Peierls-Nabarro屏障与蛋白质环的传播
Peierls-Nabarro Barrier and Protein Loop Propagation
摘要：
当自定域准粒子激发沿着离散的一维晶格传播时，它变得经受将动能转换成晶格振动的耗散。最终，动能不再使激发能够跨越相邻位置之间的最小能量势垒，并且激发变得局部化在晶格单元内。在蛋白质的情况下，晶格结构由C-α骨架组成。自定域准粒子激发是环的基本组成部分。它可以通过一个扭结来模拟，该扭结求解离散非线性薛定谔方程（DNLS）的一个变体。我们使用UNRES粗粒分子动力学力场研究了蛋白G相关白蛋白结合结构域中这种扭结的传播。我们估计的扭结需要跨越的能量障碍的高度，以沿骨干晶格传播。我们分析了这些障碍如何引起控制扭结运动的应力和救济。为此，我们变形的天然折叠的蛋白质结构，平行平移扭结沿骨干远离其天然位置。我们释放转置的扭结，并跟踪它如何沿着主干向本机位置传播。我们观察到的耗散力施加在扭结的各种能量障碍，有一个关键的作用，在确定如何向其天然状态的蛋白质折叠。
英文摘要：
When a self-localized quasiparticle excitation propagates along a discrete one dimensional lattice, it becomes subject to a dissipation that converts the kinetic energy into lattice vibrations. Eventually the kinetic energy does no longer enable the excitation to cross over the minimum energy barrier between neighboring sites, and the excitation becomes localized within a lattice cell. In the case of a protein, the lattice structure consists of the C-alpha backbone. The self-localized quasiparticle excitation is the elemental building block of loops. It can be modeled by a kink which solves a variant of the discrete non-linear Schroedinger equation (DNLS). We study the propagation of such a kink in the case of protein G related albumin-binding domain, using the UNRES coarse-grained molecular dynamics force field. We estimate the height of the energy barriers the kink needs to cross over, in order to propagate along the backbone lattice. We analyse how these barriers gives rise to both stresses and reliefs which control the kink movement. For this, we deform a natively folded protein structure by parallel translating the kink along the backbone away from its native position. We release the transposed kink, and we follow how it propagates along the backbone towards the native location. We observe that the dissipative forces which are exerted on the kink by the various energy barriers, have a pivotal role in determining how a protein folds towards its native state.
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