1,720,989 research outputs found
Supplementary Data to: "Cysteine-mediated structural stabilization of the tetrameric GlpF"
No full textSimulation files, molecular structures and trajectories tetrameric GlpF wild type and M4C mutant. in the latter, 4 cysteine residues in the transmembrane helix bundle of GlpF, in detail C11, C28, C80, and C99 are replaced by glycines. The data underlays our publication on the role of those 4 cysteine residues for stability of membrane inserted tetrameric GlpF in a simple 3-component membrane mimic of E. coli polar lipid extract (PLE).
The zips include:
1. the charmm36-july2017.ff simulation directory for GROMACS 202X
2. gromacs simulation files (topologies and mdp files)
3. snapshots of first and last (3µs) frames of two replica of the simulations including all atoms in the simulation systems
4. protein trajectories saved every 100 ps
5. protein pdb files every 100 n
Supplementary data to "Roles of ligand, phosphorylation, and membrane in assembling human β2-adrenergic receptor-β-arrestin complexes"
No full textGROMACS simulation files, initial and final snapshots (all atoms) as well as simulation trajectories (proteins, ligands, membrane) of
(i) beta-arrestin 2 (barr2) in inactive and active form interacting with a membrane with or without PIP2 lipids,
(ii) beta2-adrenergic receptor activated by adrenaline and either phosphorylated on S355 and S356 or not, each embedded in a membrane with or without PIP2,
(iii) tail complex type of beta2-adrenergic receptor inactivated by ICI, phosphorylated on S355 and S356 in complex with active beta-arrestin2 in membranes with or without PIP2
(iv) core complex type of beta2-adrenergic receptor activated by adrenaline (ADR) with active beta-arrestin2 inserted by its fingerloop in the receptor core, in membrane with or without PIP2
(vi) tail-core complex of beta2-adrenergic receptor activated by adrenaline (ADR) and phosphorylated on S355 and S356 with beta-arrestin2 bound to both, the receptor core and the phosphorylated C-tail, in membrane with or without PIP2
Supplementary Data to: "Activation mechanism of the full-length histidine kinase LvrB, a master virulence regulator in pathogenic Leptospira"
No full textInitial coordinate and simulation input files and a coordinate files of the final outputs as well as of the simulation trajectories (protein only) for all-atom MD simulations of LvrB performed using CHARMM36m/TIP4p in GROMACS2023. (pdb, xtc)
Simulation data on phosphorylated aspartic acid (residue APP) with parameters generated by CHARMM-GUI are included
Supplementary Information to "Linker-Cluster Cooperativity in Confinement of Proline- Functionalized Zr-Based Metal-Organic Frameworks and its Effect on the Organocatalytic Aldol Reaction"
No full textFiles and structures for performing all-atom molecular dynamics simulations of UiO-67 and UiO-67-based structures filled with Methanol and reactant and product molecules
Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3'
No full textSimulation files, molecular structures and trajectories, and jupyter notebooks used for analysis underlaying our publication on membrane insertion of monomeric gasdermin D to E. coli polar lipid extract (PLE).
In detail:
charmm36-july2017.ff simulation directory for GROMACS 202X
used and useful gromacs files (topologies and mdp files)
jupyter notebooks for analysis
snapshots and trajectories of monomeric gasdermin D in E. coli PLE, including umbrella sampling simulations
snapshots and trajectories of monomeric gasdermin D in POPC/30%cholesterol
snapshots and trajectories of arcs of seven gasdermin D subunits in E. coli PLE.
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Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching"
No full textGROMACS simulation files, input and final structures for CHARMM36m MD simulations including our refined parameters for phosphorylated serine in 3 different protonation states.
The directory charmm36-jul22mod.ff contains our refined parameters
Data for: ART-SM: Boosting Fragment-Based Backmapping by Machine Learning
No full textThe simulation files, molecule topologies, and analysis workflows required to generate the results of our paper 'ART-SM: Boosting Fragment-Based Backmapping by Machine Learning' published in J. Chem. Theory Comput..
In details:
simulations.tar.gz: Contains the pdb (molecular structure), xtc (trajectory), mdp (MD parameters), itp (topology), and top (topology) files. GROMACS 2021 or 2023 was used for the simulations (see paper for details). Additionally, ART-SM mapping files (generated with version 1.0) and Backward mapping files from coarse-grained to atomistic resolution are included.
workflows.tar.gz: Snakemake was used to handle the analysis workflows. The corresponding Snakefiles and python/bash scripts to reproduce the results in the paper are included. The actual results are not included (see paper instead). The main packages required for reproducing the results are listed under 'Software Metadata - Software Requirements'. If a second version is specified it was used only for 'sds_capb_section_4_4'. The first specified version was used for all other analyses.
Please have a look at the README files contained in each .tar.gz file.</p
Supplementary Information to "Molecular determinants of solvent nanoseparation by nanoporous carbon materials"
No full textFiles and structures for performing and analysing coarse-grained molecular dynamics simulations of solvent diffusion through nanoporous carbon materials
Supplementary Material for 'Entropic barrier of water permeation through single-file channels'
No full textFacilitated water permeation through narrow biological channels is fundamental for all forms of life. This process involves dehydration of bulk water entering the single-file region and hydrogen bond formation with channel lining amino acid residues. Despite its significance in health and disease as well as for biotechnological applications the energetics of water permeation are still elusive. Whereas the enthalpic contribution to Gibbs free energy is readily accessible via temperature dependent water permeability measurements, estimation of the entropic contribution requires information on the temperature dependence of the rate of water permeation. By means of accurate activation energy measurements of water permeation through AQP1 and by determining the accurate single channel permeability we were, for the first time, able to estimate the entropic barrier of water permeation through a narrow biological channel. This is a first step in understanding the energetic contributions in various biological and artificial channels exhibiting vastly different pore geometries
Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'
No full textEukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture (PMR) as the defining terminal event. PMR was long thought to be driven by osmotic pressure, until it was recently shown to be in many cases an active process, mediated by the protein ninjurin-1 (NINJ1). Here, we studied whether the newly resolved cryo-electron microscopy NINJ1 filaments are capable to cap membrane edges by multiscaling molecular dynamics simulations. Site-directed mutagenesis was employed to validate the function of the resulting supramolecular arrangement. The membrane protein NINJ1 is thus an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death
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