Abstract
Guinier analysis allows model-free determination of the radius of gyration (Rg) of a biomolecule from X-ray or neutron scattering data, in the limit of very small scattering angles. Its range of validity is well understood for globular proteins, but is known to be more restricted for unfolded or intrinsically disordered proteins (IDPs). We have used ensembles of disordered structures from molecular dynamics simulations to investigate which structural properties cause deviations from the Guinier approximation at small scattering angles. We find that the deviation from the Guinier approximation is correlated with the polymer scaling exponent ν describing the unfolded ensemble. We therefore introduce an empirical, ν-dependent, higher-order correction term, to augment the standard Guinier analysis. We test the new fitting scheme using all-atom simulation data for several IDPs and experimental data for both an IDP and a destabilized mutant of a folded protein. In all cases tested, we achieve an accuracy of the inferred Rg within ∼ 3% of the true Rg. The method is straightforward to implement and extends the range of validity to a maximum qRg of ∼ 2 versus ∼ 1.1 for Guinier analysis. Compared with the Guinier or Debye approaches, our method allows data from wider angles with lower noise to be used to analyze scattering data accurately. In addition to Rg, our fitting scheme also yields estimates of the scaling exponent ν in excellent agreement with the reference ν determined from the underlying molecular ensemble.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 2540-2553 |
| Number of pages | 14 |
| Journal | Journal of Molecular Biology |
| Volume | 430 |
| Issue number | 16 |
| DOIs | |
| State | Published - Aug 3 2018 |
| Externally published | Yes |
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Keywords
- Guinier analysis
- intrinsically disordered protein
- SAXS
ASJC Scopus subject areas
- Structural Biology
- Molecular Biology
Cite this
An Extended Guinier Analysis for Intrinsically Disordered Proteins. / Zheng, Wenwei; Best, Robert B.
In: Journal of Molecular Biology, Vol. 430, No. 16, 03.08.2018, p. 2540-2553.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - An Extended Guinier Analysis for Intrinsically Disordered Proteins
AU - Zheng, Wenwei
AU - Best, Robert B.
PY - 2018/8/3
Y1 - 2018/8/3
N2 - Guinier analysis allows model-free determination of the radius of gyration (Rg) of a biomolecule from X-ray or neutron scattering data, in the limit of very small scattering angles. Its range of validity is well understood for globular proteins, but is known to be more restricted for unfolded or intrinsically disordered proteins (IDPs). We have used ensembles of disordered structures from molecular dynamics simulations to investigate which structural properties cause deviations from the Guinier approximation at small scattering angles. We find that the deviation from the Guinier approximation is correlated with the polymer scaling exponent ν describing the unfolded ensemble. We therefore introduce an empirical, ν-dependent, higher-order correction term, to augment the standard Guinier analysis. We test the new fitting scheme using all-atom simulation data for several IDPs and experimental data for both an IDP and a destabilized mutant of a folded protein. In all cases tested, we achieve an accuracy of the inferred Rg within ∼ 3% of the true Rg. The method is straightforward to implement and extends the range of validity to a maximum qRg of ∼ 2 versus ∼ 1.1 for Guinier analysis. Compared with the Guinier or Debye approaches, our method allows data from wider angles with lower noise to be used to analyze scattering data accurately. In addition to Rg, our fitting scheme also yields estimates of the scaling exponent ν in excellent agreement with the reference ν determined from the underlying molecular ensemble.
AB - Guinier analysis allows model-free determination of the radius of gyration (Rg) of a biomolecule from X-ray or neutron scattering data, in the limit of very small scattering angles. Its range of validity is well understood for globular proteins, but is known to be more restricted for unfolded or intrinsically disordered proteins (IDPs). We have used ensembles of disordered structures from molecular dynamics simulations to investigate which structural properties cause deviations from the Guinier approximation at small scattering angles. We find that the deviation from the Guinier approximation is correlated with the polymer scaling exponent ν describing the unfolded ensemble. We therefore introduce an empirical, ν-dependent, higher-order correction term, to augment the standard Guinier analysis. We test the new fitting scheme using all-atom simulation data for several IDPs and experimental data for both an IDP and a destabilized mutant of a folded protein. In all cases tested, we achieve an accuracy of the inferred Rg within ∼ 3% of the true Rg. The method is straightforward to implement and extends the range of validity to a maximum qRg of ∼ 2 versus ∼ 1.1 for Guinier analysis. Compared with the Guinier or Debye approaches, our method allows data from wider angles with lower noise to be used to analyze scattering data accurately. In addition to Rg, our fitting scheme also yields estimates of the scaling exponent ν in excellent agreement with the reference ν determined from the underlying molecular ensemble.
KW - Guinier analysis
KW - intrinsically disordered protein
KW - SAXS
UR - http://www.scopus.com/inward/record.url?scp=85044526305&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85044526305&partnerID=8YFLogxK
U2 - 10.1016/j.jmb.2018.03.007
DO - 10.1016/j.jmb.2018.03.007
M3 - Article
VL - 430
SP - 2540
EP - 2553
JO - Journal of Molecular Biology
JF - Journal of Molecular Biology
SN - 0022-2836
IS - 16
ER -