FTIR and CD spectroscopic studies on cyclic penta- and hexa-peptides. Detailed examination of hydrogen bonding in β- and γ-turns determined by NMR

Vass, Elemér; Kurz, Michael; Konat, Robert K.; Hollósi, Miklós

doi:10.1016/s1386-1425(98)00028-6

Cited by 25 publications

(29 citation statements)

References 26 publications

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“…Table I shows the region where β-turn structures absorb and how this is effected by overlap from other structures. FTIR spectroscopy can be used to identify bands associated with this structure (58,59). The results of experimental studies are often in good agreement with the force-field calculations for such structures.…”

Section: -1675cmmentioning

confidence: 71%

“…However, bands in this region can sometimes be observed for proteins which are known to contain very little or no β-sheet structure as discussed already for alamethicin, bacteriorhodopsin and myoglobin. Band assignment in this region is further complicated by the possibility of β-turn structure also absorbing in this region (58,59). Anti-parallel β-sheet structure can be identified by the presence of another band near 1670-1695cm" 1 .…”

Section: -1675cmmentioning

confidence: 99%

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Fourier Transform Infrared Spectroscopic Studies of Peptides: Potentials and Pitfalls

Haris

1999

ACS Symposium Series

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This article presents a discussion of the advantages and drawbacks of FTIR spectroscopy for structural characterisation of peptides. FTIR spectra of small peptides can be highly complex and extremely difficult to interpret. Amide bands associated with different secondary structural elements in peptides can show large deviations from those observed with large water-soluble proteins. This is partly due to the fact small peptides are often highly flexible and are solvated to a greater extent compared to globular proteins. Peptide aggregation can also result in the appearance of additional bands in the amide I region that can be erroneously attributed to peptide structure. These are amongst a host of factors that needs to be taken into consideration when interpreting infrared spectra of peptides.Infrared spectroscopy is one of the earliest techniques to be used for protein conformational analysis (1). From the frequency, intensity and width of the amide bands in the infrared spectrum of a protein, it is possible to obtain highly detailed information on its structure. A survey of the current literature clearly indicates the popularity of Fourier transform infrared (FTIR) spectroscopy as a tool for structural characterisation of peptides and proteins (for reviews see ref [2][3][4][5][6][7][8][9][10][11][12]. This popularity can be attributed to a number of factors, including the ability to use this technique for recording spectra of biomolecules in diverse environments. It enables conformational analysis of a peptide to be carried out in aqueous solution, crystals, organic solvents, detergents, micelles as well as in phospholipid membranes. As such FTIR spectroscopy is one of the few techniques that can be used to monitor the role of the surrounding environment on protein conformation. This is important in light of increasing evidence 54

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Section: -1675cmmentioning

confidence: 71%

Section: -1675cmmentioning

confidence: 99%

Fourier Transform Infrared Spectroscopic Studies of Peptides: Potentials and Pitfalls

Haris

1999

ACS Symposium Series

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“…20 It was proposed that the region between 1625 and 1615 cm 21 is where bands of strongly bound g-turns occur.…”

Section: Introductionmentioning

confidence: 99%

Vibrational and chiroptical spectroscopic characterization of γ‐turn model cyclic tetrapeptides containing two β‐Ala residues

et al. 2010

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The optical spectroscopic characterization of gamma-turns in solution is uncertain and their distinction from beta-turns is often difficult. This work reports systematic ECD and vibrational circular dichroism (VCD) spectroscopic studies on gamma-turn model cyclic tetrapeptides cyclo(Ala-beta-Ala-Pro-beta-Ala) (1), cyclo(Pro-beta-Ala-Pro-beta-Ala) (2) and cyclo(Ala-beta-Ala-Ala-beta-Ala) (3). Conformational analysis performed at the 6-31G(d)/B3LYP level of theory using an adequate PCM solvent model predicted one predominant conformer for 1-3, featuring two inverse gamma-turns. The ECD spectra in ACN of 1 and 2 are characterized by a negative n-->pi* band near 230 nm and a positive pi-->pi* band below 200 nm with a long wavelength shoulder. The ECD spectra in TFE of 1-3 show similar spectra with blue-shifted bands. The VCD spectra in ACN-d(3) of 1 and 2 show a +/-/+/- amide I sign pattern resulting from four uncoupled vibrations in the case of 1 and a sequence of two positive couplets in the case of 2. A -/+/+/- amide I VCD pattern was measured for 3 in TFE-d(2). All three peptides give a positive couplet or couplet-like feature (+/-) in the amide II region. VCD spectroscopy, in agreement with theoretical calculations revealed that low frequency amide I vibrations (at approximately 1630 cm(-1) or below) are indicative of a C(7) H-bonded inverse gamma-turns with Pro in position 2, while gamma-turns encompassing Ala absorb at higher frequency (above 1645 cm(-1)).

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“…Spectral characterization of turns has been a long term goal in conformational analyses, with most attention on tight b-turns that reverse the strand direction and form a H-bond from position i (C¼ ¼O) to i 1 3 (NÀ ÀH). [22][23][24][25][26][27] Creating viable experimental models of stable turn peptides is challenging as well. If a turn is part of a linear peptide chain there will be considerable local conformational fluctuation unless some other construct constrains it, thereby creating a large energy barrier to transformation.…”

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 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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FTIR and CD spectroscopic studies on cyclic penta- and hexa-peptides. Detailed examination of hydrogen bonding in β- and γ-turns determined by NMR

Cited by 25 publications

References 26 publications

Fourier Transform Infrared Spectroscopic Studies of Peptides: Potentials and Pitfalls

Fourier Transform Infrared Spectroscopic Studies of Peptides: Potentials and Pitfalls

Vibrational and chiroptical spectroscopic characterization of γ‐turn model cyclic tetrapeptides containing two β‐Ala residues

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

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