Optimization of Model Parameters for Describing the Amide I Spectrum of a Large Set of Proteins
2012 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 16, 4831-4842 p.Article in journal (Refereed) Published
A new simulation protocol for the prediction of the infrared absorption of the amide I vibration of proteins was developed. The method incorporates known effects on the intrinsic frequencies (backbone conformation, interpeptide and peptide-solvent hydrogen bonding) and couplings (nearest neighbor coupling, transition dipole coupling) of amide I oscillators in a parametrized manner. Model parameters for the simulation of amide I spectra were determined through fitting and optimization of simulated spectra to experimentally measured infrared spectra of 44 proteins that represent maximum structural variation in terms of different folds and secondary structure contents. Prediction of protein spectra using the optimized parameters resulted in good agreement with experimental spectra and in a considerable improvement compared to a description involving only transition dipole coupling.
Place, publisher, year, edition, pages
2012. Vol. 116, no 16, 4831-4842 p.
Research subject Biophysics
IdentifiersURN: urn:nbn:se:su:diva-80301DOI: 10.1021/jp301095vISI: 000303173800012OAI: oai:DiVA.org:su-80301DiVA: diva2:555276
Reprinted with permission from http://pubs.acs.org/doi/abs/10.1021%2Fjp301095v. Copyright 2012 American Chemical Society.2012-09-192012-09-172012-09-19Bibliographically approved