pmx: Automated protein structure and topology generation for alchemical perturbations

Abstract

Computational protein design requires methods to accurately estimate free energy changes in protein stability or binding upon an amino acid mutation. From the different approaches available, molecular dynamics-based alchemical free energy calculations are unique in their accuracy and solid theoretical basis. The challenge in using these methods lies in the need to generate hybrid structures and topologies representing two physical states of a system. A custom made hybrid topology may prove useful for a particular mutation of interest, however, a high throughput mutation analysis calls for a more general approach. In this work, we present an automated procedure to generate hybrid structures and topologies for the amino acid mutations in all commonly used force fields. The described software is compatible with the Gromacs simulation package. The mutation libraries are readily supported for five force fields, namely Amber99SB, Amber99SB*-ILDN, OPLS-AA/L, Charmm22*, and Charmm36.

Keywords: alchemy; free energy calculations; molecular dynamics; mutations; thermostability.

Figure 1

An overall workflow of the pmx hybrid topology and structure generation. The force field specific mutation libraries are created by generate_hybrid_residue.py using the amino acid topologies, bonded, and nonbonded parameters as defined in the force field of interest. By default pmx provides mutation libraries for five commonly used force fields. A hybrid mutated structure is generated by mutate.py. The Gromacs standard tool pdb2gmx uses the hybrid structure to create its topology, which subsequently is processed by generate_hybrid_topology.py by adding the required parameters for the A and B states.

Figure 2

A schematic illustration of the two main pmx data structures used in the hybrid structure and topology generation. The top row describes the classes containing protein structure information, whereas the bottom rows describe the topological information. A detailed description can be found in the main text.

Figure 3

Thermodynamic cycles used for validation. A) The double system in a single simulation box setup. Two tripeptides with the hybrid structures, V2F and F2V, are placed in the same box. During an alchemical transition, valine is morphed into phenylalanine and phenylalanine into valine. The overall state of the system remains unchanged, therefore, the calculated ΔΔG must be equal to 0 kJ/mol. B: results of the ΔΔG calculation over a closed thermodynamic cycle for nine amino acid mutation pairs for five force fields.

Figure 4

Illustration of the input/output structures and an output topology of the pmx scripts. A) A capped Gly-Val-Gly tripeptide as a starting structure for the mutation. B) Structure of the tripeptide with the hybrid V2F amino acid. Valine (dark gray) is in the physical state A, whereas phenylalanine (light gray) is in the state B. C) An excerpt from the hybrid V2F topology.