统计合分析预测了二叶酸减少酶中相关的运动
Thomas L Kalmer1, Christine Mae F Ancajas1, Cameron I Cohen2,3
1Department of Chemistry, Vanderbilt University Nashville, TN, USA.
bioRxiv : the preprint server for biology
|July 1, 2024
概括
蛋白质动力学显著影响酶的进化. 这项研究揭示了二叶酸还原酶 (DHFR) 的合运动如何影响其进化轨迹,这对蛋白质工程有影响.
科学领域:
- 酵素学和分子进化研究
- 蛋白质动力学和阿洛斯特里
背景情况:
- 二叶酸减少酶 (DHFR) 是一种关键的酶,也是研究酶动态的一个模型系统.
- 蛋白质动态,残留网络和酶进化之间的关系仍然不完全理解.
- 以前的研究发现了影响DHFR动态和催化物的特定突变,但它们的进化影响尚不清楚.
研究的目的:
- 调查动态合的残留物网络在DHFR的演变中的作用.
- 为了确定这些网络内的全沟通是否对进化适应至关重要.
- 确定人类DHFR中潜在的突变部位,以保持动态.
主要方法:
- 统计合分析以确定共同演变的残留物网络.
- 分子动力学模拟来分析相关的运动和全沟通.
- 在大肠杆菌DHFR中进行局部定向突变发生 (N23PP/S148A),以评估对动力学和全ostery的影响.
主要成果:
- 在DHFR中确定了一个具有相关运动的共同演变残留物的网络.
- 这一网络内的所有流体通信因N23PP/S148A突变而被严重破坏.
- 在人类DHFR中确定了两个潜在的位点,它们可以容忍类似的突变,同时保持蛋白质动态.
结论:
- 蛋白质动力学是酶进化的重要驱动力.
- 动态合网络及其全性通信对于进化适应至关重要.
- 了解这些动态可以指导蛋白质工程对像DHFR这样的酶的努力.
相关概念视频
Spin–Spin Coupling: Three-Bond Coupling (Vicinal Coupling)
1.1K
Vicinal or three-bond coupling is commonly observed between protons attached to adjacent carbons. Here, nuclear spin information is primarily transferred via electron spin interactions between adjacent C‑H bond orbitals. This generally favors the antiparallel arrangement of spins, so 3J values are usually positive.
The extent of coupling depends on the C‑C bond length, the two H‑C‑C angles, any electron-withdrawing substituents, and the dihedral angle between the...
The extent of coupling depends on the C‑C bond length, the two H‑C‑C angles, any electron-withdrawing substituents, and the dihedral angle between the...
1.1K
¹H NMR: Long-Range Coupling
1.7K
The coupling interactions of nuclei across four or more bonds are usually weak, with J values less than 1 Hz. While these are usually not observed in spectra, the presence of multiple bonds along the coupling pathway can result in observable long-range coupling.
In alkenes, spin information is communicated via σ–π overlap, as seen in allylic (four-bond) and homoallylic (five-bond) couplings. These coupling interactions are stronger when the σ bond is parallel to the alkene...
In alkenes, spin information is communicated via σ–π overlap, as seen in allylic (four-bond) and homoallylic (five-bond) couplings. These coupling interactions are stronger when the σ bond is parallel to the alkene...
1.7K
Spin–Spin Coupling Constant: Overview
906
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...
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...
906
¹H NMR: Interpreting Distorted and Overlapping Signals
1.0K
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...
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...
1.0K
Protein Dynamics in Living Cells
2.1K
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
2.1K
2D NMR: Heteronuclear Single-Quantum Correlation Spectroscopy (HSQC)
683
Heteronuclear single-quantum correlation spectroscopy (HSQC) is a 2D NMR technique that reveals one-bond correlations between hydrogen and a heteronucleus. The HSQC experiment is similar to the heteronuclear correlation experiment (HETCOR) but is more sensitive. In the HSQC spectrum, the proton chemical shift is plotted on the horizontal F2 axis, while the 13C chemical shift is plotted on the vertical F1 axis. The corresponding proton and 13C spectra are also shown. The HSQC contour plot does...
683


