Laberge Monique, Yonetani Takashi
Department of Biochemistry and Biophysics and Johnson Research Foundation, University of Pennsylvania Medical Center, Philadelphia, Pennsylvania, USA.
Biophys J. 2008 Apr 1;94(7):2737-51. doi: 10.1529/biophysj.107.114942. Epub 2007 Dec 20.
Recent functional studies reported on human adult hemoglobin (HbA) show that heterotropic effector-linked tertiary structural changes are primarily responsible for modulating the oxygen affinity of hemoglobin. We present the results of 6-ns molecular dynamics simulations performed to gain insights into the dynamical and structural details of these effector-linked tertiary changes. All-atom simulations were carried out on a series of models generated for T- and R-state HbA, and for 2,3-diphosphoglycerate-bound models. Cross-correlation analyses identify both intra- and intersubunit correlated motions that are perturbed by the presence of the effector. Principal components analysis was used to decompose the covariance matrix extracted from the simulations and reconstruct the trajectories along the principal coordinates representative of functionally important collective motions. It is found that HbA in both quaternary states exists as ensembles of tertiary conformations that introduce dynamic heterogeneity in the protein. 2,3-Diphosphoglycerate induces significant perturbations in the fluctuations of both HbA states that translate into the protein visiting different tertiary conformations within each quaternary state. The analysis reveals that the presence of the effector affects the most important components of HbA motions and that heterotropic effectors modify the overall dynamics of the quaternary equilibrium via tertiary changes occurring in regions where conserved functionally significant residues are located, namely in the loop regions between helices C and E, E and F, and F and G, and in concerted helix motions. The changes are not apparent when comparing the available x-ray crystal structures in the presence and absence of effector, but are striking when comparing the respective dynamic tertiary conformations of the R and T tetramers.
近期有关成人血红蛋白（HbA）的功能研究报告显示，异促效应物相关的三级结构变化是调节血红蛋白氧亲和力的主要原因。我们展示了进行6纳秒分子动力学模拟的结果，以深入了解这些效应物相关三级变化的动力学和结构细节。对一系列为T态和R态HbA以及与2,3-二磷酸甘油酸结合的模型生成的模型进行了全原子模拟。交叉相关分析确定了亚基内和亚基间的相关运动，这些运动因效应物的存在而受到干扰。主成分分析用于分解从模拟中提取的协方差矩阵，并沿着代表功能上重要的集体运动的主坐标重建轨迹。研究发现，处于两种四级状态的HbA均以三级构象集合的形式存在，这在蛋白质中引入了动态异质性。2,3-二磷酸甘油酸在两种HbA状态的波动中均引起显著扰动，这转化为蛋白质在每个四级状态内访问不同的三级构象。分析表明，效应物的存在影响了HbA运动的最重要成分，并且异促效应物通过在保守的功能重要残基所在区域（即螺旋C和E、E和F以及F和G之间的环区域）发生的三级变化以及协同的螺旋运动来改变四级平衡的整体动力学。当比较有无效应物时可用的X射线晶体结构时，这些变化并不明显，但当比较R和T四聚体各自的动态三级构象时，变化却很显著。
