Determination of the Relationship between the Geometric Structure of a Model Peptide and Its 13C Isotope-Edited FTIR Spectroscopy by ATR in H2O

Abstract

Determination of protein structures (such as α-helix, β-sheet, unstructured conformation, and so on) is important to correlate the function of a protein with its structure.1 X-ray crystallography is a powerful technique but it requires proteins to form single crystal structure. However, lots of proteins do not meet this requirement. NMR can determine the structure of peptides/proteins in aqueous environment but the measurement is time-consuming. Thus, determination of the structure of proteins/peptides with short life-time (such as one hour) in aqueous solution is challenging for NMR. Recently, IR spectroscopy has been reported to be able to address the geometric structure of peptide with 13C isotopic labels in deuterated water (D2O) in residue level.2 Although similar to regular water, D2O is not physiologically approved.3 On the other hand, H2O has intensive absorption around 1620 cm-1 (this will cover the IR absorption of proteins/peptides) in IR spectroscopy. Thus, traditional transmission measurement of IR spectra of proteins/peptides in H2O will fail, because the thickness of normal liquid FTIR cell is in millimeter level.

In this thesis, 13C isotope edited FTIR was applied in H2O solution by attenuated total reflection (ATR) technique, which can avoid H2O background absorption because the path-length of IR in the sample solution of ATR is only several micrometers. A model helical peptide Ac-AAAAKAAAAKAAAAKAAAAY-NH2 (Ac means C-terminus and NH2 indicates the N-terminus) was synthesized and 13C labeled alanine (A) residues were introduced into the model peptide with various spacing residues. The 13C labeled residues generate a new amide I band, namely, 13C amide I band which was shown to relate to the geometry of the helical peptide. For example, the 13C amide I band was detected at 1608 cm-1 when the two 13C labeled A residues are adjacent. When the number of spacing residues increased to 2 and 3, the 13C amide I band was detected at 1599 and 1602 cm-1, respectively. Thus, the 13C amide I band can help to determine the geometry of peptides/proteins.