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Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations.

ABSTRACT: 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 III(P) (AmIII(P)) vibrations of Gln and Asn depend cosinusoidally on their side chain OCCC dihedral angles (the ?3 and ?2 angles of Gln and Asn, respectively). We use UV resonance Raman (UVRR) and visible Raman spectroscopy to experimentally correlate the AmIII(P) Raman band frequency to the primary amide OCCC dihedral angle. The AmIII(P) structural sensitivity derives from the Gln (Asn) C?-C? (C?-C?) stretching component of the vibration. The C?-C? (C?-C?) bond length inversely correlates with the AmIII(P) band frequency. As the C?-C? (C?-C?) bond length decreases, its stretching force constant increases, which results in an upshift in the AmIII(P) frequency. The C?-C? (C?-C?) bond length dependence on the ?3 (?2) dihedral angle results from hyperconjugation between the C??O? (C??O?) ?* and C?-C? (C?-C?) ? orbitals. Using a Protein Data Bank library, we show that the ?3 and ?2 dihedral angles of Gln and Asn depend on the peptide backbone Ramachandran angles. We demonstrate that the inhomogeneously broadened AmIII(P) band line shapes can be used to calculate the ?3 and ?2 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.

SUBMITTER: Punihaole D

PROVIDER: S-EPMC5065012 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature

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Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations.

Punihaole David D Hong Zhenmin Z Jakubek Ryan S RS Dahlburg Elizabeth M EM Geib Steven S Asher Sanford A SA

The journal of physical chemistry. B 20150930 41

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 III(P) (AmIII(P)) 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 AmIII(P) Raman band frequency to ...[more]

PMID: 26392216

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Project description:Alkylureas display hydrocarbon and amide groups, the primary functional groups of proteins. To obtain the thermodynamic information that is needed to analyze interactions of amides and proteins with nucleobases and nucleic acids, we quantify preferential interactions of alkylureas with nucleobases differing in the amount and composition of water-accessible surface area (ASA) by solubility assays. Using an established additive ASA-based analysis, we interpret these thermodynamic results to determine interactions of each alkylurea with five types of nucleobase unified atoms (carbonyl sp2O, amino sp3N, ring sp2N, methyl sp3C, and ring sp2C). All alkylureas interact favorably with nucleobase sp2C and sp3C atoms; these interactions become more favorable with an increasing level of alkylation of urea. Interactions with nucleobase sp2O are most favorable for urea, less favorable for methylurea and ethylurea, and unfavorable for dialkylated ureas. Contributions to overall alkylurea-nucleobase interactions from interactions with each nucleobase atom type are proportional to the ASA of that atom type with proportionality constant (interaction strength) ?, as observed previously for urea. Trends in ?-values for interactions of alkylureas with nucleobase atom types parallel those for corresponding amide compound atom types, offset because nucleobase ?-values are more favorable. Comparisons between ethylated and methylated ureas show interactions of amide compound sp3C with nucleobase sp2C, sp3C, sp2N, and sp3N atoms are favorable while amide sp3C-nucleobase sp2O interactions are unfavorable. Strongly favorable interactions of urea with nucleobase sp2O but weakly favorable interactions with nucleobase sp3N indicate that amide sp2N-nucleobase sp2O and nucleobase sp3N-amide sp2O hydrogen bonding (NH···O?C) interactions are favorable while amide sp2N-nucleobase sp3N interactions are unfavorable. These favorable amide-nucleobase hydrogen bonding interactions are prevalent in specific protein-nucleotide complexes.

Dataset Information

Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations.

Publications

Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations.

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