Department of Bioengineering, Box 355013, University of Washington, Seattle, WA 98195-5013, USA.
Department of Bioengineering, Box 355013, University of Washington, Seattle, WA 98195-5013, USA.
J Mol Biol. 2019 Apr 5;431(8):1540-1564. doi: 10.1016/j.jmb.2019.02.026. Epub 2019 Mar 3.
Protein folding/unfolding is a complicated process that defies high-resolution characterization by experimental methods. As an alternative, atomistic molecular dynamics simulations are now routinely employed to elucidate and magnify the accompanying conformational changes and the role of solvent in the folding process. However, the level of detail necessary to map the process at high spatial-temporal resolution provides an overwhelming amount of data. As more and better tools are developed for analysis of these large data sets and validation of the simulations, one is still left with the problem of visualizing the results in ways that provide insight into the folding/unfolding process. While viewing and interrogating static crystal structures has become commonplace, more and different approaches are required for dynamic, interconverting, unfolding, and refolding proteins. Here we review a variety of approaches, ranging from straightforward to complex and unintuitive for multiscale analysis and visualization of protein folding and unfolding.
蛋白质折叠/去折叠是一个复杂的过程，用实验方法很难进行高分辨率的描述。作为替代方法，现在通常采用原子分子动力学模拟来阐明和放大伴随的构象变化以及溶剂在折叠过程中的作用。然而，要以高时空分辨率绘制过程图谱，需要详细到令人望而却步的程度，从而产生了大量的数据。随着更多更好的工具被开发出来用于分析这些大数据集并验证模拟，人们仍然面临着以提供对折叠/去折叠过程深入了解的方式来可视化结果的问题。虽然查看和询问静态晶体结构已经变得很普遍，但对于动态、相互转化、展开和重新折叠的蛋白质，需要更多不同的方法。在这里，我们综述了各种方法，范围从简单到复杂和非直观的，用于蛋白质折叠和去折叠的多尺度分析和可视化。
