2D-IR Experiments and Simulations of the Coupling between Amide-I and Ionizable Side Chains in Proteins: Application to the Villin Headpiece

Abstract

The carboxylate side chains of Asp and Glu have significant coupling with the amide states of the backbone of Villin headpiece. In two dimensional spectroscopy, cross peaks are observed between these side chains and the main amide-I band. To model the absorption of the side chains, the electric field variations of vibrational frequencies of a carboxylic acid group (neutral form, CH 3 -COOH), and a carboxylate group (ionized form, CH 3 -COO -) are parametrized by means of DFT calculations. Simulations indicate that the side-chains significantly couple to only one or two amide-I modes out of all the amino acid residues which makes them useful as spectroscopic markers, providing information about the local structural behavior of the protein. Both experiment and simulations show that the cross peaks between the carboxylate and amide-I bands are significantly diminished above the melting temperature.

Ultrafast relaxation and 2D IR of the aqueous trifluorocarboxylate ion

“…A number of these parametrization schemes have been employed for describing the amide-I mode, 14 OH and OD stretch mode, 12 nitriles, 15 and lately have been extended to the symmetric and asymmetric stretch of carboxylate. 16 Of great importance to the present work on TFA is the new electrostatic map developed for the acetic acid/acetate vibrational transitions 16 which as shown in the next sections will provide sufficient insights to correlate the frequency fluctuations to microscopic processes.…”

“…The asymmetric stretching vibration of the amphiphilic trifluoroacetate ion and its 13 C v 16 O isotopologue in D 2 O were investigated with infrared spectroscopy ͑FTIR͒, ultrafast infrared pump probe, and two dimensional vibrational photon echo techniques and simulations. Trifluoroacetate ions have a nonexponential depopulation of the first vibrational excited state, which is well described by a kinetic mechanism involving a temperature dependent solvent assisted relaxation to the symmetric stretch mode.…”

“…Trifluoroacetate ions have a nonexponential depopulation of the first vibrational excited state, which is well described by a kinetic mechanism involving a temperature dependent solvent assisted relaxation to the symmetric stretch mode. The vibrational spectrum of the asymmetric stretch of the 13 C v 16 O isotopologue presents an unusual spectral shape. The frequency-frequency autocorrelation function shows a static term not present in the 13 C v 16 O form, which is caused by an accidental degeneracy with a combinational mode.…”

“…The vibrational spectrum of the asymmetric stretch of the 13 C v 16 O isotopologue presents an unusual spectral shape. The frequency-frequency autocorrelation function shows a static term not present in the 13 C v 16 O form, which is caused by an accidental degeneracy with a combinational mode. A newly developed frequency map for carboxylate is used to characterize the processes and dynamics observed in the frequency fluctuations of the carboxylate asymmetric stretch mode in aqueous solution.…”

Vibrational dynamics of a non-degenerate ultrafast rotor: The (C12,C13)-oxalate ion

“…19 The fluctuations of the site frequencies δω i (t) of the asymmetric stretches due to solvent dynamics are calculated from the DFT frequency maps and electric field parameters. 27 Similarly, the transition dipole magnitudes of the two oxalate transitions are derived from the map containing the dipole strengths and dihedral angles. 19 …”