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Electrostatic frequency shifts in amide I vibrational spectra: Direct parameterization against experiment
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Figures

Image of FIG. 1.

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FIG. 1.

(a) Experimental FTIR absorption spectra for the GG dipeptide as a function of pH. Dashed vertical lines mark the amide I peak maxima. See text for details. (b) Frequency histograms (4 cm−1 bins) for 23 standard dipeptides under acidic (yellow), neutral (red), and basic (black) conditions.

Image of FIG. 2.

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FIG. 2.

(a) Structure of a generic dipeptide; our coordinate system is defined so that the x axis points along the amide C=O bond and the y axis is in the plane of the amide unit. (b)–(e) Scatter plots of experimental peak frequencies for 23 standard dipeptides with individual electrostatic variables evaluated from 5 ns CHARMM27 MD simulations (see labels in figure).

Image of FIG. 3.

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FIG. 3.

Correlation scatter plots for experimental amide I peak frequencies (horizontal axis) and predicted frequencies (vertical axis) from linear least-squares best fit equations to various electrostatic parameters as labeled. The c values reported for each frame are Pearson correlation coefficients.

Image of FIG. 4.

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FIG. 4.

Scatter plots of experimental amide I peak frequencies with MD electrostatics for CHARMM27 (left panel) and OPLS-AA (right panel) force fields. Amino acid composition is labeled by color (see legend). The inset for each panel plots an error histogram (deviation between experimental and best-fit simulation frequencies) for the 23 standard dipeptides in each data set.

Image of FIG. 5.

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FIG. 5.

Scatter plot comparing the average electric field values for CHARMM27 and OPLS-AA trajectories. Data points are colored according to amino acid composition (see legend). The dashed line is the least-squares best fit line for the standard dipeptide data (black points): E OPLS = 0.7246 · E CHARMM − 0.033. The correlation coefficient is 0.975.

Image of FIG. 6.

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FIG. 6.

A comparison of experimental absorption spectra (blue circles) with simulated frequency histograms (dashed lines) and absorption spectra (solid lines) for the VT dipeptide under neutral and basic conditions. Note that the clipped peak near 1600 cm−1 is due to the C-terminal carboxylate absorption peak which is not included in our simulations.

Tables

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Table I.

Best-fit data for various combinations of electrostatic variables evaluated for the CHARMM27 force field against experimental frequencies for our 23 standard dipeptides. The first data column presents the sample standard deviation (σ) of the error between best-fit prediction and experimental values. The second column reports the predicted zero-field (i.e., vacuum) frequency, and the third column the linear coefficients for the respective variables (see, e.g., Eqs. (4) and (8)). The units on the potential are E h /e and on the field E h /a o e, as above. Note that for the potential fits, the coefficients are constrained to sum to zero.

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/content/aip/journal/jcp/138/13/10.1063/1.4798938
2013-04-04
2014-04-17

Abstract

The interpretation of protein amide I infrared spectra has been greatly assisted by the observation that the vibrational frequency of a peptide unit reports on its local electrostatic environment. However, the interpretation of spectra remains largely qualitative due to a lack of direct quantitative connections between computational models and experimental data. Here, we present an empirical parameterization of an electrostatic amide I frequency map derived from the infrared absorption spectra of 28 dipeptides. The observed frequency shifts are analyzed in terms of the local electrostatic potential, field, and field gradient, evaluated at sites near the amide bond in molecular dynamics simulations. We find that the frequency shifts observed in experiment correlate very well with the electric field in the direction of the C=O bond evaluated at the position of the amide oxygen atom. A linear best-fit mapping between observed frequencies and electric field yield sample standard deviations of 2.8 and 3.7 cm−1 for the CHARMM27 and OPLS-AA force fields, respectively, and maximum deviations (within our data set) of 9 cm−1. These results are discussed in the broader context of amide I vibrational models and the effort to produce quantitative agreement between simulated and experimental absorption spectra.

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Scitation: Electrostatic frequency shifts in amide I vibrational spectra: Direct parameterization against experiment
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/13/10.1063/1.4798938
10.1063/1.4798938
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