在可变温度下预测和实验NMR化学转变:蛋白质形态动力学的效应
Xu Yi1, Lichirui Zhang1, Richard A Friesner1
1Department of Chemistry, Columbia University, New York, New York 10025, United States.
The journal of physical chemistry letters
|February 21, 2024
概括
蛋白质的结构灵活性显著影响NMR化学转移. 对分子动力学模拟的预测转移的平均值改善了对二叶酸还原酶 (DHFR) 实验数据的一致性.
科学领域:
- 生物物理学的生物物理.
- 结构生物学 结构生物学
- 核磁共振 (NMR) 光谱学 核磁共振 (NMR) 光谱学
背景情况:
- 对于理解蛋白质结构和动态来说,NMR化学转移至关重要.
- 准确预测和解释NMR化学转移仍然是生物物理研究中的一个重大挑战.
研究的目的:
- 为了研究蛋白质结构分布对15N化学转移的影响.
- 为了比较量子力学/分子力学 (QM/MM) 预测的转移与二叶酸减少酶 (DHFR) 的实验性NMR数据.
主要方法:
- 利用分子动力学 (MD) 轨迹来捕获蛋白质构成组合.
- 采用QM/MM方法来预测各种蛋白质构造的15N化学转移.
- 将预测的转移与实验溶液状态和固态NMR (SSNMR) 数据进行了比较.
主要成果:
- MD快照显示预测的15N化学转移变化高达25ppm.
- 平均预测的变化在形状组合的平均值显著改善了与室温实验数据的一致性.
- 冷溶液的SSNMR线宽与MD轨迹的预测转移分布有很好的相关性.
- 在皮秒时间尺度上观察到脊柱扭转角度 (ψ) 的显著波动,有助于转移变化.
结论:
- 蛋白质结构动力学在确定观察到的NMR化学转移方面发挥着关键作用.
- 总体平均预测提供了比单个形态预测更准确的实验NMR转移的表示.
- MD模拟与QM/MM预测相结合,为蛋白质动力学和NMR光谱解释提供了宝贵的见解.
相关概念视频
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR
1.1K
The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
1.1K
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution
841
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...
841
NMR Spectroscopy: Chemical Shift Overview
1.5K
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...
1.5K
NMR Spectroscopy Of Amines
8.8K
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...
8.8K
¹H NMR of Labile Protons: Temporal Resolution
1.1K
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...
1.1K
Proton (¹H) NMR: Chemical Shift
1.7K
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...
Absorption signals of all the protium nuclei...
1.7K


