摘要
目的目前,如何从核磁共振(nuclear magnetic resonance,NMR)光谱实验中准确地确定蛋白质的三维结构是生物物理学中的一个热门课题,因为蛋白质是生物体的重要组成成分,了解蛋白质的空间结构对研究其功能至关重要,然而由于实验数据的严重缺乏使其成为一个很大的挑战。方法在本文中,通过恢复距离矩阵的矩阵填充(matrix completion,MC)算法来解决蛋白质结构确定问题。首先,初始距离矩阵模型被建立,由于实验数据的缺乏,此时的初始距离矩阵为不完整矩阵,随后通过MC算法恢复初始距离矩阵的缺失数据,从而获得整个蛋白质三维结构。为了进一步测试算法的性能,本文选取了4种不同拓扑结构的蛋白质和6种现有的MC算法进行了测试,探究了算法在不同的采样率以及不同程度噪声的情况下算法的恢复效果。结果通过分析均方根偏差(root-mean-square deviation,RMSD)和计算时间这两个重要指标的平均值及标准差评估了算法的性能,结果显示当采样率和噪声因子控制在一定范围内时,RMSD值和标准差都能达到很小的值。另外本文更加具体地比较了不同算法的特点和优势,在精确采样情况下,ScGrassMC算法计算的精度较高,LMaFit和ScaledASD算法则在计算时间上更具优势。在抗噪性方面,ASD和ScaledASD算法表现更为突出。结论本文可以得出,MC算法应用在蛋白质结构确定领域具有很好的效果,而且不同的算法在计算中具有不同的特点和优势。这些结论为新的MC算法的开发提供了参考。本文的研究结果对基于MC算法的蛋白质结构确定领域具有潜在的推动作用。
Objective Nowadays,how to determine an accurate three-dimensional protein structure from nuclear magnetic resonance(NMR)spectroscopy experiments is a hot topic in biophysics,because understanding the spatial structure of a protein is crucial to research its function.However,this is a large challenge due to the serious lack of experimental data.Methods In this paper,the problem of protein structure determination was solved by matrix completion(MC)algorithms of recovering a distance matrix.Firstly,the initial distance matrix model was established,then its missing data were recovered by the MC algorithms at different sampling ratios.The subsequent stage involved adding the noise model to evaluate the noise resistance of the algorithms.Four proteins with different topological structures and 6 off-the-shelf MC algorithms were selected for testing.Results The results show that these algorithms have good performance in a certain range of sampling ratios and noises.More specifically,the advantages of different algorithms in the case of accurate sampling and noisy sampling are compared by analyzing the average and standard deviation of the root-mean-square deviation(RMSD)and computational time,which are two important indexes about algorithms.Conclusion We can conclude that 6 different MC algorithms have different performances and advantages for the problem of protein structure determination.These characteristics provide a basis for the development of a new MC algorithm.The results of this paper have potential promotion in the field of protein research based on MC algorithms.
作者
李志诚
韦仙
李晋婷
LI Zhi-Cheng;WEI Xian;LI Jin-Ting(Department of Physics,Taiyuan Normal University,Jinzhong 030619,China;Institute of Computational and Applied Physics,Taiyuan Normal University,Jinzhong 030619,China;Department of Science,Taiyuan Institute of Technology,Taiyuan 030008,China)
出处
《生物化学与生物物理进展》
SCIE
CAS
CSCD
北大核心
2022年第6期1155-1164,共10页
Progress In Biochemistry and Biophysics
基金
supported by grants from Scientific and Technological Innovation Programs(STIP)of Higher Education Institutions in Shanxi(2020L0513)
the Shanxi Province Science Foundation for Youths(202103021223328)。
关键词
蛋白质结构确定
距离矩阵
矩阵填充
抗噪性
protein structure determination
distance matrix
matrix completion
noise resistance
