Tight β-turns in peptides. DFT-based study of infrared absorption and vibrational circular dichroism for various conformers including solvent effects

Kim, Joohyun; Kapitán, Josef; Lakhani, Ahmed; Bouř, Petr; Keiderling, Timothy A.

doi:10.1007/s00214-006-0183-4

Cited by 30 publications

(33 citation statements)

References 88 publications

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“…Slight variation (full minimization) of the modeling of the A structures revealed that the VCD pattern is very sensitive to minor geometry variations within one class of the b-turns. Particularly, the increased flexibility of the peptide chain in the vicinity of the glycine residues, observed also for other model oligopeptides, 26 can have a significant impact on the resultant spectral shape.…”

Section: IImentioning

confidence: 98%

“…One method to constrain a turn is formation of a hairpin, a topic that has prompted extensive studies involving both peptide design and spectral analyses. 26,[28][29][30][31][32][33][34][35][36][37][38][39][40][41][42] For a turnfocused study, hairpins have the disadvantage that most of the residues in the peptide are not in the turn (yet contribute to spectral overlap, thereby obscuring the turn contribution), and those in the termini (which are open and frayed) often have considerable fluctuation.…”

Section: Introductionmentioning

confidence: 99%

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Vibrational circular dichroism and IR spectral analysis as a test of theoretical conformational modeling for a cyclic hexapeptide

et al. 2008

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A model cyclohexapeptide, cyclo-(Phe-(D)Pro-Gly-Arg-Gly-Asp) was synthesized and its IR and VCD spectra were used as a test of density functional theory (DFT) level predictions of spectral intensities for a peptide with a nonrepeating but partially constricted conformation. Peptide structure and flexibility was estimated by molecular dynamics (MD) simulations and the spectra were simulated using full quantum mechanical (QM) approaches for the complete peptide and for simplified models with truncated side chains. After simulated annealing, the backbone conformation of the ring structure is relatively stable, consisting of a normal beta-turn and a tight loop (no H-bond) which does not vary over short trajectories. Only in quite long MD runs at high temperatures do other conformations appear. MD simulations were carried out for the cyclic peptide in water and in TFE, which match experimental solvents, as well as with and without protonation of the Asp carboxyl group. DFT spectral simulations were made using the annealed structure and were extended to include basis set variation, to determine an optimal computational approach, and solvent simulation with a polarized continuum model (PCM). Stepwise full DFT simulation of spectra was done for various sequences with the same backbone geometry but based on (1) solely Gly residues, (2) Ala substitution except Gly and Pro, and (3) complete sequences with side chains. Additionally, a selection of structures was used to compute IR and VCD spectra with the optimal method to determine structural variation effects. The side chains, especially the Asp-COOH and Arg-NH(2) transitions, had an impact on the computed amide frequencies, IR intensities and VCD pattern. Since experimentally these groups would have little chirality, due to conformational variation, they do not impact the observed VCD spectra. Correcting for frequency shifts, the Ala model for the cyclopeptide gives the clearest representation of the amide VCD. The experimental sign pattern for the amide I' band in D(2)O and also the sharper, more intense amide I VCD band in TFE was seen to some degree in one conformer with Type II' turns, but the data favor a mix of structures.

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Section: IImentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Vibrational circular dichroism and IR spectral analysis as a test of theoretical conformational modeling for a cyclic hexapeptide

et al. 2008

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“…A complementary technique, vibrational CD ͑VCD͒, uses circularly polarized IR light and provides spectra with detailed "fingerprints" analogous to standard IR spectra. VCD measurements in the amide I and II regions have been widely used to study conformations of small peptides, including small cyclic peptides and turns [28][29][30][31][32] that resemble the peptides analyzed in this work. These measurements can be challenging because VCD bands tend to be weaker than IR absorbance bands by a factor of 10 4 -10 5 ; however, the vibrational transitions probed by VCD are typically more localized to specific chromophores or normal modes and are sensitive to dipole coupling of nearby residues.…”

Section: Introductionmentioning

confidence: 99%

“…29 Even predictions for two-amino-acid ␤ turns vary depending on method, basis set, and choice of solvent model. 31 Therefore, in this work we aim to explore how reference data from model peptides having well-defined conformations can be used to assist in empirical interpretation of results for larger, complex, and heterogeneous peptides.…”

Section: Introductionmentioning

confidence: 99%

Vibrational circular-dichroism spectroscopy of homologous cyclic peptides designed to fold into β helices of opposite chirality

et al. 2011

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Cyclic ␤-helical peptides have been developed as model structured biomolecules for examining peptide adsorption and conformation on surfaces. As a key prerequisite to circular-dichroism ͑CD͒ analysis of these model peptides on surfaces, their conformations and the corresponding vibrational spectra in the 1400-1800 cm −1 range were analyzed by vibrational circular-dichroism ͑VCD͒ spectroscopy in solution. The two model peptides ͑"␤ Leu and ␤ Val"͒ were examined in chloroform, where they each fold into a homogeneous well-defined antiparallel double-stranded ␤-helical species, as determined previously by NMR and electronic CD spectroscopy. Because the ␤-helical conformations of ␤ Leu and ␤ Val are well characterized, the VCD spectra of these peptides can be unambiguously correlated with their structures. In addition, these two ␤-helical peptides differ from one another in two key respects that make them uniquely advantageous for CD analysis-first, while their backbone conformations are topologically similar, ␤ Leu and ␤ Val form helices of opposite chiralities; second, the two peptides differ in their sequences, i.e., composition of the side chains attached to the backbone. The observed VCD spectra for ␤ Leu and ␤ Val are roughly mirror images of each other, indicating that the VCD features are dominated by the chirality and conformation of the peptide backbone rather than by the peptide sequence. Accordingly, spectra similarly characteristic of peptide secondary structure can be expected for peptides designed to be structural analogs of ␤ Leu and ␤ Val while incorporating a variety of side chains for studies of surface adsorption from organic and aqueous solvents.

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“…This positive couplet was assigned to type II -turns. 10 A recent theoretical paper by Keiderling and coworkers 11 presents a systematic analysis of the expected amide I and II VCD band patterns associated with standard (type I-III) and mirrorimage (type I'-III') β-turn structures. Calculations were performed at BPW91/6-31G** level on Ac-Xxx-Yyy-NHMe type model peptides with different amino acids in the corner positions.…”

Section: Vcd Spectroscopy Of Proteinsmentioning

confidence: 99%

Structure analysis of proteins, peptides and metal complexes by vibrational circular dichroism

Hollósi¹,

Vass²,

Szilvágyi³

et al. 2012

Arkivoc

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There are two principal forms of vibrational optical activity (VOA), an IR form referred to as vibrational circular dichroism (VCD) and Raman form known as Raman optical activity (ROA). This paper reports examples of the application of VCD spectroscopy for the determination of the absolute configuration and conformation of chiral molecules, e.g. cyclic -lactams. VCD spectroscopy can be applied for the characterization of the conformation of proteins and peptides in solution. VCD based conformational analysis of cyclic peptides is discussed. Examples are the cyclic hexapeptide cyclo(Pro 2 -Gly-Pro 2 -Gly) and cyclic peptides comprising -homoamino acids (trans-2-aminocyclopentane or trans-2-aminocyclohexane carboxylic acid). Structure analysis by VCD of opiate peptides, glycopeptides, peptidomimetics and chiral transition metal complexes are also discussed.

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Tight β-turns in peptides. DFT-based study of infrared absorption and vibrational circular dichroism for various conformers including solvent effects

Cited by 30 publications

References 88 publications

Vibrational circular dichroism and IR spectral analysis as a test of theoretical conformational modeling for a cyclic hexapeptide

Vibrational circular dichroism and IR spectral analysis as a test of theoretical conformational modeling for a cyclic hexapeptide

Vibrational circular-dichroism spectroscopy of homologous cyclic peptides designed to fold into β helices of opposite chirality

Structure analysis of proteins, peptides and metal complexes by vibrational circular dichroism

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