期刊
CHEMISTRY-A EUROPEAN JOURNAL
卷 19, 期 19, 页码 5909-5916出版社
WILEY-V C H VERLAG GMBH
DOI: 10.1002/chem.201203809
关键词
denaturation; FRET; molecular dynamics; protein folding; proteins
资金
- National Key Basic Research Foundation of China [2010CB912302, 2012CB917304]
- National Natural Science Foundation of China [21233002, 20973015, 91027044, 21003004]
An increasing number of proteins are found to contain a knot in their polypeptide chain. Although some studies have looked into the folding mechanism of knotted proteins, why and how these complex topologies form are still far from being fully answered. Moreover, no experimental information about how the knot moves during the protein-folding process is available. Herein, by combining single-molecule fluorescence resonance energy transfer (smFRET) experiments with molecular dynamics (MD) simulations, we performed a detailed study to characterize the knot in the denatured state of TrmD, a knotted tRNA (guanosine-1) methyltransferase from Escherichia coli, as a model system. We found that the knot still existed in the unfolded state of TrmD, consistent with the results for two other knotted proteins, YibK and YbeA. More interestingly, both smFRET experiments and MD simulations revealed that the knot slid towards the C-terminal during the unfolding process, which could be explained by the relatively strong interactions between the beta-sheet core at the N terminal of the native knot region. The size of the knot in the unfolded state is not larger than that in the native state. In addition, the knot slid in a downhill mode with simultaneous chain collapse in the denatured state.
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