Atilgan Canan, Atilgan Ali Rana
Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.
PLoS Comput Biol. 2009 Oct;5(10):e1000544. doi: 10.1371/journal.pcbi.1000544. Epub 2009 Oct 23.
We study apo and holo forms of the bacterial ferric binding protein (FBP) which exhibits the so-called ferric transport dilemma: it uptakes iron from the host with remarkable affinity, yet releases it with ease in the cytoplasm for subsequent use. The observations fit the "conformational selection" model whereby the existence of a weakly populated, higher energy conformation that is stabilized in the presence of the ligand is proposed. We introduce a new tool that we term perturbation-response scanning (PRS) for the analysis of remote control strategies utilized. The approach relies on the systematic use of computational perturbation/response techniques based on linear response theory, by sequentially applying directed forces on single-residues along the chain and recording the resulting relative changes in the residue coordinates. We further obtain closed-form expressions for the magnitude and the directionality of the response. Using PRS, we study the ligand release mechanisms of FBP and support the findings by molecular dynamics simulations. We find that the residue-by-residue displacements between the apo and the holo forms, as determined from the X-ray structures, are faithfully reproduced by perturbations applied on the majority of the residues of the apo form. However, once the stabilizing ligand (Fe) is integrated to the system in holo FBP, perturbing only a few select residues successfully reproduces the experimental displacements. Thus, iron uptake by FBP is a favored process in the fluctuating environment of the protein, whereas iron release is controlled by mechanisms including chelation and allostery. The directional analysis that we implement in the PRS methodology implicates the latter mechanism by leading to a few distant, charged, and exposed loop residues. Upon perturbing these, irrespective of the direction of the operating forces, we find that the cap residues involved in iron release are made to operate coherently, facilitating release of the ion.
我们研究了细菌铁结合蛋白（FBP）的脱辅基形式和全辅基形式，该蛋白存在所谓的铁转运困境：它以极高的亲和力从宿主摄取铁，但在细胞质中又能轻易释放铁以供后续使用。这些观察结果符合“构象选择”模型，该模型提出存在一种在配体存在下稳定的低丰度、高能构象。我们引入了一种新工具，称为扰动响应扫描（PRS），用于分析所采用的远程控制策略。该方法依赖于基于线性响应理论的计算扰动/响应技术的系统应用，通过沿链顺序对单个残基施加定向力并记录残基坐标的相对变化。我们进一步获得了响应大小和方向性的封闭形式表达式。使用PRS，我们研究了FBP的配体释放机制，并通过分子动力学模拟支持了这些发现。我们发现，从X射线结构确定的脱辅基形式和全辅基形式之间逐个残基的位移，通过对脱辅基形式的大多数残基施加扰动得到了如实再现。然而，一旦在全辅基FBP中将稳定配体（Fe）整合到系统中，仅扰动少数选定的残基就能成功再现实验位移。因此，FBP摄取铁在蛋白质波动的环境中是一个有利的过程，而铁的释放则由包括螯合和变构在内的机制控制。我们在PRS方法中实施的方向性分析通过导致一些遥远、带电且暴露的环残基暗示了后一种机制。在扰动这些残基时，无论作用力的方向如何，我们发现参与铁释放的帽残基会协同作用，促进离子的释放。
