从NMR化学转移中解释蛋白质结构动态
Paul Robustelli1, Kate A Stafford, Arthur G Palmer
1Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.
Journal of the American Chemical Society
|March 3, 2012
概括
分子动力学模拟通过捕捉动态构造变化来改善核磁共振 (NMR) 对蛋白质的化学转移预测. 这种方法提高了对静态结构的准确性,有助于研究蛋白质运动.
科学领域:
- 生物物理学的生物物理.
- 计算化学计算化学
- 结构生物学 结构生物学
背景情况:
- 核磁共振 (NMR) 光谱对于确定蛋白质结构和动态是至关重要的.
- 来自X射线结晶学的静态蛋白质结构可能不能完全代表溶液动态.
- 准确预测NMR化学转移对于解释实验数据至关重要.
研究的目的:
- 用分子动力学 (MD) 模拟来评估半实证的NMR化学转移预测方法.
- 将动态平均移动的预测与静态结构的预测进行比较.
- 评估MD-平均化学转移对于特征蛋白质运动的有用性.
主要方法:
- 利用半实证的NMR化学转移预测方法.
- 对蛋白质进行了无偏向的分子动力学 (MD) 模拟.
- 从MD轨迹计算动态平均的骨干化学转移.
- 将MD平均预测与实验NMR数据和静态结构预测进行了比较.
主要成果:
- 与静态结构预测相比,MD-平均化学转移预测显示了与实验值的改进一致.
- 通过对多种形状和较小波动的群体加权采样,提高了准确性.
- 对化学转移的分析发现了X射线形状和MD模拟中的潜在不准确性.
- 平均的 (1) H 化学转移被证明对芳香环位置和键几何学的波动敏感.
结论:
- 来自MD模拟的动态平均NMR化学转移提供了一种强大的方法,用于详细描述蛋白质运动.
- 这种方法通过考虑解决方案中的结构灵活性和动态来完善结构洞察力.
- 与NMR化学转移分析相结合的MD模拟可以验证模拟质量并识别相关的 conformational ensembles.
相关概念视频
01:02¹H 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...
01:15NMR Spectroscopy: Chemical Shift Overview
The position of the absorption signal of a sample is reported relative to the position of the signal of tetramethylsilane (TMS), which is added as an internal reference while recording spectra. The difference between the absorption frequencies of the sample and TMS (in Hz) is divided by the spectrometer operating frequency (in MHz) to obtain a dimensionless quantity called the chemical shift. It is reported on the δ (delta) scale and expressed in parts per million.
For instance, the proton...
For instance, the proton...
01:07Proton (¹H) NMR: Chemical Shift
Organic molecules primarily contain carbon and hydrogen atoms. While all the hydrogen isotopes are NMR-active, protium or hydrogen-1 is the most abundant. It has a significant energy separation between its nuclear spin states due to its large gyromagnetic ratio. As per Boltzmann's distribution, an increase in the energy separation implies a greater excess population of nuclei available for excitation, resulting in a strong NMR absorption signal.
Absorption signals of all the protium nuclei in a...
Absorption signals of all the protium nuclei in a...
00:52¹H NMR of Conformationally Flexible Molecules: Temporal Resolution
At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
01:19NMR Spectroscopy Of Amines
In proton NMR spectroscopy, primary amines and secondary amines showcase their N–H protons as a broad signal in the chemical shift range between δ 0.5 and 5 ppm. The exact position in this range depends on several factors, including sample concentration, hydrogen bonding, and the type of solvent used. Since amine protons undergo fast proton exchange in solution, the protons are labile and therefore do not participate in any splitting with adjacent protons. Thus, the observed peak is broad and...
01:10¹H NMR of Labile Protons: Temporal Resolution
Protons bonded to heteroatoms such as nitrogen and oxygen exhibit a range of chemical shift values. This is due to the varying degree of hydrogen bonding between the proton and the heteroatom in other molecules. The extent of hydrogen bonding affects the electron density around the proton, thereby giving different chemical shift values for the protons in the proton NMR spectrum.
The –OH proton in alcohols typically appears in the range of δ 2 to 5 ppm but can vary depending on the specific...
The –OH proton in alcohols typically appears in the range of δ 2 to 5 ppm but can vary depending on the specific...