Saturation Mutagenesis by Efficient Free-Energy Calculation

J Chem Theory Comput. 2018 Feb 13;14(2):894-904. doi: 10.1021/acs.jctc.7b01099. Epub 2018 Jan 8.

Abstract

Single-point mutations in proteins can greatly influence protein stability, binding affinity, protein function or its expression per se. Here, we present accurate and efficient predictions of the free energy of mutation of amino acids. We divided the complete mutational free energy into an uncharging step, which we approximate by a third-power fitting (TPF) approach, and an annihilation step, which we approximate using the one-step perturbation (OSP) method. As a diverse set of test systems, we computed the solvation free energy of all amino acid side chain analogues and obtained an excellent agreement with thermodynamic integration (TI) data. Moreover, we calculated mutational free energies in model tripeptides and established an efficient protocol involving a single reference state. Again, the approximate methods agreed excellently with the TI references, with a root-mean-square error of only 3.6 kJ/mol over 17 mutations. Our combined TPF+OSP approach does show not only a very good agreement but also a 2-fold higher efficiency than full blown TI calculations.

MeSH terms

  • Amino Acids / chemistry*
  • Amino Acids / genetics
  • Molecular Dynamics Simulation*
  • Mutagenesis
  • Thermodynamics*

Substances

  • Amino Acids