The pyrrolidine ring of the amino acid proline reduces the conformational freedom of the protein backbone in its unfolded form and thus enhances protein stability. The strategy of inserting proline into regions of the protein where it does not perturb the structure has been utilized to stabilize many different proteins including enzymes. However, most of these efforts have been based on trial and error, rather than rational design. Here, we try to understand proline’s effect on protein stability by introducing proline mutations into various regions of the B1 domain of Streptococcal protein G. We also applied the Optimization of Rotamers By Iterative Techniques computational protein design program, using two different solvation models, to determine the extent to which it could predict the stabilizing and destabilizing effects of prolines. Use of a surface area dependent solvation model resulted in a modest correlation between the experimental free energy of folding and computed energies; on the other hand, use of a Gaussian solvent exclusion model led to significant positive correlation. Including a backbone conformational entropy term to the computational energies increases the statistical significance of the correlation between the experimental stabilities and both solvation models.
Submitter: Marie Ary
Submission Date: Feb. 24, 2017, 3:49 p.m.
|Number of data points||77|
|Assays/Quantities/Protocols||Experimental Assay: ΔGf (25°C) ; Experimental Assay: Tm ; Derived Quantity: ΔΔGf (25°C) ; Computational Protocol: Ecalc (LK) ; Computational Protocol: Ecalc (SM)|
|Libraries||Effect of proline mutations on Tm, ΔGf, and computed energy (Table 1)|