Conformational Properties of Neuromedin NmU-8 and Its Modified Analogs

The three-dimensional organization and conformational properties of NmU-8 neuropeptide and its modified analogs have been studied by modeling and compared with the available data on their biological activity. The effect of single amino acids substitutions on conformational states of the native neuropeptide is discussed. The low-energy conformations responsible for its contractile activity have been revealed.     

Conformational features of the Dippu-AST 8 neuropeptide from the cockroach Diploptera punctata

Spatial structure and conformational properties of the Dippu-AST 8 (allatostatin III) neuropeptide have been investigated by the molecular mechanics method. The conformational energy and geometrical parameters corresponding to the low-energy states of the molecule are obtained. A single backbone conformation with a very restricted set of Ser 3, Phe 4 and Leu 9 amino acids positions is observed for Dippu-AST 8 neuropeptide.     

Structure/activity relationships of C-terminal neuropeptide Y peptide segments and analogues composed of sequence 1-4 linked to 25-36

C-terminal analogues of neuropeptide Y have been synthesized. The influence of chain length, single-amino-acid substitutions and segment substitutions on receptor binding, biological activity and conformational properties has been investigated. Receptor binding and in vivo assays revealed biological activity already for amino acids 28-36 of neuropeptide Y [neuropeptide Y-(Ac-28-36)-peptide] which increased with increasing chain length. Replacement of Arg25 in neuropeptide Y-(Ac-25-36)-peptide had no influence on binding, whereas Arg33 and Arg35 cannot be replaced by lysine or ornithine without considerable decrease in receptor binding. The introduction of conformational constraints by the 2-aminoisobutyric acid residue (Aib) in position 30 and replacing the amino acids 28-32 by Ala-Aib-Ala-Aib-Ala decreased receptor binding. However, the corresponding Aib-Ala-Aib-Ala-Aib-substituted analogue and a more flexible analogue with Gly5 at position 28-32 exhibited considerable affinity for the receptor. All these substitutions led to a decrease in postsynaptic activity. Strong agonistic activities could be detected in a series of 10 discontinuous analogues, which are constructs of N-terminal parts linked via different spacer molecules to C-terminal segments. One of the most active molecules was neuropeptide Y amino acids 1-4 linked to amino acids 25-36 through aminohexanoic acid (Ahx) [neuropeptide Y-(1-4-Ahx-25-36)-peptide].     

The NMR-derived conformation of neuropeptide F from Moniezia expansa

The solution structure of neuropeptide F (NPF), from the flatworm (platyhelminthes) Moniezia expansa, has been determined by (1)H NMR spectroscopy at 800 MHz in 60%/40% CD(3)OH/H(2)O. NPF is the most abundant neuropeptide in platyhelminthes. The secondary structure of NPF contains an alpha helix from residues Lys(14) to Ile(31), while the N terminus, consisting of residues Pro(-2) to Asn(13), and the C-terminus, consisting of residues Gly(32) to Phe(36), are in a random conformation. The structure was calculated by a simulated annealing protocol, and the conformational data are compared to the porcine neuropeptide Y (NPY), a peptide hormone and neurotransmitter. The exact function of NPF is unknown, but structural similarity with porcine NPY indicates that its mode of action is similar. These structural data can serve as a starting point in the design of new antiparasitic drugs.     

Conformational analysis of galanin using end to end distance distribution observed by Förster resonance energy transfer

The structural dynamics of the flexible neuropeptide galanin in solution were studied by Förster resonance energy transfer measurements at different temperatures by time-resolved fluorescence spectroscopy to determine its conformational heterogeneity. Endogenous tryptophan at position 2 acted as the fluorescent donor and the non fluorescent acceptor dinitrophenyl or the fluorescent acceptor dansyl were selectively attached to lysine 25 in porcine galanin. The coexistence of different structures of the neuropeptide galanin in trifluoroethanol solution was revealed by the model independent analysis of the distribution of relaxation times from the time-resolved resonance energy transfer data. Multiple conformational states are reflected by distinct end-to-end distance populations. The conformations differ in mean donor-acceptor distance by about 15 Å, and are consistent with the extended and folded backbone conformations of two α-helical regions separated by a flexible hinge. The effect that the labelling of galanin has on binding to the receptor was also evaluated. DNP-galanin showed the same high affinity to galanin receptors as unlabelled galanin, whereas DNS-galanin had significantly reduced affinity.     

Proctolin, an insect neuropeptide.

Synthetic, biological and conformational studies on the insect neuropeptide proctolin (Arg-Tyr-Leu-Pro-Thr) and some of its analogues are reviewed.     

Membrane‐induced structure of novel human tachykinin hemokinin‐1 (hHK1)

PPT‐C encoded hemokinin‐1(hHK‐1) of Homo sapiens (TGKASQFFGLM) is a structurally distinct neuropeptide among the tachykinin family that participate in the NK‐1 receptor downstream signaling processes. Subsequently, signal transduction leads to execution of various effector functions which includes aging, immunological, and central nervous system (CNS) regulatory actions. However the conformational pattern of ligand receptor binding is unclear. The three‐dimensional structure of the hemokinin‐1 in aqueous and micellar environment has been studied by one and two‐dimensional proton nuclear magnetic resonance (2D 1H‐NMR spectroscopy) and distance geometry calculations. Data shows that hemokinin‐1 was unstructured in aqueous environment; anionic detergent SDS induces α‐helix formation. Proton NMR assignments have been carried out with the aid of correlation spectroscopy (gradient‐COSY and TOCSY) and nuclear Overhauser effect spectroscopy (NOESY and ROESY) experiments. The inter proton distances and dihedral angle constraints obtained from the NMR data have been used in torsion angle dynamics algorithm for NMR applications (CYANA) to generate a family of structures, which have been refined using restrained energy minimization and dynamics. Helical conformation is observed from residue K3‐M11. The conformational range of the peptide revealed by NMR studies has been analyzed in terms of characteristic secondary features. Observed conformational features have been compared to that of Substance P potent NK1 agonist. Thus the report provides a structural insight to study hHK‐1‐NK1 interaction that is essential for hHK1 based signaling events. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 702–710, 2015.     

Three-dimensional structure of neuropeptide k bound to dodecylphosphocholine micelles

Neuropeptide K (NPK), an N-terminally extended form of neurokinin A (NKA), represents the most potent and longest lasting vasodepressor and cardiomodulatory tachykinin reported thus far. NPK has been shown to have high selectivity for the NK2 receptor. Because the micelle-associated structure may be relevant to the NPK-receptor interaction, the three-dimensional structure of the NPK in aqueous and micellar environments has been studied by two-dimensional proton nuclear magnetic resonance (2D (1)H NMR spectroscopy) and distance geometry calculations. Proton NMR assignments have been carried out with the aid of correlation spectroscopy (DQF-COSY and TOCSY) and nuclear Overhauser effect spectroscopy (NOESY and ROESY) experiments. The interproton distances and dihedral angle constraints obtained from the NMR data have been used in torsion angle dynamics algorithm for NMR applications (DYANA) to generate a family of structures, which have been refined using restrained energy minimization and dynamics. The results show that in an aqueous environment NPK lacks a definite secondary structure, although some turn-like elements are present in the N terminus. The structure is well-defined in the presence of dodecylphosphocholine micelles. The global fold of NPK bound to DPC micelles consists of two well-defined helices from residues 9 to 18 and residues 27 to 33 connected by a noncanonical beta turn. The N terminus of the peptide is characterized by a 3(10) helix or a series of dynamic beta turns. The conformational range of the peptide revealed by NMR and circular dichroism (CD) studies has been analyzed in terms of characteristic secondary features. The observed conformational features have been further compared to a NKA and neuropeptide gamma (NPgamma) potent endogenous agonist for the NK2 receptor.     

Alpha-helical small molecular size analogues of neuropeptide Y: structure-activity relationships.

C-terminal analogues of neuropeptide Y (NPY) of small molecular size have been synthesized. The influence of chain length, single or multiple amino acid substitution, and segment substitutions on receptor binding, pre- and postsynaptic biological activity, and conformational properties have been investigated. Receptor binding and in vivo assays revealed biological activity for NPY Ac-25-36 that increased with increasing alpha-helicity. In attempts to stabilize the alpha-helical content, three independent types of modified NPY Ac-25-36 analogues were synthesized. Strong agonistic activities could be detected in a series of discontinuous analogues, which are constructs of N-terminal parts linked via different spacer molecules to C-terminal segments. One of the most active molecules was NPY 1-4-Aca-25-36 (Aca, epsilon-aminocaproic acid). For the first time conformational properties of a series of small NPY analogues have been investigated by CD, and correlated with biological activity and receptor binding. A C-terminal dodecapeptide segment of NPY with an amount of 50% substitution to the native C-terminal sequence of NPY was found to exhibit significant receptor binding.     

The conformational and vibrational behavior of the inhibitory neuropeptide derived from beta-endorphin

In this study, conformational behavior, structural, and vibrational characterization of the carboxy terminal dipeptide of β-endorphin (glycy-l-glutamine, glycyl-glutamine, beta-endorphin_30-31), which is an inhibitory neuropeptide synthesized from beta-endorphin_1-31 in brain stem regions, has been investigated. The theoretically possible stable conformers were searched by means of molecular mechanics method to determine their energetically preferred conformations. The 360 different conformations were calculated with the φ, Ψ, χ dihedral angles using the Ramachandran maps. The most stable conformation of the title molecule is characterized by the extended backbone shape (e) in the BR conformational range with ?.78 kcal/mol energy. The cis- and trans-dimeric forms of the dipeptide were also formed and energetically preferred conformations of dimers were investigated. The experimental methods (FT-IR, micro-Raman spectroscopies) coupled with quantum chemical calculations based on density functional theory (DFT) have been used to identify the geometrical, energetic, and vibrational characteristics of the dipeptide. The assignment of the vibrational spectra was performed based on the potential energy distribution of the vibrational modes. To investigate the electronic properties, such as nonlinear optical properties, the electric dipole moment, the mean polarizability, the mean first hyperpolarizability, and HOMO–LUMO energy gaps were computed using the DFT with the B3LYP/6-31++G(d,p) basis set combination. The second-order interaction energies were derived from natural bonding orbital analysis. The focus of this study is to determine possible stable conformation on inhibitory neuropeptide and to investigate molecular geometry, molecular vibrations of monomeric and dimeric forms, and hydrogen bonding interactions of glycy-l-glutamine dipeptide.     

Conformations of neurotensin in solution and in membrane environments studied by 2-D NMR spectroscopy

Two-dimensional HOHAHA and ROESY nuclear magnetic resonance techniques are used to obtain complete proton resonance assignments and to perform a conformational investigation of the neuropeptide neurotensin (pGlu-Leu-Tyr-Glu-Asn-Lys-Pro-Arg-Arg-Pro-Tyr-Ile-Leu) in aqueous solution, methanol, and membrane-mimetic [deuterated sodium dodecylsulfate (SDS)] environments. Results suggest the absence of discernible elements of secondary structure in water and methanol. ROESY spectra confirm that Lys-Pro and Arg-Pro peptide bonds are all-trans, but that a significant population of cis Arg-Pro bonds arises in aqueous solution, which increases in the environment of SDS micelles. The conformational ensemble of the peptide is observed to narrow as it becomes bound through its cationic mid-region to SDS micelles, with the accompanying advent of local extended structure. The overall results indicate the inherent conformational flexibility of neurotensin, and emphasize the environmental dependence of conformation in peptides of medium length.     

Structuro-functional organization of delta sleep-inducing peptide

Theoretical conformational analysis was carried out for a nonapeptide hormone (delta sleep-inducing peptide). Possible structure of the neuropeptide under physiological conditions may be described by a set of low-energy conformations belonging to nine different forms of the backbone. A solution of the "reverse conformational problem" for delta sleep inducing peptide enables one to predict modified amino acid sequences (D-Ala3-, Pro4-, Pro6-, Pro7, and Tyr7-analogs), which may assume one of the low-energy states of the native hormone. The influence of the solute was not taken into account in our calculations.     

Regulation of endogenous human NPFF2 receptor by neuropeptide FF in SK-N-MC neuroblastoma cell line

Neuropeptide FF has many functions both in the CNS and periphery. Two G protein-coupled receptors (NPFF1 and NPFF2 receptors) have been identified for neuropeptide FF. The expression analysis of the peptide and receptors, together with pharmacological and physiological data, imply that NPFF2 receptor would be the primary receptor for neuropeptide FF. Here, we report for the first time a cell line endogenously expressing hNPFF2 receptor. These SK-N-MC neuroblastoma cells also express neuropeptide FF. We used the cells to investigate the hNPFF2 receptor function. The pertussis toxin-sensitive inhibition of adenylate cyclase activity upon receptor activation indicated coupling to Gi/o proteins. Upon agonist exposure, the receptors were internalized and the mitogen-activated protein kinase cascade was activated. Upon neuropeptide FF treatment, the actin cytoskeleton was reorganized in the cells. The expression of hNPFF2 receptor mRNA was up-regulated by neuropeptide FF. Concomitant with the receptor mRNA, the receptor protein expression was increased. The homologous regulation of hNPFF2 receptor correlates with our previous results in vivo showing that during inflammation, the up-regulation of neuropeptide FF mRNA precedes that of NPFF2 receptor. The regulation of hNPFF2 receptor by NPFF could also be important in the periphery where neuropeptide FF has been suggested to function as a hormone.     

Distribution, quantitation, and origin of immunoreactive neuropeptide Y in the human gastrointestinal tract

A radioimmunoassay for measurement of immunoreactive neuropeptide Y has been developed using antiserum from a rabbit (221) immunized with porcine neuropeptide Y. Antibody 221 has been characterized for both sensitivity and specificity. To determine the distribution of neuropeptide Y in the human gastrointestinal tract, fresh tissue specimens were separated by microdissection into the muscularis externa and the mucosa-submucosa. To examine the origin of neuropeptide Y in human colon, specimens of aganglionic and ganglionic colon were obtained from patients with Hirschsprung's disease. Immunoreactive neuropeptide Y in human gut was present in highest concentrations in the muscularis externa of the stomach and in lowest concentrations in the muscularis externa of the ileum and descending colon. Neuropeptide Y in the stomach was present in higher concentrations in the muscularis externa than in the mucosa-submucosa, but in the descending colon there were lower concentrations of neuropeptide Y in the muscularis externa than in the mucosa-submucosa. In Hirschsprung's disease, concentrations of neuropeptide Y were increased in aganglionic colon in both the muscularis externa and the mucosa-submucosa, compared to corresponding layers from proximal ganglionic colon. Extracts of the gastric muscularis externa and the colonic mucosa-submucosa were separated by C18 reverse-phase high-performance liquid chromatography. One major immunoreactive species was identified by radioimmunoassay which eluted in a position similar to synthetic human neuropeptide Y. These results demonstrated both regional and layer differences in concentrations of neuropeptide Y in human gut. Increased concentrations of neuropeptide Y in aganglionic colon from Hirschsprung's disease most likely result from enlargement of neuropeptide Y-containing extrinsic nerve fibers in both the mucosa-submucosa and the muscularis externa.     

Differences in conformational behavior of ATA and TAT sequences in single strand DNA trimer.

The conformational behavior of single strand (ss) TAT and ATA trimers of DNA have been studied by computational chemistry tools including CICADA software interfaced with AMBER molecular mechanics and dynamics. The Single-Coordinate-Driving (SCD) method has been used in conjunction with molecular dynamics simulated annealing. It has been revealed that the conformational flexibility of each sequence differs substantially from the other one. Four common conformational families have been found for both trimers. These are: helical, reverse-stacked (base 3), half-stacked (base 3), reverse-stacked (base 1). However, the energies of conformers representing the families are different for both the studied systems. An additional conformational family, bulged, has been found for ss(ATA), while ss(TAT) has been found also in half-stacked (base 1) conformation. In general, ss(TAT) exhibits a higher number of low energy conformations while ss(ATA) shows one interesting low energy conformational interconversion between reverse-stacked (A3) family and half-stacked (A3) family. The high conformational variability of the trimers has been confirmed by flexibility analysis and by molecular dynamics simulations, which have also shown the conformational stability of single conformational families. It has been concluded that the methodology used is able to provide a very detailed picture of the conformational space of these molecules.     

Differences in Conformational Behavior of ATA and TAT Sequences in Single Strand DNA Trimer

Abstract

The conformational behavior of single strand (ss) TAT and ATA trimers of DNA have been studied by computational chemistry tools including CICADA software interfaced with AMBER molecular mechanics and dynamics. The Single-Coordinate-Driving (SCD) method has been used in conjunction with molecular dynamics simulated annealing. It has been revealed that the conformational flexibility of each sequence differs substantially from the other one. Four common conformational families have been found for both trimers. These are: helical, reverse-stacked (base 3), half-stacked (base 3), reverse-stacked (base 1). However, the energies of conformers representing the families are different for both the studied systems. An additional conformational family, bulged, has been found for ss(ATA), while ss(TAT) has been found also in half-stacked (base 1) conformation. In general, ss(TAT) exhibits a higher number of low energy conformations while ss(ATA) shows one interesting low energy conformational interconversion between reverse-stacked (A3) family and half-stacked (A3) family. The high conformational variability of the trimers has been confirmed by flexibility analysis and by molecular dynamics simulations, which have also shown the conformational stability of single conformational families. It has been concluded that the methodology used is able to provide a very detailed picture of the conformational space of these molecules.     

Neuropeptide K-(1-24)-peptide: storage and release by carcinoid tumors

An antiserum directed against the COOH-terminal region of neuropeptide K-(1-24)-peptide that shows only 0.5% reactivity with neuropeptide K has been used in radioimmunoassay to study the posttranslation processing of human beta-preprotachykinin. A primary midgut carcinoid tumor contained high concentration of substance P (2970 pmol/g), neurokinin A (3660 pmol/g) and neuropeptide K-(1-24)-peptide (3430 pmol/g) but only a very low concentration (less than 5 pmol/g) of intact neuropeptide K. Neuropeptide K-(1-24)-peptide was also detected in extracts of metastatic tumor tissue from four patients with midgut carcinoid tumors. The amino acid sequence of tumor neuropeptide K-(1-24)-peptide was identical to that predicted from the nucleotide sequence of a human beta-preprotachykinin cDNA. The fasting plasma concentration of neuropeptide K-(1-24)-peptide was elevated in a patient with the carcinoid syndrome (821 fmol/ml compared with less than 18 fmol/ml in healthy subjects) and rose approximately 2-fold after intravenous pentagastrin. The study has demonstrated that the Lys25-Arg26 bond in neuropeptide K (corresponding to Lys96-Arg97 in the precursor) is an important processing site in human beta-preprotachykinin.     

Evidence of neuropeptide bivalency in the interaction of substance P with cerebroside sulfate.

A precipitin effect has been observed with mixtures of cerebroside sulfate and the neuropeptide substnace P. This phenomenon is attributed to multivalency of the lipid due to its existence in micellar form, and to bivalency of substance P. One of those neuropeptide sites is almost certainly the basic residue(s) located at the N-terminal of substance P, whereas the hydrophobic residues at the C-terminus are suggested as candidates for the other site on the basis of turbidimetric, circular dichroic, and fluorometric studies. An intrinsic association constant of 3.6 x 10(4)M-1 has been obtained from the cerebroside sulfate concentration associated with maximal turbidity of mixtures containing a fixed concentration of the neuropeptide.     

Evidence of a specific pancreatic polypeptide receptor in rat arterial smooth muscle.

Pancreatic polypeptide (PP) is a member of the PP fold family of regulatory peptides. Studies have shown that neuropeptide Y, peptide YY, and PP increased gastrointestinal motility. The GI effects of neuropeptide Y and peptide YY were accompanied by an increase in mean arterial blood pressure; however, PP decreased mean arterial blood pressure. Cloning of a receptor of the neuropeptide Y family with high affinity for PP has been reported. This Y4 receptor is present in intestine, pancreas, and prostate, and its mRNA has been detected in brain and coronary artery. We found in vitro evidence of PP-mediated inhibition of arterial neurogenic vasoconstriction. We have also detected Y4 mRNA in rat peripheral arteries. These findings suggest a potential role for the Y4 receptor in regulating vascular tone.     

Isolation of less than Glu-Gly-Leu-Arg-Trp-NH2 (Antho-RWamide II), a novel neuropeptide from sea anemones

Using a radioimmunoassay for the peptide sequence Arg-Phe-NH2 (RFamide), a novel peptide has been purified from acetic acid extracts of the sea anemone Anthopleura elegantissima. This peptide has the structure less than Glu-Gly-Leu-Arg-Trp-NH2, and was named Antho-RWamide II. Antho-RWamide II is a neuropeptide. Its structure is closely related to an earlier characterized neuropeptide from Anthopleura less than Glu-Ser-Leu-Arg-Trp-NH2 (Antho-RWamide I).