Surface salt bridges, double-mutant cycles, and protein stability: an experimental and computational analysis of the interaction of the Asp 23 side chain with the N-terminus of the N-terminal domain of the ribosomal protein L9

Experimental and theoretical double-mutant cycles have been used to investigate a salt bridge in the N-terminal domain of the protein L9. Aspartic acid 23 is the only acidic residue involved in a well-defined pairwise interaction, namely, a partially solvent-exposed salt bridge with the protonated N-terminus of the protein. Mutations were studied in which Asp 23 was substituted by alanine, asparagine, and nitrile alanine. Interactions with the N-terminus were probed by comparisons between proteins with a protonated and acetylated N-terminus. The mutants were all folded, and the structures were unchanged from wild type as judged by CD and 2-D NMR. The coupling free energy between the N-terminus and the side chain of Asp 23 measured through double-mutant cycle analysis was favorable and ranged from -0.7 to -1.7 kcal mol(-1), depending upon the set of mutants used. This relatively large coupling free energy for a surface salt bridge likely arises from geometric factors that reduce the entropy loss associated with salt-bridge formation and from structural relaxation in the mutants. Coupling free energies computed with continuum electrostatic calculations agreed well with the experimental values when full account was taken of all potential interactions, particularly those involving Asp 23 and the acetylated N-terminus as well as interactions with solvent. The measured and calculated coupling free energy decreased only slightly when the salt concentration was increased from 100 to 750 mM NaCl. The calculations suggest that the coupling free energy between D23 and the N-terminus measured through the experimental double-mutant cycle analysis is significantly smaller than the actual interaction free energy between the groups in the wild-type structure because of the inapplicability of assumptions frequently used to interpret double-mutant cycles.