Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations

We
identified vibrational spectral marker bands that sensitively
report on the side chain structures of glutamine (Gln) and asparagine
(Asn). Density functional theory (DFT) calculations indicate that
the Amide IIIP (AmIIIP) vibrations of Gln and
Asn depend cosinusoidally on their side chain OCCC dihedral angles
(the χ3 and χ2 angles of Gln and
Asn, respectively). We use UV resonance Raman (UVRR) and visible Raman
spectroscopy to experimentally correlate the AmIIIP Raman
band frequency to the primary amide OCCC dihedral angle. The AmIIIP structural sensitivity derives from the Gln (Asn) Cβ–Cγ (Cα–Cβ) stretching component of the vibration. The Cβ–Cγ (Cα–Cβ) bond
length inversely correlates with the AmIIIP band frequency.
As the Cβ–Cγ (Cα–Cβ) bond length decreases, its stretching
force constant increases, which results in an upshift in the AmIIIP frequency. The Cβ–Cγ (Cα–Cβ) bond length dependence
on the χ3 (χ2) dihedral angle results
from hyperconjugation between the CδOϵ (CγOδ) π*
and Cβ–Cγ (Cα–Cβ) σ orbitals. Using a Protein Data
Bank library, we show that the χ3 and χ2 dihedral angles of Gln and Asn depend on the peptide backbone
Ramachandran angles. We demonstrate that the inhomogeneously broadened
AmIIIP band line shapes can be used to calculate the χ3 and χ2 angle distributions of peptides.
The spectral correlations determined in this study enable important
new insights into protein structure in solution, and in Gln- and Asn-rich
amyloid-like fibrils and prions.