Institute of Chemistry - Centre for Glycomics, Dubravska cesta 9, 84538 Bratislava, Slovakia.
Agency for Medical Research and Development (AMED), Chiyoda-ku, Japan.
J Chem Inf Model. 2020 Mar 23;60(3):1559-1567. doi: 10.1021/acs.jcim.9b00942. Epub 2020 Feb 24.
The analysis of folding trajectories for proteins is an open challenge. One of the problems is how to describe the amount of folded secondary structure in a protein. We extend the use of Estradas' folding degree ( , , 697) for the analysis of the evolution of the folding stage during molecular dynamics (MD) simulation. It is shown that residue contribution to the total folding degree is a predominantly local property, well-defined by the backbone dihedral angles at the given residue, without significant contribution from the backbone conformation of other residues. Moreover, the magnitude of this residue contribution can be quite easily associated with characteristic motifs of secondary protein structures such as the α-helix, β-sheet (hairpin), and so on by means of a Ramachandran-like plot as a function of backbone dihedral angles φ,ψ. Additionally, the understanding of the free energy profile associated with the folding process becomes much simpler. Often a 1D profile is sufficient to locate global minima and the corresponding structure for short peptides.
蛋白质折叠轨迹的分析是一个开放性的挑战。其中一个问题是如何描述蛋白质中折叠二级结构的数量。我们扩展了 Estradas 的折叠度（ ， ， 697）的使用，用于分析分子动力学（MD）模拟过程中折叠阶段的演化。结果表明，残基对总折叠度的贡献主要是局部性质，可以通过给定残基的主链二面角很好地定义，而与其他残基的主链构象没有显著贡献。此外，通过类似于 Ramachandran 的图谱，该残基贡献的大小可以很容易地与二级蛋白质结构的特征模体（如α-螺旋、β-折叠（发夹）等）相关联，作为主链二面角 φ， ψ 的函数。此外，与折叠过程相关的自由能分布的理解变得更加简单。对于短肽，通常一维分布足以定位全局最小值和相应的结构。
