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1.
Cyclic hexapeptides of the type cyclo(L -Xxx-L -Pro-D -Yyy)2 or cyclo(L -Xxx-L -Pro-Gly)2 exist in solution predominantly in two forms of C2 average symmetry, one with all-trans peptide bonds and generally well-established conformation, and another with both Xxx-Pro peptide bonds cis. We have been measuring the thermodynamic parameters of this equilibrium using carbon and proton nmr spectroscopy. Data have been obtained for peptides in which Yyy = Gly, D -Ala, or D -Phe, and Xxx = Gly, L -Ala, L -Leu, and L -Val. In a given solvent, stability of the all-trans form decreases (ΔG0 increases) as Xxx is changed through the series Gly, L -Ala-, L -Leu, and L -Val, consistent with expected increasing repulsion between the Xxx side chain and the proline δ methylene across the trnas Xxx-Pro bond. Also, for a given set of side chains, the stability of the all-trnas form increases as the polarity of the solvent decreases, consistent with models in which all C?O and N? H groups are accessible for solvation in the two-cis form, but two C?O and two N? H groups are somewhat sequestered in the all-trans form. With the available data it is not possible to identify pure intramolecular (solvent-independent) or pure peptide-bond solvation (side chain-independent) terms in ΔH° or ΔS°, although trends are discernible.  相似文献   

2.
Combinations of L - and D -proline residues are useful compounds for finding new structures and properties of cyclic peptides. This is demonstrated with one striking example, the cyclic tetrapeptide c(D -Pro-L -Pro-D -Pro-L -Pro). For this molecule composed of strictly alternating D - and L -configurated residues, a highly symmetrical structure is expected, which should be an optically inactive meso-form. Cyclization of the enantiomeric pure linear precursor D -Pro-L -Pro-D -Pro-L -Pro, however, yields a racemic mixture of two enantiomeric cyclotetrapeptides, both with twofold symmetry and a cistranscistrans sequence of the peptide bonds. Remarkably, this formation of a racemate was not caused by racemization, but by cis/trans isomerization of all peptide bonds in the ring. This process may occur in the linear precursor during the ring formation (cyclization of conformers with transcistrans or cistranscis arrangement of the amide bonds) as well as in the enantiomeric pure cyclic tetrapeptide at higher temperature. In the latter case, an all-cis structure should exist as the intermediate, which can form a cistranscistrans sequence in two equivalent ways, leading finally to two enantiomeric cyclotetrapeptides. In the first one, the cis peptide bonds are attributed to the L -residues and the trans peptide bonds to the D -residues; in the second one, the cis bonds belong to the D and the trans bonds to the L -residues. The mixture of these two enantiomers does not crystallize in the racemic form, but in enantiomeric pure separate crystals. The structural properties could be proved by 1H- and 13C-nmr spectroscopy and x-ray analysis. The cis/trans isomerization process was confirmed by optical rotation measurements and CD spectroscopy, as well as DREIDING model studies. Calorimetric measurements in the solid state suggest the existence of the expected all-cis intermediate. The backbone conformation of the 12-membered medium-sized ring shows only slight deviations—up to 6° —from the planarity of the peptide bonds. On the other hand, the four pyrrolidine rings show different types of puckering of the Cγ or the Cβ atoms.  相似文献   

3.
Ian Mc Ewen 《Biopolymers》1993,33(4):693-702
The cyclic hexapeptide cyclo[-Pro1-Gly2-Glu3(OBzl)-Pro4-Phe5-Leu6-] ( 1 ; OBzl: benzyl ester) was modeled and synthesized to be used as a chiral site for the separation of enantiomers. Total correlation spectroscopy and nuclear Ovehauser effect spectroscopy spectra of the peptide in CDCl3 showed the presence of three stereoisomers. The two dominant stereoisomers 1a and 1b exchanged chemically with each other, while the minor stereoisomer 1c exchanged exclusively with the stereoisomer 1b . Stereoisomer 1a had two cis proline peptide bonds while stereoisomer 1b had all-trans peptide bonds. The stereoisomer 1c had, for nonstrained peptides, an unusual cis phenylalanine peptide bond while both proline peptide bonds were trans. © 1993 John Wiley & Sons, Inc.  相似文献   

4.
Molecular dynamics of the cyclic dipeptides cyclo(Gly-L -Pro), cyclo-(L-Pro-L -Pro), and cyclo(L-Pro-D-Pro) and the linear dipeptides L-Pro-Gly and cis and trans Gly-L -Pro were studied in neutral aqueous solution by 13C nuclear magnetic resonance. Spinlattice relaxation times (T1) were determined for each individual carbon atom. The correlation times, τ, were derived from a semiquantitative analysis of the T1 data. The correlation times of the proline ring carbons, β, γ, and δ suggest that the cyclic dipeptides have more restriction of conformational freedom in the proline ring than the linear dipeptides. This effect is most pronounced on the γ carbon.  相似文献   

5.
Cyclo(L -Pro-Sar)n (n = 2–4) with moderate flexibility and hydrophobicity of molecular structure was synthesized, and the characteristics of these cyclic peptides and their metal complexes in acetonitrile were investigated in connection with the residual properties using 13C-nmr measurements. The cyclic tetrapeptide cyclo(L -Pro-Sar)2 showed a sterically hindered phenomenon in acetonitrile in which the amide backbone adopted a cis-trans-cis-trans sequence. The cyclic hexapeptide cyclo(L -Pro-Sar)3 existed as a mixture of several conformers whose interconversion is slow on the nmr time scale, including cis-cis-trans and/or cis-trans-trans arrangement of the Sar-Pro bond. Finally, it was demonstrated that the cyclic octapeptide cyclo(L -Pro-Sar)4 behaved as a mixture of multiple conformers which allowed for cis-trans isomerism about the Pro-Sar peptide bond, of which 20–30% had the all-cis Sar-Pro bond isomer and the remaining 70–80% had one (or more) cis Sar-Pro bond isomer. 13C-nmr spectra also demonstrated that cyclo(L -Pro-Sar)n (n = 3,4) formed a 1:1 ion complex whose conformation was characterized by an all-trans peptide bond in the presence of excess metal salt. Cation binding studies, using CD measurements, established that the ion selectivity of cyclo(L -Pro-Sar)4 in acetonitrile decreased in the order, Ba2+ > Ca2+ > Na+ > Mg2+ > Li+.  相似文献   

6.
The results of classifying into various types the 68 examples of isolated α-turns in the X-ray diffraction crystal structures of peptides documented in the literature are presented and discussed in this review article. α-Turns characterized by the trans disposition of all ω torsion angles are common for the backbone linear peptides investigated. In contrast, the cis arrangement of the N-terminal (ωi + 1) torsion angle, among those generated by the three residues internal to the α-turn, is a peculiar feature of 65% of the cyclic peptides. Among linear and cyclic peptides featuring the all-trans disposition of the ω torsion angles, only one third of the α-turns display φ,ψ values not too far from those characterizing regular α-helices. In general, our findings, taken together, suggest that a significant conformational diversity is compatible with the formation of an intramolecularly H-bonded C13-member pseudocycle (α-turn) in linear and cyclic peptides.  相似文献   

7.
Cyclic octapeptides, cyclo(X-Pro)4, where X represents Phe, Leu, or Lys(Z), were synthesized and their conformations investigated. A C2-symmetric conformer containing two cis peptide bonds was found in all of these cyclic octapeptides. The numbers of available conformations due to the cistrans isomerization of Pro peptide bonds depended on the nature of the solvent and X residue: they decreased in the following order: cyclo[Lys(Z)-Pro]4 > cyclo(Leu-Pro)4 > cyclo(Phe-Pro)4 in CDCl3. 13C spin-lattice relaxation times (T1) of these cyclic octapeptides were measured, and the contribution of segmental mobility to T1 was found to vary with the nature of the X residue.  相似文献   

8.
Data are presented on the position of the equilibria of cyclo(Xxx-Pro-Yyy)2 backbones between forms with two cis Xxx-Pro peptide bonds and forms with only trans peptide bonds. These data are interpreted in terms of two factors: a solvent-independent steric interaction between the Xxx and Pro side chains, and the ability of solvent to influence the transannular electrostatic interaction between N? H and C?O groups of the Xxx units in the all-trans form.  相似文献   

9.
D J Patel  A E Tonelli 《Biopolymers》1976,15(8):1623-1635
Conformations containing all trans peptide bonds have previously been proposed for N-methylleucine gramicidin-S and (di-N-methylleucine) gramicidin-S based on an evaluation of proton nuclear magnetic resonance parameters in a series of solvents. These gramicidin-S derivatives exhibit full biological activity despite the fact that the proposed solution conformations differ in backbone topology and relative orientation of the Phe and Orn side chains compared to gramicidin-S. The present authors discuss conformations for N-methylleucine gramicidin-S and (di-N-methylleucine) gramicidin-S which incorporate cis peptide bonds at L -Orn-L -N-MeLeu, where the gramicidin-S backbone is essentially retained, and the relative orientation of the Pro, Orn, Val, and Phe side chains correspond to those observed for gramicidin-S. A novel hydrogen-bond arrangement involving one carbonyl group interacting with two peptide protons (1 ←4 and 1 ←5 types) is proposed to stabilize the backbone conformation in the gramicidin-S derivatives. A recent report on the cyclic heptapeptide antibiotic, Ilamycin B1, shows the presence of cis peptide bonds at N-CH3 amino acids, as well as the novel hydrogen-bond arrangement presented above.  相似文献   

10.
1H-Nmr was used to measure the rate of cistrans interconversion of X-Pro bonds in linear and cyclic oligopeptides. k(cis → trans) = 2.5 × 10?3 s?1 at 25°C was found for the zwitterionic form of H-Ala-Pro-OH, in good agreement with earlier measurements. Replacement of Ala by Phe, Tyr, or Trp resulted in a 10-fold slower interconversion rate, whereas after substitution of Ala by His or Glu, the rate decreased only slightly. Independent of the residues X, the interconversion rate was increased by a factor of ca. 20 when the peptide chain was elongated by addition of Ala to the C-terminal Pro. An additional increase by a factor of 6 was observed when going from the protected linear peptide CF3CO-Gly-Gly-Pro-Ala-OCH3 to the closely related cyclic compound c[-Gly-Gly-Pro-Gly-Ala-]. These data are evaluated with regard to their possible use in future studies on the role of X-Pro cistrans isomerization in the kinetics of protein folding.  相似文献   

11.
Analysis of two isomeric cyclic hexapeptides of composition (Asp, Arg, Gly2, Pro, D -Pro) by a nuclear Overhauser effect constrained distance geometry conformation search yielded a narrowly defined backbone conformation for one and considerable ambiguity about the conformation in part of the other. Preliminary 13C relaxation studies of these peptides suggest that it is possible that this difference may correspond to a physical difference in internal mobility. In connection with this observation, other experimental evidence bearing on the backbone conformational mobility of cyclic oligopeptides with 4–10 residues, frequently considered to have well-defined backbones, is reviewed. Conformational heterogeneity involving rotation of a peptide bond plane relative to the overall ring plane is identified as a common phenomenon. Nuclear magnetic resonance line-shape studies at temperatures down to 200 K can detect backbone motions with activation free energy barriers down to about 10 kcal/mole, but conformational exchange with lower barriers, though detectable in other ways, will not be obvious from nmr spectra alone. © 1993 John Wiley & Sons, Inc.  相似文献   

12.
Janosi L  Gorfe A 《Biophysical journal》2010,99(9):2957-2966
The precise role of the sphingosine base trans double bond for the unique properties of sphingomyelins (SMs), one of the main lipid components in raftlike structures of biological membranes, has not been fully explored. Several reports comparing the hydration, lipid packing, and hydrogen-bonding behaviors of SM and glycerophospholipid bilayers found remarkable differences overall. However, the atomic interactions linking the double-bond geometry with these thermodynamic and structural changes remained elusive. A recent report on ceramides, which differ from SMs only by their hydroxyl headgroup, has shown that replacing the trans double bond of the sphingosine base by cis weakens the hydrogen-bonding potential of these lipids and thereby alters their biological activity. Based on data from extensive (a total 0.75 μs) atomistic molecular dynamics simulations of bilayers composed of all-trans, all-cis, and a trans/cis (4:1 ratio) racemic mixture of sphingomyelin lipids, here we show that the trans configuration allows for the formation of significantly more hydrogen bonds than the cis. The extra hydrogen bonds enabled tighter packing of lipids in the all-trans and trans/cis bilayers, thus reducing the average area per lipid while increasing the chain order and the bilayer thickness. Moreover, fewer water molecules access the lipid-water interface of the all-trans bilayer than of the all-cis bilayer. These results provide the atomic basis for the importance of the natural sphingomyelin trans double-bond conformation for the formation of ordered membrane domains.  相似文献   

13.
Conformations of the cyclic tetrapeptide cyclo(L -Pro-Sar)2 in solution were studied by 1H- and 13C-nmr spectrometry and model building. The nmr data provide definite evidence that this cyclic peptide exists chiefly in two conformations, namely, a C2-symmetric conformation and an asymmetric structure. The former was demonstrated to be predominant in polar solvents (100% in Me2SO-d6). This structure contains all cis-peptide bond linkages and all trans′ Pro Cα?CO bonds. It represents the first cyclic tetrapeptide in which all four peptide bonds have been found in the cis-conformation. As the polarity of the solvent decreases, the population of C2-symmetric conformers decreases (88% in CD3CN and 65% in CDCl3). At the same time, a minor asymmetric conformer, characterized by cis-cis-cis-trans peptide bond sequences (two cis Sar-Pro bonds, one cis Pro-Sar bond, and one trans Pro-Sar bond), is seen to increase (9% in CD3CN and 30% in CDCl3). A proposed predominant conformation in solution for cyclo(L -Pro-Sar)2 was compared with a crystal structure, as reported in an accompanying paper. Both structures show striking overall similarities.  相似文献   

14.
Vincent Madison 《Biopolymers》1977,16(12):2671-2692
A survey of over 50 crystal structures indicates that both imino acid and peptide derivatives of proline populate ring conformers consistent with the torsional potentials about single bonds. In both cases, lower barriers for rotation about C? N bonds relative to those about C? C bonds favor smaller values for dihedral angles about the former bonds. In peptides a minimum in the torsional potential about C? N bonds occurs at zero dihedral angle, further favoring small angles. The pyrrolidine-ring dihedral angles of the proline compounds in the solid state obey a cyclopentane-type pseudorotation function. Thus the puckering of the five-membered ring can be quantitatively described by two parameters. Consistent with small dihedral angles about C? N bonds, Cβ and/or Cγ are puckered out of the mean plane of the ring in nearly all of the nonstrained compounds. Utilizing the consistent force-field method of Lifson and coworkers [see A. Warshel, M. Levitt, and S. Lifson (1970) J. Mol. Spectrosc. 33 , 84] the intramolecular energy of five proline peptides was minimized with respect to all internal coordinates. In addition, the energy surface near minima was explored by constraining a particular dihedral angle and reminimizing the energy with respect to all remaining variables. In linear peptides two types of pyrrolidine-ring conformers have identical predicted energies. In the cyclic dipeptide cyclo (Pro-Gly) one of the ring conformers is favored by about 3 kcal/mol, while the cyclic tripeptide cyclo(Pro-Gly-Gly) favors the other conformer by a comparable margin. In agreement with observations in the solid state and in solution, Cβ and/or Cγ are puckered in the predicted conformers. A correlation between proline Φ and the details of the puckered conformation was predicted and found to match precisely conformers observed in crystals. For the diamides N-acetyl-L -proline-N′-methyl-amide and N-acetyl-L -proline-N′,N′-dimethylamide (AcProMe2A) 30% and 60% cis acetyl peptide bonds were predicted in good agreement with observations in nonpolar solvents for the respective compounds. The conformational distributions with respect to proline Ψ are also in accord with experimental observations. For AcProMe2A, a model for a -Pro-Pro-sequence in a peptide chain, this study is the first to predict stable conformers for proline Ψ either ca. ?50° or 140° for both cis and trans peptides.  相似文献   

15.
A new method of high-performance liquid chromatography (HPLC) analysis to quantify isomers of retinol, retinal and retinoic acid simultaneously was established. The HPLC system consisted of a silica gel absorption column and a linear gradient with two kinds of solvents containing n-Hexane, 2-propanol, and glacial acetic acid in different ratios. It separated six retinoic acid isomers (13-cis, 9-cis, all-trans, all-trans-4-oxo, 9-cis-4-oxo, 13-cis-4-oxo), three retinal isomers (13-cis-, 9-cis-, and all-trans) and two retinol isomers (13-cis- and all-trans). Human serum samples were subjected to this HPLC analysis and at least, all-trans retinol, 13-cis retinol, and all-trans retinoic acid were detectable. This HPLC system is useful for evaluating retinoic acid formation from retinol via a two-step oxidation pathway. Moreover, it could be applied to monitoring the concentrations of various retinoids, including all-trans retinoic acid in human sera.  相似文献   

16.
The molecular conformations of the linear oligopeptides H-(L -Ala)n-L -Pro-OH, with n = 1,2 and 3, have been investigated. 13C nmr observation of the equilibrium between the cis and trans forms of the Ala-Pro peptide bond indicated the occurrence of nonrandom conformations in solutions of these flexible peptides. The formation of the nonrandom species containing the cis form of the Ala-Pro bond was found to depend on the deprotonation of the carboxylic acid group of proline, the solvent, and the ionic strength in aqueous solution. The influence of intramolecular hydrogen bonding on the relative conformational energies of the species containing the cis and trans Ala-Pro peptide bond was studied by comparison of the peptides H-(Ala)n-Pro-OH with analogous molecules where hydrogen bond formation was excluded by the covalent structure. In earlier work a hydrogen bond between the protonated terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue had been suggested to stabilize conformations including trans proline. For the systems described here this hypothesis can be ruled out, since the cis:trans ratio is identical for molecules with methyl ester protected and free protonated terminal carboxylic acid groups of proline. Direct evidence for hydrogen bond formation between the deprotonated terminal carboxylic acid group and the amide proton of the penultimate amino acid residue in the molecular species containing cis proline was obtained from 1H nmr studies. However, the cis:trans ratio of the Ala-Pro bond was not affected by N-methylation of the penultimate amino acid residue, which prevents formation of this hydrogen bond. Overall the experimental observations lead to the conclusion that the relative energies of the peptide conformations including cis or trans proline are mainly determined by intramolecular electrostatic interactions, whereas in the molecules considered, intramolecular hydrogen bonding is a consequence of specific peptide backbone conformations rather than a cause for the occurrence of energetically favored species. Independent support for this conclusion was obtained from model consideration which indicated that electrostatic interactions between the terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue could indeed account for the observed relative conformational energies of the species containing cis and trans proline, respectively.  相似文献   

17.
In the present paper we describe the synthesis, purification, single crystal x-ray analysis, and nmr solution characterization, combined with restrained molecular dynamic simulations, of the cyclic hexapeptide cyclo-(L -Pro-L -Phe-β-Ala)2. The peptide was synthesized by classical solution methods and the cyclization of the free hexapeptide was accomplished in good yields in diluted methylene chloride solution using N,N-dicyclohexyl-carbodiimide. The compound crystallizes in the monoclinic space group P21 from methanol-dichloro-methane solution. The two identical halves of the molecule adopt in the solid state two different conformations. One β-Ala-L -Pro peptide bond is trans, while the second is cis. The molecule is present in dimethylsulfoxide d6 solutions as a mixture of conformational families. One of these corresponds to a C2 symmetrical molecule with both β-Ala-Pro cis peptide bonds, while the second major conformation is very similar to that observed in the solid state. All Pro-Phe segments, both in the solid state and the symmetrical and unsym-metrical solution conformations, display ?,ψ angles close to that of position i + 1 and i + 2 of type II β-turns. In addition, the segments preceeded by a trans β-Ala-Pro peptide bond are characterized by a typical ii + 3 hydrogen bond, which is absent in the conformer containing a cis β-Ala-Pro peptide bond. The latter conformation corresponds to a new structural domain we define as the “pseudo type II β-turn.” © 1994 John Wiley & Sons, Inc.  相似文献   

18.
All-trans-retinoic acid (all-trans-RA) and 13-cis-retinoic acid (13-cis-RA), due to their effects on cell differentiation, proliferation and angiogenesis, improved treatment results in some malignancies. Pharmacokinetic studies of all-trans-RA and 13-cis-RA along with monitoring of retinoic acid metabolites may help to optimize retinoic acid therapy and to develop new effective strategies for the use of retinoic acids in cancer treatment. Therefore, we developed a HPLC method for the simultaneous determination in human plasma of the physiologically important retinoic acid isomers, all-trans-, 13-cis- and 9-cis-retinoic acid, their 4-oxo metabolites, 13-cis-4-oxoretinoic acid (13-cis-4-oxo-RA) and all-trans-4-oxoretinoic acid (all-trans-4-oxo-RA), and vitamin A (all-trans-retinol). Analysis performed on a silica gel column with UV detection at 350 nm using a binary multistep gradient composed on n-hexane, 2-propanolol and glacial acetic acid. For liquid-liquid extraction a mixture of n-hexane, dichloromethane and 2-propanolol was used. The limits of detection were 0.5 ng/ml for retinoic acids and 10 ng/ml for all-trans-retinol. The method showed good reproducibility for all components (within-day C.V.: 3.02–11.70%; day-to-day C.V.: 0.01–11.34%. Furthermore, 9-cis-4-oxoretinoic acid (9-cis-4-oxo-RA) is separated from all-trans-4-oxo-RA and 13-cis-4-oxo-RA. In case of clinical use of 9-cis-retinoic acid (9-cis-RA) the pharmacokinetics and metabolism of this retinoic acid isomer can also be examined.  相似文献   

19.
A series of proline-containing linear oligopeptides (4 dipeptides and 15 tripeptides) were synthesized and examined in aqueous and nonaqueous solutions using 13C-nmr spectroscopy. Spectra of linear tripeptides showing cis-trans isomerism about the X-Pro bond (X = Pro, Gly, and Ala) also show neighboring effects on the chemical shifts of residues both preceding and following the prolyl moiety. The extent of cis-trans isomerism observed about the X-Pro peptide bond correlates not only with the nature of X, but also depends on the size of the residue following proline; the larger substituents favor an increase in cis content about the X-Pro bond.  相似文献   

20.
K Akasaka 《Biopolymers》1974,13(11):2273-2280
Proton and phosphorus-31 nuclear spin-lattice relaxation times (T1) have been measured with the Fourier-transform method at 100 and 40.5 MHz, respectively, on single-stranded polyriboadenylic acid (poly(A)) in a neutral D2O solution in the temperature range of 14–82°C. T1 minimum is observed around 35–45°C for H(8), H(1′), and phosphorus resonances. Rotational correlation times have been deduced from the T1 data, which indicate that the sugar–phosphate backbone as well as the base–sugar segment is undergoing rapid internal motion of 10?8–10?10 sec range. The molecular motion of the sugar–phosphate backbone as deduced from the phosphorus relaxation is well-characterized by a single activation enthalpy of 8.1 kal/mole for the whole temperature range of 14–82°C. Activation enthalpies of similar magnitude have been obtained for the motion of the adenine–ribose moiety from H(8) and H(1′) relaxation. The relative magnitude of T1 for H(8) and H(1′) infers that the poly(A) nucleotide exists on the average as anti in the single-stranded form. The phosphorus T1 value is consistent with a conformation such that both C(4′)–C(5′) and C(4′)–C(3′) bonds are nearly trans to their connected O–P bonds.  相似文献   

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