X-ray diffraction studies of enkephalins. Crystal structure of [(4'-bromo) Phe4,Leu5]enkephalin

Dominant Chemical Interactions Governing the Folding Mechanism of Oligopeptides

The hydrophobic effect is the main factor that drives the folding of polypeptide chains. In this study, we have examined the influence of the hydrophobic effect in the context of the main mechanical forces approach, mainly in relation to the establishment of specific interplays, such as hydrophobic and CH-π cloud interactions. By adopting three oligopeptides as model systems to assess folding features, we demonstrate herein that these finely tuned interactions dominate over electrostatic interactions, including H-bonds and electrostatic attractions/repulsions. The folding mechanism analysed here demonstrates cooperation at the single-residue level, for which we propose the terminology of "single residues cooperative folding". Overall, hydrophobic and CH-π cloud interactions produce the main output of the hydrophobic effect and govern the folding mechanism, as demonstrated in this study with small polypeptide chains, which in turn represent the main secondary structures in proteins.

miR-4651 inhibits cell proliferation of gingival mesenchymal stem cells by inhibiting HMGA2 under nifedipine treatment

Drug-induced gingival overgrowth (DIGO) is recognized as a side effect of nifedipine (NIF); however, the underlying molecular mechanisms remain unknown. In this study, we found that overexpressed miR-4651 inhibits cell proliferation and induces G0/G1-phase arrest in gingival mesenchymal stem cells (GMSCs) with or without NIF treatment. Furthermore, sequential window acquisition of all theoretical mass spectra (SWATH-MS) analysis, bioinformatics analysis, and dual-luciferase report assay results confirmed that high-mobility group AT-hook 2 (HMGA2) is the downstream target gene of miR-4651. Overexpression of HMGA2 enhanced GMSC proliferation and accelerated the cell cycle with or without NIF treatment. The present study demonstrates that miR-4651 inhibits the proliferation of GMSCs and arrests the cell cycle at the G0/G1 phase by upregulating cyclin D and CDK2 while downregulating cyclin E through inhibition of HMGA2 under NIF stimulation. These findings reveal a novel mechanism regulating DIGO progression and suggest the potential of miR-4651 and HMGA2 as therapeutic targets.

Dihedral Angle Calculations To Elucidate the Folding of Peptides through Its Main Mechanical Forces

This study reports a general method to calculate dihedral angles (φ and ψ) of a given amino acid sequence, focusing on potential energy and torque moment concepts. By defining these physical measures in relation to the chemical interactions that occur on each single amino acid residue within a peptide, we analyze the folding process as the result of main mechanical forces (MMFs) exerted in the specific amino acid chain of interest. As a proof of concept, Leu-enkephalin was initially used as a model peptide to carry out the theoretical study. Our data show agreement between calculated Leu-enkephalin backbone dihedral angles and the corresponding experimentally determined X-ray values. Hence, we used calcitonin to validate our MMF-based method on a larger peptide, i.e., 32 amino acid residues forming an α-helix. Through a similar approach (although simplified with regard to electrostatic interactions), the calculations for calcitonin also demonstrate a good agreement with experimental values. This study offers new opportunities to analyze peptides' amino acid sequences and to help in the prediction of how they must fold, assisting in the development of new computational techniques in the field.

[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.

Stereochemical basis for a unified structure activity theory of aromatic and heterocyclic rings in selected opioids and opioid peptides

This paper presents a novel unified theory of the structure activity relationship of opioids and opioid peptides. It is hypothesized that a virtual or known heterocyclic ring exists in all opioids which have activity in humans, and this ring occupies relative to the aromatic ring of the drug, approximately the same plane in space as the piperidine ring of morphine. Since the rings of morphine are rigid, and the aromatic and piperidine rings are critical structural components for morphine's analgesic properties, the rigid morphine molecule allows for approximations of the aromatic and heterocyclic relationships in subsequent drug models where bond rotations are common. This hypothesis and five propositions are supported by stereochemistry and experimental observations.Proposition #1 The structure of morphine provides a template. Proposition #2 Steric hindrance of some centric portion of the piperidine ring explains antagonist properties of naloxone, naltrexone and alvimopam. Proposition #3 Methadone has an active conformation which contains a virtual heterocyclic ring which explains its analgesic activity and racemic properties. Proposition #4 The piperidine ring of fentanyl can assume the morphine position under conditions of nitrogen inversion. Proposition #5 The first 3 amino acid sequences of beta endorphin (l-try-gly-gly) and the active opioid dipeptide, l-tyr-pro, (as a result of a peptide turn and zwitterion bonding) form a virtual piperazine-like ring which is similar in size, shape and location to the heterocyclic rings of morphine, meperidine, and methadone. Potential flaws in this theory are discussed.This theory could be important for future analgesic drug design.

Conformational stability and three-dimensional model of the δ-opioid pharmacophore for the extended antiparallel dimer structure of Met-enkephalin in water

The conformational stability of the extended antiparallel dimer structure of Met-enkephalin in water was analyzed by examining the hydration structure of enkephalin using molecular dynamics simulations. The result shows that, despite of the hydrophicility of the terminal atoms in the pentapeptide, the main contributor for the stability of the dimer in water is the four intermolecular hydrogen bonds between the Gly(2) and Phe(4) groups. The three-dimensional model of the delta-opioid pharmacophore for this dimer structure was also established. Such a model was demonstrated to match the delta-opioid pharmacophore query derived from the non-peptides SIOM, TAN-67, and OMI perfectly. This result thus strongly supports the assumption that the dimer structure of Met-enkephalin is a possible delta-receptor binding conformation.

The role of crystallography in drug design

Structure and function are intimately related. Nowhere is this more important than the area of bioactive molecules. It has been shown that the enantioselectivity of an enzyme is directly related to its chirality. X-ray crystallography is the only method for determining the "absolute" configuration of a molecule and is the most comprehensive technique available to determine the structure of any molecule at atomic resolution. Results from crystallographic studies provide unambiguous, accurate, and reliable 3-dimensional structural parameters, which are prerequisites for rational drug design and structure-based functional studies.

Enkephalins: Raman spectral analysis and comparison as function of pH 1-13

Raman spectral studies are carried out on Leu- and Met-enkephalin as a function of the pH value in the range of 1-13. The molecules are dissolved in KCl solvent and the pH is controlled at each value. Spectral analyses reveal the dependence of the structural conformation on the pH, and a comparison of the two molecules is made in three frequency regions: the tyrosine Fermi doublet (850-830 cm(-1)), aromatic side chains (1650-1550 cm(-1)), and carboxylate (1430-1400 cm(-1)). All regions and frequencies are presented, discussed, and compared for the two molecules.

The structure of an endomorphin analogue incorporating 1-aminocyclohexane-1-carboxlylic acid for proline is similar to the beta-turn of Leu-enkephalin

Endomorphin (EM2, Tyr-Pro-Phe-Phe-NH(2)) can assume various conformations related to cis/trans-rotamers of the amide linkage of Tyr-Pro. To control isomerization, restricted or flexible components have been introduced at the Pro position. We focused on [Chx(2)]EM2, an EM2 analogue substituting 1-aminocyclohexane-1-carboxlylic acid (Chx) for Pro. X-ray diffraction analysis revealed that [Chx(2)]EM2 is folded into the trans-form of Tyr-Chx. The manner of folding resembled that seen in D-TIPP, an EM analogue incorporating tetrahydroisoquinoline carboxylic acid, as well as the beta-turn of Leu-enkephalin. Selectivity for the opioid mu-receptor was fairly well conserved by [Chx(2)]EM, suggesting that the folded form is important for mu-selectivity.

A designed beta-hairpin peptide in crystals

Beta-hairpin structures have been crystallographically characterized only in very short acyclic peptides, in contrast to helices. The structure of the designed beta-hairpin, t-butoxycarbonyl-Leu-Val-Val-D-Pro-Gly-Leu-Val-Val-OMe in crystals is described. The two independent molecules of the octapeptide fold into almost ideal beta-hairpin conformations with the central D-Pro-Gly segment adopting a Type II' beta-turn conformation. The definitive characterization of a beta-hairpin has implications for de novo peptide and protein design, particularly for the development of three- and four-stranded beta-sheets.

Crystal structures of peptides and modified peptides

The X-ray diffraction experiments on peptides and related molecules which have been carried out in Western Europe, except Italy, in the last eight years are reviewed. The crystal structures of some bioactive peptides such as Leu-enkephalin (a neurotransmitter), cyclosporin A (an immunomodulator in both the free and protein-bound state), balhimycin (an antibiotic) and octreotide (a somatostatin analogue) are briefly presented. Crystallized N- and C-protected model peptides have given an insight into the folding tendency and folding modes depending on the peptide sequences. The crystal structures of various pseudopeptide molecules reveal how the three-dimensional structure of peptide analogues can be modulated by substituting non-peptide groups for the peptide bond. A few examples of structural mimetics of the beta- and gamma-turns, and of templates for alpha-helix induction are also presented.

Structural studies of opioid peptides: a review of recent progress in x-ray diffraction studies

The solid state structures of many opioid peptide agonists have been elucidated by x-ray diffraction analysis. Recently, the first structure of an opioid peptide antagonist has been determined. Theoretically, linear peptides can have many different backbone conformations, yet early x-ray studies (1983-1987) on enkephalin and its analogues showed only two different backbone conformations: extended and single beta-bend. In 1989 enkephalin was observed in a third conformation, a double beta-bend. Since that time diffraction studies have been completed on the rationally designed linear opioid peptide agonists DTLET (Tyr-D-Thr-Gly-Phe-Leu-Thr) and DADLE (D-Ala2,D-Leu5-enkephalin) as well as on several cyclic enkephalin analogues including DPDPE (Tyr-[D-Pen-Gly-Phe-D-Pen]) and JOM-13 (Tyr-[D-Cys-Phe-D-Pen]). The most recent review of the x-ray studies on this class of compounds was written in 1988. This paper will update that review to include the results of studies completed since that time.

Conserved delta-activity in reverse enantiomeric opioid peptide

A reverse enantiomeric peptide has a reversed amino acid sequence with enantiomeric amino acid residues compared with its parent peptide. In most cases the random change of amino acid sequence or chirality might be expected to bring about significant changes in peptide activity. However, the reverse enantiomeric peptides of Leu-enkephalin and Tyr-D-Ala-Gly-Phe-D-Leu (DADLE) have shown affinity for the opioid delta-receptor, but not for mu- or kappa-receptors. This suggests that delta-opioid receptor recognition occurs primarily through interaction with the peptide side chains, since the native opioid peptide and its reverse enantiomer are able to have similar side-chain conformation.

Characteristic molecular packing in the crystal structure of tert-butoxycarbonyl-L-phenylalanyl-L-methionine methyl ester

The molecular conformation and association of the peptide Boc-L-Phe-L-Met-OMe have been studied in the solid state by X-ray diffraction. The peptide crystallizes in the orthorhombic system, space group P2(1)2(1)2(1), with cell parameters of a = 9.821(2), b = 25.394(6), c = 28.714(8) A, V = 7161(3) A3. The structure has been solved by direct methods and refined to a final R of 0.079 for 5464 independent reflections with Fo > or = sigma(Fo). The crystal consists of three independent molecular conformations per asymmetric unit. Respective peptide backbones adopt an extended conformation with the side-chains of Phe and Met residues being arranged below and above the backbone chains. Contrary to the sheet structure most frequently observed in the crystal packing of the extended peptide conformations, three independent molecules lie spirally along the c-axis and form a pin-wheel-like crystal packing. The sheet structures formed by two of three independent molecules are almost at right angles to the backbone of the remaining molecule. This molecular packing mode would provide a possible interaction model between the intersecting beta-sheet structure and single-strand structure of polypeptide.

Crystal structure of deltakephalin: a delta-selective opioid peptide with a novel beta-bend-like conformation

The solid-state structure of deltakephalin (Tyr-DThr-Gly-Phe-Leu-Thr) has been determined by single-crystal X-ray diffraction. Deltakephalin (DTLET) is a synthetic opioid peptide which differs from enkephalin in that a D-Thr has been substituted for Gly2 and a sixth residue, L-Thr, has been added. Clear colorless plates obtained using vapor diffusion and macro-seeding crystallization techniques were monoclinic; space group C2 with a = 27.389(5), b = 9.205(2), c = 16.788(2) A, beta = 98.87(2) degrees and V = 4181.4(14) A3. The asymmetric unit contained one molecule of DTLET and six molecules of water, giving a calculated density of 1.28 g cm-3. The crystal structure revealed that DTLET has a pseudo type I' beta-bend which is stabilized by an intramolecular side-chain to backbone hydrogen bond. This is the first reported observation of a pseudo beta-bend conformation in a solid-state structure of an enkephalin analog.

Conserved and novel structural characteristics of enantiomorphic Leu-enkephalin. X-ray crystal analysis of Leu-enkephalin enantiomer, L-Tyr-Gly-Gly-L-Phe-L-Leu and D-Tyr-Gly-Gly-D-Phe-D-Leu

The crystal of the Leu-enkephalin racemate (L-Tyr-Gly-Gly-L-Phe-L-Leu and D-Tyr-Gly-Gly-D-Phe-D-Leu) was obtained as a centrosymmetric space group. Crystal data: C28H37N5O7 x 1.5H2O, Mw = 582.6, triclinic, space group P1, a = 11.176(3), b = 16.115(3), c = 10.204(4) A, alpha = 92.41(3), beta = 104.86(2), gamma = 85.35(2)degrees, V = 1770(1)A3, Z = 2; F(000) = 640, mu(CuK alpha) = 6.50 cm-1, D chi = 1.081 g cm-3. The structure was determined by X-ray diffraction. The conformation of the Leu-enkephalin racemate was classified into the extended form which has been often observed in natural enkephalin. The symmetry-related molecules were connected by hydrogen bonds and arranged in an antiparallel fashion. The molecular packing showed a sheet structure similar to that of natural enkephalin.

Investigation of conformational equilibrium of polypeptides by internal coordinate stochastic dynamics. Met5-enkephalin

The equilibrium population of different conformational states of a polypeptide can in principle be obtained by a very long molecular dynamics simulation. The method of internal coordinate molecular dynamics earlier developed in this laboratory (A.K. Mazur and R.A. Abagyan J. Biomol. Struct. Dyn. 6,833 (1989)) allows one to use time steps much larger than usual for computing molecular trajectories. It is shown here that the sampling of the conformational space can be additionally enhanced by adding a random component to the set of forces applied to atoms. We describe the algorithms by which the random force is introduced and also a special method which excludes the fast rotation of polar hydrogens from equations of motion but keeps them movable. As a result the task stated in the title becomes realistic. Internal coordinate stochastic dynamics is applied for scanning the conformational space of the pentapeptide Met5-enkephalin which is a common test example widely used in theoretical studies. A large number of conformational transitions is observed during the 20 ns simulation starting from the global energy minimum thus allowing us to arrive at a nearly Boltzmann distribution of populations of conformational states. A few states are found which are distinguished by high apparent configurational entropy which turn out to correspond well to experimentally observed conformations of enkephalins.

A supermolecule study of the effect of hydration on the conformational behaviour of leucine-enkephalin

A theoretical conformational study was performed on leu-enkephalin in its zwitterionic form, both in vacuo and in the presence of a number, n, of up to 13 water molecules saturating its first hydration shell. The intramolecular energy of enkephalin as well as the intermolecular enkephalin-water and water-water interaction energies were computed with the SIBFA procedure (Sum of Interactions Between Fragments Ab initio computed), which uses additive ab initio multipole systematics and analytical formulas grounded on ab initio SCF computations. Energy minimizations were performed with a polyvalent minimizer, Merlin, with which three distinct derivative and three distinct nonderivative minimizers can be activated in a sequential fashion. Eight different candidate conformations of enkephalin were used as starting points. These conformations are either those found in distinct X-ray structures, or those proposed on the basis of theoretical computations by other authors. In the absence of hydration, they converged towards distinct folded energy-minima, the best four ones being separated by an energy gap of 8.7 kcal/mol. In marked contrast, with up to n = 13, the energetical separation between the six best conformers narrowed down to congruent to 4 kcal/mol. They can be characterized by: (a) either a direct or a water-mediated ammonium-carboxylate interaction; b) either a close proximity (as in morphine) or a large separation between the aromatic rings of Tyr and Phe (intercenter separations of congruent to 4.5 A and congruent to 10.5 A, respectively), with each of the four mutual combinations of (a) and (b) being represented.

An attempt to structurally convert mu-selective morphine toward delta-receptor binding: dimerization based on enkephalin conformation

In order to elucidate the substrate specificities for mu- and delta-opioid receptors, dimerization of the mu-specific morphine molecule was attempted, based on the hypothesis of the possible relationship between the molecular conformation of endogenous enkephalin and its selectivity for each opioid receptor. The NOR2 ([normorphine]N-CH2-CH2-N[normorphine]) thus synthesized exhibited agonist activity showing a preference for binding with the delta-opioid receptor, compared with the parent morphine molecule. Antagonist activity was also observed for NOR3 ([normorphine]N-CH2-CH2-CH2-N[normorphine]).

17O- and 14N-NMR studies of Leu-enkephalin and enkephalin-related fragments in aqueous solution

17O- and 14N-nmr chemical shifts and line widths of the carboxyl and amino terminal groups of Leu-enkephalin--Tyr-Gly-Gly-Phe-[17O]Leu-Oh--and enkephalin-related fragments--[17O]Leu-OH, Phe-[17O]Leu-OH, Gly-Phe-[17O]Leu-OH, and Gly-Gly-Phe-[17O]Leu-OH--were measured in aqueous solution over the entire H pH range. Enrichment in 17O was achieved by saponification of the corresponding O-methyl esters. Ionization constants and titration shifts were obtained by nonlinear least-squares fits to one-proton titration curves. [17O]Leu-OH exhibits a profound pH-dependent solvation change on deprotonation of the carboxyl group, as shown by 17O- and 14N-nmr line widths. In contrast, the peptides studied do not exhibit pH-dependent conformational (solvation) changes on deprotonation of the carboxyl group, and a head-to-tail intramolecular association between the ionic terminal groups should be excluded. It is shown that the peptides do not exhibit isotropic overall molecular motion and that segmental motion rather than fast internal motion influences the effective correlation times at the sites of the carboxyl oxygens and the amino nitrogen.

A crystal molecular conformation of leucine-enkephalin related to the morphine molecule

Leucine-enkephalin (Try1-Gly2-Gly3-Phe4-Leu5) has been crystallized as a trihydrate from water solution. X-ray diffraction reveals a tightly folded molecular conformation with two fused beta III- (Gly2-Gly3) and beta I- (Gly3-Phe4) turns. The Tyr1 and Phe4 aromatic rings have a close orthogonal arrangement analogous to the tyramine and cyclohexenyl rings in morphine. This suggests that the conformation found in the trihydrate crystal structure could be required for recognition by mu-receptor sites.

Importance of folded monomer and extended antiparallel dimer structures as enkephalin active conformation. Molecular dynamics simulations of [Met5]enkephalin in water

Simulations of the molecular dynamics of the [Met5]enkephalin monomer and dimer structures in water have been carried out. The dynamic trajectories have been analyzed in terms of the distances between intra- or intermolecular polar atoms. The time-correlated conformational transitions of an extended monomer structure have been converged into a stationary state among the beta-bend folded forms. However, the dynamics simulation of an extended antiparallel dimer structure has shown no noticeable conformation change. These results imply that both the beta-bend monomer and the extended dimer structures exist together as the fundamental conformation of enkephalins.

Molecular-dynamics simulations of [Met5]- and [D-Ala2,Met5]-enkephalins. Biological implication of monomeric folded and dimeric unfolded conformations

To investigate the biologically active conformation of enkephalin, molecular-dynamics simulations were applied to [Met5]- and [D-Ala2,Met5]-enkephalins. The dynamic trajectory of monomeric extended [Met5]-enkephalin was analysed in terms of relative mobility between respective torsions of backbone chain. After 10 ps of the dynamics simulation, the conformational transition was converged into a stationary state among the beta-bend folded forms, where they are stabilized by several intramolecular hydrogen-bond formations. Similar conformational transition was also observed in the dynamics simulation of [D-Ala2,Met5]enkephalin, which is a more mu-receptor-specific peptide than [Met5]enkephalin. The geometrical correspondence between the monomeric enkephalin conformation in the stationary state and morphine molecule (a mu-specific rigid opiate) was surveyed by virtue of the triangular substructures generated by choosing three functional atoms in each molecule, and good resemblances were observed. On the other hand, the dynamics simulation of the antiparallel extended [Met5]enkephalin dimer showed a trajectory different from that of the monomeric one. Two intermolecular hydrogen bonds at Tyr1 (NH3+)...Met5(CO2-) end residues were held throughout the 100 ps simulation, the dimeric structure being consequently kept. The conformational transition of the backbone chains from the antiparallel extended form to the twisted one took place via an intermediate state. Many conformations revealed during the dynamics simulation showed that the relative orientations of each two Tyr1, Gly3, Phe4 and Met5 residues in the dimer are nearly related by a pseudo-C2-symmetry respectively, and both halves of the dimer structure could be further fitted to the monomeric folded enkephalin conformation. The monomeric and dimeric conformations of enkephalin at their stationary states are discussed in relation to the substrate-specificity for mu- and delta-opioid receptors.

Conformational characteristics of receptor-selective opioid peptides. 1H n.m.r. and c.d. spectroscopic studies of delta-kephalin and [Val4]morphiceptin

An investigation on the conformations of highly receptor-selective opioid peptides was carried out to gain further understanding of the structure-activity relationship of endogenous enkephalins. The preferred conformations of a highly mu-selective [Val4]morphiceptin and a highly delta-selective delta-kephalin have been probed by 1H n.m.r. solvent-, concentration- and temperature-dependences of amide protons to take the folded conformations stabilized by an intramolecular hydrogen bond and the anti-parallely extended dimeric structures respectively. Their possible stereo-conformations were proposed, based on the analyses of the vicinal coupling constants (JHNC alpha H). The conformational difference between the mu- and delta-selective opioid peptides was further ascertained by the c.d. measurements. The c.d. spectra of the mu-selective peptides show negative bands in the range of 210-230 nm, while those of the delta-selective ones show the opposite positive bands. A correlation between c.d. spectra and receptor-selectivity was possible.

Catecholamines bind to enkephalins, morphiceptin, and morphine

Nuclear magnetic resonance spectroscopy, pH titration, and color reactions demonstrate that the catecholamines dopamine, epinephrine, and norepinephrine bind to the enkephalins. Binding constants are c. 6 X 10(3) per mole. Catecholamines also bound to the mu opiate receptor agonist morphiceptin (Tyr-Pro-Phe-Pro-NH2). Very little binding was found to enkephalin and morphiceptin fragments and analogues, indicating that the entire molecules are necessary. Serotonin binding peptides do not bind the catecholamines. Morphine and apomorphine, however, do bind these catecholamines (with a binding constant for morphine of c. 4 X 10(4) per mole). The opiate antagonist naloxone and a number of other drugs do not bind catecholamines. Morphine, morphiceptin, and the enkephalins also retard the formation of colored reaction products by catecholamines in vitro. These results may help to explain observations that the enkephalins are co-stored and co-transmitted with dopamine and norepinephrine, and may provide a basis for the elucidation of other known cases of peptide-monoamine co-transmission. Possible implications for understanding opiate effects on catecholamines during addiction and withdrawal are discussed, and suggestions concerning drug design are made.

The three-dimensional similarity between a dimeric antiparallel extended structure and a beta-turn folded form of enkephalin

The three-dimensional similarity between two fundamental conformations, a dimeric antiparallel extended structure and a type I' beta-turn folded form, of enkephalin was examined by computer graphic and empirical energy calculation methods. By the rotation of Tyr and Phe side chains, one half of the former structure could mimic the three-dimensional form of the latter without a large loss of conformational energy. This result provides a new idea for considering the conformation of enkephalin suitable for the multiple opioid receptors. The active conformation of enkephalin for mu- and delta-opioid receptors is discussed in the light of the present study.

Molecular mechanics studies of dermorphin

Molecular mechanical simulations have been carried out on dermorphin. Presence of D-Ala2 at the N-terminus and L-Pro6 residue at the C-terminus indicated the probability of beta-turns. From the stereochemical considerations, three types- II', III' and V' - for the beta-turn at the N-terminus of the peptide and two types-I and III- for the C-terminus side of the peptide are possible. In our molecular mechanics calculations, we considered six folded and one extended conformations for dermorphin to asses the relative stabilities. Three of the six folded conformations are lower in energy and have the following general feature-similar in energy, three hydrogen bonds, semirigid beta-sheet segment and favorable Tyr1-Tyr5 interaction. The presence of beta-sheet structure might play a role in mu-receptor selective interaction of dermorphin.

Ethanol induced conformational changes of the peptide ligands for the opioid receptors and their relevance to receptor interaction

The FT-IR (Fourier Transform Infrared) Spectrum of [Met 5]-enkephalinamide in aqueous solution shows the presence of both the beta-turn and beta-sheet conformations. The beta-turn and beta-sheet conformations of enkephalins have been proposed to play a role in receptor selectivity. Addition of ethanol alters these secondary structural features and hence the effect of ethanol on ligand-receptor interaction may be mediated primarily through conformational changes of the ligand rather than those of the receptor.

The crystal structures of [Met5]enkephalin and a third form of [Leu5]enkephalin: observations of a novel pleated beta-sheet

The structures of [Met5]enkephalin (Tyr-Gly-Gly-Phe-Met) and [Leu5]enkephalin (Tyr-Gly-Gly-Phe-Leu) have been determined from single crystal x-ray diffraction data and refined to residuals of 0.100 and 0.092, respectively. The [Met5]enkephalin structure consists of dimers forming antiparallel beta-sheets extending in the monoclinic ac plane with 10.6 water molecules per dimer. The two molecules, related by pseudo two-fold axes, have similar backbone conformations and similar tyrosine and phenylalanine side-chain conformations. Both methionine residues are disordered and the disorder is different in the two independent molecules. Additional hydrogen bonds connect adjacent dimers to form infinite sheets normal to the b axis. The water molecules are found mainly in the interstices between the sheets. [Leu5]Enkephalin crystallizes as a monohydrate that is isomorphous with the [Met5]enkephalin structure with respect to the beta-sheet but different with respect to the tyrosine and phenylalanine side-chain conformations and water content. The peptide chains in both structures are fully extended and more nearly planar than pleated. The planes of the peptide chains in the dimers form an angle of 143.3 degrees with one another in [Met5]enkephalin and 156.0 degrees in [Leu5]enkephalin. This produces a zigzag pattern or pleat in the beta-sheets perpendicular to the direction of the peptide chains and, therefore, perpendicular to the normal beta-sheet pleat. The average repeat distance between Ni and Ni+2 in the peptide chains of both structures is 7.10 A, versus an ideal value of 6.68 A.

Crystal structure of methionine-enkephalin

The crystal structure of methionine-enkephalin has been determined by X-ray crystallography. There are two independent pentapeptides in the asymmetric unit and both display extended backbone conformations with their side chains arranged alternately below and above the backbone plane. The two molecules form a hydrogen-bonded head-to-tail dimer similar in conformation to one dimeric pair of leucine-enkephalin molecules in a previously reported crystal structure.