Hydrogen bond interactions of G proteins with the guanine ring moiety of guanine nucleotides

We have utilized Raman difference spectroscopy to investigate hydrogen bonding interactions of the guanine moiety in guanine nucleotides with the binding site of two G proteins, EF‐Tu (elongation factor Tu from Escherichia coli) and the c‐Harvey ras protein, p21 (the gene product of the human c‐H‐rus proto‐oncogene). Raman spectra of proteins complexed with GDP (guanosine 5′ diphosphate), IDP (inosine 5′ diphosphate), 6‐thio‐GDP, and 6‐¹⁸O‐GDP were measured, and the various difference spectra were determined. These were compared to the difference spectra obtained in solution, revealing vibrational features of the nucleotide that are altered upon binding. Specifically, we observed significant frequency shifts in the vibrational modes associated with the 6‐keto and 2‐amino positions of the guanine group of GDP and IDP that result from hydrogen bonding interactions between these groups and the two proteins. These shifts are interpreted as being proportional to the local energy of interaction (δH) between the two groups and protein residues at the nucleotide binding site. Consistent with the tight binding between the nucleotides and the two proteins, the shifts indicate that the enthalpic interactions are stronger between these two polar groups and protein than with water. In general, the spectral shifts provide a rationale for the stronger binding of GDP and IDP with p21 compared to EF‐Tu. Despite the structural similarity of the binding sites of EF‐Tu and p21, the strengths of the observed hydrogen bonds at the 6‐keto and 2‐amino positions vary substantially, by up to a factor of 2. The hydrogen bond between the protein and the 6‐keto group is stronger for GDP in EF‐Tu compared to p21, but this comparison is reversed for bound IDP. Thus, the removal of the 2‐amino group from GDP to form IDP affects binding properties distal to the amino site.