Stretching vibrational frequencies and pKa differences in H-bond networks of protein environments

The experimentally measured stretching vibrational frequencies of O-D [vO-D(donor)] and C=O [vC=O(donor)] Hbond donor groups can provide valuable information about the H-bonds in proteins. Here, using a quantum mechanical/molecular mechanical approach, the relationship between these vibrational frequencies and the difference in pKa values between H-bond donor and acceptor groups [ApKa(donor ... acceptor)] in bacteriorhodopsin and photoactive yellow protein environments was investigated. The results show that vO-D(donor) is correlated with ApKa(donor ... acceptor), regardless of the specific protein environment. vC=O(donor) is also correlated with ApKa(donor ... acceptor), although the correlation is weak because the C=O bond does not have a proton. Importantly, the shifts in vO-D(donor) and vC=O(donor) are not caused by changes in pKa (donor) alone, but rather by changes in ApKa(donor ... acceptor). Specifically, a decrease in ApKa(donor ... acceptor) can lead to proton release from the H-bond donor group toward the acceptor group, resulting in shifts in the vibrational frequencies of the protein environment. These findings suggest that changes in the stretching vibrational frequencies, in particular vO-D(donor), can be used to monitor proton transfer in protein environments.

Automated summary

The experimentally measured stretching vibrational frequencies of O-D and C=O Hbond donor groups can provide valuable information about the H-bonds in proteins. The relationship between these vibrational frequencies and the difference in pKa values between H-bond donor and acceptor groups in bacteriorhodopsin and photoactive yellow protein environments was investigated using a quantum mechanical/molecular mechanical approach. The results show that the vibrational frequencies are correlated with the pKa values, and the shifts in the frequencies are caused by changes in pKa values.