First-principles calculations of protein circular dichroism in the near ultraviolet.
Electronic transitions in aromatic side chains are responsible for the characteristics of proteins in the near UV. We present the first systematic study of a large number of proteins focused on the accurate calculation of near-UV circular dichroism (CD) spectra. We report new parameter sets derived from ab initio calculations for benzene, phenol, and indole that describe the valence electronic transitions to the (1)L(b), (1)L(a), (1)B(b), and (1)B(a) states in the side chains of amino acids phenylalanine, tyrosine, and tryptophan. CD spectra were calculated, using the matrix method with the new side-chain parameters, for 30 proteins whose CD spectra and crystal structures have been made publicly available. The new parameter sets are fully self-consistent and yield near-UV spectra better than those obtained using previous parameter sets. The mean absolute errors for computed wild-type spectra in the near UV are reduced by a factor of approximately 2. A similiar reduction is found for the near-UV spectra (and difference spectra) of mutants involving aromatic amino acids. Empirical modifications to model vibronic coupling in the side-chain chromophore of phenylalanine offer no overall improvement. Protein CD calculations from first principles coupled with atomic-level modeling enhance the utility and interpretability of CD measurements in the near UV.
School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
David M
DM
Rogers
Jonathan D
JD
Hirst
D000595:Amino Acid Sequence; D024322:Amino Acids, Aromatic / Q000737:chemistry*; D000818:Animals; D007611:Aprotinin / Q000737:chemistry / Q000235:genetics; D001426:Bacterial Proteins; D024402:Carbonic Anhydrase II / Q000737:chemistry / Q000235:genetics; D002417:Cattle; D002942:Circular Dichroism / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D009154:Mutation; D010649:Phenylalanine / Q000737:chemistry / Q000235:genetics; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D012260:Ribonucleases / Q000737:chemistry / Q000235:genetics; D055672:Static Electricity; D014364:Tryptophan / Q000737:chemistry / Q000235:genetics; D014443:Tyrosine / Q000737:chemistry / Q000235:genetics; D014466:Ultraviolet Rays
D024322:Amino Acids, Aromatic; D001426:Bacterial Proteins; D011506:Proteins; D014443:Tyrosine; D010649:Phenylalanine; D014364:Tryptophan; D007611:Aprotinin; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease; D024402:Carbonic Anhydrase II