All-atom molecular dynamics of the HBV capsid supports a role for structural asymmetry in biological function, reveals the potential for triangular pores to mediate cellular signaling, and indicates that capsid flexibility may limit resolution attainable by cryo-EM.
Unbiased molecular dynamics simulations reveal the insertion mechanism of the lipidated tail of the matrix domain of HIV-1 Gag into realistic membrane models and show its effect on lipid sorting.
Antonija Kuzmanic, Ludovico Sutto ... Modesto Orozco
Extensive molecular dynamics simulations enhanced by advanced sampling techniques give a detailed view of p38α canonical activation mechanism, which reveals novel key electrostatic interactions that are put in context of existing experimental data.
Luca Casiraghi, Francesco Mambretti ... Tommaso Bellini
A variant of SELEX introduced here to induce abiotic evolution in a molecular system enables to observe and study speciation, the nature of fitness, and the interplay between use of resources and interactions between individuals.
Simulations of the unliganded human hemoglobin tetramer, which for the first time yield a thermodynamically stable system, cast doubts on the use of standard solvent box sizes for molecular dynamics studies of biological macromolecules.
Tone Bengtsen, Viktor L Holm ... Kresten Lindorff-Larsen
Molecular simulations, small-angle X-ray and neutron scattering experiments and previously measured NMR experiments were combined to study the structure and dynamics of the proteins and lipids in a nanodisc.
New hybrid structure determination methods leveraging the inherent biophysical properties of a macromolecule through molecular dynamics simulations provide accurate and cost-efficient ways of achieving atomic structures from high resolution cryo-electron density maps.
Molecular simulations show how hydrophobicity and conformational disorder underlie the phase separation of elastin-like peptides and the elasticity of human tissues.
George L Hamilton, Nabanita Saikia ... Mark E Bowen
A combination of single molecule fluorescence with DMD simulations and disulfide mapping resolved the multistate structural landscape of the PSG supramodule from PSD-95, which explains how interdomain interactions within PSD-95 enable PDZ3 binding of the critical synaptic adhesion protein neuroligin.