The probability distribution of side-chain conformations in [Leu] and [Met]enkephalin determines the potency and selectivity to μ and δ opiate receptors

Gas-phase structures reflect the pain-relief potency of enkephalin peptides

We use cold ion spectroscopy and quantum-chemical computations to solve the structures of opioid peptides enkephalins in the gas phase. The derived structural parameters clearly correlate with the known pharmacological efficiency of the studied drugs, suggesting that gas-phase methods, perhaps, can be used for predicting the relative potency of ligand drugs that target the hydrophobic pockets of receptors.

Nonstatistical UV Fragmentation of Gas-Phase Peptides Reveals Conformers and Their Structural Features

Solving the 3D structure of a biomolecule requires recognition of its conformers and measurements of their individual structural identities, which can be compared with calculations. We employ the phenomenon of nonstatistical photofragmentation, detected by a combination of UV cold ion spectroscopy and high-resolution mass spectrometry, to identify the main conformers of gas-phase peptides and to recover individual UV absorption and mass spectra of all of these conformers in a single laser scan. We first validate this approach with a benchmark dipeptide, Tyr-Ala, and then apply it to a decapeptide, gramicidin S. The revealed characteristic structural difference between the conformers of the latter identifies some of the previously calculated structures of gramicidin S as the most likely geometries of its remaining unsolved conformer.

Conformational heterogeneity of a leucine enkephalin analogue in aqueous solution and sodium dodecyl sulfate micelles: comparison of time-resolved FRET and molecular dynamics simulations

We have undertaken time-resolved Förster resonance energy transfer (FRET) and molecular dynamics simulations to analyze conformations and conformational heterogeneity of an analogue of leucine enkephalin in solution and in the presence of sodium dodecyl sulfate (SDS) micelles. Enkephalins are opioid pentapeptides that interact with opioid receptors in the central nervous system. We used time-correlated single-photon counting to detect energy transfer between the N-terminal tyrosine and a tryptophan residue substituted for phenylalanine at the 4 position. FRET from Tyr to Trp was measured over a temperature range from 5 to 55 degrees C in aqueous solution. By taking into account Tyr rotamer interconversion rates measured previously, we determined average distances between Tyr and Trp for the two populated rotameric conformations of Tyr. Molecular dynamics simulations (100 ns) support this analysis and indicate extensive conformational heterogeneity. The simulations also predict that the FRET orientational factor is correlated with the Tyr-Trp separation. Failure to account for the correlation between orientation and distance results in errors that appear to be largely offset in the leucine enkephalin analogue (YGGWL) by a weighting bias inherent in the R(-6) dependence of the energy-transfer rate. The Tyr lifetimes decrease upon titration of the peptides with SDS, indicating formation of compact conformations of the peptide in the micelle environment. This result is consistent with the conjecture that the lipid environment may induce formation of bioactive conformations of the peptide.

Tracking the evolution of the proenkephalin gene in tetrapods

In gnathostomes there is remarkable consistency in the organization of the proenkephalin gene. This opioid precursor encodes seven opioid (YGGF) sequences: five pentapeptide sequences, a met-enkephalin-7 sequence and a met-enkephalin-8 sequence. Yet, within vertebrate lineages there can be distinct sets of pentapeptide opioids (YGGFM or YGGFL). In the Sarcopterygii, the sixth opioid position in lungfishes and anuran amphibian proenkephalin genes encodes a met-enkephalin (YGGFM) sequence. However, in mammalian proenkephalin there is a leu-enkephalin (YGGFL) sequence at this position. This study was done to test the hypothesis that the presence of the leu-enkephalin sequence in mammals is a feature common to amniote vertebrates, but not present in anamniote vertebrates. To resolve this issue, proenkephalin cDNAs were cloned from the urodele amphibians, Amphiuma means and Necturus maculosus, and two amniote vertebrates, the turtle, Chrysemys scripta, and the brown snake, Storeria dekayi. As predicted, a met-enkephalin sequence is present at the sixth opioid position in urodele amphibians; whereas, a leu-enkephalin sequence is present at this opioid site in the reptile proenkephalin sequences. These data are consistent with the conclusion that the transition from a met-enkephalin sequence to a leu-enkephalin sequence at the sixth opioid position in tetrapod proenkephalins occurred in the ancestral proto-reptiles. Phylogenetic analyses, using the Maximum Parsimony and Neighbor-Joining algorithms, of the amphibian proenkephalin sequences supported the position that anuran and urodele amphibians are a monophyletic assemblage. The same analysis of reptile-related proenkephalin sequences, including the deduced amino acid sequence of a partially characterized alligator proenkephalin cDNA, could not conclusively resolve the phylogeny of the major reptilian orders.

Tyrosyl rotamer interconversion rates and the fluorescence decays of N-acetyltyrosinamide and short tyrosyl peptides

It has long been recognized that the fluorescence lifetimes of amino acid residues such as tyrosine and tryptophan depend on the rotameric configuration of the aromatic side chain, but estimates of the rate of interchange of rotameric states have varied widely. We report measurements of the rotameric populations and interchange rates for tyrosine in N-acetyltyrosinamide (NATyrA), the tripeptide Tyr-Gly-Gly (YGG), and the pentapeptide Leu-enkephalin (YGGFL). The fluorescence lifetimes were analyzed to determine the rotameric interchange rates in the context of a model incorporating exchange among three rotameric states. Maximum entropy method analysis verified the presence of three fluorescence decay components for YGGFL and two for YGG and NATyrA. Rotameric exchange between the gauche(-) and trans states occurred on the nanosecond time scale, whereas exchange with the gauche(+) state occurred on a longer time scale. Good agreement was obtained with rotameric populations and exchange rates from molecular dynamics simulations. Quenching by iodide was used to vary the intrinsic fluorescence lifetimes, providing additional constraints on the determined interchange rates. The temperature dependence was measured to determine barriers to exchange of the two most populated rotamers of 3, 5, and 7 kcal/mol for NATyrA, YGG, and YGGFL, respectively.

Structure-activity relationships of Leu-enkephalin analog with (4-carboxamido)phenylalanine substituted for tyrosine: A molecular dynamics study

Motivated by recent experimental work on Leu-Enkephalin modification with (4-Carboxamido)phenylalanine (Cpa), we perform MD simulations to study the structure-activity relationships of the [Cpa(1), Leu(5)]-enkephalin (Cpa-LE) for better understandings of the binding affinity in delta-selective opioid ligands. Recently, Tyr(1) substituted into Cpa(1) form was experimentally found to be the first example of an amino acid that acts as a surrogate for Tyr(1) in opioid peptide ligands, which challenges a long-standing belief that a phenolic residue is required for high affinity binding. Our simulations show the Cpa-LE structure in aqueous solution revealed that the occurrence of single-bend packed state can be stabilized by an intramolecular hydrogen bond from Leu(5)-NH to Gly(2)-CO (5-->2). In addition, an intramolecular sidechain to backbone hydrogen bond, i.e., hydrogen bond binding between the sidechain carbonyl CO group of the Cpa residue and backbone amide NH group of the Phe residue was examined. Furthermore, the hydration effects of carboxamido group (CONH(2)) for Cpa residue and 5-->2 hydrogen bond were calculated via the solute-solvent radial distribution functions g(alpha-beta) (r), providing direct evidence of strong hydrogen bond interactions. Our simulation results further reveal the chi(1) rotamers of the Cpa(1) and Phe(4) that show preferences for trans and gauche (-), respectively. Finally, we elucidate the probability distributions of two aromatic rings among the Cpa-LE, Leu-enkephalin, and delta pharmacophore model. The results show that modified the Tyr(1) to Cpa(1) can lead to increase the potency and selectivity for delta-opioid receptor (DOR), consistent with experimental findings.