Raman Spectroscopy of Proteins and Nucleoproteins

Abstract

A protein Raman spectrum comprises discrete bands representing vibrational modes of the peptide backbone and its side chains. The spectral positions, intensities, and polarizations of the Raman bands are sensitive to protein secondary, tertiary, and quaternary structures and to side-chain orientations and local environments. In favorable cases, the Raman spectrum serves as an empirical signature of protein three-dimensional structure, intramolecular dynamics, and intermolecular interactions. Quantitative analysis of Raman spectral series can be further boosted by advanced statistical approaches of factor analysis that allow fitting of specific theoretical models while reducing the amount of analyzed data. Here, the strengths of Raman spectroscopy are illustrated by considering recent applications from the authors' work that address (1) subunit folding and recognition in assembly of the icosahedral bacteriophages, (2) orientations of subunit main chains and side chains in native filamentous viruses, (3) roles of cysteine hydrogen bonding in the folding, assembly, and function of virus structural proteins, and (4) structural determinants of protein/DNA recognition in gene regulatory complexes. Conventional Raman and polarized Raman techniques are surveyed.

Appearance of annular ring-like intermediates during amyloid fibril formation from human serum albumin

“…63,[78][79][80] In our study, we monitored the Raman spectra of HSA aggregates in a time dependent manner, especially the amide I and amide III bands (Fig. 63,[78][79][80] In our study, we monitored the Raman spectra of HSA aggregates in a time dependent manner, especially the amide I and amide III bands (Fig.…”

“…78,79 The I 850 /I 830 ratio for the native conformation was B1.3 which decreased to B1.0 during aggregation. After gaining information about protein backbone conformational changes, we investigated the side chain vibrations at the residue-specific level.…”

Zinc oxide nanoparticle and bovine serum albumin interaction and nanoparticles influence on cytotoxicity in vitro

“…Amide I and amide III bands are expected in the spectral intervals of 1640 to 1680 cm -1 and 1230 to 1310 cm -1 , respectively, and the band shapes and peak positions are sensitive to the protein secondary structure. Accordingly, these Raman amide bands are often used as indicators of protein secondary structure [32]. The amide I deconvoluted spectral region is shown in supplementary Fig.…”

Nucleation of Amyloid Oligomers by RepA‐WH1‐Prionoid‐Functionalized Gold Nanorods

“…[5,17] Thea mide III region of the native conformation is dominated by bands at 1222 and 1265 cm À1 ,w hich are linked to aromatic residues and ar andom structure,w hereas amide Id oes not show any Raman signal. [22] The latter might reflect the formation of a b-solenoid, ah elical arrangement of b-strands common to some amyloid proteins. [22] The latter might reflect the formation of a b-solenoid, ah elical arrangement of b-strands common to some amyloid proteins.…”

“…[21] SERS spectra were collected using 785 nm laser light as the excitation source,a tl ow intensity (1.4 mWcm À2 )toavoid damaging the samples.Under such conditions,the typical band broadening characteristic of the Raman spectra of proteins was observed. [22] SERS spectra were obtained for the native protein and at the initial (1 day) and final (22 days) stages of oligomerization. Incubation of H6-RepA-WH1(A31V) with AuNRs induced variations in A) The dot-blot assay with B3h7, an antibody specific for amyloidogenic RepA-WH1 oligomers, [13c] reveals that the H6-RepA-WH1(A31V) protein assemblies around the AuNRs (even rows) are amyloids, whereas the soluble protein molecules (odd rows) are not.…”