2026-10-14T15:51:20Z https://www.scidb.cn/oai

10.57760/sciencedb.0128s 2026-09-11T09:41:34Z

2026-09-11 Steered molecular dynamics trajectories for: Ultrastable De Novo SuperMyo Proteins Enable High-Performance Macroscopic Fibers from Minimal Repeats doi:10.57760/sciencedb.0128s en Steered molecular dynamics (SMD) trajectories==============================================Associated manuscript:"Ultrastable De Novo SuperMyo Proteins Enable High-Performance MacroscopicFibers from Minimal Repeats" (Nature Communications, in revision).Contents--------Three archives, one per protein construct (the wild-type titin I27 domain andthe two de novo designed SuperMyo domains A339 and B42): smd_trj_I27.tar  - 100 independent SMD replicas for I27 smd_trj_A339.tar - 100 independent SMD replicas for A339 smd_trj_B42.tar  - 100 independent SMD replicas for B42Each archive contains 100 folders (smd_rep1 ... smd_rep100), and each foldercontains: init.gro    - starting structure of the dimeric interchain beta-interface          for that replica (GROMACS coordinate file), taken from an          equilibrium MD snapshot. smd_noPBC.xtc  - SMD pulling trajectory (GROMACS trajectory, PBC removed).Methods-------SMD simulations were performed with GROMACS 2025.3 using the CHARMM36m forcefield to estimate the resistance of the modeled interchain beta-interfaces toforced separation, as described in the Methods section of the associatedmanuscript ("Steered molecular dynamics simulations"). The maximum force ineach trajectory was used to quantify beta-interface dissociation resistance(manuscript Fig. 5d-f).The starting structures were derived from equilibrium MD simulations initiatedfrom AlphaFold3-predicted tetrameric complex models; the AlphaFold3 models andthe representative equilibrium final frames are provided in SupplementaryData 1 of the manuscript.How to read the files---------------------.gro and .xtc files can be opened with standard molecular simulation tools,e.g. GROMACS (gmx trjconv), MDAnalysis (Python), VMD or UCSF ChimeraX.Archives are uncompressed tar files (tar -xf smd_trj_I27.tar). steered molecular dynamics; GROMACS; protein fiber; beta-sheet interface; de novo protein design Peng Zheng PUBLIC https://creativecommons.org/licenses/by/4.0/ dataset Science Data Bank