2008/02/29 by Francesco Piazza, Yves‐Henri Sanejouand, Yves-Henri Sanejouand · 76 citations
Biochemistry, Genetics and Molecular Biology · Computer Science · Physics and Astronomy · #Breather #Nonlinear Dynamics and Pattern Formation #Nonlinear Photonic Systems #Nonlinear system #Physics #Quantum mechanics #Simple (philosophy) #Spectroscopy and Quantum Chemical Studies #Statistical physics #Zero (linguistics) #cond-mat.soft #nlin.PS #q-bio.BM
paper · pdf · doi:10.1088/1478-3975/5/2/026001
published in Physical Biology 5(2), 026001 (IOP Publishing) · 26 pages, 8 figures, to be published in Physical Biology, 2008 (IOP)
arxiv created 2008/04/29 · openalex publication_date 2008/05/01 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
Recently, using a numerical surface cooling approach, we have shown that highly energetic discrete breathers (DBs) can form in the stiffest parts of nonlinear network models of large protein structures. In the present study, using an analytical approach, we extend our previous results to low-energy discrete breathers as well as to smaller proteins. We confirm and further scrutinize the striking site selectiveness of energy localization 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 a result of the impossibility of exciting small-amplitude modes in the first place. In contrast, in the latter case, a small subset of linear edge modes acts as accumulation points, whereby DBs can be continued to arbitrary small energies, while unavoidably approaching one of such normal modes. In particular, the case of the edge mode seems peculiar, its dispersion relation being simple and little system dependent. 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 catalysis tend to be located in such regions. This finding reinforces the idea that localized 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.