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Updated: Jul 9, 2025

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在分子动力学模拟中处理诱导的适合性,符合性选择和次要姿势,以便可靠地预测自由能量

Piero Procacci1

  • 1Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.

Journal of chemical theory and computation
|December 1, 2023
PubMed
概括

标准的分子动力学 (MD) 模拟可以有效地采用诱导适合或简单的构造选择的样本系统. 然而,具有长期转移稳定状态的复杂系统需要增强的采样技术来获得可靠的结果.

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Molecular Chaperones and Protein Folding03:00

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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
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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...
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