RNA to domains 1 and 2, respectively, induces domain closure, which completes the formation of an ATPase active site at the domain interface and introduces steric clashes in the RNA binding site, leading to the displacement of one of the RNA strands (6, 7). ATP hydrolysis and inorganic phosphate release are then thought to regenerate the open enzyme conformation (4, 8, 13). Unlike conventional helicases, DEAD-box proteins have not been found to translocate, limiting the unwinding activity to short helices that can be disrupted in a single cycle of ATP binding and hydrolysis (4, 8, 9, 14–16). This mechanism is compatible with the physiological roles of DEAD-box proteins, because cellular RNAs rarely contain continuous base-paired regions that are longer than one or two helical turns.The interactions of DEAD-box proteins with structured RNAs have been extensively studied using two homologous proteins that function as general RNA chaperones: CYT-19 from Neurospora crassa and Mss116 from Saccharomyces cerevisiae. In vivo, CYT-19 is required for efficient splicing of several mitochondrial group I introns and can promote splicing of group I and group II introns in yeast mutants that lack functional Mss116 (17, 18). Both proteins have been shown to act as general RNA chaperones during group I and group II intron folding in vitro and are thought to act primarily by reversing misfolding of the intron RNAs, although additional mechanisms may be used for some substrates (17–23). Importantly, the chaperone activities of these and other DEAD-box proteins correlate with their ATP-dependent helix unwinding activities, suggesting that DEAD-box proteins function by lowering the energy barriers for transitions between alternative structures that involve disruption of base pairs (24, 25).In vitro studies using the group I intron ribozyme from Tetrahymena thermophila have been instrumental in probing the chaperone mechanism of CYT-19 (17, 26–28). This ∼400-nt RNA folds into a compact, globular structure composed of a conserved core and a series of peripheral elements that encircle the core by forming long-range tertiary contacts (Fig. 1) (29–31). Upon addition of Mg²⁺ ions, the majority of the ribozyme population becomes trapped in a long-lived misfolded conformation, which then slowly refolds to the native state (32). The misfolded intermediate is remarkably similar to the native ribozyme, forming a complete native network of secondary and tertiary interactions and a globally compact fold (33, 34). Despite these similarities, refolding to the native state requires extensive unfolding, including disruption of all five peripheral tertiary contacts and the core helix P3 (33, 35). To explain these results, a topological error has been proposed, wherein two single-stranded joining elements are crossed incorrectly in the core of the misfolded ribozyme, and transient disruption of the surrounding native structure is required for refolding (33, 35).Open in a separate windowFig. 1.The Tetrahymena group I intron ribozyme. (A) Secondary structure and mutations. Peripheral elements are colored and thick arrows mark the long-range peripheral tertiary contacts. Paired regions (P) and loops that were mutated in this study (L) are labeled based on group I intron nomenclature in ref. 31. The mutated regions are enclosed in dashed boxes and labeled in bold, with sequence substitutions indicated nearby. Sequences that were deleted to construct the helix truncation mutants (Fig. 6) are enclosed in gray dashed boxes and the replacement nucleotides are shown in gray italic font. (B) Tertiary structure model of the ribozyme (31). Peripheral elements (colored surface) and the locations of the long-range peripheral tertiary contacts (circles) are highlighted using the same color scheme as in A. The ribozyme core is shown in silver. The block arrows indicate the approximate positions of tertiary contacts not visible in each respective view of the ribozyme. The figures were prepared using PyMOL.Given the structural similarity between the native and misfolded ribozyme, it is interesting that CYT-19 can accelerate refolding of the misfolded intermediate by at least an order of magnitude without detectably unfolding the native ribozyme (26). Insights into this apparent preference for the misfolded ribozyme came from studies of two ribozyme mutants in which the tertiary structure was destabilized, making the stability of the native ribozyme comparable to that of the misfolded intermediate (28). CYT-19 unfolded the native and misfolded conformers of these mutants with comparable efficiencies, suggesting that the efficiency of chaperone-mediated unfolding depended on the stability of ribozyme tertiary structure. However, the mutations studied were concentrated in one region of the ribozyme, leaving open the possibility that CYT-19 recognizes local disruptions rather than global stability.Here we investigate the roles of RNA stability in CYT-19-mediated unfolding of the Tetrahymena ribozyme by using a series of ribozyme mutants with disruptions of each of the five peripheral tertiary contacts. We observe a strong correlation between CYT-19 activity and global stability of ribozyme tertiary structure. Further, we find that the RNA-dependent ATPase activity of CYT-19 depends on the accessibility of secondary structure in the ribozyme. Our results lead to a general model for recognition and remodeling of unstable or incorrectly folded RNAs by a DEAD-box protein.     

Covalent agonists for studying G protein-coupled receptor activation

Structural studies on G protein-coupled receptors (GPCRs) provide important insights into the architecture and function of these important drug targets. However, the crystallization of GPCRs in active states is particularly challenging, requiring the formation of stable and conformationally homogeneous ligand-receptor complexes. Native hormones, neurotransmitters, and synthetic agonists that bind with low affinity are ineffective at stabilizing an active state for crystallogenesis. To promote structural studies on the pharmacologically highly relevant class of aminergic GPCRs, we here present the development of covalently binding molecular tools activating G_s-, G_i-, and G_q-coupled receptors. The covalent agonists are derived from the monoamine neurotransmitters noradrenaline, dopamine, serotonin, and histamine, and they were accessed using a general and versatile synthetic strategy. We demonstrate that the tool compounds presented herein display an efficient covalent binding mode and that the respective covalent ligand-receptor complexes activate G proteins comparable to the natural neurotransmitters. A crystal structure of the β₂-adrenoreceptor in complex with a covalent noradrenaline analog and a conformationally selective antibody (nanobody) verified that these agonists can be used to facilitate crystallogenesis.One of the major obstacles to the investigation of the structural basis of G protein-coupled receptor (GPCR) activation is the flexibility of their seven-transmembrane core, particularly in the active state (1), and the resulting biochemical instability of the solubilized protein (2, 3). Protein crystallography, the most powerful tool for the study of GPCR structure, requires the formation of stable and conformationally homogeneous ligand-receptor complexes (4). High-affinity agonists with dissociation constants in the low to subnanomolar range and low off-rates facilitate stabilization of the protein throughout the process of expression, purification, and crystallogenesis (2); however, endogenous neurotransmitters usually show poor binding affinity. Low binding affinity with rapid association and dissociation rates leads to conformational heterogeneity that prevents the formation of diffraction-quality crystals. The rapid dissociation rate of agonists also makes it difficult to generate active-state stabilizing proteins, such as the camelid antibodies (nanobodies) that have been used to obtain active-state structures of the β₂-adrenergic receptor (β₂AR) (5) and M2 muscarinic receptor (6).To prevent ligand dissociation, irreversible ligation of electrophilic moieties like halomethylketones, isothiocyanates, Michael acceptors, or aziridinium groups of small-molecule ligands with a suitably positioned nucleophilic residue in the receptor has been used (7–16). However, irreversible ligands often suffer from incomplete cross-linking (15) and reduced receptor activation when covalent binding leads to loss of agonist efficacy (10, 16). Furthermore, their highly electrophilic nature and the abundance of nucleophilic groups in biological systems may lead to a low coupling selectivity (7, 8).Disulfide-based cross-linking approaches (17, 18) offer the advantage that the covalent binding of disulfide-containing compounds is chemoselective for cysteine and enforced by the affinity of the ligand-pharmacophore rather than by the electrophilicity of the cross-linking function (19). We refer to the described ligands as covalent rather than irreversible agonists because cleavage may be promoted by reducing agents and the disulfide transfer process is a reversible chemical reaction in general.Structural information on the target protein facilitates the development of covalent ligand-receptor pairs. Mutation of H93^2.64 in the β₂AR to cysteine introduced an anchor for the disulfide-based covalent agonist FAUC50, which does not perturb ligand binding or the activation of the receptor, and thus enabled, to our knowledge, the first agonist-bound GPCR structure (20). Taking advantage of the high structural homology among aminergic GPCRs, we reasoned that the introduction of cysteine into position X^2.64 should also result in a covalently binding receptor mutant for other aminergic GPCRs.We here report a methodology to generate disulfide-based covalent ligand-receptor pairs to promote structural and functional studies on GPCRs. We demonstrate that even the low-affinity endogenous agonists noradrenaline, dopamine, and serotonin can be converted into efficient covalently binding molecular tools for the β₂AR, the dopamine D₂ receptor (D₂R), and the 5-hydroxytryptamine 2A (5-HT_2A) serotonergic subtype representing G_s-, G_i-, and G_q-coupled GPCRs, respectively. Analogous studies were conducted starting from histamine and the receptor subtype H₁. We applied this strategy to obtain an active-state crystal structure of the β₂AR^H93C and a covalent (nor)adrenaline analog.     

Protective hinge in insulin opens to enable its receptor engagement

Insulin provides a classical model of a globular protein, yet how the hormone changes conformation to engage its receptor has long been enigmatic. Interest has focused on the C-terminal B-chain segment, critical for protective self-assembly in β cells and receptor binding at target tissues. Insight may be obtained from truncated “microreceptors” that reconstitute the primary hormone-binding site (α-subunit domains L1 and αCT). We demonstrate that, on microreceptor binding, this segment undergoes concerted hinge-like rotation at its B20-B23 β-turn, coupling reorientation of Phe^B24 to a 60° rotation of the B25-B28 β-strand away from the hormone core to lie antiparallel to the receptor''s L1–β₂ sheet. Opening of this hinge enables conserved nonpolar side chains (Ile^A2, Val^A3, Val^B12, Phe^B24, and Phe^B25) to engage the receptor. Restraining the hinge by nonstandard mutagenesis preserves native folding but blocks receptor binding, whereas its engineered opening maintains activity at the price of protein instability and nonnative aggregation. Our findings rationalize properties of clinical mutations in the insulin family and provide a previously unidentified foundation for designing therapeutic analogs. We envisage that a switch between free and receptor-bound conformations of insulin evolved as a solution to conflicting structural determinants of biosynthesis and function.How insulin engages the insulin receptor has inspired speculation ever since the structure of the free hormone was determined by Hodgkin and colleagues in 1969 (1, 2). Over the ensuing decades, anomalies encountered in studies of analogs have suggested that the hormone undergoes a conformational change on receptor binding: in particular, that the C-terminal β-strand of the B chain (residues B24–B30) releases from the helical core to expose otherwise-buried nonpolar surfaces (the detachment model) (3–6). Interest in the B-chain β-strand was further motivated by the discovery of clinical mutations within it associated with diabetes mellitus (DM) (7). Analysis of residue-specific photo–cross-linking provided evidence that both the detached strand and underlying nonpolar surfaces engage the receptor (8).The relevant structural biology is as follows. The insulin receptor is a disulfide-linked (αβ)₂ receptor tyrosine kinase (Fig. 1A), the extracellular α-subunits together binding a single insulin molecule with high affinity (9). Involvement of the two α-subunits is asymmetric: the primary insulin-binding site (site 1^*) comprises the central β-sheet (L1–β₂) of the first leucine-rich repeat domain (L1) of one α-subunit and the partially helical C-terminal segment (αCT) of the other α-subunit (Fig. 1A) (10). Such binding initiates conformational changes leading to transphosphorylation of the β-subunits’ intracellular tyrosine kinase (TK) domains. Structures of wild-type (WT) insulin (or analogs) bound to extracellular receptor fragments were recently described at maximum resolution of 3.9 Å (11), revealing that hormone binding is primarily mediated by αCT (receptor residues 704–719); direct interactions between insulin and L1 were sparse and restricted to certain B-chain residues. On insulin binding, αCT was repositioned on the L1–β₂ surface, and its helix was C-terminally extended to include residues 711–714. None of these structures defined the positions of C-terminal B-chain residues beyond B21. Support for the detachment model was nonetheless provided by entry of αCT into a volume that would otherwise be occupied by B-chain residues B25–B30 (i.e., in classical insulin structures; Fig. 1B) (11).Open in a separate windowFig. 1.Insulin B-chain C-terminal β-strand in the μIR complex. (A) Structure of apo-receptor ectodomain. One monomer is in tube representation (labeled), the second is in surface representation. L1, first leucine-rich repeat domain; CR, cysteine-rich domain; L2, second leucine-rich repeat domain; FnIII-1, -2 and -3; first, second and third fibronectin type III domains, respectively; αCT, α-subunit C-terminal segment; coral disk, plasma membrane. (B) Insulin bound to μIR; the view direction with respect to L1 in the apo-ectodomain is indicated by the arrow in A. Only B-chain residues indicated in black were originally resolved (11). The brown tube indicates classical location of residues B20-B30 in free insulin, occluded in the complex by αCT. (C) Orthogonal views of unmodeled 2F_obs-F_calc difference electron density (SI Appendix), indicating association of map segments with the αCT C-terminal extension (transparent magenta), insulin B-chain C-terminal segment (transparent gray), and Asn^A21 (transparent yellow). Difference density is sharpened (B_sharp = −160 Ų). (D–F) Refined models of respective segments insulin B20–B27, αCT 714–719, and insulin A17-A21 within postrefinement 2F_obs-F_calc difference electron density (B_sharp = −160 Ų). D is in stereo.We describe here the structure and interactions of the detached B-chain C-terminal segment of insulin on its binding to a “microreceptor” (μIR), an L1–CR domain-minimized version of the α-subunit (designated IR310.T) plus exogenous αCT peptide 704–719 (11). Our analysis defines a hinge in the B chain whose opening is coupled to repositioning of αCT between nonpolar surfaces of L1 and the insulin A chain. To understand the role of this hinge in holoreceptor binding and signaling, we designed three insulin analogs containing structural constraints (d-Ala^B20, d-Ala^B23]-insulin, ∆Phe^B25-insulin, and ∆Phe^B24-insulin, where ∆Phe is (α,β)-dehydrophenylalanine (Fig. 2) (12). The latter represents, to our knowledge, the first use of ∆Phe—a rigid “β-breaker” with extended electronic conjugation between its side chain and main chain (SI Appendix, Fig. S1)—as a probe of induced fit in macromolecular recognition. In addition, a fourth analog, active but with anomalous flexibility in the B chain (5, 6) (

The nature of protein folding pathways

How do proteins fold, and why do they fold in that way? This Perspective integrates earlier and more recent advances over the 50-y history of the protein folding problem, emphasizing unambiguously clear structural information. Experimental results show that, contrary to prior belief, proteins are multistate rather than two-state objects. They are composed of separately cooperative foldon building blocks that can be seen to repeatedly unfold and refold as units even under native conditions. Similarly, foldons are lost as units when proteins are destabilized to produce partially unfolded equilibrium molten globules. In kinetic folding, the inherently cooperative nature of foldons predisposes the thermally driven amino acid-level search to form an initial foldon and subsequent foldons in later assisted searches. The small size of foldon units, ∼20 residues, resolves the Levinthal time-scale search problem. These microscopic-level search processes can be identified with the disordered multitrack search envisioned in the “new view” model for protein folding. Emergent macroscopic foldon–foldon interactions then collectively provide the structural guidance and free energy bias for the ordered addition of foldons in a stepwise pathway that sequentially builds the native protein. These conclusions reconcile the seemingly opposed new view and defined pathway models; the two models account for different stages of the protein folding process. Additionally, these observations answer the “how” and the “why” questions. The protein folding pathway depends on the same foldon units and foldon–foldon interactions that construct the native structure.     

Dissociation of the trimeric gp41 ectodomain at the lipid–water interface suggests an active role in HIV-1 Env-mediated membrane fusion

The envelope glycoprotein gp41 mediates the process of membrane fusion that enables entry of the HIV-1 virus into the host cell. The actual fusion process involves a switch from a homotrimeric prehairpin intermediate conformation, consisting of parallel coiled-coil helices, to a postfusion state where the ectodomains are arranged as a trimer of helical hairpins, adopting a six-helix bundle (6HB) state. Here, we show by solution NMR spectroscopy that a water-soluble 6HB gp41 ectodomain binds to zwitterionic detergents that contain phosphocholine or phosphatidylcholine head groups and phospholipid vesicles that mimic T-cell membrane composition. Binding results in the dissociation of the 6HB and the formation of a monomeric state, where its two α-helices, N-terminal heptad repeat (NHR) and C-terminal heptad repeat (CHR), become embedded in the lipid–water interface of the virus and host cell. The atomic structure of the gp41 ectodomain monomer, based on NOE distance restraints and residual dipolar couplings, shows that the NHR and CHR helices remain mostly intact, but they completely lose interhelical contacts. The high affinity of the ectodomain helices for phospholipid surfaces suggests that unzippering of the prehairpin intermediate leads to a state where the NHR and CHR helices become embedded in the host cell and viral membranes, respectively, thereby providing a physical force for bringing these membranes into close juxtaposition before actual fusion.The first step of HIV infection involves fusion of the viral and target cell membranes, a process mediated by the viral envelope glycoprotein Env, consisting of subunits gp120 and gp41 (1). The envelope proteins form a noncovalent complex on the viral surface with the trimerized gp41 transmembrane subunit sequestered by three gp120 surface subunits (2–5). Binding of gp120 to the cell surface receptors CD4 and chemokine receptors CXCR4 or CCR5 triggers a cascade of conformational changes that disrupt the interactions between gp41 and gp120 and result in an extended gp41 conformation (1, 6). In this extended prefusion state, the highly hydrophobic N-terminal fusion peptide (FP) of gp41 anchors in the host cell membrane, while being spatially remote from its transmembrane domain (TM), which traverses the viral membrane (7, 8). After the host cell and viral membranes have fused, the gp41 ectodomain, which links the FP and TM domains, has transitioned into a C3-symmetric six-helix bundle (6HB), with the FP in physical proximity to the TM domain (9). The refolding of gp41 trimers into the highly stable 6HB arrangement is believed to overcome the large free-energy barrier of membrane fusion. Several atomic resolution structures of the 6HB postfusion state have been solved by X-ray crystallography, confirming that the C-terminal heptad repeat (CHR) helices pack in an antiparallel manner into the conserved hydrophobic grooves formed at the surface of the central trimer of N-terminal heptad repeat (NHR) helices (10–12).Contrary to the postfusion state, structural features of the prehairpin intermediates of HIV-1 gp41 remain the subject of much debate. The functional requirement that gp41’s fusion peptide engages the membrane of spatially distant host cells dictates an extended conformation for the time point where FP engages the membrane of the host cell. Cartoon models commonly depict this prehairpin intermediate as an extended trimer of linear NHR and CHR helices (13–17). Recent cryo-EM studies provide more detailed insights into the relatively subtle rearrangement of the trimeric helical NHR core, which is associated with rearrangements of gp120 relative to gp41 on receptor activation of Env, that leads to the release of FP from its hydrophobic burial site at the gp41–gp120 interface (5, 18, 19). Subsequent dissociation of the gp120 subunits leaves the gp41 core in a state somewhat similar to the common cartoon models, lacking the trimer-stabilizing interactions supplied by gp120.Although it seems clear that, initially, gp41 directly engages the viral and host cell membranes only by means of its TM and FP domains, there is evidence that, subsequently, the NHR region also interacts directly with the membranes and actively participates in the fusion process. In particular, the NHR-derived peptide, N36, binds to both zwitterionic and negatively charged phospholipid vesicles (20), whereas the N70 peptide, which encompasses the FP and NHR domains, is four times more fusogenic than FP alone for negatively charged membranes (21). The latter result suggests that the NHR segment takes an active role in destabilizing membranes and works synergistically with FP to increase the efficiency of lipid mixing. In another elegant set of experiments, Wexler-Cohen and Shai (14) showed that NHR-mimicking peptides, designed to interfere with formation of gp41’s 6HB state by competing with gp41 NHR insertion into the 6HB, have strongly increased inhibitory activity when they carry a membrane-anchoring alkyl chain. Increased inhibition is seen regardless of whether the alkyl chain is attached at the N or C terminus of the NHR peptide, suggesting that the gp41 NHR domain is embedded in the membrane surface. 6HB oligomers formed by NHR- and CHR-derived synthetic peptides dissociate in the presence of either zwitterionic or negatively charged phospholipid vesicles (20, 22). This lipid binding property has been postulated to facilitate membrane fusion by introducing an additional destabilization of the viral and target cell membranes, thereby lowering the free-energy barrier for fusion (23).In the present study, we show that the 6HB complex formed by an ectodomain that contains large segments of the NHR and CHR helices, connected by a six-residue linker (Core^S), dissociates and forms stable monomers on binding to either dodecyl phosphocholine (DPC) micelles or phospholipid vesicles of a lipid composition that mimics the T-cell membrane. The transition from trimers to monomers is associated with a significant decrease in α-helicity and also observed for a longer ectodomain construct (Core^IL) that encompasses the native immunodominant loop (IL) connecting the NHR and CHR helices. The Core^S construct was chosen for detailed characterization of the structure and dynamics of the gp41 ectodomain monomer in the presence of DPC micelles. An atomic structure determination by NMR spectroscopy of the gp41 ectodomain monomer, based on residual dipolar coupling (RDC) and NOE restraints, reveals a monomeric, flexibly linked two-helical structure lying on the surface of the DPC micelle without any specific interaction between the stable and well-defined NHR and CHR helices. We propose that formation of this lipid-bound state, where CHR embeds in the viral membrane and NHR in the membrane of the host cell, provides the force for pulling the two membranes into close juxtaposition, thereby priming the system for membrane fusion. After fusion, close spatial proximity between the opposite ends of the ectodomain then permits their tight interaction, which is seen in 6HB crystal structures of the full-length gp41 ectodomain (9).