Arginine: II. Interactions of Its Salt Bridges with Branched Aliphatic Side Chains

Previous analyses of the structures deposited in the PDB revealed that arginine (Arg) side chains are often in close contact with leucine (Leu) side chains. In the previous paper, we studied interactions between Leu and Arg side chains alone [Ng et al. https://doi.org/10.1021/acs.jpcb.5c02168]. In this work, we have focused on the interactions between Leu side chains and salt bridges formed between Arg and acidic side chains. We inspected the trimer structures of the three side chains: Leu, Arg, and an acidic residue in the high-resolution files in the PDB. We also performed optimization of the model trimers with the ωB97X-D density functional and aug-cc-pVTZ basis set. We found that the salt bridges in a relatively low-polarity environment are most likely in a dynamic equilibrium between an ionic form and two neutral tautomers. That leads to the increased distances between Arg and the acidic residue as well as to the increased density of low-energy vibrational states, consequently increasing specific heat and entropy. The Leu residue controls the polarity of the environment. These findings explain why an increased number of salt bridges provides increased stability to the thermophilic enzymes and increases the fluctuations and mobility of psychrophilic proteins. Further studies are needed to find out whether methyl protons are scrambled with amino protons. We also performed calculations on the trimers with the doubly protonated Arg side chain. Energy of such trimers is lower than the energy of the monoprotonated trimers. Their lowest energy is obtained after a proton transfer to an acidic residue, and the guanidinium ion returns to the lowest energy planar structure. Such proton transfer may occur in membrane proteins where salt bridges are interspersed between nonpolar residues.