CNR-Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, via Madonna del Piano 10, I-50019 Sesto Fiorentino, Italy.
Phys Biol. 2011 Aug;8(4):046008. doi: 10.1088/1478-3975/8/4/046008. Epub 2011 Jun 14.
We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin, discrete breathers (DBs), emerge naturally as continuations of a subset of high-frequency normal modes residing at specific sites dictated by the native fold. DBs are time-periodic, space-localized vibrational modes that exist generically in nonlinear discrete systems and are known for their resilience and ability to concentrate energy for long times. In the case of the small β-barrel structure that we consider, DB-mediated localization occurs on the turns connecting the strands. At high energies, DBs stabilize the structure by concentrating energy on a few sites, while their collapse marks the onset of large-amplitude fluctuations of the protein. Furthermore, we show how breathers develop as energy-accumulating centres following perturbations even at distant locations, thus mediating efficient and irreversible energy transfers. Remarkably, due to the presence of angular potentials, the breather induces a local static distortion of the native fold. Altogether, the combination of these two nonlinear effects may provide a ready means for remotely controlling local conformational changes in proteins.
我们报告了一个无格点蛋白质模型的分子动力学模拟结果，该模型具有物理力场和氨基酸序列。我们表明，局部非线性起源的模式，离散呼吸子（DBs），自然地作为居住在特定位置的高频正常模式的子集的延续而出现，这些位置由天然折叠决定。DBs 是时间周期性的，空间局部的振动模式，在非线性离散系统中普遍存在，以其弹性和长时间集中能量的能力而闻名。在我们考虑的小 β-桶结构的情况下，DB 介导的定位发生在连接链的转角处。在高能下，DB 通过将能量集中在少数几个位置来稳定结构，而它们的崩溃标志着蛋白质的大幅度波动的开始。此外，我们展示了呼吸子如何在远离位置的情况下作为能量积累中心发展，从而介导有效的不可逆能量转移。值得注意的是，由于存在角势，呼吸子会引起局部的天然折叠的静态变形。总的来说，这两种非线性效应的结合可能为远程控制蛋白质的局部构象变化提供一种简便的方法。
