Bauer Jacob, Žoldák Gabriel
Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia.
Center for Interdisciplinary Biosciences, P. J. Šafárik University, Technology and Innovation Park, Trieda SNP 1, 041 54 Košice, Slovakia.
Nanomaterials (Basel). 2021 Oct 22;11(11):2795. doi: 10.3390/nano11112795.
Single-molecule force spectroscopy experiments allow protein folding and unfolding to be explored using mechanical force. Probably the most informative technique for interpreting the results of these experiments at the structural level makes use of steered molecular dynamics (MD) simulations, which can explicitly model the protein under load. Unfortunately, this technique is computationally expensive for many of the most interesting biological molecules. Here, we find that normal mode analysis (NMA), a significantly cheaper technique from a computational perspective, allows at least some of the insights provided by MD simulation to be gathered. We apply this technique to three non-homologous proteins that were previously studied by force spectroscopy: T4 lysozyme (T4L), Hsp70 and the glucocorticoid receptor domain (GCR). The NMA results for T4L and Hsp70 are compared with steered MD simulations conducted previously, and we find that we can recover the main results. For the GCR, which did not undergo MD simulation, our approach identifies substructures that correlate with experimentally identified unfolding intermediates. Overall, we find that NMA can make a valuable addition to the analysis toolkit for the structural analysis of single-molecule force experiments on proteins.
单分子力谱实验能够利用机械力来探究蛋白质的折叠与去折叠过程。在结构层面解释这些实验结果时，可能最具信息量的技术要数引导分子动力学（MD）模拟，它能够明确地模拟处于负载状态下的蛋白质。不幸的是，对于许多最具研究价值的生物分子而言，这项技术的计算成本很高。在此，我们发现，从计算角度来看成本显著更低的正常模式分析（NMA），至少能够获取一些MD模拟所提供的见解。我们将这项技术应用于先前通过力谱研究过的三种非同源蛋白质：T4溶菌酶（T4L）、热休克蛋白70（Hsp70）以及糖皮质激素受体结构域（GCR）。将T4L和Hsp70的NMA结果与之前进行的引导MD模拟结果进行比较，我们发现能够重现主要结果。对于未进行MD模拟的GCR，我们的方法识别出了与实验确定的去折叠中间体相关的子结构。总体而言，我们发现NMA能够为蛋白质单分子力实验的结构分析工具集增添有价值的内容。
