相关实验视频

Updated: Jul 19, 2025

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

由两个短线性动图段采样的合形多面体,通过循环二元化,振动和核磁共振光谱检测

Reinhard Schweitzer-Stenner¹, Raghed Kurbaj¹, Nichole O'Neill¹

¹Department of Chemistry, Drexel University, Philadelphia, PA19104Pennsylvania,United States.

|August 18, 2023

概括

短线性图案 (SLiM) 呈现出明显的形状偏好,受残留相互作用的影响. 这些发现揭示了对SLiM功能和生物过程中的调节的结构性见解.

科学领域:

生物化学生物化学
结构生物学结构生物学
分子生物学分子生物学

背景情况:

短线性图案 (SLiM) 是对各种生物过程至关重要的无序蛋白质段.
尽管缺乏正规的二次结构,但SLiM的功能是识别站点,准信号和绑定站点.
了解SLiM的符合性是解读它们的监管作用的关键.

研究的目的:

为了研究两个特定的SLiM图案 (GRRDSG和GRRTSG) 的形状景观,代表RxxS类.
阐明残留物-残留物相互作用对SLiM结构和动态的影响.
将实验结果与分子动力学模拟进行比较.

主要方法:

使用了光谱技术的组合:核磁共振 (NMR),红外 (IR) 光谱,振动光谱和紫外线循环二极化.
为所选的SLiM图案确定了Ramachandran图案.
使用Amber ff14SB和CHARMM 36m力场进行了分子动力学模拟.

主要成果:

其余物相互作用显著地重新分配了聚烯II和β-链盆地之间的构造群体.
由于这些相互作用,延伸结构在转折形和螺旋形状上得到稳定.
温度上升有利于比聚烯II更有利于β-链种群.
分子动力学模拟虽然表明了残留物-残留物相互作用,但并没有完全复制实验观察到的结构变化.

结论:

SLiMs具有独特的形状倾向,受到局部和非局部残留物相互作用的影响.
这些相互作用稳定了特定的结构状态 (延伸,β-链) 并影响了它们的温度依赖行为.
实验光谱数据揭示了SLiM形态动力学的细微差别,这些细微差别并未完全被当前分子动力学力场所捕获.

更多相关视频

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

CD Spectroscopy to Study DNA-Protein Interactions

CD Spectroscopy to Study DNA-Protein Interactions

Published on: February 10, 2022

相关概念视频

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

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.

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

¹H 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...

¹H NMR: Interpreting Distorted and Overlapping Signals

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...

2D NMR: Overview of Homonuclear Correlation Techniques

2D NMR: Overview of Homonuclear Correlation Techniques

Homonuclear correlation spectroscopy (COSY) is a powerful technique used in Nuclear Magnetic Resonance (NMR) spectroscopy to study the correlations between nuclei of the same type within a molecule. It provides information about scalar couplings between adjacent nuclei, which helps determine connectivity and structural information. There are several COSY variants, each with its unique strengths and experimental parameters.
COSY90 is the standard two-dimensional (2D) COSY experiment that...

¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)

¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)

When proton-coupled carbon-13 spectra are simplified by a broadband proton decoupling technique, structural information about the coupled protons is lost. Distortionless enhancement by polarization transfer (DEPT) is a technique that provides information on the number of hydrogens attached to each carbon in a molecule. While the DEPT experiment utilizes complex pulse sequences, the pulse delay and flip angle are specifically manipulated. The resulting signals have different phases depending on...

2D NMR: Heteronuclear Single-Quantum Correlation Spectroscopy (HSQC)

2D NMR: Heteronuclear Single-Quantum Correlation Spectroscopy (HSQC)

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...