posted on 2024-01-18, 15:04authored byYlène Aboulfath, Sana Bougueroua, Alvaro Cimas, Dominique Barth, Marie-Pierre Gaigeot
A novel approach based on a coarse-grained
representation of topological
graphs is proposed for the automatic analysis of molecular dynamics
(MD) trajectories of hydrogen-bonded (H-Bonded) flexible biomolecules.
Herein, our approach models an H-Bonded biomolecule by its H-Bonded
cycles and its graph of cycles in which the vertices and links represent
the intersections between these cycles. We propose a methodology in
which each identified conformer/isomer from the MD is represented
by a well-chosen set of H-Bonded cycles called a minimum cycle basis.
The key component is the “polycycles” that distinguish
the cycles that play the same polymorphic role in the molecule from
the ones that lead to an actual conformational change of the molecule.
The relevance of our proposed method is evaluated on MD trajectories
of gas-phase biomolecules, for which the covalent bonds are unchanged
over time and only the hydrogen bonds change over time. The polygraphs
and their time evolution are shown to reveal the dynamicity of the
metastructure(s) of the H-Bonded biomolecules while providing polymorphic
information on the cycles. Such information on the dynamics and changes
in the H-bond network, as some cycles change identity while retaining
the same role in the overall structure, is not easily captured at
the atomic level of representation. Such information can instead be
captured by polymorphic cycles.