Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments

Abstract

Protein-protein complex assembly is one of the major drivers of biological response. Understanding the mechanisms of protein oligomerization/dimerization would allow one to elucidate how these complexes participate in biological activities and could ultimately lead to new approaches in designing novel therapeutic agents. However, determining the exact association pathways and structures of such complexes remains a challenge. Here, we use parallel tempering metadynamics simulations in the well-tempered ensemble to evaluate the performance of Martini 2.2P and Martini open-beta 3 (Martini 3) force fields in reproducing the structure and energetics of the dimerization process of membrane proteins and proteins in an aqueous solution in reasonable accuracy and throughput. We find that Martini 2.2P systematically overestimates the free energy of association by estimating large barriers in distinct areas, which likely leads to overaggregation when multiple monomers are present. In comparison, the less viscous Martini 3 results in a systematic underestimation of the free energy of association for proteins in solution, while it performs well in describing the association of membrane proteins. In all cases the near-native dimer complexes are identified as minima in the free energy surface albeit not always as the lowest minima. In the case of Martini 3 we find that the spurious supramolecular protein aggregation present in Martini 2.2P multimer simulations is alleviated and thus this force field may be more suitable for the study of protein oligomerization. We propose that the use of enhanced sampling simulations with a refined coarse-grained force field and appropriately defined collective variables is a robust approach for studying the protein dimerization process, although one should be cautious of the ranking of energy minima. File list (2) download file view on ChemRxiv Protein-Dimerization-MARTINI.pdf (3.46 MiB) download file view on ChemRxiv SUPPORTING INFORMATION_martini-dimerization.pdf (8.58 MiB)

Impact of bilayer composition on the dimerization properties of the Slg1 stress sensor TMD from a multiscale analysis †

“…Therefore, we attribute these differences to the lack of molecular details in the Martini representation. It has been shown that the protein-protein interactions are overestimated in Martini 2.2 70,71 , as also explicitly seen in our previous work 38 . Therefore, it might be possible that also the protein-lipid interactions suffer from a similar overestimation.…”

Lipid-Mediated Association of the Slg1 Transmembrane Domains in Yeast Plasma Membranes

“…To check this overestimation, we tested the case of DOPC complex mixtures without ergosterol using MARTINI 2.2 and MARTINI 3, and we observed that MARTINI 2.2 slightly overestimates the free energy of association, however, the PS lipids still do not show any considerable effect on the binding energy. Moreover, this overestimation is expected to be systematic, also shown to be the case in a membrane environment and a solution in a recent computational work . Taking the dimer structures, generated via MARTINI 2.2, as the starting point for atomistic simulations, preliminary results suggests that these structures remain stable.…”

“…Of course, there would still be limitations to distinguish RH and LH configurations in the latter case. Concerning the coarse-grained force field, MARTINI 2.2 has been shown to overestimate the protein–protein interactions, , and recently, it was shown that scaling the protein–lipid interaction in MARTINI 2.2 destabilizes protein aggregates while it still preserves the membrane properties . To check this overestimation, we tested the case of DOPC complex mixtures without ergosterol using MARTINI 2.2 and MARTINI 3, and we observed that MARTINI 2.2 slightly overestimates the free energy of association, however, the PS lipids still do not show any considerable effect on the binding energy.…”

Improving Martini 3 for Disordered and Multidomain Proteins

“…One of the most widely used coarse-grained force fields for biomolecular systems is Martini. , Martini maps two to four non-hydrogen atoms to one bead and is mainly parametrized against thermodynamic partitioning data. While Martini has been used successfully to study a wide range of biomolecular systems, earlier versions of the force field have been found to underestimate the global dimensions of flexible multidomain proteins − and overestimate protein–protein interactions. − In order to favor more expanded conformations of multidomain proteins, we have previously used an approach based on increasing the strength of nonbonded interactions between protein and water beads, , improving the agreement with SAXS experiments. Similarly, others have decreased the strength of nonbonded interactions between protein beads to improve the accuracy of IDP phase partitioning and protein–protein interactions …”