单分子荧光共振能量转移数据处理的优化算法

吕袭明; 李辉; 尤菁; 李伟; 王鹏业; 李明; 奚绪光; 窦硕星

doi:10.7498/aps.66.118701

摘要

单分子荧光共振能量转移（smFRET）技术是当今单分子生物物理研究领域的重要实验手段，该技术通过测量供体、受体荧光光强以及二者间的共振能量转移效率，揭示标记位点间的距离，用于研究DNA、蛋白质等生物大分子的构象变化.然而，当前传统数据处理方法大量依赖人工干预，噪音大，严重影响了实验效率和数据的可靠性.本文提出了一种针对smFRET数据的自动分析算法.该算法主要包括三个部分：基于计算供体与受体荧光光强的相关系数来确定受体与供体对应荧光点的自动匹配算法、甄别错误点的筛选算法以及基于隐马尔可夫模型的全局拟合算法.经改进后的算法大大简化了传统算法中需要人工干预的步骤，而且自动筛除了实验数据中主要的几类噪音.将改进的算法应用于人类端粒重复序列G-四联体（G4）DNA折叠动力学的数据分析，结果显示优化算法比传统算法能够更快地得到更高信噪比的数据，而且该数据结果清晰地表明G4的折叠体现出多态性并受到钾离子浓度的影响.

关键词:

Abstract

The single-molecule fluorescence resonance energy transfer (smFRET) technique plays an important role in the development of biophysics. Measuring the changes of the fluorescence intensities of donor and acceptor and of the FRET efficiency can reveal the changes of distance between the labeling positions. The smFRET may be used to study conformational changes of DNA, proteins and other biomolecules. Traditional algorithm for smFRET data processing is highly dependent on manual operation, leading to high noise, low efficiency and low reliability of the outputs. In the present work, we propose an automatic and more accurate algorithm for smFRET data processing. It consists of three parts: algorithm for automatic pairing of donor and acceptor fluorescence spots based on negative correlation between their intensities; algorithm for data screening by eliminating invalid fluorescence spots sections; algorithm for global data fitting based on Baum-Welch algorithm of hidden Markov model (HMM). Based on the law of energy conservation, the light intensity of one pair of donor and acceptor shows a negative correlation. We can use this feature to find the active smFRET pairs automatically. The algorithm will first find out three active smFRET pairs with correlation coefficient lower than the threshold we set. This three active smFRET pairs will provide enough coordinate data for the algorithm to calculate the pairing matrix in the rest of automatic pairing work. After obtaining all the smFRET pairs, the algorithm for data screening will check the correlation coefficient for each pair. The invalid pairs with correlation coefficient higher than the threshold value will be eliminated. The rest of smFRET pairs will be analyzed by the data fitting algorithm. The Baum-Welch algorithm can be used for learning the global parameters. The global parameters we obtained will then be used to fit each FRET-time curve with Viterbi algorithm. The global parameter learning part will help us find the specific FRET efficiency for each state and the curve fitting part will provide more kinetic parameters. The optimization algorithm significantly simplifies the procedures of manual operation in the traditional algorithm and eliminate several types of noises from the experimental data automatically. We apply the new optimization algorithm to the analyses of folding kinetics data for human telomere repeat sequence, the G-quadruplex DNA. It is demonstrated that the optimization algorithm is more efficient to produce data with higher S/N ratio than the traditional algorithm. The final results reveal clearly the folding of G-quadruplex DNA in multiple states that are influenced by the K+ concentration.

Keywords:

作者及机构信息

1.
中国科学院物理研究所, 软物质物理重点实验室, 北京凝聚态物理国家实验室, 北京 100190;

2.
中国科学院大学物理科学学院, 北京 100049;

3.
西北农林科技大学生命科学院, 杨凌 712100

通信作者: 李辉, huili@iphy.ac.cn;sxdou@iphy.ac.cn ; 窦硕星, huili@iphy.ac.cn;sxdou@iphy.ac.cn

基金项目: 国家自然科学基金（批准号：11674383，11474346，11274374）、国家重点基础研究发展计划（批准号：2013CB837200）和国家重点研究发展计划（批准号：2016YFA0301500）资助的课题.

Authors and contacts

1.
Beijing National Laboratory for Condensed Matter Physics, Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China;

2.
School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;

3.
College of Life Sciences, Northwest A & F University, Yangling 712100, China

Corresponding author: Li Hui, huili@iphy.ac.cn;sxdou@iphy.ac.cn ; Dou Shuo-Xing, huili@iphy.ac.cn;sxdou@iphy.ac.cn

Funds: Project supported by the National Natural Science Foundation of China (Grant Nos. 11674383, 11474346, 11274374), the National Basic Research Program of China (Grant No. 2013CB837200), and the National Key Research and Development Program of China (Grant No. 2016YFA0301500).

参考文献

[1]	Zhou R, Kozlov A G, Roy R, Zhang J, Korolev S, Lohman T M, Ha T 2011 Cell 146 222
[2]	Honda M, Park J, Pugh R A, Ha T, Spies M 2009 Mol. Cell 35 694
[3]	Liu C, Mckinney M C, Chen Y H, Earnest T M, Shi X, Lin L J, Ishino Y, Dahmen K, Cann I K, Ha T 2011 Biophy. J. 100 1344
[4]	Wu J Y, Stone M D, Zhuang X 2010 Nucl. Acids Res. 38 e16
[5]	Hengesbach M, Kim N K, Feigon J, Stone M D 2012 Angew. Chem. 51 5876
[6]	Ha T, Tinnefeld P 2012 Annu. Rev. Phys. Chem. 63 595
[7]	He Z C, Li F, Li M Y, Wei L 2015 Acta Phys. Sin. 64 046802 (in Chinese) [何志聪, 李芳, 李牧野, 魏来 2015 64 046802]
[8]	Li M Y, Li F, Wei L, He Z C, Zhang J P, Han J B, Lu P X 2015 Acta Phys. Sin. 64 108201 (in Chinese) [李牧野, 李芳, 魏来, 何志聪, 张俊佩, 韩俊波, 陆培祥 2015 64 108201]
[9]	Roy R, Hohng S, Ha T 2008 Nat. Methods 5 507
[10]	Mckinney S A, Joo C, Ha T 2006 Biophys. J. 91 1941
[11]	Lee N K, Kapanidis A N, Wang Y, Michalet X, Mukhopadhyay J, Ebright R H, Weiss S 2005 Biophys. J. 88 2939
[12]	Sabanayagam C R, Eid J S, Meller A 2005 J. Chem. Phys. 122 061103
[13]	Deniz A A, Dahan M, Grunwell J R, Ha T J, Faulhaber A E, Chemla D S, Weiss S, Schultz P G 1999 PNAS 96 3670
[14]	Rabiner L R 1989 Proc. IEEE 77 257
[15]	Ambrus A, Chen D, Dai J, Bialis T, Jones R A, Yang D 2006 Nucl. Acids Res. 34 2723
[16]	Gray R D, Trent J O, Chaires J B 2014 J. Mol. Biol. 426 1629
[17]	Tippana R, Xiao W, Myong S 2014 Nucl. Acids Res. 42 8106
[18]	Li Y, Liu C, Feng X, Xu Y, Liu B F 2014 Anal. Chem. 86 4333
[19]	Cordes T, Vogelsang J, Tinnefeld P 2009 J. Am. Chem. Soc. 131 5018
[20]	Hubner C G, Renn A, Renge I, Wild U P 2001 J. Chem. Phys. 115 9619
[21]	Lee J Y, Okumus B, Kim D S, Ha T 2005 PNAS 102 18938
[22]	Noer S L, Preus S, Gudnason D, Aznauryan M, Mergny J L, Birkedal V 2016 Nucl. Acids Res. 44 464

施引文献

[1]	Zhou R, Kozlov A G, Roy R, Zhang J, Korolev S, Lohman T M, Ha T 2011 Cell 146 222
[2]	Honda M, Park J, Pugh R A, Ha T, Spies M 2009 Mol. Cell 35 694
[3]	Liu C, Mckinney M C, Chen Y H, Earnest T M, Shi X, Lin L J, Ishino Y, Dahmen K, Cann I K, Ha T 2011 Biophy. J. 100 1344
[4]	Wu J Y, Stone M D, Zhuang X 2010 Nucl. Acids Res. 38 e16
[5]	Hengesbach M, Kim N K, Feigon J, Stone M D 2012 Angew. Chem. 51 5876
[6]	Ha T, Tinnefeld P 2012 Annu. Rev. Phys. Chem. 63 595
[7]	He Z C, Li F, Li M Y, Wei L 2015 Acta Phys. Sin. 64 046802 (in Chinese) [何志聪, 李芳, 李牧野, 魏来 2015 64 046802]
[8]	Li M Y, Li F, Wei L, He Z C, Zhang J P, Han J B, Lu P X 2015 Acta Phys. Sin. 64 108201 (in Chinese) [李牧野, 李芳, 魏来, 何志聪, 张俊佩, 韩俊波, 陆培祥 2015 64 108201]
[9]	Roy R, Hohng S, Ha T 2008 Nat. Methods 5 507
[10]	Mckinney S A, Joo C, Ha T 2006 Biophys. J. 91 1941
[11]	Lee N K, Kapanidis A N, Wang Y, Michalet X, Mukhopadhyay J, Ebright R H, Weiss S 2005 Biophys. J. 88 2939
[12]	Sabanayagam C R, Eid J S, Meller A 2005 J. Chem. Phys. 122 061103
[13]	Deniz A A, Dahan M, Grunwell J R, Ha T J, Faulhaber A E, Chemla D S, Weiss S, Schultz P G 1999 PNAS 96 3670
[14]	Rabiner L R 1989 Proc. IEEE 77 257
[15]	Ambrus A, Chen D, Dai J, Bialis T, Jones R A, Yang D 2006 Nucl. Acids Res. 34 2723
[16]	Gray R D, Trent J O, Chaires J B 2014 J. Mol. Biol. 426 1629
[17]	Tippana R, Xiao W, Myong S 2014 Nucl. Acids Res. 42 8106
[18]	Li Y, Liu C, Feng X, Xu Y, Liu B F 2014 Anal. Chem. 86 4333
[19]	Cordes T, Vogelsang J, Tinnefeld P 2009 J. Am. Chem. Soc. 131 5018
[20]	Hubner C G, Renn A, Renge I, Wild U P 2001 J. Chem. Phys. 115 9619
[21]	Lee J Y, Okumus B, Kim D S, Ha T 2005 PNAS 102 18938
[22]	Noer S L, Preus S, Gudnason D, Aznauryan M, Mergny J L, Birkedal V 2016 Nucl. Acids Res. 44 464

[1]	周晗, 耿轶钊, 晏世伟. p53活性四聚体全原子分子动力学分析. , 2024, 73(4): 048701. doi: 10.7498/aps.73.20231515
[2]	罗泽伟, 武戈, 陈挚, 邓驰楠, 万蓉, 杨涛, 庄正飞, 陈同生. 双通道结构光照明超分辨定量荧光共振能量转移成像系统. , 2023, 72(20): 208701. doi: 10.7498/aps.72.20230853
[3]	张宇航, 薛振勇, 孙皓, 张珠伟, 陈虎. 酰基辅酶A结合蛋白去折叠动力学的单分子磁镊研究. , 2023, 72(15): 158702. doi: 10.7498/aps.72.20230533
[4]	张悦悦, 韩伟静, 陈同生, 王爽. 解旋酶Sen1行走机制的研究. , 2023, 72(10): 108701. doi: 10.7498/aps.72.20230187
[5]	徐一丹, 姜雯昱, 童继红, 韩露露, 左子潭, 许理明, 宫晓春, 吴健. NO分子形状共振阿秒动力学精密测量. , 2022, 71(23): 233301. doi: 10.7498/aps.71.20221735
[6]	朱栋, 徐晗, 周寅, 吴彬, 程冰, 王凯楠, 陈佩军, 高世腾, 翁堪兴, 王河林, 彭树萍, 乔中坤, 王肖隆, 林强. 基于扩展卡尔曼滤波算法的船载绝对重力测量数据处理. , 2022, 71(13): 133702. doi: 10.7498/aps.71.20220071
[7]	朱琪, 王升涛, 赵福祺, 潘昊. 层错四面体对单晶铜层裂行为影响的分子动力学研究. , 2020, 69(3): 036201. doi: 10.7498/aps.69.20191425
[8]	王琼, 王凯歌, 孟康康, 孙聃, 韩仝雨, 高爱华. 基于单分子成像技术研究λ-DNA分子穿越微米通道端口的电动力学特性. , 2020, 69(16): 168202. doi: 10.7498/aps.69.20200074
[9]	李兴欣, 李四平. 退火温度调控多层折叠石墨烯力学性能的分子动力学模拟. , 2020, 69(19): 196102. doi: 10.7498/aps.69.20200836
[10]	潘登, 刘长鑫, 张泽洋, 高玉金, 郝秀红. 速度对聚四氟乙烯摩擦系数影响的分子动力学模拟. , 2019, 68(17): 176801. doi: 10.7498/aps.68.20190495
[11]	陆越, 马建兵, 滕翠娟, 陆颖, 李明, 徐春华. 单分子动力学研究大肠杆菌单链结合蛋白与单链DNA的结合过程. , 2018, 67(8): 088201. doi: 10.7498/aps.67.20180109
[12]	陈泽, 马建兵, 黄星榞, 贾棋, 徐春华, 张慧东, 陆颖. 单分子技术研究T7解旋酶的解旋与换链. , 2018, 67(11): 118201. doi: 10.7498/aps.67.20180501
[13]	秦亚强, 陈瑞云, 石莹, 周海涛, 张国峰, 秦成兵, 高岩, 肖连团, 贾锁堂. 共轭聚合物单分子构象和能量转移特性研究. , 2017, 66(24): 248201. doi: 10.7498/aps.66.248201
[14]	赵振业, 徐春华, 李菁华, 黄星榞, 马建兵, 陆颖. 用全内反射瞬逝场照明磁镊研究Bloom解旋G-四联体. , 2017, 66(18): 188701. doi: 10.7498/aps.66.188701
[15]	何志聪, 李芳, 李牧野, 魏来. CdTe量子点-铜酞菁复合体系荧光共振能量转移的研究. , 2015, 64(4): 046802. doi: 10.7498/aps.64.046802
[16]	张哲, Obergfell Kyle, 韩先明, 陈向军. Monte-Carlo拟合算法及其在电子动量谱学实验数据处理中应用的研究. , 2010, 59(3): 1695-1701. doi: 10.7498/aps.59.1695
[17]	曹莉霞, 王崇愚. α-Fe裂纹的分子动力学研究. , 2007, 56(1): 413-422. doi: 10.7498/aps.56.413
[18]	余大启, 陈民. 刚性多原子分子的正则系综分子动力学算法. , 2006, 55(4): 1628-1633. doi: 10.7498/aps.55.1628
[19]	池凌飞, 林揆训, 姚若河, 林璇英, 余楚迎, 余云鹏. Langmuir单探针诊断射频辉光放电等离子体及其数据处理. , 2001, 50(7): 1313-1317. doi: 10.7498/aps.50.1313
[20]	黄世华, 楼立人. 荧光动力学的转移函数理论. , 1989, 38(3): 422-429. doi: 10.7498/aps.38.422

计量

文章访问数: 7260
PDF下载量: 246
被引次数: 0

姓名
邮箱
手机号码
标题
留言内容
验证码

搜索

留言板