Investigation of synthetic hosts that model cation-pi sites found at protein binding domains

Small cyclophanes containing aromatic groups and dialkyl ammonium ions were created as model systems of the cation-pi complexes found at some protein binding domains. The hosts had different shapes in order to investigate the effect the arrangement of ammonium ions to aromatic surfaces has on their reactivity. pK(a) values of the hosts were substantially different in DMSO or (95/5) DMSO/D(2)O solutions, which showed that the ions existed in different environments of the hosts. Electrostatic charges, as determined by density functional calculations, revealed that the magnitude of a cationic charge depends on its position relative to an aromatic ring. Association constants of the hosts bound to the sodium salt of N-acetyl phenylalanine in d(6)-DMSO and in (95/5) d(6)-DMSO/D(2)O solutions were inversely proportional to the magnitude of the hosts' acidity constants. These results suggest that the magnitude of the positive charge for cationic groups of cation-pi complexes is reduced by being associated with electron-rich faces of aromatic rings. The aromatic rings, however, lessen the desolvation penalty that must be overcome for ligand binding, giving an overall more favorable association.

Synthesis and physical properties of protein core mimetics

A series of mimetic cores composed of a synthetic scaffold and amino acids have been constructed and their properties investigated in chloroform. A relative measure of H-bond strength was obtained by comparing temperature coefficients derived from variable-temperature (1)H NMR experiments. Although most templates had a strong H-bond, only a single template composed of D- and L-phenylalanines was able to form two strong H-bonds. Templates containing D- and L-leucines formed only a single H-bond. The results of these studies suggest that aromatic edge-to-face interactions provide greater stabilization energy than aliphatic-aromatic interactions in the tightly packed hydrophobic cores of proteins. Partial structures of the templates were derived by analyzing a series of two-dimensional (1)H NMR spectra and performing molecular mechanics calculations using AMBER and MMFF94 force fields.

Tripodal peptide hydroxamates as siderophore models. Iron(III) binding with ligands containing H-(alanyl)n-beta-(N-hydroxy)alanyl strands (n = 1-3) anchored by nitrilotriacetic acid

Combining three units of one of H-(alanyl)n-beta-(HO)alanyl peptides (n = 1-3) with nitrilotriacetic acid affords tripodal peptide hydroxamate ligands (1L, 1D, 2LL, 2DL, and 3LLL, where each L or D denotes the L- or D-alanyl residue). These ligands form six-coordinate octahedral complexes (Fe-1L, Fe-1D, Fe-2LL, Fe-2DL, and Fe-3LLL) with iron(III) in aqueous near neutral pH solution, and the stability and the chirality of the complexes formed depend on the alanyl residues incorporated. Thus Fe-2LL is the most stable against attack of H+ and OH- ions and the least labile in the iron(III) removal by EDTA. The CD spectra show a predominance of the A configuration for Fe-1D, Fe-2LL, Fe-2DL, and Fe-3LLL, but the opposite delta configuration for Fe-1L. These ligands and their gallium(III) complexes are studied by 1H NMR spectroscopy in DMSO-d6 solution. CD and NMR spectral analysis, aided by molecular model examinations, indicates that critical factors in controlling the configuration and the stability of the complexes are (1) the hydroxamate-carrying alanyl residue, (2) the expanse of an interior space in the ligand, and (3) an interstrand amide NH hydrogen bond; the latter bonding is possible with ligands 2LL and 2DL. A microbial growth promotion activity test shows that ligands 1L, 2LL, and 3LLL all act as iron-transporting agents.

Mimicry of beta II'-turns of proteins in cyclic pentapeptides with one and without D-amino acids

The solution structure of eight cyclic pentapeptides has been determined by two-dimensional 1H-NMR spectroscopy combined with spectra simulations and restrained molecular dynamic simulations. Six of the cyclic pentapeptides were derived from the C-terminal cholecystokinin fragment CCK-4 enlarged with Asp1 resulting in the sequence (Asp-Trp-Met-Asp-Phe), one L-amino acid after the other was substituted by its D-analog. In addition, two peptides, including an all-L-amino-acid-containing cyclic pentapeptide, cyclo(Asp-Phe-Lys-Ala-Thr) and cyclo(Asp-Phe-Lys-Ala-D-Thr) were investigated. All D-amino-acid-containing peptides show beta II'-turn conformations with the D-amino acid in the i + 1 position, excepting the D-aspartic-acid-containing peptides. These two peptides are characterized by the lack of beta-turns at pH values less than 4, suggesting that D-aspartic acid in the full-protonized state avoids the formation of beta-turns in these compounds. At pH values greater than 5, a conformational change into the beta II'-turn conformation was also observed for these peptides. Conformations without beta-turns are expected for cyclic all-L pentapeptides, but both cyclo(Asp-Phe-Lys-Ala-Thr) and the D-Thr analog cyclo(Asp-Phe-Lys-Ala-D-Thr) exhibit beta II'-turn conformations around Thr-Asp and D-Thr-Asp. Thus cyclic all-L pentapeptides and those with one D-amino acid are able to form similar structures preferably with a beta II'-turn. The beta-turn formation in cyclic pentapeptides containing a D-aspartic acid is dependent on the ionization state. The relevance of the work to the design of beta'-turn mimetics is discussed.

Multiple solution conformations of the integrin-binding cyclic pentapeptide cyclo(-Ser-D-Leu-Asp-Val-Pro-). Analysis of the (phi, psi) space available to cyclic pentapeptides

The aqueous solution structure of the cyclic pentapeptide cyclo(-Ser-D-Leu-Asp-Val-Pro-) has been determined by two-dimensional 1H-NMR spectroscopy, combined with a conformational search and distance-geometry calculations. As many as five conformers in slow exchange were observed, and the rate of interconversion between components was measured from the build-up rates of exchange peaks. NMR data allowed the structures of the two predominant conformers to be determined. The major component (66%) contained a cis-proline as part of a type-VIa2 beta-turn encompassing residues Asp-Val-cis-Pro-Ser. The second component (16%) contained only trans-amide bonds, and a type-VIII beta-turn formed by residues Val-Pro-Ser-D-Leu. These structures are discussed in relation to the (phi, psi), space available to the cyclic pentapeptide, determined by a conformational search, and in relation to previously published cyclic-pentapeptide structures. The molecule exhibits activity in a scintillation-proximity assay for the inhibition of the interaction between the integrin very-late antigen-4 (VLA-4; alpha 4 beta 1) and vascular-cell-adhesion molecule-1 (VCAM-1). The structure/activity relationship of the LDV sequence is discussed and related to the recently published X-ray structure of VCAM-1. The relevance of the work to the design of anti-inflammatory drugs is discussed.

Synthesis and NMR conformational analysis of a beta-turn mimic incorporated into gramicidin S. A general approach to evaluate beta-turn peptidomimetics

The solution structure of a gramicidin S (GS) analog containing a beta-turn mimic [BTD4-5, Lys2.2']GS has been compared to that of native GS. The linear [BTD4-5, Lys2.2']GS was synthesized by solid phase methodology and the cyclized peptide was analyzed by NMR. In the peptide portion of [BTD4-5, Lys2.2']GS, the intramolecular hydrogen bonding pattern, inter-residue NOEs, including a transannular H alpha-H alpha NOE, and JN alpha coupling constants all describe a solution structure which is equivalent to that of native GS. These data confirm that the BTD group is a competent Type II' beta-turn mimic since it does not disrupt the native conformation of GS. It also supports the use of GS as a conformational model in which to test beta-turn mimics.

A 500 MHz 1H NMR spectroscopic study of Met5-enkephalinamide in aqueous solution: ethanol induced conformational changes

An analysis of spin coupling constants, less than 3J greater than C alpha H-NH, from a high resolution 500 MHz 1H NMR study of [Met5]-enkephalinamide in aqueous solution, suggested that beta-sheet structure is the likely conformer. The effect of ethanol on the conformation of [Met5]-enkephalinamide in aqueous solution was investigated. From the upfield drift of observed chemical shifts and changes in coupling constants, especially of the amide NH resonances, it is concluded that ethanol disrupts the conformation possibly by influencing the hydrogen bonding. The above observation is consistent with a recent study of the ethanol induced conformational changes occurring in [Met5]enkephalinamide [Rapaka, R.S. et al. (1986) Life Sciences 39, 837-842].

Conformational analysis of pGlu-His-Amph and pGlu-His-Pro-Amph related to their central nervous system activity

The compounds pGlu-His-Pro-Amph and pGlu-His-Amph obtained from the condensation of TRH or a fragment of TRH with amphetamine show activities which are different regarding the parent compounds. Although the two derivatives exhibit about the same low toxicity they differ in several pharmacological properties. Physicochemical analysis by 1H-NMR and CD spectroscopy was carried out in order to detect in the two compounds conformational differences that might explain their different activities. The results show that in the proline containing peptide the amphetamine has a hindered rotation in comparison with the compounds devoid of proline. This, together with the occurrence of a cis conformer having different properties than the trans conformer could be the origin of the biological difference observed between the two hybrid compounds.

Reverse turns in peptides and proteins

The evidence that reverse turns frequently occur as structural components of proteins, as well as of linear and cyclic peptides, is overwhelming. This review summarizes and examines critically the experimental evidence derived from physical methods such as 1H and 13C nuclear magnetic resonance spectroscopy, spin-lattice relaxation time, circular dichroism, IR spectroscopy, and X-ray crystallography. Secondly, theoretical evidence obtained from energy calculations, which rely on empirical energy functions, and correlative methods, which rely on algorithms based on the frequency of occurrence of amino acids, is evaluated. In particular, those theoretical studies for which complementary physical studies have been completed are emphasized. Finally, examples of structure-function relationships involving reverse turns and their biological recognition are demonstrated.

Proton magnetic resonance and conformational energy calculations of repeat peptides of tropoelastin. A permutation of the hexapeptide

The conformation of a hexapeptide sequence occurring in tropoelastin is discussed from the results obtained using a combined approach of theoretical conformational energy calculations on HCO-Val-Ala-Prb-Gly-OMe and 1h nmr studies on t-Boc-Val-Ala-Pro-Gly-Val-Gly-OMe in a dilute solution of methanol. Both studies have reasonable concurrence with respect to the preferred conformation of the hexapeptide and an analysis of the combined results suggests that the hexapeptide is stabilized by a beta-turn involving the Ala1,iC=O and Val4,iNH groups and a gamma-turn involving Gly5,iC=O and Gly3,iNH groups. A weaker interaction between Gly3,iC=O and Gly5,iNH groups is also found to be possible. Conformational features of the first valyl residue in the sequence Val-Ala-Pro-Gly-Val-Gly and the last valyl residue in Ala-Pro-Gly-Val-Gly-Val are compared and found to have similar torsion angles. The implications of such a similarity are discussed with respect to the conformation of the polyhexapeptide.

Conformational studies on [Pro3, Gly4]-oxytocin in dimethyl sulfoxide by 1H nuclear magnetic resonance spectroscopy: evidence for a type II beta turn in the cyclic moiety

A model for oxytocin has been previously proposed in which residues 3 and 4 occupy the corner positions in a beta turn (Urry, D. W., & Walter, R (1971) Proc. Natl. Acad. Sci. U.S.A. 68, 956). The analogue [Pro(3),Gly(4)]-oxytocin (PGO) was used in proton magnetic resonance (1H NMR) studies designed to probe the contribution of these corner positions in forming a beta turn. Comparison of various 1H NMR parameters obtained at 220 MHz for backbone amide protons of PGO with those for the corresponding protons of oxytocin suggests that, to a first approximation, these two peptides may have similar backbone conformations in )CD3)2SO. Theoretically, the L-Pro lead toGly sequence in positions 3 and 4 of PGO would allow the formation of either a type I or type II beta turn. The two coupling constants between vicinal amide and C alpha protons for Gly(4) of PGO in (CD3)2SO are compatible with a type II beta turn in which 04, the dihedral angle about the bond between the backbone C alpha and N' atoms of Gly4, is appromximately +92 degrees, but not with a type I beta turn. A survey of peptides studied in other laboratories by X-ray and/or 1H NMR with reported type II beta turns with L-Pro lead toGly or Gly lead to Gly sequences in the corner positions revealed a close correlation between chemical shifts and vicinal coupling constants for the glycl residue in the second corner position. It is suggested that this criterion can form an additional basis for the characterization of beta turns. More studies are needed to determine the particular type of beta turn manifest in the cyclic moiety of oxytocin per se, although a reasonable working hypothesis is that oxytocin, similar to PGO, has a type II beta turn.