Solvent effects on the conformation of cyclo(-D-Trp-D-Asp-Pro-D-Val-Leu-). An NMR spectroscopy and molecular modeling study

LowModeMD--implicit low-mode velocity filtering applied to conformational search of macrocycles and protein loops

We present a method for conformational search of complex molecular systems such as macrocycles and protein loops. The method is based on perturbing an existing conformation along a molecular dynamics trajectory using initial atomic velocities with kinetic energy concentrated on the low-frequency vibrational modes, followed by energy minimization. A novel Chebyshev polynomial filter is used to heavily dampen the high-frequency components of a randomly generated Maxwell-Boltzmann velocity vector. The method is very efficient, even for large systems; it is straightforward to implement and requires only standard force-field energy and gradient evaluations. The results of several computational experiments suggest that the method is capable of efficiently sampling low-strain energy conformations of complex systems with nontrivial nonbonded interaction networks.

Molecular modeling of the complex of endothelin-1 (ET-1) with the endothelin type A (ET(A)) receptor and the rational design of a peptide antagonist

ET-1 is the most potent vasoconstrictor known to date, causing vasoconstriction when bound to the ET(A) receptor. Inhibitors of the binding of ET-1 to the ET(A) receptor would be of immense value as potential therapeutic agents in the treatment of cardiovascular disorders such as angina and hypertension. We present here the rational design of such an inhibitor, which is arrived at on the basis of a model of the ET-1/ET(A) receptor complex proposed by us. The model is found to be consistent with binding and mutagenesis studies of ET-1 as well as of BQ123, a known, potent ET(A)-selective antagonist which competes with ET-1 for receptor binding. BQ123 is a peptidic antagonist which is constrained to adopt a definite conformation on account of its cyclic nature. The noncyclic peptide antagonist designed by us also has a unique conformation because it contains two dehydro-Alanine (deltaAla) residues which, on account of their planarity, cause the peptide backbone to bend in a specific and predictable manner. The folding rules for peptides containing deltaAla were derived in our earlier studies. Energy minimization and modelling of the complex of the designed peptide with the ET(A) receptor indicate that the antagonist is ET(A)-selective and the binding is more stable and more specific as compared to that of BQ123.

Novel sodium binding properties of some cyclopentapeptide endothelin A selective receptor antagonists: electrospray and fast-atom-bombardment mass spectrometric studies

Electrospray ionization and fast atom bombardment mass spectrometric methods reveal novel interactions of endothelin A selective receptor antagonists, cyclo(D-Trp-D-Asp-Pro-D-Val-Leu), cyclo(D-Trp-D-Glu-Ala-D-allo-Ile-Leu) and cyclo(D-Trp-D-Asp-Pro-D-Ile-Leu) with sodium ions. The peptides have very high intrinsic affinities for sodium ions, and form multiple sodium adducts and sandwich structures: [M + Na]+, [M + 2Na - H]+, [M + 3Na - 2H]+, [M + 4Na - 3H]+, [M + 5Na - 4H]+, [2M + Na]+, [2M + 2Na - H]+, [2M + 3Na - 2H]+, [2M + 4Na - 3H]+, [2M + 5Na - 4H]+, [2M + 6Na - 5H]+, and [2M + 7Na - 6H]+. The three cyclic peptides exhibit similar sodium binding stoichiometries despite differences in their amino acids. The observed sodium binding properties may have implications in understanding their protective effects against ischemia-induced acute renal failure. Those cyclic peptides that offer protection may be those that have high affinities for multiple sodium ions.

Nuclear magnetic resonance studies of the C-terminal human growth hormone fragment I179-C182-[SS]-C189-P191 and the related trisulfide peptide I179-C182-[SSS]-C189-P191

The synthetic C-terminal hGH fragment I179-C182-[SS]-C189-P191 and the related trisulfide peptide I179-C182-[SSS]-C189-P191 have been studied using homonuclear 1H-NMR methods and distance geometry calculations. The 1H-NMR spectra of both the disulfide (diS) and the trisulfide (triS) were completely assigned. Amide proton exchange rates, NOEs and the temperature dependence of the NH chemical shifts indicate a hydrogen bond in triS between Val185 and Ser188 stabilizing a turn in this region. 3JH,H coupling constants and NOEs were measured and used as input for distance geometry calculations. For triS two families of structures with averaged pairwise backbone root mean square deviations for Cys182-Cys189 of 1.3-1.5 A were found, only one of which is compatible with experimental data. For diS only one family of structures was found, but with such a low structural definition (back bone rmsd > 2 A) that no interpretation into a consensus structure is useful. The generated structures were compared to the crystal structure of the terminal loop in hGH, complexed to its binding proteins. The resemblance was low between the solution structures of the tridecapeptides and the terminal hGH loop.

Synthesis and conformational analysis of cyclic pentapeptide endothelin antagonists

Two endothelin antagonists cyclo(D-Leu-D-Val-Pro-D-Asp-Trp) (IPI-147), and cyclo (D-Trp-D-Asp-Ac3c-D-Val-Leu) (IPI-725) have been synthetized. Their solution conformations have been studied in aqueous solution by NMR spectroscopy and dynamics simulation. Activity studies show that IPI-725 is a strong ETA antagonist, while IPI-147 is a weak ETA antagonist. Comparison of the solution conformations of these two ETA antagonists suggests that the difference in their activities results from their structural differences. IPI-147 contains a type II beta-turn with a hydrogen bond between NH of D-Val and the C = O of D-Asp. IPI-725, on the other hand, contains two turns, a type II beta-turn with a hydrogen bond between NH of D-Asp and C = O of D-Val, as well as a gamma'-turn with a hydrogen bond formed between D-Val NH and D-Asp carbonyl group. Therefore IPI-147 appears to be more flexible than IPI-725. Although both beta-turns contain the same residues, their orders in the turn are reversed. The beta-turn in IPI-725 is formed with D-Val:Leu:D-Trp:D-Asp, while in IPI-147, the beta-turn is formed with D-Asp:Trp:D-Leu:D-Val. The activities and solution conformations of IPI-147 and IPI-725 were also compared with BQ-123 [cyclo(D-Trp-D-Asp-Pro-D-Val-Leu)], a well characterized, highly potent endothelin antagonist.

Synthesis and solution structure of the antimicrobial peptide protegrin-1

Protegrins are members of a family of five Cys-rich, cationic antimicrobial peptides recently isolated from porcine cells. We have synthesised an 18-amino-acid peptide that corresponds to protegrin-1. After Cys oxidation, the peptide has bactericidal activity against gram-positive and gram-negative bacteria, similar to that described for the natural peptide. The solution structure of protegrin-1 was investigated by means of 1H-NMR spectroscopy in water and in (CD3)2SO, with distance-geometry and simulated-annealing calculations. The C6-C15 and C8-C13 disulfide pattern was determined on the basis of NMR-derived constraints. These two parallel disulfide bridges stabilised a beta-sheet structure which comprised two antiparallel strands (residues 5-9 and 12-16) linked by a distorted beta-turn (residues 9-12). The N-terminus and C-terminus were essentially disordered. The distribution of hydrophobic and hydrophilic residues at the peptide surface was found to be a structural feature shared with tachyplesin-1, a related peptide which displays cytolytic activity, and, to a lesser extent, with mammalian defensins. These findings led us to assume that the distribution pattern could be required for the cytolytic activity of these peptides.

Comparison of the structures of the endothelin A receptor antagonists BQ123 and N-methyl leucine BQ123 with the crystal structure of the C-terminal tail of endothelin-1

The functionally important regions of the cyclic pentapeptide endothelin A receptor antagonist BQ123 are shown to correlate with the structure of the C-terminal tail of endothelin-1, as found in the recently-determined X-ray crystal structure. Residues 18 and 21 of endothelin-1 are spatially juxtaposed such that they superpose extremely well with D-Asp and D-Trp of the antagonist, consistent with the residues on this surface of the endothelin helix being important for binding. This study provides new information on the three-dimensional nature of the endothelin A receptor binding site which may prove useful for rational drug design.

Solution conformational dynamics of the C-terminal residues in endothelin-1 and some analogues: a time-resolved fluorescence study

The rotational relaxation times of the single tryptophan residues in endothelin-1, [Ala1,3,11,15]endothelin-1, human pro-endothelin-1, the linear hexapeptide Ac-His-Leu-Asp-Ile-Ile-Trp which corresponds to the C-terminal residues 16-21 in endothelin-1, the cyclic pentapeptide BQ123, and several di- and tri-peptides possessing C-terminal tryptophan residues have been determined from time-resolved fluorescence anisotropy decays obtained by phase/modulation techniques. Fluorescence lifetime distribution widths have also been examined as predictors of conformational heterogeneity/restriction. A significant contribution from a slow rotational component supports either the persistence, on the nano-second timescale at least, of a non-flexible alpha-helical structure for the C-terminal tail residues of endothelin-1 in water as solvent, as seen in the X-ray crystallographic structure, or the interaction of the C-terminal tail residues 16-21 with the constrained disulfide-bridged core residues 1-15. This slow rotational contribution is less evident in the linear, acyclic tetraalanine analogue but greatly increased in pro-endothelin-1. In BQ123 the fluorescence characteristics support the occurrence of a dominant rotameric form involving the indole sidechain of the D-tryptophan residue (C alpha-C beta torsion angle chi 1 of 60 degrees, as previously determined by NMR.