Characterizing Protein Dynamics with Integrative Use of Bulk and Single-Molecule Techniques

doi:10.1021/acs.biochem.7b00817

	Characterizing Protein Dynamics with Integrative Use of Bulk and Single-Molecule Techniques
	Liu, Zhu 2,3,4,5; Gong, Zhou 2,3; Cao, Yong ; Ding, Yue-He 1,6; Dong, Meng-Qiu 1; Lu, Yun-Bi 4,5; Zhang, Wei-Ping 4,5; Tang, Chun 2,3
刊名	BIOCHEMISTRY
	2018-01-23
卷号	57 期号:3 页码:305-313
ISSN号	0006-2960
DOI	10.1021/acs.biochem.7b00817
文献子类	Article
英文摘要	A protein dynamically samples multiple conformations, and the conformational dynamics enables protein function. Most biophysical measurements are ensemble-based, with the observables averaged over all members of the ensemble. Though attainable, the decomposition of the observables to the constituent conformational states can be computationally expensive and ambiguous. Here we show that the incorporation of single-molecule fluorescence resonance energy transfer (smFRET) data resolves the ambiguity and affords protein ensemble structures that are more precise and accurate. Using K63-linked diubiquitin, we characterize the dynamic domain arrangements of the model system, with the use of chemical cross-linking coupled with mass spectrometry (CXMS), small-angle X-ray scattering (SAXS), and smFRET techniques. CXMS allows the modeling of protein conformational states that are alternatives to the crystal structure. SAXS provides ensemble-averaged low-resolution shape information. Importantly, smFRET affords state-specific populations, and the FRET distances validate the ensemble structures obtained by refining against CXMS and SAXS restraints. Together, the integrative use of bulk and single-molecule techniques affords better insight into protein dynamics and shall be widely implemented in structural biology.
WOS关键词	PARAMAGNETIC RELAXATION ENHANCEMENT ; ALTERNATING-LASER EXCITATION ; RAY SOLUTION SCATTERING ; MASS-SPECTROMETRY ; BIOLOGICAL MACROMOLECULES ; DISTANCE RESTRAINTS ; UBIQUITIN BINDING ; CROSS-LINKING ; FRET ; NMR
WOS研究方向	Biochemistry & Molecular Biology
语种	英语
出版者	AMER CHEMICAL SOC
WOS记录号	WOS:000423418500008
资助机构	National Key R&D Program of China(2016YFA0501200) ; National Key R&D Program of China(2016YFA0501200) ; 973 program from the Chinese Ministry of Science and Technology(2013CB910200) ; 973 program from the Chinese Ministry of Science and Technology(2013CB910200) ; National Natural Science Foundation of China(31400735 ; National Natural Science Foundation of China(31400735 ; China Postdoctoral Science Foundation(2015M571860 ; China Postdoctoral Science Foundation(2015M571860 ; 31500595 ; 31500595 ; 2016T90537) ; 2016T90537) ; 81573400) ; 81573400) ; National Key R&D Program of China(2016YFA0501200) ; National Key R&D Program of China(2016YFA0501200) ; 973 program from the Chinese Ministry of Science and Technology(2013CB910200) ; 973 program from the Chinese Ministry of Science and Technology(2013CB910200) ; National Natural Science Foundation of China(31400735 ; National Natural Science Foundation of China(31400735 ; China Postdoctoral Science Foundation(2015M571860 ; China Postdoctoral Science Foundation(2015M571860 ; 31500595 ; 31500595 ; 2016T90537) ; 2016T90537) ; 81573400) ; 81573400) ; National Key R&D Program of China(2016YFA0501200) ; National Key R&D Program of China(2016YFA0501200) ; 973 program from the Chinese Ministry of Science and Technology(2013CB910200) ; 973 program from the Chinese Ministry of Science and Technology(2013CB910200) ; National Natural Science Foundation of China(31400735 ; National Natural Science Foundation of China(31400735 ; China Postdoctoral Science Foundation(2015M571860 ; China Postdoctoral Science Foundation(2015M571860 ; 31500595 ; 31500595 ; 2016T90537) ; 2016T90537) ; 81573400) ; 81573400) ; National Key R&D Program of China(2016YFA0501200) ; National Key R&D Program of China(2016YFA0501200) ; 973 program from the Chinese Ministry of Science and Technology(2013CB910200) ; 973 program from the Chinese Ministry of Science and Technology(2013CB910200) ; National Natural Science Foundation of China(31400735 ; National Natural Science Foundation of China(31400735 ; China Postdoctoral Science Foundation(2015M571860 ; China Postdoctoral Science Foundation(2015M571860 ; 31500595 ; 31500595 ; 2016T90537) ; 2016T90537) ; 81573400) ; 81573400)
内容类型	期刊论文
源URL	[http://ir.wipm.ac.cn/handle/112942/12840]
专题	中国科学院武汉物理与数学研究所
通讯作者	Gong, Zhou; Tang, Chun
作者单位	1.Natl Inst Biol Sci, Beijing 102206, Peoples R China 2.Chinese Acad Sci, Wuhan Inst Phys & Math, State Key Lab Magnet Resonance & Atom Mol Phys, CAS Key Lab Magnet Resonance Biol Syst, Wuhan 430071, Hubei, Peoples R China 3.Chinese Acad Sci, Wuhan Inst Phys & Math, Natl Ctr Magnet Resonance Wuhan, Wuhan 430071, Hubei, Peoples R China 4.Zhejiang Univ, Sch Med, Minist Hlth China, Dept Pharmacol,Inst Neurosci,Key Lab Med Neurobio, Hangzhou 310058, Zhejiang, Peoples R China 5.Zhejiang Univ, Sch Med, Zhejiang Prov Key Lab Mental Disorders Management, Hangzhou 310058, Zhejiang, Peoples R China 6.Univ Massachusetts, Sch Med, RNA Therapeut Inst, 368 Plantat St, Worcester, MA 01605 USA
推荐引用方式 GB/T 7714	Liu, Zhu,Gong, Zhou,Cao, Yong,et al. Characterizing Protein Dynamics with Integrative Use of Bulk and Single-Molecule Techniques[J]. BIOCHEMISTRY,2018,57(3):305-313.
APA	Liu, Zhu.,Gong, Zhou.,Cao, Yong.,Ding, Yue-He.,Dong, Meng-Qiu.,...&Tang, Chun.(2018).Characterizing Protein Dynamics with Integrative Use of Bulk and Single-Molecule Techniques.BIOCHEMISTRY,57(3),305-313.
MLA	Liu, Zhu,et al."Characterizing Protein Dynamics with Integrative Use of Bulk and Single-Molecule Techniques".BIOCHEMISTRY 57.3(2018):305-313.