Key motif to gain selectivity at the neuropeptide Y5-receptor: structure and dynamics of micelle-bound [Ala31, Pro32]-NPY

Crystal structures of human neuropeptide Y (NPY) and peptide YY (PYY)

Neuropeptide Y (NPY), peptide YY (PYY) and pancreatic polypeptide (PP) form the evolutionarily conserved pancreatic polypeptide family. While the fold is widely utilized in nature, crystal structures remain elusive, particularly for the human forms, with only the structure of a distant avian form of PP reported. Here we utilize a crystallization chaperone (antibody Fab fragment), specifically recognizing the amidated peptide termini, to solve the structures of human NPY and human PYY. Intriguingly, and despite limited sequence identity (~50%), the structure of human PYY closely resembles that of avian PP, highlighting the broad structural conservation of the fold throughout evolution. Specifically, the PYY structure is characterized by a C-terminal amidated α-helix, preceded by a backfolded poly-proline N-terminus, with the termini in close proximity to each other. In contrast, in the structure of human NPY the N-terminal component is disordered, while the helical component of the peptide is observed in a four-helix bundle type arrangement, consistent with a propensity for multimerization suggested by NMR studies.

Binding of Natural Peptide Ligands to the Neuropeptide Y5 Receptor

The binding mode of natural peptide ligands to the Y5 G protein-coupled receptor (Y5 R), an attractive therapeutic target for the treatment of obesity, is largely unknown. Here, we apply complementary biochemical and computational approaches, including scanning of the receptor surface with a genetically encoded crosslinker, Ala-scanning of the ligand and double-cycle mutagenesis, to map interactions in the ligand-receptor interface and build a structural model of the NPY-Y5 R complex guided by the experimental data. In the model, the carboxyl (C)-terminus of bound NPY is placed close to the extracellular loop (ECL) 3, whereas the characteristic α-helical segment of the ligand drapes over ECL1 and is tethered towards ECL2 by a hydrophobic cluster. We further show that the other two natural ligands of Y5 R, peptide YY (PYY) and pancreatic polypeptide (PP) dock to the receptor in a similar pose.

Neuropeptide Y and its C-terminal fragments acting on Y2 receptor: Raman and SERS spectroscopy studies

In this paper, we present spectroscopic studies of neuropeptide Y (NPY) and its native NPY(3-36), NPY(13-36), and NPY(22-36) and mutated acetyl-(Leu(28,31))-NPY(24-36)C-terminal fragments acting on Y2 receptor. Since there is some evidence for the correlation between the SERS patterns and the receptor binding ability, we performed a detailed analysis for these compounds at the metal/water interface using Raman spectroscopy (RS) and surface-enhanced Raman spectroscopy (SERS) methods. Many studies have suggested that interactions of this kind are crucial for a variety of biomedical and biochemical phenomena. The identification of amino acids in these peptide sequences by SERS allowed us to determine which molecular fragments were responsible for the interaction with the silver nanoparticle surface. Our findings demonstrated that in all of the investigated compounds, the NPY(32-36)C-terminal fragment (Thr(32)-Arg(33)-Gln(34)-Arg(35)-Tyr(36)NH2) was involved in the adsorption process onto metal substrate. The results of the present study suggest that the same molecular fragment interacts with the Y2 receptor, what proved the usefulness of the SERS method in the study of these biologically active compounds. The search for analogs acting on Y2 receptor may be important from the viewpoint of possible future clinical applications.

The investigation of membrane binding by amphibian peptide agonists of CCK2R using (31)P and (2)H solid-state NMR

It has been proposed that some neuropeptides may be anchored to the cell membranes prior to attaching to the adjacent active sites of transmembrane receptors. The three amphibian skin neuropeptides signiferin 1 [RLCIPYIIPC(OH)] (smooth muscle active and immunomodulator), riparin 1.1 [[RLCIPVIFPC(OH)] (immunomodulator) and rothein 1 [SVSNIPESIGF(OH)] (immunomodulator) act via CCK2 transmembrane receptors. A combination of (31)P and (2)H solid state NMR studies of each of these three peptides in eukaryotic phospholipid models at 25°C shows that rothein 1 does not interact with the membrane at all. In contrast, both of the cyclic disulfides signiferin 1 and riparin 1.1 interact with phospholipid head groups and partially penetrate into the upper leaflet of the model bilayer, but to different extents. These interactions are not sufficiently effective to cause disruption of the lipid bilayer since the peptides are not antimicrobial, anticancer, antifungal nor active against enveloped viruses.

Non-specific binding and general cross-reactivity of Y receptor agonists are correlated and should importantly depend on their acidic sectors

Non-specific binding of Y receptor agonists to intact CHO cells, and to CHO cell or rat brain particulates, is much greater for human neuropeptide Y (hNPY) compared to porcine peptide Y (pPYY), and especially relative to human pancreatic polypeptide (hPP). This binding of hNPY is reduced by alkali cations in preference to non-ionic chaotrope urea, while the much lower non-specific binding of pPYY is more sensitive to urea. The difference could mainly be due to the 10-16 stretch in 36-residue Y agonists (residues 8-14 in N-terminally clipped 34-peptides), located in the sector that contains all acidic residues of physiological Y agonists. Anionic pairs containing aspartate in the 10-16 zone could be principally responsible for non-specific attachments, but may also aid the receptor site binding. Two such pairs are found in hNPY, one in pPYY, and none in hPP. The hydroxyl amino acid residue at position 13 in mammalian PYY and PP molecules could lower conformational plasticity and the non-selective binding via intrachain hydrogen bonding. The acidity of this tract could also be important in agonist selectivity of the Y receptor subtypes. The differences point to an evolutionary reduction of promiscuous protein binding from NPY to PP, and should also be important for Y agonist selectivity within NPY receptor group, and correlate with partial agonism and out-of group cross-reactivity with other receptors.

Recognition of Neurohormones of the NPY Family by Their Receptors

In this review a structural approach developed to answer the question whether hormones from the neuropeptide Y (NPY) family are recognized directly from solution or from the membrane-bound state is described. The chosen strategy is built onto a comparison of a set of peptides with well-known pharmacology and investigates whether similarities of structures of pharmacologically related peptides are higher in solution or in the membrane-bound state. Moreover, we have established the membrane-association mode of these peptides and contributed to our understanding of the structural features of these hormones both when placed in bulk solution and when bound to membranes. As a result we propose a receptor recognition pathway that includes initial association with the membrane and requires the peptides to come off the membrane to diffuse into the binding pocket of the receptor. This review also presents methodology recently developed by us to simulate the structural transition the peptides undergo when diffusing from bulk solution onto the membrane.

Recognition of GPCRs by Peptide Ligands and Membrane Compartments theory: Structural Studies of Endogenous Peptide Hormones in Membrane Environment

One of the largest family of cell surface proteins, G-protein coupled receptors (GPCRs) regulate virtually all known physiological processes in mammals. With seven transmembrane segments, they respond to diverse range of extracellular stimuli and represent a major class of drug targets. Peptidergic GPCRs use endogenous peptides as ligands. To understand the mechanism of GPCR activation and rational drug design, knowledge of three-dimensional structure of receptor–ligand complex is important. The endogenous peptide hormones are often short, flexible and completely disordered in aqueous solution. According to “Membrane Compartments Theory”, the flexible peptide binds to the membrane in the first step before it recognizes its receptor and the membrane-induced conformation is postulated to bind to the receptor in the second step. Structures of several peptide hormones have been determined in membrane-mimetic medium. In these studies, micelles, reverse micelles and bicelles have been used to mimic the cell membrane environment. Recently, conformations of two peptide hormones have also been studied in receptor-bound form. Membrane environment induces stable secondary structures in flexible peptide ligands and membrane-induced peptide structures have been correlated with their bioactivity. Results of site-directed mutagenesis, spectroscopy and other experimental studies along with the conformations determined in membrane medium have been used to interpret the role of individual residues in the peptide ligand. Structural differences of membrane-bound peptides that belong to the same family but differ in selectivity are likely to explain the mechanism of receptor selectivity and specificity of the ligands. Knowledge of peptide 3D structures in membrane environment has potential applications in rational drug design.

Are Hormones from the Neuropeptide Y Family Recognized by Their Receptors from the Membrane-Bound State?

Hormones and many other neurotransmitters, growth factors, odorant molecules, and light all present stimuli for a class of membrane-anchored receptors called G protein-coupled receptors (GPCRs). The GPCRs are the largest family of cell-surface receptors involved in signal transduction. About 1% of all known genes of Drosophila and more than 5% of the genes of Caenorhabditis elegans encode GPCRs. In addition, more than 50% of current therapeutic agents on the market target these receptors. When the enormous biological and pharmaceutical importance of these receptors is considered, it is surprising how little is known about the mechanism with which these receptors recognize their natural ligands. In this review we present a structural approach, utilizing techniques of high-resolution NMR spectroscopy, to address the question of whether peptides from the neuropeptide Y family of neurohormones are recognized directly from solution or from the membrane-bound state. In our studies we discovered that the structures of the membrane-bound species are better correlated to the pharmacological properties of these peptides than the solution structures are. These findings are supported by the observation that many biophysical properties of these peptides seem to be optimized for membrane binding. We finally present a scenario of possible events during receptor recognition.

Novel modified and radiolabelled neuropeptide Y analogues to study Y-receptor subtypes

To better characterize neuropeptide Y (NPY) receptor subtypes, several novel selective analogues of the NPY sequence have been developed in the last few years. These analogues show high selectivity towards single NPY receptors and facilitate insights into the localisation and physiological role of each receptor subtype in health and disease. Besides the important role of NPY in the regulation of food intake and other physiological functions, recently NPY receptors have been identified to play an important role in several types of cancer. To further enlighten all these numerous functions the radioactive labelling of peptides is still an indispensable and versatile tool. By using the appropriate radioisotope and labelling strategy several different radioisotopes can be incorporated into the sequence of subtype selective NPY analogues. Depending on the radioisotope the resulting radiolabelled NPY analogues can be used for diagnostic or therapeutic applications and enable us to better investigate single receptor subtypes in vitro and in vivo.

Characterization of the Proto-oncogenic and Mutant Forms of the Transmembrane Region of Neu in Micelles

We have investigated peptides corresponding to the complete transmembrane region of both proto-oncogenic (Val(664)) and mutant (Glu(664)) forms of the receptor Neu in detergent micelles by NMR and CD spectroscopy. Both forms of the peptide appear to adopt similar levels of helicity and dimeric interactions based on the analysis of CD spectra and nuclear Overhauser effect connectivity profiles. There are considerable differences in the chemical shifts of amide and, to a lesser extent, CHalpha resonances between the two forms of the peptides, and these differences are most pronounced in residues upstream of the mutation site and close to the N terminus of the transmembrane domain. Similarly, there are substantial differences in the amide hydrogen-deuterium exchange rates for residues close to and upstream of the mutation site; amide protons in this region of the protooncogenic peptide are much more resistant to exchange than those in the mutant form. In both molecules, residues downstream of the mutation site exhibit slow exchange. We therefore demonstrate that, although transmembrane Neu peptides exhibit similar levels of secondary structure when dispersed in detergent, there are detectable differences in their adopted micellar states that may provide insight into the dimer-promoting ability of the polar transforming mutation.

Structural Similarities of Micelle-bound Peptide YY (PYY) and Neuropeptide Y (NPY) are Related to their Affinity Profiles at the Y Receptors

Here, we investigate the structure of porcine peptide YY (pPYY) both when unligated in solution at pH 4.2 and when bound to dodecylphosphocholine (DPC) micelles at pH 5.5. pPYY in solution displays the PP-fold, with the N-terminal segment being back-folded onto the C-terminal alpha-helix, which extends from residue 17 to 31. In contrast to the solution structure of Keire et al. published in the year 2000 the C-terminal helix does not display a kink around residue 23-25. The root mean square deviation (RMSD) for backbone atoms of the NMR ensemble of conformers to the mean structure is 0.99(+/-0.35) Angstrom for residues 14-31. The back-fold is supported by values of 0.60+/-0.1 for the (15)N(1)H-NOE and by generalized order parameters S(2) of 0.74+/-0.1 for residues 5-31 which indicate that the peptide is folded in that segment. We have additionally used DPC micelles as a membrane model and determined the structure of pPYY when bound to it. Therein, an alpha-helix occurs in the segment comprising residues 17-31 and the N terminus freely diffuses in solution. The hydrophobic side of the amphipathic helix forms the micelle-binding interface and hydrophobic side-chains extend into the micelle interior. A significant stabilization of helical conformation occurs in the C-terminal pentapeptide, which is important for receptor binding. The latter is supported by positive values of the heteronuclear NOE in that segment (0.52+/-0.1 compared to 0.08+/-0.4 for the unligated form) and by values of S(2) of 0.6+/-0.2 (versus 0.38+/-0.2 for the unligated form). The structures of micelle-bound pPYY and pNPY are much more similar than those of pPYY and bPP with pairwise RMSDs of 1.23(+/-0.21)A or 3.21(+/-0.39) Angstrom, respectively. In contrast to the conformational similarities in the DPC-bound state their structures in solution are very different. In fact pPYY is more similar to bPP, which with its strong preference for the Y(4) receptor displays a completely different binding profile. Considering the high degree of sequence homology of pNPY and pPYY (>80%) and the fact, that their binding affinities at all receptor subtypes are high and, more importantly, rather similar, it is much more likely that PYY and NPY are recognized by the Y receptors from the membrane-bound state. As a consequence of the latter the PP-fold is not important for recognition of PYY or NPY at the Y receptors. To our knowledge this work provides for the first time strong arguments derived from structural data that support a membrane-bound receptor recognition pathway.

Bovine pancreatic polypeptide (bPP) undergoes significant changes in conformation and dynamics upon binding to DPC micelles

The pancreatic polypeptide (PP), a 36-residue, C-terminally amidated polypeptide hormone is a member of the neuropeptide Y (NPY) family. Here, we have studied the structure and dynamics of bovine pancreatic polypeptide (bPP) when bound to DPC-micelles as a membrane-mimicking model as well as the dynamics of bPP in solution. The comparison of structure and dynamics of bPP in both states reveals remarkable differences. The overall correlation time of 5.08ns derived from the 15N relaxation data proves unambiguously that bPP in solution exists as a dimer. Therein, intermolecular as well as intramolecular hydrophobic interactions from residues of both the amphiphilic helix and of the back-folded N terminus contribute to the stability of the PP fold. The overall rigidity is well-reflected in positive values for the heteronuclear NOE for residues 4-34. The membrane-bound species displays a partitioning into a more flexible N-terminal region and a well-defined alpha-helical region comprising residues 17-31. The average RMSD value for residues 17-31 is 0.22(+/-0.09)A. The flexibility of the N terminus is compatible with negative values of the heteronuclear NOE observed for the N-terminal residues 4-12 and low values of the generalized order parameter S(2). The membrane-peptide interface was investigated by micelle-integrating spin-labels and H,2H exchange measurements. It is formed by those residues which make contacts between the C-terminal alpha-helix and the polyproline helix. In contrast to pNPY, also residues from the N terminus display spatial proximity to the membrane interface. Furthermore, the orientation of the C terminus, that presumably contains residues involved in receptor binding, is different in the two environments. We speculate that this pre-positioning of residues could be an important requirement for receptor activation. Moreover, we doubt that the PP fold is of functional relevance for binding at the Y(4) receptor.