Assignment of side-chain conformation using adiabatic energy mapping, free energy perturbation, and molecular dynamic simulations

The effect of Asp54 phosphorylation on the energetics and dynamics in the response regulator protein Spo0F studied by molecular dynamics

The response regulator protein Spo0F acts as an intermediate phospho-messenger in the signal transduction pathway that controls initiation of the differentiation process of sporculation in the bacterium Bacillus subtilis. The regulatory domain of Spo0F contains a triad of three conserved aspartate residues, whereof one aspartate (Asp54) is phosphorylated. Using molecular dynamics simulations, we have studied the changes in flexibility induced by phosphorylation and estimated the free energy cost of introducing a phosphate group at this position using alchemical free energy calculations. The deduced conformational flexibility compares well with experimental NMR results. We find that the apo-conformation of the protein explores a rough energy landscape resulting in a broad population of conformational substates. Phosphorylation of Spo0F reduces protein flexibility, and in particular, the so-called anchor and recognition regions exhibit lower mobility relative to the apo-conformation. Phosphorylation of Asp54 (P-Asp54), in which the apo-structure coordinates to the magnesium ion, results in extension of the sidechain, and depending on which carboxylate oxygen is phosphorylated, distinct interactions between P-Asp54 and magnesium ion as well as residues in its proximity are established. However, phosphorylation does not affect the coordination number of the magnesium ion yielding, within the statistical uncertainties, the same free energy change.

Direct observation of structural heterogeneity in a beta-sheet

Structural heterogeneity is thought to be inherent in many proteins and may be important for their folding and/or function. However, it is difficult to detect by conventional methods. Carbon-deuterium bonds are environmentally sensitive, nonperturbative probes of protein environments whose observation and characterization are facilitated by their unique stretching absorption frequency in an otherwise unobscured region of the IR spectrum. We demonstrate that deuterium atoms incorporated at C(alpha) backbone positions (C(alpha)-D bonds) are sensitive to the local backbone structure and thus may be used not only to detect structural heterogeneity but also to help characterize it structurally. Density functional theory calculations are used to predict that C(alpha)-D bonds of glycine are sensitive to their local structure, with the absorptions red-shifted for an extended beta-sheet relative to gamma- and alpha-helix-like turns. These predictions are confirmed using the N-terminal Src homology 3 (nSH3) domain from the human CrkII adaptor protein, whose function as a signaling domain may require structural heterogeneity. Four nSH3 variants were synthesized in which individual glycine residues were site-specifically modified with C(alpha)D(2) glycine residues. Not only were the C(alpha)-D bonds incorporated within the beta-sheet of nSH3 more red-shifted than those incorporated within loops, but the data also reveal that nSH3 populates at least two discrete beta-sheet core structures. Moreover, the data suggest that the folded core of nSH3 may be less ordered than previously believed and also that the unfolded state may be more ordered than previously thought, and both of these factors may influence the folding and function of these important signaling domains. The C-D-based IR technique should be generally useful in the characterization of structure and heterogeneity of both folded and unfolded states.