Conformational analysis of polyoxyethylene-bound homo-oligo-L-glutamates in aqueous environment

A detailed conformational analysis of homo-oligo-L -glutamates was carried out in aqueous solution using ¹H-nmr spectroscopy. Three series of side-chain protected (α-OMe) glutamate oligopeptides, attached to polyoxyethylene (POE) to enhance their solubility, were synthesized. The effect of the N-terminal blocking groups—Boc, Ac, and pGlu—on the conformations of these peptides in water is discussed. Unequivocal assignments were obtained for all amide NH resonances through use of selectively α-deuterated oligo-glutamates. Analysis of vicinal coupling constants, temperature dependence of NH chemical shifts, transfer of saturation experiments, and titration studies with a denaturing solvent (DMSO) were used to investigate the peptide structure. These data suggest that the Glu¹ and Glu² NH protons of each heptamer are solvent exposed, while the NH protons of interior glutamate residues chain are solvent sequestered. The nmr data are consistent with the onset of helical structure at the heptamer of each series in aqueous solution. The POE-peptides with pGlu at the N-terminus showed considerably reduced stability of structure than those with the Boc or acetyl blocking groups. Peptide conformations and their stability in water are compared to those in other solvents.     

Conformational analyses of polyoxyethylene-bound homo-oligo-L-glutamates in a helix-supporting environment trifluoroethanol

A detailed conformational analysis of C-terminal polyoxyethylene-bound homo-oligo-L -glutamates (dimer, penta-heptamer) with N-terminal blocking groups, X = Boc, Ac, or pGlu, was carried out in the helix-supporting environment, trifluorethanol, using ¹H-nmr spectroscopy to observe backbone NH resonances. The nmr structural investigations for the three glutamate POE series were based on the assignment of individual amide NH resonances through deuteration, analyses of vicinal coupling constants (³J_NH-α-CH), measurements of the temperature-dependence of NH chemical shifts, saturation-transfer experiments, stable free radical titration studies, and titration experiments using a denaturing solvent (DMSO). From these investigations, a detailed picture was derived for the possible conformations of these POE-peptides.     

Preferred conformations of protected homo-oligo-L-glutamate peptides in CDCl3 and CDCl3/TFA mixtures

A conformational analysis of protected glutamate homo-oligopeptides Z-[Glu(OEt)]_n-OEt (n = 2–7) was carried out in chloroform solution using high-resolution ¹H-nmr spectroscopy. At dilute peptide concentrations, the backbone NH and α-CH resonances are well resolved and can be assigned by combining extensive homonuclear decoupling experiments with data for co-oligopeptide derivatives. The structure of these peptides in solution was then assessed using information from chemical shifts, coupling constants, temperature coefficients, and titration of each oligomer with trifluoroacetic acid (TFA). The di- and tripeptides are found to be in disordered forms in deuterochloroform (CDCl₃) and CDCl₃/TFA mixtures. The tetrapeptide exhibits a folded structure with intramolecular hydrogen bonding at Glu² in CDCl₃ and undergoes a transition to increasingly disordered forms as TFA is added. The pentamer to heptamer show a folded structure with a strong intramolecular hydrogen bond at Glu² and a weaker hydrogen bond at Glu³, which are disrupted as these peptides go to random coils at high TFA/CDCl₃ ratios. In addition, the N-terminal portions of these glutamate peptides appear to be involved in side chain–main chain interactions. The results support the hypothesis that protected linear homo-oligopeptides may possess two or more segments of conformation with intramolecular folding preferred near the N-terminal portion.     

Conformational analysis of muscimol, a GABA agonist

The potential energy barriers for rotation around the C₅C₆ bond in muscimol and two related isoxazoles have been calculated using the MINDO/3 molecular orbital method. The preferred conformations have N₇C₆C₅C₄ torsion angles near ± 100 °, in agreement with crystallographic data. The activities of muscimol and related isoxazoles as bicuculline-sensitive inhibitors of neuronal firing, however, are best accounted for in terms of “active conformations” with N₇C₆C₅C₄ torsion angles in the range +(32–46) °. These findings predict a limited range of possible “active conformations” for the flexible neurotransmitter GABA at postsynaptic receptors common to GABA, (+)-bicuculline salts and muscimol.     

Mathematical analysis of the possibility of detecting correlation between spike trains of weakly interacting neurons

The number of spikes which must be recorded in order to detect significant correlation between spike trains of two synaptically connected neurons was estimated by a mathematical model. Dependence of this number of spikes on importance of interneuronal connection (measured as the amplitude of the EPSP evoked by a single spike of the input neuron in the output cell) and on the intensity of total spontaneous excitatory influences on the output neuron and on its own parameters was studied. For cells which corresponded in the weight of connections between them, their intrinsic parameters, and characteristics of spontaneous activity to real spinal neurons, the necessary number of spikes was 10⁷–10⁸. An increase in amplitude of the single EPSP and also a decrease in the intensity of the input spontaneous spike train and parameters of after-hyperpolarization of the postsynaptic neuron led to a decrease in the number of spikes necessary for the detection of significant correlation. On the basis of the results of this and previous investigations the possible principles for construction of a spinal locomotor generator are discussed.A. A. Bogomolets Institute of Physiology, Academy of Sciences of the Ukrainian SSR, Kiev. Translated from Neirofiziologiya, Vol. 12, No. 3, pp. 290–296, May–June, 1980.     

Conformational analysis of d(C3G3), a B-family duplex in solution

NMR and circular dichroism studies of the duplex formed by the self-complementary DNA hexanucleotide d(C3G3) indicate that it is a B-type structure but differs from standard B-form. An analysis of NMR coupling constants within the deoxyribose moieties yields a 70% or greater contribution from pseudorotation phase angles corresponding to the C3'-exo conformation, a conformation similar to the C2'-endo conformation associated with B-form DNA. Intranucleotide interproton distances are consistent with a B-form structure, but some internucleotide distances are intermediate between A- and B-form structures. Circular dichroism spectra have B-form characteristics but also include an unusual negative band at 282 nm. The solution spectroscopic results are in contrast with X-ray crystallographic studies which find A-form structures for similar sequences.     

Conformational analysis of bacitracin A, a naturally occurring lariat

The proton nmr spectra of bacitracin A in H2O and DMSO-d6 have been assigned and the conformational behavior of the peptide in the two solvents has been compared. Although bacitracin A shows a conformational equilibrium between at least two conformations differing in the relative position of the cyclic and linear domains of the molecule, the spectra in water can be interpreted in terms of a preferred conformation in which the linear part is folded over the cyclic moiety and a turn is present around Ile(8)-DPhe(9).     

Detection of weakly interacting anti-carbohydrate scFv phages using surface plasmon resonance

Methods to characterise and confirm specificity of scFv displayed on phages are important during panning procedures, especially when selecting for antibody fragments with weak affinities in the millimole to micromole range. In this report the surface plasmon resonance (SPR) biosensor was used to study and verify specificity of phages displaying weak anti-carbohydrate scFvs. The variable immunoglobulin light (VL) and heavy (VH) chain genes of the weak monoclonal antibody 39.5 were amplified and cloned into a phagemid and displayed as a scFv-pIII fusion protein on filamentous phage. This monoclonal antibody recognises with weak affinity the structural sequence Glcalpha1-4Glc present in a variety of carbohydrate molecules. Injection of the 39.5 phages over a biosensor chip immobilised with a (Glc)4-BSA conjugate confirmed selective binding of the scFv to its antigen. Inhibition studies verified the specificity. These results clearly show that SPR technology can be used to evaluate in terms of binding and specificity weakly interacting scFv displayed on the phage surface.     

Synthesis and nmr conformational studies of polyoxyethylene-bound, alpha-deuterated glutamate oligopeptides

The syntheses of three series of glutamate oligopeptides attached to a macromolecular solubilizing polyoxyethylene (POE) group Boc-[Glu(OMe)]_n-OPOE, Ac-[Glu(OMe)]_n-OPOE, pGlu-[Glu(OMe)]_n?1-OPOE (n ? 1–7) and their various analogs specifically deuterated at individual α-CH positions using the liquid-phase method of peptide synthesis are described. It was shown that stepwise synthesis using the symmetrical anhydride gave homo-oligopeptides that are analytically pure. Fragment condensation methods using DCC-HOBt yield POE-peptides with POE-HOBt impurities but the peptide synthesis may be carried stoichiometrically with smaller quantities of amino acid derivatives. 360 MHz ¹H-nmr conformational studies of these homo-oligopeptides in DMSO-d₆ are presented. The α-deuterated peptides are shown to allow unequivocal homoligopeptide backbone NH assignments.     

Conformational motion correlations in the formation of polypeptide secondary structure in a viscous medium

The Langevin dynamics method and statistical correlation analysis were used to study the α-helical structure folding dynamics of the (Ala)₅₀, (AlaGly)₂₅, and (AlaGly)₇₅ polypeptides depending on the viscosity of the medium. Friction forces that arise when the effective viscosity of the medium is similar to the viscosity of water were found to result in strong correlations between the backbone torsion angles. The polypeptides under study folded mainly to produce α-helical structures. A structure of two contacting α-helices that were approximately equal in length and had a loop between them was observed for a longer chain of 150 residues. A method to visualize the correlation matrix of the dihedral angles of a polypeptide chain was developed for analyzing the effects of the dynamic correlation of conformational degrees of freedom. The analysis of the dynamics of the correlation matrix showed that rotations involving angles of the same type (φ–φ and ψ–ψ) occur predominantly in one direction. Rotations invoving different angles (φ–ψ) occur predominantly in opposite directions, so that the total macromolecule does not rotate. A significant reduction in the effective viscosity of the medium disrupts the correlation and makes the rotations stochastic, thus distorting the formation of the regular (helical) structure. The effects of correlated conformational motions are consequences of viscous friction forces. This conclusion agrees with our previous results that outlined the principle of the minimum rate of energy dissipation and the equipartition of energy dissipation rate between conformational degrees of freedom.     

Conformational analysis of lipid-associating proteins in a lipid environment

Two major types of helical structures have been identified in lipid-associating proteins, being either amphipathic or transmembrane domains. A conformational analysis was carried out to characterize some of the properties of these helices. These calculations were performed both on isolated helices and in a lipid environment. According to the results of this analysis, the orientation of the line joining the hydrophobic and hydrophilic centers of the helix seems to determine the orientation of the helix at the lipid/water interface. The calculation of this parameter should be useful to discriminate between an amphipathic helix, parallel to the interface and a transmembrane helix orientated perpendicularly. The membrane-spanning helices are completely immersed in the phospholipid bilayer and their length corresponds to about the thickness of the hydrophobic core of the DPPC bilayer. The energy of interaction, expressed per phospholipid is significantly higher for the transmembrane compared to the amphipathic helices. For the membrane-spanning helices the mean energy of interaction is higher than the interaction energy between two phospholipids, while it is lower for most amphipathic helices. This might account for the stability of these protein-anchoring domains. This computer modeling approach should usefully complement the statistical analysis carried out on these helices, based on their hydrophobicity and hydrophobic moment. It represents a more refined analysis of the domains identified by the prediction techniques and stress the functional character of lipid-associating domains in membrane proteins as well as in soluble plasma lipoproteins.     

Conformational analysis of the anomeric forms of kojibiose, nigerose, and maltose using MM3

Energy surfaces were computed for relative orientations of the relaxed pyranosyl rings of the two anomeric forms of kojibiose, nigerose, and maltose, the (1 → 2)-, (1 → 3)-- and (1 → 4)--linked -glucosyl disaccharides, respectively. Twenty-four combinations of starting conformations of the rotatable side-groups were considered for each disaccharide. Optimized structures were calculated using MM3 on a 20° grid spacing of the torsional angles about the glycosidic bonds. The energy surfaces of the six disaccharides were similar in many respects but differed in detail within the low-energy regions. The maps also illustrate the importance of the exo-anomeric effect and linkage type in determining the conformational flexibility of disaccharides. Torsional conformations of known crystal structures of maltosyl-containing molecules lie in a lower MM3 energy range than previously reported.     

Conformational analysis using a truth maintenance system

This paper describes Rotamer, a program we wrote to assist chemists in identifying the likely three-dimensional (3D) shapes (conformations) that a flexible molecule might assume. The search of the space of all possible conformations is approached as a constraint-satisfaction problem. The structure generator in Rotamer uses a simplified truth maintenance system (TMS) to cache information acquired in the course of exploring the conformation space. The computational benefits of using this TMS increase with the size of the problem.     

Conformational analysis of a potent SSTR3-selective somatostatin analogue by NMR in water solution.

The three-dimensional structure of a potent SSTR3-selective analogue of somatostatin, cyclo(3-14)H-Cys(3)-Phe(6)-Tyr(7)-D-Agl(8)(N(beta) Me, 2-naphthoyl)-Lys(9)-Thr(10)-Phe(11)-Cys(14)-OH (des-AA(1, 2, 4, 5, 12, 13)[Tyr(7), D-Agl(8)(N(beta) Me, 2-naphthoyl)]-SRIF) (peptide 1) has been determined by (1)H NMR in water and molecular dynamics (MD) simulations. The peptide exists in two conformational isomers differing mainly by the cis/trans isomerization of the side chain in residue 8. The structure of 1 is compared with the consensus structural motifs of other somatostatin analogues that bind predominantly to SSTR1, SSTR2/SSTR5 and SSTR4 receptors, and to the 3D structure of a non-selective SRIF analogue, cyclo(3-14)H-Cys(3)-Phe(6)-Tyr(7)-D-2Nal(8)-Lys(9)-Thr(10)-Phe(11)-Cys(14)-OH (des-AA(1, 2, 4, 5, 12, 13)[Tyr(7), D-2Nal(8)]-SRIF) (peptide 2). The structural determinant factors that could explain selectivity of peptide 1 for SSTR3 receptors are discussed.     

Kermit, a frizzled interacting protein, regulates frizzled 3 signaling in neural crest development

Wnts are a family of secreted glycoproteins that are important for multiple steps in early development. Accumulating evidence suggests that frizzled genes encode receptors for Wnts. However, the mechanism through which frizzleds transduce a signal and the immediate downstream components that convey that signal are unclear. We have identified a new protein, Kermit, that interacts specifically with the C-terminus of Xenopus frizzled-3 (Xfz3). Kermit is a 331 amino acid protein with a central PDZ domain. Kermit mRNA is expressed throughout Xenopus development and is localized to neural tissue in a pattern that overlaps Xfz3 expression temporally and spatially. Co-expression of Xfz3 and Kermit results in a dramatic translocation of Kermit to the plasma membrane. Inhibition of Kermit function with morpholino antisense oligonucleotides directed against the 5' untranslated region of Kermit mRNA blocks neural crest induction by Xfz3, and this is rescued by co-injection of mRNA encoding the Kermit open reading frame. These observations suggest that Kermit is required for Wnt/frizzled signaling in neural crest development. To the best of our knowledge, Kermit is the first protein identified that interacts directly with the cytoplasmic portion of frizzleds to modulate their signaling activity.     

Conformational analysis of xyloglucans

Xyloglucan isolated from the elongating regions of pea stems was examined using X-ray diffraction and energy calculations. The X-ray fibre pattern suggested that the backbone (1----4)-beta-D-glucan takes an extended two-fold helix similar to common cellulose. In order to study side chains (xylosyl or fucosyl-galactosyl-xylosyl residues) of the polysaccharide, energetically preferable conformations were searched by calculation of interactions between non-bonded atom pairs. A stepwise calculation for the conformation of fucosyl-galactosyl-xylosyl residue gave 10 allowed area (phi-psi) maps which are useful to deduce xyloglucan conformations of both monocotyledons and dicotyledons in the walls of growing plant cells.     

Conformational study of poly(L-lysine) interacting with acidic phospholipid vesicles

Circular dichroism measurements were carried out on poly(L-lysine) in the presence of vesicles of the negatively charged phospholipids, phosphatidylserine (PS; from bovine brain), phosphatidic acid (PA; prepared from egg yolk lecithin) and dimyristoylphosphatidylglycerol (DMPG). PS vesicles induced a conformational change in poly(L-lysine) from random coil to alpha-helix structure in 5 mM Tes (pH 7.0), whereas PA vesicles gave rise to beta-structure in the same buffer. The fraction of alpha-helix, F alpha (or beta-structure, F beta), increased with increasing PS (or PA) concentration, reaching a saturation value of about 0.7 (or about 1). Mixed vesicles comprising PS and dilauroylphosphatidylcholine (DLPC) also induced alpha-helix conformation, however, the saturation value of F alpha diminished with decreasing PS content in mixed vesicles. On the other hand, the spectral patterns for poly(L-lysine) in DMPG vesicle suspensions exhibited the coexistence of alpha-helix and beta-structure. Both F alpha and F beta increased with DMPG concentration and reached saturation values of about 0.5. Mixed vesicles composed of DMPG and dimyristoylphosphatidylcholine (DMPC) led to a reduction in F beta, while F alpha remained almost constant. The diversity in ordered structure induced by different phospholipid vesicles suggests the participation of lipid head groups in determining the secondary structure of poly(L-lysine) adsorbed on the vesicular surface.