Molywood movies gallery
Rotation of the F1-ATP synthase γ subunit in all possible conformational states of βᵀᴾ (T, blue) and βᴱ (E, red). As the catalytic subunits assume an open or closed geometry, they maintain different number of contacts with the central γ subunit during the two shorter (25 and 30 degree) rotary substeps, moving from 65 to 120 degrees in the synthesis direction. The plots show γ-βᴱ and γ-βᵀᴾ contacts, and color-coding maps the contact frequency onto the structure of the enzyme.
D-ribose binding protein conformational transition from a closed to an open conformation studied by means of an informational biased discrete Molecular Dynamics (dMD) method, using a double Go-like potential with biasing schemes based on Maxwell Demon dynamics and metadynamics methods. The coarse-grained method allows tracing smooth and chemically meaningful transitions between initial (closed conformation, PDB 1BA2) and target (open conformation, PDB 2DRI) structures, identifying intermediate states from the physically reliable generated trajectory.
Pedro Sfriso, Adam Hospital, Agustí Emperador, Modesto Orozco.
Exploration of Conformational Transition Pathways from Coarse-Grained Simulations.
Bioinformatics. (2013) 29(16):1980-6.
https://doi.org/10.1093/bioinformatics/btt324
http://mmb.irbbarcelona.org/TransAtlas/
A double-length channel formed by amphotericin B, composed of 8 drug molecules in each membrane leaflet. The Computational Electrophysiology protocol implemented in Gromacs maintains a constant ion imbalance, which in turn creates an electrochemical gradient. As a result, potassium ions pass through the channel.
Detailed presentation of p38α structural elements and binding sites which play an important role in its activation. The structural elements shown in the generated video are the smaller N-terminal lobe, the α-helical C-terminal lobe, the activation loop (A-loop), the key residues which participate in the stabilisation of ATP, the MAPK insert (MKI) forming a lipid-binding site, the L16 loop that extends from the C-lobe to the N-lobe, the common docking (CD) motif and finally the peptide docking site recognized by the conserved docking motif present in activators, substrates, and regulators of MAPKs.
Kuzmanic A, Sutto L, Saladino G, Nebreda AR, Gervasio FL, Orozco M.
Changes in the free-energy landscape of p38alpha MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations.
Elife. 2017 Apr 26;6:e22175. DOI: 10.7554/eLife.22175
https://doi.org/10.7554/eLife.22175.003
Sample DNA-to-PNA transformation using the dna2pna script (gitlab.com/KomBioMol/dna2pna) based on PDB entry 2MB2. A parallel DNA G-quadruplex morphs into the corresponding PNA G4. The script can also produce Gromacs-compatible topologies based on a recent parametrization by Jasiński et al. (JCTC, 2018).
Formation of a covalent protein-DNA cross-link in the complex of TRF1 with telomeric DNA. The QM subsystem is shown in the context of the full system, and preliminary free energies of bond formation are compared for the 5 and 8 position of guanine. In separate runs, other oxidative intermediates are also considered: guanine cation radical, guanine radical, 8-oxoguanine (8-oxoG), and oxidized 8-oxoG cation radical.
A set of nucleic acid systems simulated with an early version of the experimental machine-learned force field. Each system was simulated in two replicas for 1 microsecond.
