IR spectroscopy of isotope-labeled helical peptides: Probing the effect of N-acetylation on helix stability

Decatur, Sean M.

doi:10.1002/1097-0282(200009)54:3<180::aid-bip40>3.0.co;2-9

Cited by 71 publications

(142 citation statements)

References 23 publications

(34 reference statements)

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“…The general feature of the model are significantly higher helical probabilities for the central residues compared to the chain termini in agreement with numerous other statistical mechanical models for helix‐coil transition7, 17, 30 as well as experimental results 39–41. In addition, Figure 4 shows that the helical probability of each individual residue in the chain increases with the increasing value of μ.…”

Section: Resultssupporting

confidence: 84%

Beyond the nearest‐neighbor Zimm–Bragg model for helix‐coil transition in peptides

Murza

Kubelka

2008

Biopolymers

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The nearest-neighbor (micro = 1) variant of the Zimm and Bragg (ZB) model has been extensively used to describe the helix-coil transition in biopolymers. In this work, we investigate the helix-coil transition for a 21-residue alanine peptide (AP) with the ZB model up to fourth nearest neighbor (micro = 1, 2, 3, and 4). We use a matrix approach that takes into account combinations of any number of helical stretches of any length and therefore gives the exact statistical weight of the chain within the assumptions of the ZB model. The parameters of the model are determined by fitting the temperature-dependent circular dichroism and Fourier transform infrared experimental spectra of the AP. All variants of the model fit the experimental data, thus giving similar results in terms of the macroscopic observables, such as temperature-dependent fractional helicity. However, the resulting microscopic parameters, such as distributions of the individual residue helical probabilities and free energy surfaces, vary significantly depending on the variant of the model. Overall, the mean residue enthalpy and entropy (in the absolute value) both increase with micro, but combined yield essentially the same "effective" value of the ZB propagation parameters for all micro. Greater helical probabilities for individual residues are predicted for larger micro, in particular, near the center of the sequence. The ZB nucleation parameters increase with increasing micro, which results in a lower free energy barrier to helix nucleation and lower apparent "cooperativity" of the transition. The significance of the long-range interactions for the predictions of ZB model for helix-coil transition, the calculated model parameters and the limitations of the model are discussed.

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Section: Resultssupporting

confidence: 84%

Beyond the nearest‐neighbor Zimm–Bragg model for helix‐coil transition in peptides

Murza

Kubelka

2008

Biopolymers

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“…Here, the value of x is 3. Generally, helical peptides typically form partly helical conformations, often with a central helix and frayed, disordered ends, rather than in the fully folded or unfolded state 27, 28. We applied the ZB model to the present CD results (see Material and methods) and obtained Δ H helix →unfold (25.0°C) = 5.4 ± 0.1 kJ mol −1 res −1 for the AK20 peptide.…”

Section: Resultsmentioning

confidence: 99%

Effect of pressure on helix‐coil transition of an alanine‐based peptide: An FTIR study

Imamura

Kato

2008

Proteins

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Effects of pressure and temperature on the helix-coil transition of an alanine-based peptide (Ac- AA(AAKAA)(3)AAY-NH(2)) have been investigated using CD and FTIR spectroscopy. From the correlation between CD and FTIR data, we showed that the change in infrared intensity of the amide I' band at 1633 cm(-1) is almost identical to the change in the helical content calculated from the CD result. Thus, we monitored the amide I' band intensity at 1633 cm(-1) to determine the helical content at high pressures. We determined free energy, enthalpy, and volume changes upon unfolding of the alpha-helix. The obtained volume change (0.98 +/- 0.04 cm(3) mol(-1) res(-1) at 25.4 degrees C) is not consistent with a recent molecular dynamics simulation study by Pascheck et al. who used temperature-pressure replica exchange methods (Paschek, Gnanakaran, and Garcia, Proc Natl Acad Sci USA 2005;102:6765-6770). They reported a small negative volume change upon unfolding of the alpha-helix, indicating that pressure induced the peptide to unfold. Pressure dependence of the band-width of the amide I' band also supported the present experimental results in which pressure induces the peptide to fold, which is also apparently inconsistent with the pressure-induced protein unfolding that is generally observed. We propose a hypothesis to unravel the paradox of pressure-induced peptide folding and protein unfolding.

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“…The basis of the sensitivity of the vibrational spectroscopies to polypeptide secondary structure arises from coupling between the amide vibrational modes which is sensitive to the peptide backbone conformation (f, c torsional angles) as well as to the hydrogen bonding. Recent developments in femtosecond laser-based 2D IR methods [8][9][10]11,12,13], site specifically isotope-labeled structurespectra studies [14][15][16][17]18,19,20,21], vibrational circular dichroism (VCD) [22][23][24][25] and coupled IR, Raman and VCD studies [3,4,26] have emphasized the need to establish reliable understanding of the structural basis for vibrational coupling between amides.…”

Section: Introductionmentioning

confidence: 99%

Contribution of transition dipole coupling to amide coupling in IR spectra of peptide secondary structures

Kubelka

Kim

Bouř

et al. 2006

Vibrational Spectroscopy

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IR spectroscopy of isotope-labeled helical peptides: Probing the effect of N-acetylation on helix stability

Cited by 71 publications

References 23 publications

Beyond the nearest‐neighbor Zimm–Bragg model for helix‐coil transition in peptides

Beyond the nearest‐neighbor Zimm–Bragg model for helix‐coil transition in peptides

Effect of pressure on helix‐coil transition of an alanine‐based peptide: An FTIR study

Contribution of transition dipole coupling to amide coupling in IR spectra of peptide secondary structures

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