Modeling Vibrational Spectra of Amino Acid Side Chains in Proteins: The Carbonyl Stretch Frequency of Buried Carboxylic Residues

Andrei K. Dioumaev, Mark S. Braiman

Research output: Contribution to journalArticlepeer-review

64 Scopus citations


To improve the use of vibrational spectra for modeling Asp and Glu environments buried in proteins, vc=o frequencies of aliphatic carboxylic acids and N-acetylaspartic acid a-amide were compared in several different solvents. These data indicate that propionic acid and longer-chain aliphatic carboxylic acids are all quite similar, and serve as better models for Asp and Glu residues buried in proteins than does acetic acid. For propionic acid, vc-o frequencies above 1745 cm-1 are observed only in non-H-bonding solvents. Furthermore, in such non-H-bonding solvents, the vc=o frequency exhibits a linear correlation with Onsager's parameter, 2 (ε - l)/ (2ε + 1), which is expected to be proportional to the strength of the solute-induced electrostatic (“reaction”) field of the solvent. We also measured a vc=o frequency of 1742 cm-1 for the protonated Asp-26 residue of thioredoxin which is known to be surrounded principally by nonpolar groups. These results are used to model the environment of the Asp-85 residue of bacteriorhodopsin, for which the vc=o frequency has been measured previously in several photointermediate states. In the unphotolyzed (bR) state, the Asp-85 residue (vc=o ≃ 1730 cm-1) is in a relatively polar hydrogen-bonding environment, but this environment is drastically changed upon photoconversion to the M state (vc-o = 1762 cm-1). We conclude that in the latter state, the Asp-85 COOH group is in a highly nonpolar environment, characterized by the absence not only of hydrogen bonding but also of other forms of external dielectric stabilization.

Original languageEnglish (US)
Pages (from-to)10572-10574
Number of pages3
JournalJournal of the American Chemical Society
Issue number42
StatePublished - 1995
Externally publishedYes

ASJC Scopus subject areas

  • Catalysis
  • General Chemistry
  • Biochemistry
  • Colloid and Surface Chemistry


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