Characterization of β‐bend ribbon spiral forming peptides using electronic and vibrational CD

Yoder, Gorm; Keiderling, Timothy A.; Formaggio, Fernando; Crisma, Marco; Toniolo, Claudio

doi:10.1002/bip.360350111

Cited by 47 publications

(64 citation statements)

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“…205 and 230 nm, and a positive band near 195 nm. This spectrum differs from those of helical peptides and is similar to the spectra of peptides in righthanded b-bend ribbon spiral conformation [24] [53]. At the same time, the Aam-I CD spectra in DHPC/DMPC bicelles and in POPC vesicles display a steadily growing amplitude and show two negative bands at ca.…”

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confidence: 72%

Antiamoebin I in Methanol Solution: Rapid Exchange between Right‐Handed and Left‐Handed 3₁₀‐Helical Conformations

Шенкарев

Paramonov

Nadezhdin

et al. 2007

Chemistry & Biodiversity

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Antiamoebin I (Aam-I) is a membrane-active peptaibol antibiotic isolated from fungal species belonging to the genera Cephalosporium, Emericellopsis, Gliocladium, and Stilbella. Antiamoebin I has the amino acid sequence: Ac-Phe(1)-Aib-Aib-Aib-Iva-Gly-Leu-Aib(8)-Aib-Hyp-Gln-Iva-Hyp-Aib-Pro-Phl(16). By using the uniformly (13)C,(15)N-labeled sample of Aam-I, the set of conformationally dependent J couplings and (3h)J(NC) couplings through H-bonds were measured. Analysis of these data along with the data on magnetic nonequivalence of the (13)C(beta) nuclei (Deltadelta((13)C(beta))) in Aib and Iva residues allowed us to draw the univocal conclusion that the N-terminal part (Phe(1)-Gly(6)) of Aam-I in MeOH solution is in fast exchange between the right-handed and left-handed 3(10)-helical conformations, with an approximately equal population of both states. An additional conformational exchange process was found at the Aib(8) residue. The (15)N-NMR-relaxation and CD-spectroscopy measurements confirmed these findings. Molecular modeling and Monte Carlo simulations revealed that both exchange processes are correlated and coupled with significant hinge-bending motions around the Aib(8) residue. Our results explain relatively low activity of Aam-I with respect to other 15-amino acid residue peptaibols (for example, zervamicin) in functional and biological tests. The high dynamic 'propensity' possibly prevents both initial binding of the antiamoebin to the membrane and subsequent formation of stable ionic channels according to the barrel-stave mechanism.

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confidence: 72%

Antiamoebin I in Methanol Solution: Rapid Exchange between Right‐Handed and Left‐Handed 3₁₀‐Helical Conformations

Шенкарев

Paramonov

Nadezhdin

et al. 2007

Chemistry & Biodiversity

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“…As the chain increases in length, the influence of the terminal group is less, particularly for a shorter range dependent phenomenon such as VCD, 13.45, 46 and helices of the opposite chirality become ener- getically competitive. There is a complication due to the odd-even dependence of the oligomer VCD, but this appears to yield a consistent pattern over each subset.…”

Section: Discussionmentioning

confidence: 98%

Conformational study of linear alternating and mixed D‐ and L‐proline oligomers using electronic and vibrational CD and fourier transform IR

et al. 1995

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Vibrational CD (VCD) spectra of a series of blocked linear, alternating D- and L-proline containing oligopeptides, dissolved in D2O and in CDCl3, are reported. For the Boc-LDL-Pro3 to Boc-DLDLDLDL-Pro8 oligomers, the VCD spectra in the amide I band is a positive couplet, opposite in sense to that obtained for (L-Pro)n oligomers. While this admits the possibility of their favoring a right-handed helical chain conformation, the amide I ir spectra for these DL oligomers in D2O indicate a mixed, apparently alternate, cis-trans conformation that prevents a simple conclusion. Their VCD in D2O evidence no narrowing and has a progressive loss in intensity (measured as delta A/A) with an increase in chain length. In CDCl3 a similar pattern of positive VCD couplets decreasing in intensity with length was seen, but the ir spectra are narrower. Their electronic CD (ECD), in the uv, also indicates a loss in intensity with increasing length. Oligomers with odd or even numbers of Pro residues have different ECD patterns, indicating that those spectra are strongly influenced by local contributions arising in the N-terminal groups. The VCD arises from dipolar and vibrational coupling of the amides in the helical structure. All the spectra are consistent with the chiral end groups leading to formation of an excess of one helical handedness. With an increase in length, the influence of this selectiveness is less and the overall CD measured decreases.

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“…[3][4][5][6][7] The amide I and A modes originate from the stretching motion of the CdO and N-H bond, respectively, whereas the amide II and III are attributed to bending motion of the N-H coupled to C-N stretching. The vibrational circular dichroism (VCD) of the amide I, II, and III has been extensively applied to protein structure determination, [8][9][10][11][12] and normal-mode analysis of ab initio calculations has been performed. 13,14 However, most simulation effort has focused on the amide I vibrations [15][16][17][18][19][20] which are highly localized (mostly CdO stretch) and the easiest to model.…”

Section: Introductionmentioning

confidence: 99%

Vibrational−Exciton Couplings for the Amide I, II, III, and A Modes of Peptides

2007

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The couplings between all amide fundamentals and their overtones and combination vibrational states are calculated. Combined with the level energies reported previously (Hayashi, T.; Zhuang, W.; Mukamel, S. J. Phys. Chem. A 2005, 109, 9747), we obtain a complete effective vibrational Hamiltonian for the entire amide system. Couplings between neighboring peptide units are obtained using the anharmonic vibrational Hamiltonian of glycine dipeptide (GLDP) at the BPW91/6-31G(d,p) level. Electrostatic couplings between non-neighboring units are calculated by the fourth rank transition multipole coupling (TMC) expansion, including 1/R 3 (dipoledipole), 1/R 4 (quadrupole-dipole), and 1/R 5 (quadrupole-quadrupole and octapole-dipole) interactions. Exciton delocalization length and its variation with frequency in the various amide bands are calculated. The simulated infrared amide I and II absorptions and CD spectra of 24 residue R-helical motifs (SPE 3 ) are in good agreement with experiment.

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Characterization of β‐bend ribbon spiral forming peptides using electronic and vibrational CD

Cited by 47 publications

References 35 publications

Antiamoebin I in Methanol Solution: Rapid Exchange between Right‐Handed and Left‐Handed 3₁₀‐Helical Conformations

Antiamoebin I in Methanol Solution: Rapid Exchange between Right‐Handed and Left‐Handed 3₁₀‐Helical Conformations

Conformational study of linear alternating and mixed D‐ and L‐proline oligomers using electronic and vibrational CD and fourier transform IR

Vibrational−Exciton Couplings for the Amide I, II, III, and A Modes of Peptides

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Characterization of β‐bend ribbon spiral forming peptides using electronic and vibrational CD

Cited by 47 publications

References 35 publications

Antiamoebin I in Methanol Solution: Rapid Exchange between Right‐Handed and Left‐Handed 310‐Helical Conformations

Antiamoebin I in Methanol Solution: Rapid Exchange between Right‐Handed and Left‐Handed 310‐Helical Conformations

Conformational study of linear alternating and mixed D‐ and L‐proline oligomers using electronic and vibrational CD and fourier transform IR

Vibrational−Exciton Couplings for the Amide I, II, III, and A Modes of Peptides

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Antiamoebin I in Methanol Solution: Rapid Exchange between Right‐Handed and Left‐Handed 3₁₀‐Helical Conformations

Antiamoebin I in Methanol Solution: Rapid Exchange between Right‐Handed and Left‐Handed 3₁₀‐Helical Conformations