New Simulation Methods at Multi-Scale and -Resolutions

描述（由申请人提供）：许多大型生物分子含有高度柔性的结构成分，这些结构成分会发生大规模的各向异性和集体变形。理想情况下，使用各向异性温度b因子可以更准确地描述这些变形。然而，通常情况下，含有高柔性组分的大配合物产生的晶体只能衍射到有限的分辨率（3~4.5¿）。因此，由于唯一反射的数量相对较少，对于许多这样的系统来说，需要每个原子三个位置参数和六个热参数的全尺寸传统各向异性精化是不切实际的。因此，它们通常在最佳情况下为每个原子提供一个各向同性b因子。由于无法以合理的精度对这些各向异性变形进行建模，进而影响了位置参数的精化，减缓了整体收敛速度，导致精化结构模型误差较大。因此，在结构测定和功能研究中，迫切需要新的方法来应对蛋白质结构的大变形。假设：生物分子的大规模变形对结构测定的误差有很大影响，可以通过使用少量的集体正态模的各向异性精化来减少这种误差。总体目标：我们的重点是开发新的模拟方法，以更真实和有效地表示生物分子在结构确定和功能研究中的大规模变形。在这个资金周期中，将开发一种新的基于正态模式的x射线细化方案（NM-XREF），并在大量有限分辨率结构中进行测试。具体目标：1)算法和软件开发。为了提高NM-XREF的效率和精度，将继续开发新的算法。此外，将投入大量精力将NM-XREF协议开发成一个用户友好的软件包，为整个结构生物学社区服务。2) NM-XREF的系统基准。我们将系统地测试NM-XREF，并将其与TLS在50多个生物分子体系上进行比较。研究结果有望为纳米- xref的应用提供一个总体指导。3)一组选定的生物系统的细化。我们选择了一些最具挑战性的生物系统，通过多次NM-XREF细化和手动调整进行更彻底的调查。最终的结构模型有望为系统的重要功能动力学提供新的见解。4)哺乳动物脂肪酸合酶的结构测定。通过使用NM-XREF，我们希望解决一些在以往的研究中缺失的移动结构部件。我们广泛的初步结果表明，对于使用常规方法精炼的大量有限分辨率结构，NM-XREF对模型质量的改善仍然是实质性的。此外，NMXREF不仅优于TLS方法，而且在某些情况下，当顺序使用TLS时，还可以最大化TLS的增益。因此，将NM-XREF开发成一个对社区友好的工具是当务之急。

DESCRIPTION (provided by applicant): Many large biomolecules contain highly flexible structural components that undergo large-scale anisotropic and collective deformations. Ideally, these deformations should be more accurately described using anisotropic temperature B-factors. However, very frequently, large complexes containing highly flexible components yield crystals that only diffract to limited resolutions (3~4.5¿). Thus, limited by the relatively small number of unique reflections, a full-scale conventional anisotropic refinement that requires three positional and six thermal parameters for each atom is impractical for many such systems. As a result, they are often refined with one isotropic B-factor for each atom at the best scenario. The inability to model these anisotropic deformations with reasonable accuracy in turn deteriorates the refinement of positional parameters, slows down the overall convergence, and results in large errors in refined structural models. Therefore, new methods are urgently needed to cope with large deformations of protein structures in structure determination and functional study. Hypotheses: Large-scale deformations of biomolecules contribute significantly to the errors in structure determination, which can be reduced by anisotropic refinement using a small number of collective normal modes. General Objectives: Our focus has been on developing new simulation methods to represent more realistically and efficiently large-scale deformations of biomolecules in structure determination and functional study. In this funding cycle, a new normal-mode-based X-ray refinement protocol (NM-XREF) will be developed and tested in a large set of limited-resolution structures. Specific Aims: 1) Algorithmic and software development. New algorithmic development will be pursued to improve the efficiency and accuracy of NM-XREF. Furthermore, substantial efforts will be invested to develop the NM-XREF protocol into a user-friendly software package for serving the entire structural biology community. 2) Systematic benchmark of NM-XREF. We will systematically test NM-XREF and compare it with TLS on over 50 biomolecular systems. The outcome is expected to provide a general guideline for the application of NM-XREF. 3) Refinement of a selected group of biological systems. We have selected some of the most challenging biological systems for a more thorough investigation through multiple cycles of NM-XREF refinement and manual adjustment. The final structural models are expected to provide new insights into the functionally important dynamics of the systems. 4) Structure determination of mammalian fatty acid synthase. By using NM-XREF, we hope to resolve some of the mobile structural components missing in previous studies. Our extensive preliminary results suggest that, for a large number of limited-resolution structures refined using conventional methods, the improvement of model quality by NM-XREF is still substantial. Moreover, NMXREF not only outperforms the TLS method, but also maximizes the gain by TLS when they are sequentially utilized in some cases. Thus, it is of a high priority to develop NM-XREF into a friendly tool for the community. PUBLIC HEALTH RELEVANCE Atomic structures of biomolecules are critical to the understanding of their cellular functions, which often involve large-scale conformational deformations, especially for large protein assemblies. Although functionally important, those large-scale deformations impose enormous difficulties on structural refinement in X-ray crystallography. This proposal aims to develop a new X-ray refinement protocol that, with fewer refinement parameters, provides a more accurate description of conformational deformations in structure determination at limited resolutions (3~4.5¿).