一种自旋标记蛋白质的多频电子自旋共振光谱是从分子动力学模拟中计算的
Deniz Sezer1, Jack H Freed, Benoît Roux
1Department of Physics, Cornell University, Ithaca, New York 14853, USA.
Journal of the American Chemical Society
|February 5, 2009
概括
分子动力学模拟和马尔科夫模型准确地预测了旋转标记T4Lysozyme的多频电子自旋共振 (ESR) 光谱. 这种方法揭示了详细的旋转标签动态和相互作用,有助于光谱解释.
科学领域:
- 生物物理学的生物物理.
- 计算生物学 计算生物学
- 频谱学是一种光谱学.
背景情况:
- 电子自旋共振 (ESR) 光谱通过自旋标签提供了对蛋白质结构和动态的洞察.
- 与分子运动相关的复杂ESR光谱的解释仍然是一个重大挑战.
研究的目的:
- 开发一种严格的方法来解释多频ESR频谱.
- 阐明T4Lysozyme上的旋转标签的分子动力学和相互作用.
主要方法:
- 广泛的分子动力学 (MD) 模拟自旋标记的T4溶酶 (MTSSL在位置72和131).
- 从MD轨迹构建随机马尔科夫模型,以扩展旋转标签动态的时间尺度.
- 用实验数据计算和比较多频ESR光谱.
主要成果:
- 计算的ESR光谱与实验数据在多个磁场强度之间表现出很好的一致性,而无需对参数进行调整.
- 模拟MD显示,旋转标签探索众多形状,并与非邻近的蛋白质残留物相互作用.
- 这项研究提供了关于旋转标签行为的详细分子图像.
结论:
- 结合的MD和马尔科夫模型方法为解释ESR频谱提供了可靠的工具.
- 这种方法增强了对旋转标签动态及其局部蛋白质环境的理解.
- 这些发现为标记蛋白质的光谱和结晶学数据提供了宝贵的见解.
相关概念视频
¹H NMR: Interpreting Distorted and Overlapping Signals
Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are slanted or...
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are slanted or...
NMR Spectroscopy: Spin–Spin Coupling
The spin state of an NMR-active nucleus can have a slight effect on its immediate electronic environment. This effect propagates through the intervening bonds and affects the electronic environments of NMR-active nuclei up to three bonds away; occasionally, even farther. This phenomenon is called spin–spin coupling or J-coupling. Coupling interactions are mutual and result in small changes in the absorption frequencies of both nuclei involved. While nuclei of the same element are involved in...
NMR Spectrometers: Resolution and Error Correction
When magnetic nuclei in a sample achieve resonance and undergo relaxation, the signal detected in NMR is an approximately exponential free induction decay. Fourier transform of an exponential decay yields a Lorentzian peak in the frequency domain. Lorentzian peaks in an NMR spectrum are defined by their amplitude, full width at half maximum, and position, where the peak width is governed by the spin-spin relaxation time alone. In real experiments, however, the applied magnetic field is rendered...
Atomic Nuclei: Magnetic Resonance
The number of nuclear spins aligned in the lower energy state is slightly greater than those in the higher energy state. In the presence of an external magnetic field, as the spins precess at the Larmor frequency, the excess population results in a net magnetization oriented along the z axis. When a pulse or a short burst of radio waves at the Larmor frequency is applied along the x axis, the coupling of frequencies causes resonance and flips the nuclear spins of the excess population from the...
Electron Paramagnetic Resonance (EPR) Spectroscopy: Organic Radicals
Ideally, an unpaired electron shows a single peak in the EPR spectrum due to the transition between the two spin energy states. However, coupling interactions can occur between the spins of the unpaired electron and any neighboring spin-active nuclei. This hyperfine coupling results in hyperfine splitting, where the EPR signal is split into multiplets. The signals split into 2nI + 1 peaks, where n is the number of equivalent nuclei and I is the nuclear spin. These splitting patterns provide...
Spin–Spin Coupling Constant: Overview
In bromoethane, the three methyl protons are coupled to the two methylene protons that are three bonds away. In accordance with the n+1 rule, the signal from the methyl protons is split into three peaks with 1:2:1 relative intensities. The methylene protons appear as a quartet, with the relative intensities of 1:3:3:1.
Qualitatively, any spin plus-half nucleus polarizes the spins of its electrons to the minus-half state. Consequently, the paired electron in the hydrogen–carbon bond must have a...
Qualitatively, any spin plus-half nucleus polarizes the spins of its electrons to the minus-half state. Consequently, the paired electron in the hydrogen–carbon bond must have a...


