Saturation Mutagenesis by Efficient Free-Energy Calculation.

Zuzana Jandova,Chris Oostenbrink,Daniel Fast,Martina Setz,Maria Pechlaner

doi:10.1021/acs.jctc.7b01099

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.

Highlights

One-point mutation in a carefully chosen position in a protein may have a huge impact on a number of various properties, such as protein stability,[1] protein secondary structure,[2] catalytic function,[3] oligomerization,[4] binding of small ligands,[5] DNA,[6] or protein−protein interactions.[7]
The total rootmean-square error (RMSE) over all compounds in Table 1 between ΔGQLR>AN and ΔGQTI>N amounts to 11.8 kJ/mol, whereas between ΔGQTP>FN and ΔGQTI>N this is reduced to 3.3 kJ/mol
The only two cases where third-power fitting (TPF) deviates from thermodynamic integration (TI) by more than 4 kJ/ mol are the compounds with a full positive charge (Arg and Lys side chain analogues)

Summary

Introduction

One-point mutation in a carefully chosen position in a protein may have a huge impact on a number of various properties, such as protein stability,[1] protein secondary structure,[2] catalytic function,[3] oligomerization,[4] binding of small ligands,[5] DNA,[6] or protein−protein interactions.[7] It is of a great interest to understand and be able to predict these effects, for which it is highly relevant to compute the associated free energy of mutation

Objectives

Methods

Results

Conclusion