Andrea Amadei

TL;DR: Analysis of extended molecular dynamics simulations of lysozyme in vacuo and in aqueous solution reveals that it is possible to separate the configurational space into two subspace: an “essential” subspace containing only a few degrees of freedom and the remaining space in which the motion has a narrow Gaussian distribution and which can be considered as “physically constrained.”

TL;DR: Using a detailed analysis of long molecular dynamics trajectories in combination with a statistical assessment of the significance of the measured convergence, it is obtained that simulations of a few hundreds of picoseconds are in general sufficient to provide a stable and statistically reliable definition of the essential and near constraints subspaces.

TL;DR: Applications to an IgG‐binding domain, an SH3 binding domain, HPr, calmodulin, and lysozyme are presented which illustrate the use of the method as a fast and simple way to predict structural variability in proteins.

TL;DR: A comparison of a series of extended molecular dynamics simulations of bacteriophage T4 lysozyme in solvent with X‐ray data is presented, revealing that the N‐terminal helix rotates together with either of these two domains.

TL;DR: The analysis of the thermolysin trajectories indeed revealed a large rigid body hinge‐bending motion of the Nterminal and C‐terminal domains, similar to the motion hypothesized from the crystal structure comparisons.