Modeling protein stability: a theoretical analysis of the stability of T4 lysozyme mutants |
| |
Authors: | Veenstra DL; Kollman PA |
| |
Affiliation: | University of California San Francisco, Department of Pharmaceutical Chemistry, 94143-0446, USA. |
| |
Abstract: | Free energy calculations were conducted to determine the relative stability
of the unnatural amino acid mutants of T4 lysozyme norvaline (Nvl) and
O-methyl-serine (Mse) and of alanine at residue 133, which is leucine in
the native sequence. These calculations were performed both to assess the
validity of the methodology and to gain a better understanding of the
forces which contribute to protein stability. Peptides of different length
were used to model the denatured state. Restraints were employed to force
sampling of the side chain chi1 dihedral of the perturbed side chain, and
the effect of protein repacking in response to mutation was studied through
the use of different constraint sets. In addition, the convergence behavior
and hysteresis of the simulations in the folded and unfolded states were
determined. The calculated results agree well with experiment, + 1.84
versus + 1.56 kcal/mol for Mse-->Nvl and -3.48 versus -2.2 to -3.6
kcal/mol for Nvl-->Ala. We find that free energy calculations can
provide useful insights to protein stability when conducted carefully on a
well chosen system. Our results suggest that loss of packing interactions
in the native state is a major source of destabilization for mutants which
decrease the amount of buried nonpolar surface area and that subtle
responses of the backbone affect the magnitude of the loss of stability. We
show that the conformational freedom of the chi1 dihedral has a noticeable
effect on protein stability and that the solvation of amino acid side
chains is strongly influenced by interactions with the peptide backbone.
|
| |
Keywords: | |
本文献已被 Oxford 等数据库收录! |
|