Structure of Leu5-enkephalin bound to a model membrane as determined by high-resolution NMR

Tailoring the nuclear Overhauser effect for the study of small and medium-sized molecules by solvent viscosity manipulation

The nuclear Overhauser effect (NOE) is a consequence of cross-relaxation between nuclear spins mediated by dipolar coupling. Its sensitivity to internuclear distances has made it an increasingly important tool for the determination of through-space atom proximity relationships within molecules of sizes ranging from the smallest systems to large biopolymers. With the support of sophisticated FT-NMR techniques, the NOE plays an essential role in structure elucidation, conformational and dynamic investigations in liquid-state NMR. The efficiency of magnetization transfer by the NOE depends on the molecular rotational correlation time, whose value depends on solution viscosity. The magnitude of the NOE between ¹H nuclei varies from +50% when molecular tumbling is fast to -100% when it is slow, the latter case corresponding to the spin diffusion limit. In an intermediate tumbling regime, the NOE may be vanishingly small. Increasing the viscosity of the solution increases the motional correlation time, and as a result, otherwise unobservable NOEs may be revealed and brought close to the spin diffusion limit. The goal of this review is to report the resolution of structural problems that benefited from the manipulation of the negative NOE by means of viscous solvents, including examples of molecular structure determination, conformation elucidation and mixture analysis (the ViscY method).

Evidence for effect of GM1 on opioid peptide conformation: NMR study on leucine enkephalin in ganglioside-containing isotropic phospholipid bicelles

Enkephalins are endogenous neuropeptides that have opioid-like activities and compete with morphines for the receptor binding. The binding of these neuropeptides to membrane appears crucial since enkephalins interact with the nerve cell membranes to achieve bioactive conformations that fit onto multiple receptor sites (micro, delta, and kappa). Using NMR spectroscopy, we have determined the solution structure of the small opiate pentapeptide leucine enkephalin in the presence of isotropic phospholipid bicelles: phosphocholine bicelles (DMPC:CHAPS 1:4) and phosphocholine bicelles doped with ganglioside GM1 (DMPC:CHAPS:GM1 1:4:0.3). Bicelles containing GM1 were found to interact strongly with leucine enkephalin, whereas a somewhat weaker interaction was observed in the case of bicelles without GM1. Structure calculation from torsion angles, chemical shifts, and NOE-based distance constraints explored that the peptide could flexibly switch between several mu- and delta-selective conformations in both the bicelles though micro-selective conformations turned out to be geometrically preferred in each bicellar system. A detailed analysis of the structures presented supports the variance over the singly associated conformation of enkephalin in nerve cell membranes.

Glycopeptide-membrane interactions: glycosyl enkephalin analogues adopt turn conformations by NMR and CD in amphipathic media

Four enkephalin analogues (Tyr-D-Thr-Gly-Phe-Leu-Ser-CONH(2), 1, and the related O-linked glycopeptides bearing the monosaccharide beta-glucose, 2, the disaccharide beta-maltose, 3, and the trisaccharide beta-maltotriose, 4) were synthesized, purified by HPLC, and biophysical studies were conducted to examine their interactions with membrane model systems. Glycopeptide 2 has been previously reported to penetrate the blood-brain barrier (BBB), and produce potent analgesia superior to morphine in mice (J. Med. Chem.2000, 43, 2586-90 and J. Pharm. Exp. Ther. 2001, 299, 967-972). The parent peptide and its three glycopeptide derivatives were studied in aqueous solution and in the presence of micelles using 2-D NMR, CD, and molecular mechanics (Monte Carlo studies). Consistent with previous conformational studies on cyclic opioid agonist glycopeptides, it was seen that glycosylation did not significantly perturb the peptide backbone in aqueous solution, but all four compounds strongly associated with 5-30 mM SDS or DPC micelles, and underwent profound membrane-induced conformational changes. Interaction was also observed with POPC:POPE:cholesterol lipid vesicles (LUV) in equilibrium dialysis experiments. Although the peptide backbones of 1-4 possessed random coil structures in water, in the presence of the lipid phase they each formed a nearly identical pair of structures, all with a stable beta-turn motif at the C-terminus. Use of spin labels (Mn(2+) and 5-DOXYL-stearic acid) allowed for the determination of the position and orientation of the compounds relative to the surface of the micelle.

Interaction of a bacterially expressed peptide from the receptor binding domain of Pseudomonas aeruginosa pili strain PAK with a cross-reactive antibody: conformation of the bound peptide

The C-terminal receptor binding region of Pseudomonas aeruginosa pilin protein strain PAK (residues 128-144) has been the target for the design of a vaccine effective against P. aeruginosa infections. We have recently cloned and expressed a (15)N-labeled PAK pilin peptide spanning residues 128-144 of the PAK pilin protein. The peptide exists as a major (trans) and minor (cis) species in solution, arising from isomerization around a central Ile(138)-Pro(139) peptide bond. The trans isomer adopts two well-defined turns in solution, a type I beta-turn spanning Asp(134)-Glu-Gln-Phe(137) and a type II beta-turn spanning Pro(139)-Lys-Gly-Cys(142). The cis isomer adopts only one well-defined type II beta-turn spanning Pro(139)-Lys-Gly-Cys(142) but displays evidence of a less ordered turn spanning Asp(132)-Gln-Asp-Glu(135). These turns have been implicated in cross-reactive antibody recognition. (15)N-edited NMR spectroscopy was used to study the binding of the (15)N-labeled PAK pilin peptide to an Fab fragment of a cross-reactive monoclonal antibody, PAK-13, raised against the intact PAK pilus. The results of these studies are as follows: the trans and cis isomers bind with similar affinity to the Fab, despite their different topologies; both isomers maintain the conformational integrity of their beta-turns when bound; binding leads to the preferential stabilization of the first turn over the second turn in each isomer; and binding leads to the perturbation of resonances within regions of the trans and cis backbone that undergo microsecond to millisecond motions. These slow motions may play a role in induced fit binding of the first turn to Fab PAK-13, which would allow the same antibody combining site to accommodate either trans or cis topology. More importantly for vaccine design, these motions may also play a role in the development of a broad-spectrum vaccine capable of generating an antibody therapeutic effective against the multiple strains of P. aeruginosa.

NMR of drugs and ligands bound to membrane receptors

NMR methods are now able to give detailed structural, dynamic and electronic information about drugs and ligands while constrained at their site of action in membrane-embedded receptors, information which is essential for mechanistic descriptions of their action and design of new ligands. Using solid state NMR methods, a peptic ulcer drug analogue has been described at atomic resolution (to +/- 0.3 A between two atoms) at its site of action in the gastric H+/K+-ATPase, and the aromaticity of the agonist binding site of the nicotinic acetylcholine receptor has been demonstrated, with both targets in functionally competent membranes under conditions similar to those used in screening assays. G-protein-coupled receptor ligands and prosthetic groups are also being resolved using NMR methods.

Conformational sampling of bioactive conformers: a low-temperature NMR study of 15N-Leu-enkephalin

Conformational studies of enkephalins are hampered by their high flexibility which leads to mixtures of quasi-isoenergetic conformers in solution and makes NOEs very difficult to detect in NMR spectra. In order to improve the quality of the NMR data, Leu-enkephalin was synthesized with 15N-labelled uniformly on all amide nitrogens and examined in a viscous solvent medium at low temperature. HMQC NOESY spectra of the labelled Leu-enkephalin in a DMSOd6/H2O) mixture at 275 K do show numerous NOEs, but these are not consistent with a single conformer and are only sufficient to describe the conformational state as a mixture of several conformers. Here a different approach to the structure-activity relationships of enkephalins is presented: it is possible to analyse the NMR data in terms of limiting canonical structures (i.e. beta- and gamma-turns) and finally to select only those consistent with the requirements of delta selective agonists and antagonists. This strategy results in the prediction of a family of conformers that may be useful in the design of new delta selective opioid peptides.

Solution secondary structure of a bacterially expressed peptide from the receptor binding domain of Pseudomonas aeruginosa pili strain PAK: A heteronuclear multidimensional NMR study

The C-terminal receptor binding region of Pseudomonas aeruginosa pilin protein strain PAK (residues 128-144) has recently been the target for the design of a synthetic peptide vaccine effective against multiple strains of P. aeruginosa infection. We have successfully cloned and bacterially expressed a 15N-labeled PAK pilin peptide spanning residues 128-144 of the intact PAK pilin protein, PAK 128-144(Hs145), and have determined the solution secondary structure of this peptide using heteronuclear multidimensional NMR spectroscopy. The oxidized recombinant peptide exists as a major (trans) and minor (cis) species in solution, arising from isomerization around the Ile138-Pro139 peptide bond. The pattern of NOEs, temperature coefficients, and coupling constants observed for the trans isomer demonstrate the presence of a type I beta-turn and a type II beta-turn spanning Asp134-Glu-Gln-Phe137 and Pro139-Lys-Gly-Cys142, respectively. This is in agreement with the NMR solution structure of the trans isomer of a synthetic PAK 128-144 peptide which showed a type I and a type II beta-turn in these same regions of the sequence [McInnes, C., Sönnichsen, F. D., Kay, C. M., Hodges, R. S., and Sykes, B. D. (1993) Biochemistry 32, 13432-13440; Campbell, A. P., McInnes, C., Hodges, R. S., and Sykes, B. D. (1995) Biochemistry 34, 16255-16268]. The pattern of NOEs, temperature coefficients, and coupling constants observed for the cis isomer also demonstrate a type II beta-turn spanning Pro139-Lys-Gly-Cys142, but suggest a second beta-turn spanning Asp132-Gln-Asp-Glu135. Thus, the cis isomer may also possess a double-turn motif (like the trans isomer), but with different spacing between the turns and a different placement of the first turn in the sequence. The discovery of a double-turn motif in the trans (and cis) recombinant PAK pilin peptide is an extremely important result since the double turn has been implicated as a structural requirement for the recognition of both receptor and antibody. These results pave the way for future isotope-edited NMR studies of the labeled recombinant PAK pilin peptide bound to antibody and receptor, studies integral to the design of an effective synthetic peptide vaccine.

Structural model of a cyclic dynorphin A analog bound to dodecylphosphocholine micelles by NMR and restrained molecular dynamics

The compound c[Cys5,11]dynorphin A-(1-11)-NH2, 1, is a cyclic dynorphin A analog that shows similar selectivity and potency at the kappa-opioid receptor when compared to the native form of the peptide in central nervous system assays. Previous molecular mechanics calculations have shown that the ring portion of the isoform that is trans about the Arg9-Pro10 omega bond contains either a beta-turn from residues Arg6 to Arg9 or an alpha-helical conformation. Our results from solution state NMR indicate that the compound exhibits cis-trans isomerism about the Arg9-Pro10 omega bond in both aqueous solution and when bound to dodecylphosphocholine micelles. Restrained molecular dynamics calculations show that the cis isoform of the peptide contains a type III beta-turn from residues Arg7 to Pro10. Similar calculations on the trans isoform show it to contain a beta-turn from residues Cys5 and Arg8. In this report we describe the generation of three-dimensional models from NMR data for the ring portions of both the cis and trans isoforms of 1 bound to dodecylphosphocholine micelles. Comparison with other dynorphin A structural information indicates that both the cis and trans isoforms of the peptide may be active as kappa-opioid agonists.

Role of tryptophan-14 in the interaction of dynorphin A(1-17) with micelles

Fluorescence spectroscopy has been used to examine the interaction between the opioid peptide dynorphin A(1-17) (dynorphin) and dodecylphosphocholine (DPC) micelles. Fluorescence emission spectra as a function of added lipid indicate insertion of the Trp14 side chain into the hydrophobic portion of the micelle, supporting NMR results from this laboratory. A model of interaction with micelles consistent with the fluorescence results and earlier NMR results is proposed. The critical micelle concentration in the presence of peptide was also determined, and is discussed in the context of relevance to both NMR spectroscopy and peptide-lipid interactions.

NMR and structural model of dynorphin A (1-17) bound to dodecylphosphocholine micelles

Dynorphin A (1-17) (dynorphin) acts preferentially and with high affinity at the kappa-opioid receptor, for which it is the natural, endogenous ligand. Interest in designing new ligands to interact at the kappa-opioid receptor is based in part on the desire to circumvent some of the problems associated with mu-opioid ligands such as morphine. The high-resolution structure of dynorphin in an environment which closely resembles its environment in vivo could be considered as an important lead for new drugs. The interactions that occur between dynorphin and a model membrane are potentially important, as peptide hormone activity is thought to be mediated by interactions with the cell membrane. Therefore, we have determined the high-resolution structures of dynorphin in a model membrane. Results from our laboratory have shown the existence of an alpha-helical region in dynorphin from residues Gly3 through Arg9 when bound to perdeuterated dodecylphosphocholine (DPC) micelles. In this report we show that dynorphin is bound to DPC micelles and describe a family of dynorphin structures that is alpha-helical from residues Gly3 through Pro10 and that contains a beta-turn from residues Trp14 through Gln17. A model of interaction with the micelle is also reported and is discussed in the context of hormone action in vivo. The structures were determined with 1D and 2D nuclear magnetic resonance spectroscopy, distance geometry in dihedral angle space, and restrained molecular dynamics simulations.

Lipid-induced secondary structures and orientations of (Leu5)-enkephalin: helical and crystallographic double-bend conformers revealed by IRATR and molecular modelling

Lipid-induced secondary structures and orientations of the two enantiomeric [Leu5]-enkephalins, L-Tyr-Gly-Gly-L-Phe-L-Leu, and D-Tyr-Gly-Gly-D-Phe-D-Leu, on flat multi-bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) were examined with polarized attenuated total reflection IR (IRATR) spectroscopy and molecular mechanics procedures. The membrane-bound peptides showed identical IR spectra in the amide I and II band regions that indicated membrane-induced secondary structures and specific orientations of the non-zwitterionic molecules. A Lorentzian band shape analysis based on second derivatives of the original curves and observed band polarizations suggested the presence of helical structures (beta III- and alpha-turns), oriented more or less perpendicular to the membrane surface. Other folded structures, e.g. beta I- and gamma turns, were not excluded. Molecular modelling of non-zwitterionic (Leu5)-enkephalin with two beta III-turns or an alpha-turn resulted in essentially four low-energy conformers containing (i) two beta III-turns, (ii) one alpha-turn, (iii) a beta III-turn fused to an alpha-turn, and (iv) a beta III-turn fused to a beta I-turn as in the crystallographic molecular conformation described by Aubry et al. [Biopolymers 28, 27-40 (1989)]. Zwitterionic [Leu5]-enkephalin with two beta III-turns collapsed to a C13 turn (a distorted alpha-turn) bridged by a gamma I-turn (v). The alignment of the amide I oscillators within the helical structures, (i), (ii) and (iii), and the double-bend structures, (iv) and (v), explained the observed amide I and II polarizations. Differences between these and other lipid-induced [Leu5]-enkephalin conformers reported in the literature may be caused by the lipid polymorphism of the model membranes used. Possible implications of the new conformers for the molecular mechanism of opioid receptor selection are discussed in terms of the membrane compartments theory.