Ishima Rieko, Torchia Dennis A
Molecular Structural Biology Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892-4307, USA.
J Biomol NMR. 2006 Apr;34(4):209-19. doi: 10.1007/s10858-005-6226-7.
The transverse relaxation rate, R2, measured as a function of the effective field (R2 dispersion) using a Carr-Purcell-Meiboom-Gill (CPMG) pulse train, is well suited to detect conformational exchange in proteins. The dispersion data are commonly fitted by a two-site (sites a and b) exchange model with four parameters: the relative population, pa, the difference in chemical shifts of the two sites, deltaomega, the correlation time for exchange, tau(ex), and the intrinsic relaxation rate (i.e., transverse relaxation rate in the absence of chemical exchange), R2(0). Although the intrinsic relaxation rates of the two sites, R2(0a) and R2(0b), can differ, they are normally assumed to be the same (i.e., R2(0a) = R2(0b) = R2(0)) when fitting dispersion data. The purpose of this investigation is to determine the magnitudes of the errors in the optimized exchange parameters that are introduced by the assumption that R2(0a) = R2(0b). In order to accomplish this goal, we first generated synthetic constant-time CPMG R2 dispersion data assuming two-site exchange with R2(0a) not equal R2(0b), and then fitted the synthetic data assuming two-site exchange with R2(0) = R2(0a) = R2(0b). Although all the synthetic data generated assuming R2(0a) not equal R2(0b) were well fitted (assuming R2(0a) = R2(0b)), the optimized values of pa and tau(ex) differed from their true values, whereas the optimized values of deltaomega values did not. A theoretical analysis using the Carver-Richards equation explains these results, and yields simple, general equations for estimating the magnitudes of the errors in the optimized parameters, as a function of (R2(0a) - R2(0b)).
使用Carr-Purcell-Meiboom-Gill（CPMG）脉冲序列测量作为有效场函数的横向弛豫率R2（R2色散），非常适合检测蛋白质中的构象交换。色散数据通常用具有四个参数的双位点（位点a和b）交换模型拟合：相对丰度pa、两个位点的化学位移之差δω、交换的相关时间τ(ex)以及固有弛豫率（即不存在化学交换时的横向弛豫率）R2(0)。尽管两个位点的固有弛豫率R2(0a)和R2(0b)可能不同，但在拟合色散数据时通常假定它们相同（即R2(0a)=R2(0b)=R2(0)）。本研究的目的是确定由R2(0a)=R2(0b)这一假设引入的优化交换参数中的误差大小。为了实现这一目标，我们首先生成了假定R2(0a)不等于R2(0b)的双位点交换的合成恒时CPMG R2色散数据，然后假定R2(0)=R2(0a)=R2(0b)对合成数据进行拟合。尽管所有假定R2(0a)不等于R2(0b)生成的合成数据都得到了很好的拟合（假定R2(0a)=R2(0b)），但pa和τ(ex)的优化值与它们的真实值不同，而δω值的优化值则没有。使用Carver-Richards方程进行的理论分析解释了这些结果，并得出了简单的通用方程，用于估计优化参数中的误差大小，作为(R2(0a)-R2(0b))的函数。
