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TitleCharacterizing Protein Dynamics with Integrative Use of Bulk and Single-Molecule Techniques.
Journal, issue, pagesBiochemistry, Vol. 57, Issue 3, Page 305-313, Year 2018
Publish dateJan 23, 2018
AuthorsZhu Liu / Zhou Gong / Yong Cao / Yue-He Ding / Meng-Qiu Dong / Yun-Bi Lu / Wei-Ping Zhang / Chun Tang /
PubMed AbstractA protein dynamically samples multiple conformations, and the conformational dynamics enables protein function. Most biophysical measurements are ensemble-based, with the observables averaged over ...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.
External linksBiochemistry / PubMed:28945353
MethodsSAS (X-ray synchrotron)
Structure data

SASDCG7: Lys63-linked diubiquitin at pH7.4 (Polyubiquitin-C, ubiquitin)
Method: SAXS/SANS

Source
  • Homo sapiens (human)

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