Conformational analysis of the Ca(2+)-bound opioid peptides: implications for ligand-receptor interaction

Role of metal ions in ligand-receptor interaction: insights from structural studies

Experimental data indicate that metal ions such as Na(+), Ca(2+) and Mg(2+), which are present in millimolar concentrations in the extracellular environment, modulate binding of ligands to plasma membrane receptors. Here, we briefly review structural studies that demonstrate that various types of ligands, including peptide hormones and drugs, bind metal ions, in particular Ca(2+), in the lipid milieu. We propose that the metal ion-bound forms of ligands represent their bioactive conformations. With a view to understanding the mechanism of modulation of ligand-receptor interactions by metal ions, we have computed a homology model of the mu-opioid receptor, a G protein-coupled receptor (GPCR), and performed docking of specific agonist and antagonist ligands in the receptor. This resulted in the formation of a ligand-metal ion-receptor (ternary) complex which accounted for the data on the structure-activity relationships of ligands and mutation data on the receptor. Based on experimental and modeling data, we have proposed a general mechanism of activation of GPCRs by their corresponding ligands wherein metal ions play a pivotal role. Studies on overexpressed segments of mu-receptor are in progress to verify the above proposal.

Radiosensitivity of DNA in a specific protein-DNA complex: the lac repressor-lac operator complex

PURPOSE

To calculate the probability of radiation-induced frank strand breakage (FSB) at each nucleotide in the Escherichia coli lac repressor-lac operator system using a simulation procedure. To compare calculated and experimental results. To asses the contribution of DNA conformational changes and of the masking by the protein to DNA protection by the repressor.

MATERIALS AND METHODS

Two structures of the complex were extracted from the PDB databank: crystallography- and NMR-based structures. Calculations were made of the accessibility of the atoms mainly involved in strand breakage (H4' and H5') to O&Hdot; and of the FSB probabilities, along: (1) DNA in the complex; (2) DNA in the complex depleted of the repressor; and (3) a linear DNA having the same sequence. An 80bp fragment bearing the operator was irradiated alone or in presence of the repressor. The relative probabilities of FSB at each nucleotide were determined using sequencing gel electrophoresis.

RESULTS

Calculations predict modulation of the accessibility of H4' and H5' atoms and of the probabilities of FSB along the DNA fragments of complexes. This is due to the protein-induced conformational change and to masking by bound protein. The best agreement with the experimental FSB was observed for calculations that use the crystallography-based structure.

CONCLUSIONS

For specific DNA-protein complexes, our calculations can predict the protein radiolytic footprints on DNA. They show the significant contribution of the protein-induced DNA conformational change to DNA protection.

Interaction of oxytocin with Ca2+: II. Proton magnetic resonance and molecular modeling studies of conformations of the hormone and its Ca2+ complex

Drastic changes in the CD and fluorescence spectra of oxytocin [cyclo(Cys1-Tyr2-Ile3-Gln4-Asn5-Cys6)-Pro7-Leu8-Gly 9-NH2] occur on binding Ca2+ in trifluoroethanol (Ananthanarayanan and Brimble, preceding paper). To further characterize the conformation of the Ca(2+)-bound hormone, we carried out 1H-nmr measurements in deuterated trifluorethanol of oxytocin and its 1:1 Ca2+ complex. The one-dimensional nmr data identified residues involved in Ca2+ binding and the extent of their perturbation on Ca2+ addition. The 3JNH-CH coupling constants and two-dimensional nuclear Overhauser effect (NOE) spectral cross peaks confirmed the helical nature of the Ca2+ complex deduced from CD data. Interproton distances in the free hormone and its Ca2+ complex were estimated from the respective NOE data. Apparent global minimum-energy conformations of free and Ca2+ bound oxytocin were computed using the Monte Carlo with energy minimization protocol, with and without incorporating the NOE-derived distance constraints. Taken together, our results show Ca2+ binding to oxytocin to be a two-step process. The binding of the first Ca2+ brings the otherwise extended tail segment of oxytocin closer to the ring moiety so that it wraps around the cation. This causes the maximal extent of change in all the spectral parameters. The subsequent formation of the 2:1 Ca-oxytocin complex results in the tail detaching itself away from the ring so as to bind the second Ca2+ ion. This leads to further spectral changes in the hormone molecule. The tail segment plays a major role in both steps. These observations may be useful in understanding the structural basis of oxytocin action.

Homology models of mu-opioid receptor with organic and inorganic cations at conserved aspartates in the second and third transmembrane domains

Metal ions affect ligand binding to G-protein-coupled receptors by as yet unknown mechanisms. In particular, Na(+) increases the affinity for antagonists but decreases it for agonists. We had modeled the mu-opioid receptor (muR) based on the low-resolution structure of rhodopsin by G. F. X. Schertler, C. Villa, and R. Henderson (1993, Nature 362, 770-772) and proposed that metal ions may be directly involved in the binding of ligands and receptor activation (B. S. Zhorov and V. S. Ananthanarayanan, 1998, J. Biomol. Struct. Dyn. 15, 631-637). Developing this concept further, we present here homology models of muR using as templates the structure of rhodopsin elaborated by I. D. Pogozheva, A. L. Lomize, and H. I. Mosberg (1997, Biophys. J. 70, 1963-1985) and J. M. Baldwin, G. F. X. Schertler, and V. M. Unger (1997, J. Mol. Biol., 272, 144-164). Using the Monte Carlo minimization (MCM) method, we docked the Na(+)-bound forms of muR ligands: naloxone, bremazocine, and carfentanyl. The resultant low-energy complexes showed that the two positive charges in the protonated metal-bound ligands interact with the two negative charges at Asp(3.32) and Asp(2.50) (for notations, see J. A. Ballesteros and H. Weinstein, 1995, Methods Neurosci. 25, 366-426). MCM computation on morphine docked inside the model of muR by I. D. Pogozheva, A. L. Lomize, and H. I. Mosberg (1998, Biophys. J. 75, 612-634) yielded two binding modes with the ligand's ammonium group salt-bridged either to Asp(3.32) (generally regarded as the ligand recognition site) or to Asp(2.50). The latter is the presumed site for Na(+) ion, which is known to modulate ligand binding. Assuming that in the low-dielectric transmembrane region of muR, organic and inorganic cations would compete for Asp(3.32) and Asp(2.50), we propose that ligand binding, as visualized in the above models, would first displace Na(+) from Asp(3.32). A subsequent progress of the ligand toward Asp(2.50) would result in either the retention of Na(+) at Asp(2.50) in the case of antagonists or the displacement of Na(+) from Asp(2.50) in the case of agonists. The displaced Na(+) would move toward the salt-bridged Asp(3.49)-Arg(3.50) and disengage the salt bridge. This, in turn, would result in conformational changes at the cytoplasmic face of the receptor that facilitate the interaction with the G-protein.

Interaction of gonadotropin-releasing hormone and its agonist analogs with Ca2+ in a nonpolar milieu. Correlation with biopotencies

Extracellular Ca2+ is necessary for the action of gonadotropin-releasing hormone (GnRH). Assuming that this partly because of the interaction of the hormone with the relatively abundant extracellular Ca2+ in the low dielectric milieu of the bilayer plasma membrane, we studied the interaction of GnRH and five of its agonist analogs with Ca2+ under membrane-mimetic conditions. The peptides used, in increasing order of their reported gonadotropin-releasing activities, were: des-amide GnRH (or GnRH-OH); [Ala6]GnRH; [D-Ala6]GnRH; des-Gly10[D-Ala6,Pro9-NHEt]GnRH and, des-Gly10[D-Trp6,Pro9-NHEt]GnRH. Changes in the far-UV CD and fluorescence spectra of these peptides in trifluoroethanol were used to monitor conformational changes and obtain the Ca2+-binding isotherms. The data show that GnRH and its active analogs contain two Ca2+ binding sites, whereas the inactive analogs have only one. The extent of Ca2+ binding by the agonist peptides paralleled their biological potency ranking. The superactive analog des-Gly10[D-Trp6,Pro9-NHEt]GnRH exhibited the ability to transport Ca2+ ions across large unilamellar vesicles of dimyristoylphosphatidylcholine. Our study shows that significant differences among the GnRH and its analog peptides, suggestive of differences in their conformations, are manifested only in the presence of Ca2+. This observation would provide a basis for understanding GnRH action in terms of the hormone's interaction with Ca2+ in the lipid milieu.

Signal transduction within G-protein coupled receptors via an ion tunnel: a hypothesis

Based on molecular modeling of the complexes between the mu-opioid receptor and its ligands, we present a hypothesis that accounts for several of the experimental data including the importance of conserved polar residues in rhodopsin-like G-protein-coupled receptors and the effect of Na+ on the binding of ligands to these receptors. We propose that agonists, but not antagonists, would displace Na+ from its initial binding site at the conserved D2.50 residue in the second transmembrane alpha-helical segment, H2. The displaced Na+ would pass through a "gate" of conserved hydrophobic residues and move along a tunnel-like interface (formed of H2, H3 and H7) enriched with several conserved hydrophilic residues including D3.49. Interaction of Na+ with D3.49 would result in the breaking of a salt-bridge between D3.49 and the conserved R3.50 residue thus exposing the latter for interaction with the G-protein.

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.

Conformational and electrostatic similarity between polyprotonated and Ca(2+)-bound mu-opioid peptides

In a previous paper (Zhorov and Ananthanarayanan, J. Biomol, Struct. Dynam. 1995, 13:1-13) we had calculated the minimum-energy conformations of monoprotonated and zwitterionic mu-opioid peptides and demonstrated the remarkable similarity between Ca(2+)-bound morphine on the one hand and the Ca(2+)-bound forms of these peptides on the other. We postulated that the Ca(2+)-bound forms of mu-opioids would activate the mu-receptor. To assess further the involvement of multiple positive charges on some of the mu-opioid ligands in their interaction with the receptor, we have, in this work, studied the geometry of five mu-opioid peptides containing two to four protonated groups and having chemical structures essentially different from the endogenous mu-opioid peptide Met-enkephalin (EK). Conformational space was searched using the Monte Carlo-with-energy-minimization method. Ca(2+)-bound forms of the selected peptides were found to be energetically unfavourable implying that one of the protonated groups plays a role similar to that Ca2+ plays in EK-Ca2+ complex. Bioactive conformations of the polyprotonated peptides were then selected using the criteria formulated earlier for Ca(2+)-bound ligands as well as additional criteria requiring ligands to have an elongated conical overall shape complementary to the interface between the transmembrane segments of mu-receptor. Low-energy conformations meeting these criteria were found in all the peptides considered, the protonated groups being separated from each other by about 8 and 16 A. The possible role of the ligands' cationic groups in mu-receptor activation is discussed.