QM/MM simulation of the amide-I band in the Raman spectrum of insulin

Abstract

ABSTRACTRaman spectroscopy is an effective tool to detect conformational changes and secondary structures of biological molecules. The amide-I band representing the amide carbonyl (C=O) stretching, with smaller contributions of C–N stretching and N–H bending is a signature band for protein secondary structure conformation. We have simulated the Raman spectra of insulin by a hybrid quantum-mechanics and molecular-mechanics (QM/MM) method with an aim to provide an accurate description of the amide-I band. To fulfil this aim we have considered three different QM/MM models with increasingly accurate description of the electrostatic environment for tyrosine (TYR), phenylalanine (PHE) and cystine (CYS) residues of insulin. All three models successfully describe the experimental Raman spectral features associated with the vibrational modes of the amino acid side chains. However, an accurate simulation of the amide-I band is achieved only in one of the three models, where the peptide backbone atoms together with its hydrogen bonding partners are treated with QM method. This work indicates that the accurate treatment of electrostatic interactions of the peptide backbone is crucial for correct simulation of the amide-I region, which acts as a spectral signature of proteins.