Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field

Abstract

Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges in achieving an accurate structural and dynamical description of many biological assemblies, particularly to coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or not available for the vast majority of CG force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations using the SIRAH force field. We provide a set of interaction parameters for calcium, magnesium, and zinc ions, which cover more than 80% of the metal-bound structures reported in the PDB. Simulations performed on several proteins and DNA systems show that it is possible to preclude the use of topological constraints by modifying specific Lennard-Jones interactions.

The SIRAH-CoV-2 Initiative: A Coarse-Grained Simulations' Dataset of the SARS-CoV-2 Proteome

“…Simulations were performed using the SIRAH force field 2.0 ( 29 ) running with the Amber18 suite ( http://ambermd.org ) at ClusterUY. Interaction parameters for bound divalent cations and glycans were reported by Klein et al ( 30 ) and Garay et al ( 31 ), respectively.…”

Enhanced Expansion and Reduced Kiss-and-Run Events in Fusion Pores Steered by Synaptotagmin-1 C2B Domains

“…In the reduced resolution space, the parameterization of metal ions is still approximated or unavailable for the most of coarse-grained force fields. 41 For Martini, ions are modeled with single beads representing both the ion itself and the first hydration shell. 42 Therefore, in this work we have described Syt1-C2B binding mechanisms in a calcium-independent manner.…”

SIRAH late harvest: coarse-grained models for protein glycosylation

“…This makes the glycan representation consistent with the existing force field by construction, and opens the possibility to easily expand the current library of residues using the other functional groups already present in SIRAH. For instance, hydroxyl, N-acetyl, propyl, carboxylic, phosphate and sulfate groups 25,26 will allow covering carbohydrates families like polysaccharides glycosaminoglycans and proteoglycans, and other glycoconjugates.…”

“…Our group have developed the SIRAH force field (Southamerican Initiative for a Rapid and Accurate Hamiltonian), which contains parameters for DNA 19 , proteins, solvents and ions [20][21][22] , lipids 23,24 , posttransductional modifications (PTMs) 25 , and metal ions 26 . In this work, we introduce a CG mapping scheme and parameterization generalizable for arbitrary pyranoses.…”