Circular dichroism spectrum of peptides in the poly(Pro)II conformation.
The poly(Pro)II (P(II)) conformation is increasingly recognized as an important element in peptide and protein conformation. Circular dichroism (CD) is one of the most useful methods for detecting and characterizing P(II). Although the standard exciton-based model for predicting peptide CD spectra works well for alpha-helices and beta-sheets, it fails to reproduce the P(II) CD spectrum because it does not account for mixing of the n pi* and pi pi* transitions with transitions in the deep UV, which is significant for the P(II) conformation. In this work, the exciton model is extended to include this mixing, using ab initio-derived bond polarizability tensors to calculate the contributions of the high-energy transitions. The strong negative 195-nm and weaker positive 220-nm CD bands of P(II) are reproduced for (Ala)(n) conformers in the P(II) region of the Ramachandran map. For the canonical P(II) conformation from fiber diffraction of poly(Pro)II (-77, +146), the results are poor, but conformations with less negative phi (approximately -60 degrees) and more positive psi (> or = 160 degrees) give spectra showing the P(II) characteristics. The CD of (Pro)(n) is not reproduced by the calculations, probably because variations in (phi,Psi), ring puckering, and cis-trans isomerism are not included in the model The extended model also gives improved results for alpha-helical polypeptides, leading to increased amplitude for the 205-nm band and decreased amplitude for a negative band predicted near 180 nm.
Woody
Robert W
RW
Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA. robert.woody@colostate.edu
D002942:Circular Dichroism; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary
D010455:Peptides; C011083:polyproline