Overall Efficiency of the Methodology

Although the overall correlation seems good, some significant deviations between experimental and predicted pK values are apparent, and some improvements and modifications of the procedure are still required. 

Total Charge of BPTI Along a Molecular Dynamics Trajectory 

In a recent study, Wlodek et al. investigated the extent to which the assumed protonation state of a protein influences its molecular dynamics trajectory. The authors also determined how often their titration algorithm predicted ionization states identical to those imposed on the groups, when applied to a set of structures derived from a molecular dynamics trajectory. As a model they took the bovine pancreatic trypsin inhibitor (BPTI), a 58-residue protein that is often used as the prototypical small protein in many experimental and theoretical studies. 

There are several examples of application of the FDPB model in theoretical analysis of protein stability. Fiere we discuss experimental and theoreticaP results for the pFi dependence of barnase stability. Barnase is a ribonuclease from Bacillus amyloliquefaciens, a small (110 residues), monomeric, single-domain enzyme that lacks disulfide bonds and undergoes reversible unfolding by a two-state process.  

As was shown before, the PB model, using two assumptions (that the pK s computed for the crystal structure represents the native protein, and that models adequately characterize denatured states of the protein), reproduces fairly well the overall shapes of stability versus pH curves for a number of 

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Nevertheless, the search for alternative amination systems is still ongoing, aiming to increase the overall efficiency of the methodology and, therefore, making the strategy more attractive for practical applications. 

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