The Static Modes: an alternative approach for the treatment of macro- and bio-molecular induced-fit flexibility

Enhancing DFT-based energy landscape exploration by coupling Quantum Mechanics and Static Modes

Unravelling the atomic scale diffusion that can occur at the surface, at the interface or into the bulk is challenging: multi-scale modelling approach usually requires intensive prospective calculations and moreover...

Toward in silico biomolecular manipulation through static modes: atomic scale characterization of HIV-1 protease flexibility

Probing biomolecular flexibility with atomic-scale resolution is a challenging task in current computational biology for fundamental understanding and prediction of biomolecular interactions and associated functions. This paper makes use of the static mode method to study HIV-1 protease considered as a model system to investigate the full biomolecular flexibility at the atomic scale, the screening of active site biomechanical properties, the blind prediction of allosteric sites, and the design of multisite strategies to target deformations of interest. Relying on this single calculation run of static modes, we demonstrate that in silico predictive design of an infinite set of complex excitation fields is reachable, thanks to the storage of the static modes in a data bank that can be used to mimic single or multiatom contact and efficiently anticipate conformational changes arising from external stimuli. All along this article, we compare our results to data previously published and propose a guideline for efficient, predictive, and custom in silico experiments.

Mimicking DNA stretching with the Static Mode method: shear stress versus transverse pulling stress

DNA sequencing using nanopores is closer than ever to become a reality, but further research and development still need to be done, especially to unravel the atomic-scale mechanisms of induced DNA stretching. At this level, molecular modeling and simulation are essential to investigate DNA conformational flexibility and its response to the forces involved. In this work, through a "Static Mode" approach, we present a directed exploration of the deformations of a 27-mer subjected to externally imposed forces, as it could be in a nanopore. We show how the DNA sugar-phosphate backbone undergoes the majority of the induced deformation, before the base pairing is affected, and to what extent unzipping initiation depends on the force direction.

The electrostatic probe: a tool for the investigation of the Aβ(1-16) peptide deformations using the static modes

We investigate the conformational changes of the Amyloid β(1-16) peptide induced by moving Zn(2+) ions in the solvent, which we call the electrostatic probe. We use our recently developed approach of static modes which allows treating the flexibility of biological molecules at the atomic scale. Starting from an experimental apostructure, we find that several ion impacts allow the transition of the peptide toward its folded conformation, observed experimentally in the presence of Zn(2+) ions. This result shows the ability of our model and its associated software tool to describe properly the conformational changes and opens a new path toward the molecule/molecule docking problem.