A Quantitative Reconstruction of the Amide I Contour in the IR Spectra of Globular Proteins:  From Structure to Spectrum

Abstract

The Amide I contours of six globular proteins of varied secondary structure content along with a peptide model for collagen and pulmonary surfactant protein C have been simulated very closely by using a modified GF matrix method. The starting point for the method uses the three-dimensional structure as obtained from the Protein Data Bank. Elements of the interactions between peptide groups (e.g., transition dipole coupling) are very sensitive to tertiary structure, thus the current formalism demonstrates that the Amide I contour may be useful for a more detailed probe of 3-D conformation that goes beyond the traditional use of this band to probe the percentages of particular elements of secondary structure. For example, postulated changes to a known structure can be tested by comparing the new simulated band to the experimental band. A number of refinements to the transition dipole interaction calculation have been made. Most of the important interactions between the C=O oscillators that define the Amide I mode appear to have been identified, including through space transition dipole coupling, through valence bond and through hydrogen bond coupling. The eigenvector matrix produced by the method permits the contribution of each peptide group to the spectrum to be precisely determined. Analysis of the results shows that the often-used structure-frequency correlations are at best approximate and at worst misleading. The subbands from helices, sheets, turns, and loops are much broader and more overlapped than has been commonly assumed. Furthermore, the traditional alpha-helical marker band may be substantially distorted in short segments. Difference spectra based on isotope editing, a technique thought capable of revealing the spectral contributions of individual peptide groups, are shown to be prone to misinterpretation.

Raman spectroscopy of proteins: from peptides to large assemblies

“…However, these methods employ unwarranted assumptions about intrinsic Raman and IR intensities and tend to underestimate R. Tuma spectral overlaps between marker for different secondary structures. 18 Fortunately, the rapid increase in computational capacity and the availability of suitable model compounds has been driving steady progress in ab initio vibrational analyses. 19 -21 This renewed interest has also been fueled by the advent of two-dimensional (pump-and-probe) vibrational spectroscopy which allowed an experimental determination of the nearest-neighbor coupling constants in model peptides.…”

“…24 -28 A similar amide I mode description has been used to simulate IR amide I envelopes of proteins with reasonable success. 18 Although the information extractable from the amide bands alone is not sufficient for three-dimensional structure determination, one can envision Raman-assisted database comparisons used for fold classification and Raman-assisted modeling of structural changes and homologous proteins. 29 Generally, analysis of the side-chain marker bands is far from quantitative.…”

Extraction of Proteins from Biological Fluids by Use of an Ionic Liquid/Aqueous Two‐Phase System

“…The absorption bands most widely used as structure probes in protein FTIR spectroscopy have been the amide I vibrations, which fall between 1690 and 1600 cm À1 . [48] FTIR spectra for BSA, BmimCl, and BSA in BmimCl are illustrated in Figure 8, and it is obvious that the very broad absorption band around 3400 cm À1 provides no useful information in this particular case, while the absorption bands from 1700 to 1500 cm À1 are most informative. In Figure 8 a (right), the two marker bands of the protein components (i.e., the amide I band at 1665 cm À1 and the amide II band at 1540 cm À1 ) [49] were readily identifiable in the FTIR spectra of BSA.…”

Vibrational Absorption

“…IR spectra of polypeptides and proteins are affected by coupling of the vibrations of neighboring peptide groups [33,[36][37][38][39]. This coupling is analogous to exciton interactions of electronic transitions (Chap.…”