Séminaire LJK-Modèles et Algorithmes Déterministes: CASYS

 

Le Mardi 25 Mars 2008 à 11h00 en Salle 1 - Tour IRMA

 

Séminaire de Mr Francesco PIAZZA (EPFL)

 

Discrete breathers in protein structures: a mechanism for energy storage in enzymes

 

Résumé:

 

Recently, using a numerical surface cooling approach, we have shown that
highly energetic discrete breathers (DB) can form in the stiffest parts of
nonlinear network models of large protein structures [1].
In the present study, using an analytical approach, we extend our previous results to
low-energy discrete breathers as well as to smaller proteins [2].
We confirm and further scrutinize the striking site selectiveness of energy
localisation in the presence of spatial disorder. In particular, we find that, as a sheer
consequence of disorder, a non-zero energy gap for exciting a DB at a
given site either exists or not. Remarkably, in the former case, the gaps arise as
result of the impossibility of exciting small-amplitude modes in the
first place. On the contrary, in the latter case, a small subset of
linear edge modes act as accumulation points, whereby DBs can be
continued to arbitrary small energies, while unavoidably approaching one of
such normal modes.

Concerning the structure-dynamics relationship, we find that the regions of protein structures
where DBs form easily (zero or small gaps) are unfailingly the most highly connected ones, also
characterized by weak local clustering. Remarkably, a systematic analysis on a large database of enzyme structures reveals that amino-acid residues involved in enzymatic activity tend to be located in such regions. This finding reinforces the idea that localised modes of nonlinear origin may play an important biological role, e.g. by providing a ready channel for energy storage and/or contributing to lower energy barriers of chemical reactions.



References

[1] B. Juanico, Y.-H. Sanejouand, F. Piazza and P. De Los Rios,
Physical Review Letters, 99, 238104 (2007).

[2] F. Piazza and Y.-H. Sanejouand, submitted to Phys. Biol.,
preprint: http://arxiv.org/abs/0802.3593 (2008).