Azido Homoalanine is a Useful Infrared Probe for Monitoring Local Electrostatistics and Side-Chain Solvation in Proteins

The use of IR probes to monitor protein structure, deduce local electric field, and investigate the mechanism of enzyme catalysis and protein folding has attracted increasing attention. Here the azidohomoalanine (Aha) is considered to be a useful IR probe. The intricate details of the distinct effects of backbone peptide bonds and H-bonded water molecules on the azido stretch mode of the IR probe Aha were revealed by carrying out QM/MM MD simulations of two variants of the protein NTL9, NTL9-Met1Aha, and NTL9-Ile4Aha and comparing the resulting simulated IR spectra with experiments.