• 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>Journal of Molecular Biology >Can morphing methods predict intermediate structures?
【24h】

Can morphing methods predict intermediate structures?

机译：变形方法可以预测中间结构吗？

获取原文
获取原文并翻译 | 示例
           
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Movement is crucial to the biological function of many proteins, yet crystallographic structures of proteins can give us only a static snapshot. The protein dynamics that are important to biological function often happen on a timescale that is unattainable through detailed simulation methods such as molecular dynamics as they often involve crossing high-energy barriers. To address this coarse-grained motion, several methods have been implemented as web servers in which a set of coordinates is usually linearly interpolated from an initial crystallographic structure to a final crystallographic structure. We present a new morphing method that does not extrapolate linearly and can therefore go around high-energy barriers and which can produce different trajectories between the same two starting points. In this work, we evaluate our method and other established coarse-grained methods according to an objective measure: how close a coarse-grained dynamics method comes to a crystallographically determined intermediate structure when calculating a trajectory between the initial and final crystal protein structure. We test this with a set of five proteins with at least three crystallographically determined on-pathway high-resolution intermediate structures from the Protein Data Bank. For simple hinging motions involving a small conformational change, segmentation of the protein into two rigid sections outperforms other more computationally involved methods. However, large-scale conformational change is best addressed using a nonlinear approach and we suggest that there is merit in further developing such methods.
机译：运动对许多蛋白质的生物学功能至关重要，但是蛋白质的晶体结构只能为我们提供静态快照。对于生物学功能重要的蛋白质动力学通常发生在无法通过详细的模拟方法（例如分子动力学）获得的时间尺度上，因为它们经常涉及跨越高能障碍。为了解决这种粗粒度的运动，已经将几种方法实现为Web服务器，其中通常将一组坐标从初始晶体结构线性插入到最终晶体结构。我们提出了一种新的变形方法，该方法不能线性外推，因此可以绕过高能垒，并且可以在相同的两个起点之间产生不同的轨迹。在这项工作中，我们根据一种客观的方法评估了我们的方法和其他已建立的粗粒度方法：当计算初始和最终晶体蛋白质结构之间的轨迹时，粗粒度动力学方法与晶体学确定的中间结构的接近程度。我们用一组五个蛋白质进行测试，该蛋白质具有至少三个晶体学确定的来自蛋白质数据库的途中高分辨率中间结构。对于涉及小的构象变化的简单铰接运动，将蛋白质分割为两个刚性部分的性能优于其他更多的涉及计算的方法。但是，使用非线性方法最好地解决大规模构象变化的问题，我们建议进一步开发此类方法是有益的。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号