Coarse-Grained RNA Model for the Martini 3 Force Field DOI Creative Commons

Danis Yangaliev,

S. Banu Ozkan

Опубликована: Апрель 17, 2025

Abstract In this work we developed a coarse-grained model for RNA that is compatible with the Martini 3 force field. The parameterized following philosophy combining top-down and bottom-up approaches. nonbonded interactions in are derived from partitioning of nucleobases between polar nonpolar solvents, along calculations potential mean bases. For bonded interactions, parameters were refined based on atomistic simulations double-stranded RNA. Additionally, an elastic network was incorporated to maintain structural integrity complex molecules, such as transfer RNA, other specific configurations. We present implementation demonstrate its ability capture properties individual bases, single-stranded RNA−protein complexes. Compared 2 version, current offers several key advantages. It fully updated field, exhibits greater numerical stability—allowing successful simulation larger RNA–protein complexes, ribosomes, using standard timestep 20 fs, it demonstrates improved agreement all-atom models experimental data. This new enables realistic large-scale explicit-solvent molecular dynamics RNA-containing systems. Significance research introduces explicit water MD software. both data, enabling more accurate computationally efficient large RNA-protein advancement facilitates study allowing modeling biological complexes paving way systems across various fields, including therapeutics, biology, synthetic where understanding crucial developing biomedical applications advancing fundamental research.

Язык: Английский

Metals in Motion: Understanding Labile Metal Pools in Bacteria DOI Creative Commons
John D. Helmann

Biochemistry, Год журнала: 2025, Номер unknown

Опубликована: Янв. 5, 2025

Metal ions are essential for all life. In microbial cells, potassium (K+) is the most abundant cation and plays a key role in maintaining osmotic balance. Magnesium (Mg2+) dominant divalent required nucleic acid structure as an enzyme cofactor. Microbes typically require transition metals manganese (Mn), iron (Fe), copper (Cu), zinc (Zn), although precise set of metal needed to sustain life variable. Intracellular pools can be conceptualized chemically complex mixture rapidly exchanging (labile) ions, complemented by those reservoirs that exchange slowly relative cell metabolism (sequestered). Labile buffered transient interactions with anionic metabolites macromolecules, ribosome playing major role. Sequestered include many metalloproteins, cofactors, storage depots, some redeployed upon depletion. Here, I review size, composition, dynamics intracellular highlight gaps understanding.

Язык: Английский

Процитировано

0
Coarse-Grained RNA Model for the Martini 3 Force Field DOI Creative Commons

Danis Yangaliev,

S. Banu Ozkan

Опубликована: Апрель 17, 2025

Abstract In this work we developed a coarse-grained model for RNA that is compatible with the Martini 3 force field. The parameterized following philosophy combining top-down and bottom-up approaches. nonbonded interactions in are derived from partitioning of nucleobases between polar nonpolar solvents, along calculations potential mean bases. For bonded interactions, parameters were refined based on atomistic simulations double-stranded RNA. Additionally, an elastic network was incorporated to maintain structural integrity complex molecules, such as transfer RNA, other specific configurations. We present implementation demonstrate its ability capture properties individual bases, single-stranded RNA−protein complexes. Compared 2 version, current offers several key advantages. It fully updated field, exhibits greater numerical stability—allowing successful simulation larger RNA–protein complexes, ribosomes, using standard timestep 20 fs, it demonstrates improved agreement all-atom models experimental data. This new enables realistic large-scale explicit-solvent molecular dynamics RNA-containing systems. Significance research introduces explicit water MD software. both data, enabling more accurate computationally efficient large RNA-protein advancement facilitates study allowing modeling biological complexes paving way systems across various fields, including therapeutics, biology, synthetic where understanding crucial developing biomedical applications advancing fundamental research.

Язык: Английский

Процитировано

0