Conformation of deltorphin-II in membrane environment studied by two-dimensional NMR spectroscopy and molecular dynamics calculations

[Overview of structural study on conformations and intermolecular interactions of biomolecules]

Information on the conformational feature and specific intermolecular interaction of biomolecules is important to understand the biological function and to develop device for treating disorder caused by the abnormal function. Thus the 3D structures of the biologically active molecules and the specific interactions with their target molecules at the atomic level have been investigated by various physicochemical approaches. Herein, the following five subjects are reviewed: (1) function-linked conformations of biomolecules including natural annular products, opioid peptides and neuropeptides; (2) π-π stacking interactions of tryptophan derivatives with coenzymes and nucleic acid bases; (3) mRNA cap recognition of eukaryotic initiation factor 4E and its regulation by 4E-binding protein; (4) conformational feature of histamine H2 receptor antagonists and design of cathepsin B inhibitors; (5) self-aggregation mechanism of tau protein and its inhibition.

Exploring deltorphin II binding to the third extracellular loop of the delta-opioid receptor

The third extracellular loop of the human delta-opioid receptor (hDOR) is known to play an important role in the binding of delta-selective ligands. In particular, mutation of three amino acids (Trp(284), Val(296), and Val(297)) to alanine significantly diminished delta-opioid receptor affinity for delta-selective ligands. To assess the changes in conformation accompanying binding of the endogenous opioid peptide deltorphin II to the delta-opioid receptor at both the receptor and ligand levels as well as to determine points of contact between the two, an in-depth spectroscopic study that addressed these points was initiated. Fragments of the delta-opioid receptor of variable length and containing residues in the third extracellular loop were synthesized and studied by NMR and CD spectroscopy in a membrane-mimetic milieu. The receptor peptides examined included hDOR-(279-299), hDOR-(283-299), hDOR-(281-297), and hDOR-(283-297). A helical conformation was observed for the longest receptor fragment between Val(283) and Arg(291), whereas a nascent helix occurred in a similar region for hDOR-(281-297). Further removal of N-terminal residues Val(281) and Ile(282) abolished helical conformation completely. Binding of the delta-selective ligand deltorphin II to hDOR-(279-299) destabilized the helix at the receptor peptide N terminus. Dramatic changes in the alpha-proton chemical shifts for Trp(284) and Leu(286) in hDOR-(279-299) also accompanied this loss of helical conformation. Large upfield displacement of alpha-proton chemical shifts was observed for Leu(295), Val(296), and Val(297) in hDOR-(279-299) following its interaction with deltorphin II, thus identifying a gain in beta-conformation at the receptor peptide C terminus. Similar changes did not occur for the shorter peptide hDOR(281-297). A hypothesis describing the conformational events accompanying selective deltorphin II binding to the delta-opioid receptor is presented.

The mu-selective heptapeptide opioid dermorphin has two conformations around Phe3 psi with no head-to-tail interaction. A quantitative 2-D NMR and molecular modeling analysis

The mu opioid heptapeptide Dermorphin (DRM) is under 70 % of trans forms for the Tyr(5)-Pro(6) peptide bond in solution (CDCl(3)/DMSO-d(6) 1/1 vol/vol). Variations of NOE integrals at 5 temperatures show apparent correlation times of 0.8 to 0.9 ns (at 280 K) in that mixed solvent. Four NOE between non-adjacent residues reveal a large population of folded structures. However, in trans DRM, 4 adjacent NOE Phe(3)/Gly(4) can only be explained by an equilibrium between folded (psi(3) > 0) and extended (psi(3) > 0) conformations. Simulated annealing modeling gave about 60% (psi(3) > 0) and 40% (psi(3) > 0) of these conformer populations. Trans DRM study and previous studies on the heptapeptide opioids, dermenkephalin (DREK) and deltorphin-I (delta selective), and DREK(1-4)-DRM(5-7) hybrid (mu selective), show in folded structures more backbone bending of the first 4 residues in the mu opioids than in the delta peptides. Also, the main difference between mu- and delta-opioid peptides is a large fraction of extended conformations in mu heptapeptides. Either bending of the N-terminus, or extension of the C-terminal part in mu-opioid heptapeptides prevent the head-to-tail interactions which allow delta-opioid peptides to bind selectively to the delta-opioid receptor.

Opiate aromatic pharmacophore structure-activity relationships in CTAP analogues determined by topographical bias, two-dimensional NMR, and biological activity assays

Topographically constrained analogues of the highly mu-opioid-receptor-selective antagonist CTAP (H-D-Phe-c[Cys-Tyr-D-Trp-Arg-Thr-Pen]-Thr-NH(2), 1) were prepared by solid-phase peptide synthesis. Replacement of the D-Phe residue with conformationally biased beta-methyl derivatives of phenylalanine or tryptophan (2R,3R; 2R,3S; 2S,3R; 2S,3S) yielded peptides that displayed widely varying types of biological activities. In an effort to correlate the observed biological activities of these analogues with their structures, two-dimensional (1)H NMR and molecular modeling was performed. Unlike the parent (1), which is essentially a pure mu antagonist with weak delta agonist activities in the MVD bioassay, the diastereomeric beta-MePhe(1)-containing peptides exhibited simultaneous delta agonism and mu antagonism by the (2R,3R)-containing isomer 2; mu antagonism by the (2R,3S)-containing isomer 3; weak mu agonism by the (2S,3R)-containing isomer 4; and delta agonism by the (2S,3S)-containing isomer 5. Incorporation of beta-MeTrp isomers into position 1 led to peptides that were mu antagonists (2R,3R), 8; (2R,3S), 9, or essentially inactive (<10%) in the MVD and GPI assays (2S,3R), 10; (2S,3S), 11. Interestingly, in vivo antinociceptive activity was predicted by neither MVD nor GPI bioactivity. When D-Trp was incorporated in position 1, the result (7) is a partial, yet relatively potent mu agonist which also displayed weak delta agonist activity. Molecular modeling based on 2D NMR revealed that low energy conformers of peptides with similar biological activities had similar aromatic pharmacophore orientations and interaromatic distances. Peptides that exhibit mu antagonism have interaromatic distances of 7.0-7.9 A and have their amino terminal aromatic moiety pointing in a direction opposite to the direction that the amino terminus points. Peptides with delta opioid activity displayed an interaromatic distance of <7 A and had their amino terminal aromatic moiety pointing in the same direction as the amino terminus.

The delta-selective opioid peptide dermenkephalin and the mu-selective hybrid peptide dermenkephalin-[1-4]-dermophin-[5-7] display strikingly different conformations despite identical tetrapeptide N-termini. A quantitative 2-D NMR and molecular modeling analysis

The selective recognition of the aminoterminal binding pharmacophore Tyr-D-Xaa-Phe of the opioid heptapeptide dermorphin, Tyr-D-Ala-Phe-Gly-Tyr-Pro-Ser-NH2 (DRM)1, and of dermenkephalin, Tyr-D-Met-Phe-His-Leu-Met-Asp-NH2 (DREK), by the mu-opioid receptor and delta-opioid receptor, respectively, depends upon the constitution / conformation of the C-terminal tripeptide. The hybrid peptide DREK-[1-4]-DRM-[5-7] is very potent at, and exquisitely selective for the mu-opioid receptor, and differs only from dermenkephalin by its C-terminal tripeptide. Comparison of the structural features of DREK-[1-4]-DRM-[5-7] and dermenkephalin by nmr analysis and molecular modeling revealed striking differences, as well in the trans (Tyr5 - Pro6) isomer (population 75%) than in the cis isomer.. Whereas the folded C-terminal tail of dermenkephalin influenced the tertiary structure of the N-terminal tetrapeptide and placed the Tyr1 and Phe3 aromatic rings in definite orientations that are best suited for the delta-receptor, there were only weak contacts, as shown by NOE data, between the aminoterminal and carboxyterminal parts of the hybrid peptide. This promoted increased flexibility of the whole backbone and relaxed orientations for the side-chains of Tyr1 and Phe3 that are compatible with the mu-receptor but unsuitable for the delta-receptor. The steric hindrance introduced by Pro6 in DREK-[1-4]-DRM-[5-7], plus the absence of large hydrophobic side-chains in positions 5 and 6 may prevent close contacts between the N-terminal and C-terminal domains and reorientation of the main pharmacophoric elements Tyr1 and Phe3.

Opioid peptides from frog skin

The skin of the South American frogs Phyllomedusa secretes, in addition to numerous mammalian-like hormones and neuropeptides, several gene-encoded opioid peptides that contain a D-amino acid in position 2 of their sequence. Dermorphin, Tyr-D-Ala-Phe-Gly-Tyr-Pro-Ser-NH2, dermenkephalin/deltorphin A, Tyr-D-Met-Phe-His-Leu-Met-Asp-NH2 and the deltorphins, Tyr-D-Ala-Phe-Xaa-Val-Val-Gly-NH2 (where Xaa is either Asp or Glu) are highly potent at, and exquisitely selective, for the mu- and delta-opioid receptors. D-Ala and D-Met present in dermorphin and related peptides are coded for by the usual codons in the corresponding messenger RNAs. Prepro-dermorphin/dermenkephalin and prepro-deltorphins have considerable sequence identities to precursors encoding 10-46-residue-long antimicrobial peptides--dermaseptins, brevinins, temporins, esculentins and gaegurins--originating from various amphibian species. The similarity between the prepro-regions of precursors encoding end products with strikingly different structures and biological activities supports the suggestion that the genes encoding these peptides are all members of the same family.

What peptides these deltorphins be

The deltorphins are a class of highly selective delta-opioid heptapeptides from the skin of the Amazonian frogs Phyllomedusa sauvagei and P. bicolor. The first of these fascinating peptides came to light in 1987 by cloning of the cDNA of from frog skins, while the other members of this family were identified either by cDNA or isolation of the peptides. The distinctive feature of deltorphins is the presence of a naturally occurring D-enantiomer at the second position in their common N-terminal sequence, Tyr-D-Xaa-Phe, comparable to dermorphin, which is the prototype of a group of mu-selective opioids from the same source. The D-amino acid and the anionic residues, either Glu or Asp, as well as their unique amino acid compositions are responsible for the remarkable biostability, high delta-receptor affinity, bioactivity and peptide conformation. This review summarizes a decade of research from many laboratories that defined which residues and substituents in the deltorphins interact with the delta-receptor and characterized pharmacological and physiological activities in vitro and in vivo. It begins with a historical description of the topic and presents general schema for the synthesis of peptide analogues of deltorphins A, B and C as a means to document the methods employed in producing a myriad of analogues. Structure activity studies of the peptides and their pharmacological activities in vitro are detailed in abundantly tabulated data. A brief compendium of the current level of knowledge of the delta-receptor assists the reader to appreciate the rationale for the design of these analogues. Discussion of the conformation of these peptides addresses how structure leads to further hypotheses regarding ligand receptor interaction. The review ends with a broad discussion of the potential applications of these peptides in clinical and therapeutic settings.

Solution conformations of deltorphin-I obtained from combined use of quantitative 2D-NMR and energy calculations: a comparison with dermenkephalin

Deltorphin-I, Tyr-D-Ala-Phe-Asp-Val-Val-Gly-NH2 and dermenkephalin, Tyr-D-Met-Phe-His-Leu-Met-Asp-NH2, two highly related opioid peptides from frog skin, display very similar N-termini but strikingly different C-terminal tails. Nevertheless, both peptides are highly potent at, and exquisitely selective for the delta-opioid receptor. To identify common determinants concuring to the remarkably efficient targeting of deltorphin-I and dermenkephalin, combined use of quantitative two-dimensional nuclear magnetic resonance (53 dipolar interactions studied at four temperatures) and energy calculations using simulated annealing generated five groups of deltorphin-I conformers. These groups were pooled into two families whose overall conformation could be described either by a left-handed helix (Family I) or by a big loop (Family II), both stabilized by H-bonds. Proximity of D-Ala2-Phe3-Asp4 and Val5-Val6-Gly7 triads is an obvious structural similarity between almost all groups in both families of structures. Whereas differences between the two families originated mostly from a transition at psi Asp4 backbone dihedral angle, the backbone structures at segment 1-4 are similar and spatial arrangements of Tyr1 (t) and Phe3 (g-) are identical in one group of each family. Moreover, these two groups have a N-terminal tetrapeptide whose conformation most closely resembles that of a well-defined group of structures for dermenkephalin. Altogether, these results suggest that conformational attributes that are common to dermenkephalin and deltorphin-I, i.e., the backbone conformation of the N-terminal tetrapeptide and preferential orientations in the side-chain of Tyr1 (t) and Phe3 (g-) underlie their ability to bind with high selectivity to the delta-opioid receptor.

Thermodynamic model of secondary structure for alpha-helical peptides and proteins

A thermodynamic model describing formation of alpha-helices by peptides and proteins in the absence of specific tertiary interactions has been developed. The model combines free energy terms defining alpha-helix stability in aqueous solution and terms describing immersion of every helix or fragment of coil into a micelle or a nonpolar droplet created by the rest of protein to calculate averaged or lowest energy partitioning of the peptide chain into helical and coil fragments. The alpha-helix energy in water was calculated with parameters derived from peptide substitution and protein engineering data and using estimates of nonpolar contact areas between side chains. The energy of nonspecific hydrophobic interactions was estimated considering each alpha-helix or fragment of coil as freely floating in the spherical micelle or droplet, and using water/cyclohexane (for micelles) or adjustable (for proteins) side-chain transfer energies. The model was verified for 96 and 36 peptides studied by 1H-nmr spectroscopy in aqueous solution and in the presence of micelles, respectively ([set 1] and [set 2]) and for 30 mostly alpha-helical globular proteins ([set 3]). For peptides, the experimental helix locations were identified from the published medium-range nuclear Overhauser effects detected by 1H-nmr spectroscopy. For sets 1, 2, and 3, respectively, 93, 100, and 97% of helices were identified with average errors in calculation of helix boundaries of 1.3, 2.0, and 4.1 residues per helix and an average percentage of correctly calculated helix-coil states of 93, 89, and 81%, respectively. Analysis of adjustable parameters of the model (the entropy and enthalpy of the helix-coil transition, the transfer energy of the helix backbone, and parameters of the bound coil), determined by minimization of the average helix boundary deviation for each set of peptides or proteins, demonstrates that, unlike micelles, the interior of the effective protein droplet has solubility characteristics different from that for cyclohexane, does not bind fragments of coil, and lacks interfacial area.

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.

Development of a model for the delta-opioid receptor pharmacophore: 3. Comparison of the cyclic tetrapeptide, Tyr-c[D-Cys-Phe-D-Pen]OH with other conformationally constrained delta-receptor selective ligands

We have previously proposed a model of the delta-opioid receptor bound conformation for the cyclic tetrapeptide, Tyr-c[D-Cys-Phe-D-Pen]OH (JOM-13) based on its conformational analysis and from conformation-affinity relationships observed for its analogues with modified first and third residues. To further verify the model, it is compared here with results of conformational and structure-activity studies for other known conformationally constrained delta-selective ligands: the cyclic pentapeptide agonist, Tyr-c[D-Pen-Gly-Phe-D-Phe]OH (DPDPE): the peptide antagonist, Tyr-Tic-Phe-PheOH (TIPP); the alkaloid agonist, 7-spiroindanyloxymorphone (SIOM); and the related alkaloid antagonist, oxymorphindole (OMI). A candidate delta-bound conformer is identified for DPDPE that provides spatial overlap of the functionally important N-terminal NH3+ and C-terminal COO- groups and the aromatic rings of the Tyr and Phe residues in both cyclic peptides. It is shown that all delta-selective ligands considered have similar arrangements of their pharmacophoric elements, i.e., the tyramine moiety and a second aromatic ring (i.e., the rings of Phe3, Phe4, and Tic2 residues in JOM-13, DPDPE, and TIPP, respectively; the indole ring system in OMI, and the indanyl ring system in SIOM). The second aromatic rings, while occupying similar regions of space throughout the analogues considered, have different orientations in agonists and antagonists, but identical orientations in peptide and alkaloid ligands with the same agonistic or antagonistic properties. These results agree with the previously proposed binding model for JOM-13, are consistent with the view that delta-opioid agonists and antagonists share the same binding site, and support the hypothesis of a similar mode of binding for opioid peptides and alkaloids.

100 years lock-and-key concept: are peptide keys shaped and guided to their receptors by the target cell membrane?

The ideas developed in the Membrane Compartments Theory which allow a quantitative prediction of receptor preference are discussed in terms of our present knowledge of opioid and neurokinin receptor structure. Furthermore, conformations of regulatory peptides interacting with artificial lipid membranes are compared with those of chemically constrained molecules that react selectively with different receptor classes. Striking similarities in the topochemistry of molecules with similar activity were observed. The membrane-induced topomers were almost congruent with the artificial topomers that are selectively recognized by the same receptors.

Comparative conformational analyses of mu-selective dermorphin and delta-selective deltorphin-II in aqueous solution by 1H-NMR spectroscopy

Two-dimensional 1H-NMR methods have been used to obtain complete proton resonance assignments and possible solution conformations of dermorphin (H-Tyr-D-Ala-Phe-Gly-Tyr-Pro-Ser-NH2) and deltorphin-II (H-Tyr-D-Ala-Phe-Glu-Val-Val-Gly-NH2), naturally occurring mu- and delta-selective opioids, respectively, in order to examine the conformational characteristics that are closely related to the selectivities towards mu/delta-opioid receptors. With the use of the proton-proton distances derived from ROESY measurements in aqueous solution, 50 possible 3D structures are generated by means of distance geometry calculations. The conformers which satisfy the distance constraints and the torsion angles estimated from JNHC alpha H vicinal coupling constants within the allowable range are then subjected to molecular dynamics simulations for 10 ps after equilibration. Although dermorphin and deltorphin-II are both in equilibrium among many flexible conformers, some conformational differences are observed between these peptides: many conformers of dermorphin show a structure rounded at the N-terminal Tyr-D-Ala-Phe-Gly-Tyr and C-terminal Gly-Tyr-Pro-Ser-NH2 moieties, which are almost at right angles to each other, while those of deltorphin-II are characterized by a 'hook'-shaped backbone structure in which the nearly extended conformation of the Val-Val-Gly-NH2 sequence is located under the folded conformation of the N-terminal Tyr-D-Ala-Phe-Glu sequence. The possible relationship between these conformational characteristics and the mu/delta-opioid receptor selectivities is discussed.