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Dimension conversion and scaling of disordered protein chains

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Molecular BioSystems Vol - 12 Issue - 8

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Dimension conversion and scaling of disordered protein chains

Content Provider	Royal Society of Chemistry (RSC)
Author	Li, Maodong Jin, Fan Sun, Tanlin Liu, Zhirong Yu, Daqi
Copyright Year	2016
Abstract	To extract protein dimension and energetics information from single-molecule fluorescence resonance energy transfer spectroscopy (smFRET) data, it is essential to establish the relationship between the distributions of the radius of gyration (Rg) and the end-to-end (donor-to-acceptor) distance (Ree). Here, we performed a coarse-grained molecular dynamics simulation to obtain a conformational ensemble of denatured proteins and intrinsically disordered proteins. For any disordered chain with fixed length, there is an excellent linear correlation between the average values of Rg and Ree under various solvent conditions, but the relationship deviates from the prediction of a Gaussian chain. A modified conversion formula was proposed to analyze smFRET data. The formula reduces the discrepancy between the results obtained from FRET and small-angle X-ray scattering (SAXS). The scaling law in a coil–globule transition process was examined where a significant finite-size effect was revealed, i.e., the scaling exponent may exceed the theoretical critical boundary [1/3, 3/5] and the prefactor changes notably during the transition. The Sanchez chain model was also tested and it was shown that the mean-field approximation works well for expanded chains.
Starting Page	2932
Ending Page	2940
Page Count	9
File Format	HTM / HTML PDF
ISSN	1742206X
Volume Number	12
Issue Number	9
Journal	Molecular BioSystems
DOI	10.1039/c6mb00415f
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	Energetics Conformational ensembles Förster resonance energy transfer Spectroscopy Intrinsically disordered proteins Normal distribution Fluorescence Molecular dynamics Sanchez Solvent Protein Small-angle X-ray scattering
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biotechnology

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