Raman structural markers of tryptophan and histidine side chains in proteins

Abstract

The Raman spectrum of a protein contains a wealth of information on the structure and interaction of the protein. To extract the structural information from the Raman spectrum, it is necessary to identify and interpret the marker bands that reflect the structure and interaction in the protein. Recently, new Raman structural markers have been proposed for the tryptophan and histidine side chains by examining the spectra-structure correlations of model compounds. Raman structural markers are now available for the conformation, hydrogen bonding, hydrophobic interaction, and cation-pi interaction of the indole ring of Trp. For His, protonation, tautomerism, and metal coordination of the imidazole ring can be studied by using Raman markers. The high-resolution X-ray crystal structures of proteins provide the basis for testing and modifying the Raman structural markers of Trp and His. The structures derived from Raman spectra are generally consistent with the X-ray crystal structures, giving support for the applicability of most Raman structural makers. Possible modifications and limitations to some marker bands are also discussed.

Raman Spectroscopic Signatures of Echovirus 1 Uncoating

“…In intact viruses, this Trp signal is a single peak centered at 877 cm Ϫ1 , and after heat treatments, the signal divides to two peaks at 873 and 881 cm Ϫ1 , indicating changes in Trp hydrogen bonding status. The frequency of the Trp signal near 1,550 cm Ϫ1 has been reported to be indicative of changes in side chain conformation (46)(47)(48), and there are heat-induced changes in this region in our data (Fig. 5D).…”

Protein Conformation Changes of HemAT-Bs upon Ligand Binding Probed by Ultraviolet Resonance Raman Spectroscopy

“…This doublet arises from Fermi resonance between the N 1 -C 8 stretching fundamental (W7 mode) and the combination of out-of-plane bending vibrations (26). The intensity ratio of the W7 doublet serves as a marker of the hydrophobicity of the environment around the indole ring; the intensity ratio of the W7 doublet decreases as the environment around the Trp residue shifts to more hydrophilic (33). The difference spectrum, O 2 Ϫ ligand-free, reveals a negative peak at 1358 cm Ϫ1 (Fig.…”

“…The W17 band of WT (spectrum a) is observed at 876 cm Ϫ1 . This frequency corresponds to a moderate strength of hydrogen bonding (33,34). The crystal structure of the CNbound form of the truncated sensor domain in the homodimer suggests that Trp 132 does not form a hydrogen bond with any nearby residues (21).…”

“…The frequency of the W17 band (ϳ875 cm Ϫ1 ) is known to serve as a marker of hydrogen bonding of the Trp indole ring (33,34). The W17 band of WT (spectrum a) is observed at 876 cm Ϫ1 .…”

Chemical and physical characterization of thermal aggregation of model proteins modulated by zinc(II) and copper(II) ions

“…In fact, the imidazole group of His side chain possesses two nitrogen atoms, which can be protonated or deprotonated, giving rise to four different protonation forms: two neutral tautomers, fully protonated imidazolium cation (His + ), and imidazolate anion (His − ) deprotonated at both the nitrogen sites (Scheme 1). Raman spectroscopy is one of the most powerful methods to study the protonation state of His in proteins since some bands are sensitive to the His tautomeric and ionic state [19,21]. Generally, three Raman bands (at 1570, 1290 and 990 cm −1 ) can be useful, which appear at different wavenumbers depending on the His tautomeric form (tautomer I or II, also referred as Nτ -H or Nπ-H) and its involvement in metal coordination.…”