相关实验视频

Updated: Jul 1, 2025

CD Spectroscopy to Study DNA-Protein Interactions

CD Spectroscopy to Study DNA-Protein Interactions

Published on: February 10, 2022

增加了对同位素标记螺旋的振动循环二元化计算的准确性

James R Cheeseman¹, Michael J Frisch¹, Timothy A Keiderling²

¹Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, CT 06492, USA.

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy

|March 8, 2024

概括

对α螺旋的精确振动循环二元化 (VCD) 光谱需要考虑溶剂效应和结构扭曲. 密度函数理论 (DFT) 的计算揭示了这些因素对于预测胺I至关重要.

科学领域:

频谱学是一种光谱学.
计算化学计算化学
生物物理学的生物物理.

背景情况:

振动循环二元化 (VCD) 光谱是确定二次结构的强大工具.
预测alpha-helical的VCD光谱,特别是关于化和同位素替代对胺I'频段的影响,一直是具有挑战性的.
以前的计算方法经常使用理想化的结构和真空条件,限制了准确性.

研究的目的:

为了提高对阿尔法螺旋的计算VCD光谱的准确性.
调查结构扭曲,溶剂效应和侧链包含对VCD光谱预测的影响.
了解影响胺I带形状和同位素置换转移的因素.

主要方法:

密度函数理论 (DFT) 的计算是对一个25残留的Ala-丰富的进行的.
计算包括隐式溶剂校正和显式侧链.
分析了完全最小化的结构,以及各种同位素替代 (例如,13C=O).

主要成果:

完全优化的DFT计算与溶剂效应准确地预测了VCD标志模式和胺I'区域的带形状.
计算重现了实验VCD光谱,包括额外的负波段和13C=O替代变异的准确模式.
包括扭曲的端子和溶剂效应,与使用真空理想螺旋结构的模型相比,显著改善了光谱预测.
侧链包含对胺I' IR和VCD光谱的影响最小.

结论:

对阿尔法螺旋的精确VCD光谱预测需要包含现实的结构特征,如扭曲的终端和溶剂效应.
当纳入这些因素时,DFT计算提供了一种可靠的方法来解释实验VCD数据和理解同位素替代效应.
以前的计算成功可能源于错误平衡,突出了全面建模的重要性.

更多相关视频

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Published on: December 12, 2017

Covalent Labeling with Diethylpyrocarbonate for Studying Protein Higher-Order Structure by Mass Spectrometry

Covalent Labeling with Diethylpyrocarbonate for Studying Protein Higher-Order Structure by Mass Spectrometry

Published on: June 15, 2021

相关概念视频

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...

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: 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...

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...

Peptide Identification Using Tandem Mass Spectrometry

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...