Vibrational CD studies of the solution conformation of simple alanyl peptides as a function of pH

The CH-stretching vibrational CD (VCD) spectra of glycyl-L-alanine, L-alanylglycine, and L-alanyl-L-alanine have been studied at neutral, high, and low pH in D2O solution. The intense positive VCD band attributed to the C alpha H stretch of the alanyl residue in glycyl-L-alanine at neutral pH is absent in L-alanylglycine. In contrast to the VCD spectra of L-alanine, the positive methine-stretching VCD band in glycyl-L-alanine and L-alanyl-L-alanine is still present at pH 2. Based on the ring current mechanism, the VCD spectra are consistent with the presence of a five-membered CO...HN intramolecular hydrogen-bonded ring between the C-terminal carboxylate and peptide NH groups at neutral and high pH; and a seven-membered COH...O = C hydrogen-bonded ring between the C-terminal carboxyl OH and peptide C = O groups at low pH. In the N-terminal alanyl residue, the peptide C = O group is hydrogen bonded to the NH trans to the methine bond. The CH-stretching VCD spectra of L-alanyl-L-alanyl-L-alanine at neutral pH are consistent with two intramolecularly hydrogen-bonded conformations for the central alanyl residue.     

Synthesis and solution conformation studies of 3-substituted uridine and pseudouridine derivatives

A series of 3-substituted uridine and pseudouridine derivatives, based on the naturally occurring 3-(3-amino-3-carboxypropyl) modification, were synthesized. Their aqueous solution conformations were determined by using circular dichroism and NMR spectroscopy. Functional group composition and chain length were shown to have only a subtle influence on the distribution of syn/anti conformations of the modified nucleosides. The dominating factor appears to be the glycosidic linkage (C- vs. N-glycoside) in determining the nucleoside conformation.     

The conformation of single-strand polynucleotides in solution: sedimentation studies of apurinic acid

To elucidate the role of the bases in single-strand polynucleolide conformation, we have studied apurinic acid, a single-strand polydeoxyribonucleotide from which almost half the bases have been removed. The conformation of apurinic acid in aqueous solution near θ condition has been investigated by sedimentation velocity and sedimentation equilibrium measurements. The unperturbed coil dimensions of apurinic acid are essentially identical to those of poly rU of the same degree of polymerization. The dimensions are also similar to those of poly rA at high temperature, where the adenine residues are not stacked upon one another. We conclude that the considerable rigidity of these polynuclotides is conferred not by residual, undetected base stacking, but by restrictions in rotation about the bonds of the backbone. Furthermore, the rigidity of the ribose-phosphate backbone cannot be attributed to interactions involving the 2'—OH group.     

Vibrational CD studies of interchain hydrogen-bonded tripodal peptides.

The solution conformations of three trispeptides--L,L,L-1,3,5-C6H3[CH2NHCOCH(X)-NHBoc++ +]3, X = CH3 (Ala) or CH2CH(CH3)2 (Leu), and L,L,L-N(CH2CH2NHCOCH[CH2-CH(CH3)2]NHBoc)3--have been determined from their ir and vibrational CD (VCD) spectra in the NH stretching and carbonyl stretching regions in apolar solution. The compounds containing L-Leu are shown to occur primarily in a propeller conformation with C3 symmetry that is stabilized by interchain hydrogen bonds. Through application of the coupled oscillator model of VCD, a right-handed sense for the hydrogen-bonded chains in the propeller is deduced, in agreement with previous empirical force field calculations. The spectra also provide evidence for interchain association between two chains, resulting in a C10-ring. For chains not involved in interchain association, the spectra reveal the presence of C7-rings within a chain. The trispeptide containing L-Ala is found to occur primarily in a random form.     

Fluorescence and CD studies on the conformation of the gastrin releasing peptide in solution and in the presence of model membranes

The conformation of the heptacosapeptide hormone, gastrin releasing peptide, has been studied in buffer and in the presence of lipids, using static and dynamic fluorescence and CD. The results obtained show that, in buffer, the hormone exists in a collection of flexible, random coil type conformers, characterized by a beta-turn between residues 14-19. On the other hand, organic solvents can induce some degree of ordered secondary structure in the peptide chain. The marked changes, observed in CD and fluorescence spectra upon addition of lysolecitin micelles and dimyristoylphosphatidylserine vesicles, clearly show that the peptide interacts with lipids, assuming a lipid specific configuration. Interestingly, no significative spectroscopic changes are produced by exposure to dimyristoylphosphatidylcholine vesicles both in the gel and liquid-chrystalline phases, suggesting a requirement for negatively charged lipids during the process of hormone-membrane interaction.     

Nuclear magnetic resonance studies of histone IV solution conformation.

The 220-MHz high-resolution proton magnetic resonance (PMR) spectrum of histone IV has been examined as a function of histone concentration, salt concentration, and pD. The hydrophobic C-terminal portion of the histone IV monomer appears to be largely PMR "invisible" indicating that this region of the polypeptide contains rigid secondary structure. Further loss of PMR resonance areas with increased histone IV concentration in neat D2O has been attributed to self-aggregation involving a monomer-dimer equilibrium. An equilibrium between the monomer and large aggregates, on the other hand, appears to dominate at NaCl concentrations above 0.01 M. pD studies reveal an abrupt increase in histone IV aggregation at pD smaller than 0.8 and precipitation of histone IV at pD values in the neighborhood of its isoelectric point, pD similar to 11.     

NMR studies of the solution conformation of the sex peptide from Drosophila melanogaster

The insect sex peptide (SP) elicits a variety of biological responses upon transfer to the mated female. SP contains 36 amino acids, including a tryptophan-rich N-terminal region, a central region containing five hydroxyproline (Hyp) residues, and a C-terminal region enclosed by a disulfide bridge. The solution structure of SP, studied here using NMR spectroscopy, includes a motif WPWN that adopts a type I β-turn in the N-terminal Trp-rich region. This turn region is connected to the central Hyp-rich region, which adopts extended and/or PPII-like conformations. The C-terminal disulfide-bonded loop populates helical turns or nascent helical structure. Overall, the results reveal a rather flexible peptide that lacks a compact folded structure in solution.     

Induced CD provides evidence for helical solution conformation in cellulosic chains

Evidence for a helical contribution to the conformation of methylcellulose in dilute solution is given by CD measurements. Congo red binds to methylcellulose in dilute aqueous solution and becomes optically active. The shape of the induced CD spectra is as predicted by exciton coupling for a helical arrangement of chromophores. The magnitude of the induced CD changes reversibly with temperature, decreasing upon heating. The dimer analogue of the polymer, prepared by acid methanolysis, does not show this effect. These observations suggest that the induced optical activity reflects the conformational dissymmetry of the polymer. Analogous experiments with the cellulose oligomers (cellotriose through cellohexaose) show that five anhydroglucose units are necessary before asymmetry is induced upon dye binding.     

Vibrational Raman optical activity of alanyl peptide oligomers: A new perspective on aqueous solution conformation

The vibrational Raman optical activity (ROA) spectra of di- and tri-L -alanine in the range 650–1750 cm^?1 have been measured in H₂O and D₂O solution at high, neutral, and low pH and pD. Corresponding ROA spectra for tetra- and penta-L -alanine have also been obtained, but over a more restricted set of pH and pD conditions. There are similarities with the ROA spectrum of L -alanine below ～ 1200 cm^?1, but the spectra are very different above this wavenumber due to the influence of the vibrational coordinates of the peptide group. The similar overall appearance of the di-, tri-, and tetrapeptide ROA under selected conditions of pH and pD, and of all four peptide ROA spectra in DCl and HCl solutions, in the backbone skeletal stretch region ～ 1050–1200 cm^?1 and the extended amide III region ～ 1250–1350 cm^?1, suggests that the backbone conformation is approximately the same in all four structures. One difference, however, is a shift of a large positive ROA band in H₂O at ～ 1341 cm^?1 in the dipeptide, assigned to C_α–H and in-plane N–H deformations, down to ～ 1331 cm ^?1 in the tripeptide and to ～ 1315 cm^?1 in the tetrapeptide and pentapeptide (the last in HCl due to insufficient solubility in H₂O), which indicates increasing delocalization of the corresponding normal mode with increasing chain length. Our results do not support the suggestion that stabilizing interactions of the zwitterionic end groups in tri-L -alanine at neutral pH leads to a different solution structure to that at high pH. © 1994 John Wiley & Sons, Inc.     

CD studies on the conformation of some deoxyoligonucleotides containing adenine and thymine residues

CD studies of the deoxyoligomer series d(pT)_n and d(pA)_n show increasing CD maxima for oligo (dT)'s with chain length variation from two to seven, while oligo (dA)'s exhibit a decreasing CD maximum. Concentrated solutions of NaClO₄ cause a decrease in the CD of longer oligo (dT)'s towards the CD of d(pT)₂ which is different from oligo dA's. Probably base-sugar interactions are important in the observed conformational effects. The chemically synthesized oligomers dpApApTpT and dpTpApTpA show deviations in their CD spectra which reflect a dominating conformational effect of d(pA)₂ in the former but not in the alternating isomer.     

The effect of homologos amini acid replacement on the conformation of oligopeptides. III. CD studies on co-oligopeptides of methionine and valine or methionine and glycine in organic solution

A conformational analyis of co-ologopeptides containing methionine and valine or methionine and glycine was carried out using circular dichrosim. The oligopeptides containing valine and methionine (dimer to hexamer) are disorder in hexafluoropropane diol·0.5 H₂O and trimethyl phospate but become helical in trifluoroethanol at the heptamer. The CD spectra for hesamers and heptamers containing methionine or methionine and one valine give evidience that one valyl residue can be inserted into these peptides wothout affecting their secondry structure. Co-oligomethionines. The effect of a glycyl residue are generally less ordered than the analogous homo-oligomethionines. The effect of a glycl residue on the structure of the longer oligopeptides depends on its position in the chain. When inserted in the center of a hexamer or heptamer, the single glycyl residue destabilizes the ordered secondry structures in solution. Finally, evidence is presented that the CD patterns observed for various pentamers and hexamers are consistent with some order at these chain lenghts.     

Vibrational CD of polypeptides. X. A study of alpha-helical oligopeptides in solution

We have measured the vibrational CD (VCD) of a series of heterooligopeptides—o-nitrophenylsulfenyl(L -Met-L -Met-L -Leu) _n-OEt, n = 6,8,10,11–in the amide A, I, and II regions. These spectra are identical in shape and magnitude, within our signal to noise limits. The VCD in each band are of exactly the shape expected for a right-handed α-helix and imply that VCD of the polypeptide α-helix is relatively unaffected by chain length down to the 18-subunit level.     

The mean conformation of N-acetylamino acid N'-methylamides in dimethyl sulfoxide solution

The mean conformation of a series of N-acetylamino acid N'-methylamides in dimethyl sulfoxide (DMSO) was determined by 1H-NMR and 13C-NMR methods.The series investigated consisted of derivatives of DL-Ala, DL-Asn, Gln, His, DL-Ile, DL-Leu, Met, DL-Pro, DL-Phe, Ser, Thr, Trp, Tyr, DL-Val, DL-Nva, and dl-Nle. It was found that the conformational equilibria in DMSO are dominated by C5 and C7eq forms.The amounts of these forms in the equibbria were found to be roughly proportional to the Boltzmann probabilities for the occurrence of a definite form, as calculated theoretically by Vasquez et al.(Macromolecules 16 (1983) 1043).Exceptions to this rule were DL-Pro and, to a lesser extent, Ser, Asn and Trp derivatives.     

Monitoring proton dissociation and solution conformation of chiral ytterbium complexes with near-IR CD

The ytterbium complex [Yb((S)-THP)](3+) ((S)-THP = (1S,4S,7S,10S-tetrakis(2-hydroxypropyl)-1,4,7,10-tetraazacyclododecane) is investigated in solution through NMR, near-IR absorption, and CD spectroscopy. Quantitative analysis of the paramagnetic pseudocontact NMR shift shows Lambda helicity of the ligand cage around the metal. The NIR CD spectrum recorded at acidic pH is found to be very similar to that of [Yb((R)-DOTMA)](-) ((R)-DOTMA = (1R,4R,7R,10R)-alpha,alpha',alpha',alpha'-tetramethyl-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid), which in solution assumes a twisted square antiprism (TSA) conformation. The similarity of the NIR CD spectra is discussed, and it is the first proof of the Lambda(lambda,lambda,lambda,lambda) conformation of [Yb((S)-THP)](3+). NIR CD spectra recorded in the pH range of 2-9 allow one to easily follow proton dissociation and to calculate the pK of this equilibrium in water (pK(A) = 6.4 +/- 0.1). This value agrees well with that determined for [Lu((S)-THP)](3+) using potentiometric methods. This demonstrates once again that NIR CD spectroscopy is a powerful technique for investigating the solution structure and dynamics of these complexes.     

Cross-linking studies on the conformation and dimerization of myelin basic protein in solution.

Myelin basic protein was isolated from both cat and bovine central nervous system. Cat and bovine myelin basic protein, which are shown to be similar by tryptic mapping, exhibit identical behavior when cross-linked with the bifunctional reagent difluorodinitrobenzene. Myelin basic protein is cross-linked into only a dimer under certain conditions in the presence of sodium dodecyl sulfate. In contrast, many oligomers are formed when myelin basic protein is cross-linked in the absence of detergent. The formation of cross-linked dimers in the absence of other oligomer formation suggests that the protein is at least partly dimeric in the presence of sodium dodecyl sulfate. The conformation of them myelin basic protein monomer in sodium dodecyl sulfate was also studied. N-Bromosuccinimide and cyanogen bromide cleavage reactions were used to demonstrate that difluorodinitrobenzene had introduced intramolecular cross-links between the two peptides resulting from each of the cleavage ractions. However, these types of intramolecular cross-links cannot be detected under conditions in which only dimers have formed. Some of the lysine residues which are modified by difluorodinitrobenzene were identified by tryptic mapping. In several respects, the conformation of myelin basic protein in a sodium dodecyl sulfate solution appears to be similar to the conformation of the protein in the membrane.     

Adenine nucleosides in solution: circular dichroism studies and base conformation.

Adenosine, AMP, S-adenosylhomocysteine, S-adenosylmethionine, aristeromycin and 25 other synthetic adenosine analogs modified in the 4' or 5' positions show certain groups of different circular dichroism (CD) spectra. Both positive and negative Cotton effects can occur in the long-wavelength part (250-270 nm) of the spectra. Molar ellipticities [theta] range from -6000 (in adenosine 5'-carboxylate) to +4000 deg. cm2 dmol-1 (in 5'-deoxy-5'iodoadenosine), including some compounds with small, polar 5'-substituents in which low-intensity bands are found in signed pairs. Most of these adenosine derivatives that have the same adenine chromophore and a ribofuranose moiety unsubstituted in the 2' and 3' positions prefer an anti-conformation of the adenine base, as evidenced by proton magnetic resonance spectroscopy. In the majority of cases, electronic perturbations of the chromophore or major alterations of the assymmetric sugar residue can be excluded as sources of the CD variations. Therefore a correlation of the long-wavelength CD bands with the glycosyl torsion angle phiCN is suggested, where the gauche, gauche/anti combination which is typical of AMP in the crystal and in solution (phiCN approximately -40degrees, [theta] negative) is one reference point and a region for phiCN = 0degrees ([theta] positive) is assigned to compounds with space-filling substituents such as S-adenosylmethionine. Both negative and positive Cotton effects can be associated with the anti conformation range. Within this series, the base conformation of novel nucleoside structures could be predicted from CD measurements. The CD spectrum gives no indication, however, of whether a certain torsion angle is the result of a rigid structure (as in AMP) or the average value of a molecule with high rotational freedom (as in 5'-deoxyadenosine). The conformations of aristeromycin and 4'-thioadenosine are discussed in relation to adenosine, and a structure-determining effect of the 4' bridge atom is noted.