Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
J Biomol NMR. 2012 Dec;54(4):355-76. doi: 10.1007/s10858-012-9678-6. Epub 2012 Oct 21.
NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements from NMR-monitored chemical shift titrations, for which the dependence of K ( D ) on the chemical shift difference (Δω) between free and bound states is extrapolated to Δω = 0. The demonstrated accuracy and precision for k ( off ) will be valuable for the interpretation of biological kinetics in weakly interacting protein-protein networks, where a small change in the magnitude of the underlying kinetics of a given pathway may lead to large changes in the associated downstream signaling cascade.
NMR 监测的化学位移滴定法可用于研究弱蛋白-配体相互作用,为研究提供丰富的信息,包括热力学参数,如微摩尔至毫摩尔范围内的离解常数(K(D))、游离态和配体结合态的比例,以及状态之间的转换动力学等,这些通常处于 NMR 时间尺度上的快速交换状态。我们最近开发了两种化学位移滴定方法,其中总蛋白和配体浓度的共变给出了 1:1 蛋白-配体相互作用的 K(D)值更高的精度(Markin 和 Spyracopoulos 在 J Biomol NMR 53: 125-138, 2012)。在这项研究中,我们证明了应用于我们开发的精确的蛋白-配体化学位移滴定方法获得的单个(1)H-(15)N 2D HSQC NMR 谱的经典线宽分析,可产生准确和精确的动力学参数,如离解速率(k(off))。对于在 NMR 时间尺度上的快速交换状态下的实验确定的动力学,在这项工作中为 k(off)3000 s(-1),通过对化学位移滴定方法进行量子力学 NMR 模拟,使用磁共振工具包 GAMMA,确定经典线宽分析的准确性优于 5%。通过使用蒙特卡罗模拟,从 NMR 谱的线宽分析确定 k(off)的实验精度为 13%,与 GAMMA 模拟中线宽分析的理论精度(存在噪声和蛋白浓度误差时为 12%)一致。此外,还使用 GAMMA 模拟证明了线宽分析有可能在很宽的范围内(从 100 到 15,000 s(-1))提供合理准确和精确的 k(off)值。对于接近中间交换(100 s(-1))的 k(off)值的线宽分析的有效性,可以通过 NMR 监测的化学位移滴定法获得更准确的 K(D)测量来促进,其中 K(D)对游离态和结合态之间的化学位移差(Δω)的依赖性被外推到 Δω=0。对于解释弱相互作用的蛋白-蛋白网络中的生物学动力学,k(off)的这种已证明的准确性和精度将非常有价值,因为给定途径的基础动力学的微小变化可能导致相关下游信号级联的巨大变化。