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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

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Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level
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Published on: April 19, 2019

A quantitative measure for protein conformational heterogeneity.

Nicholas Lyle1, Rahul K Das, Rohit V Pappu

  • 1Computational and Systems Biology Program, Division of Biology and Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, Missouri 63130, USA.

The Journal of Chemical Physics
|October 5, 2013
PubMed
Summary

Researchers developed a new parameter to measure protein conformational heterogeneity. This tool helps distinguish between coupled folding and coil-to-globule transitions, aiding studies of intrinsically disordered proteins (IDPs).

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Area of Science:

  • Protein dynamics and biophysics
  • Computational biology and structural bioinformatics

Background:

  • Proteins exhibit conformational heterogeneity, with intrinsically disordered proteins (IDPs) and denatured states representing extreme examples.
  • Polymeric properties like size and shape help infer globule versus coil formation, but a direct measure of ensemble heterogeneity is lacking.

Purpose of the Study:

  • To introduce a novel parameter for quantifying the degree of conformational heterogeneity within protein ensembles.
  • To differentiate systems where unfolding-folding transitions are coupled with coil-to-globule transitions from those with homogeneous collapsed states.

Main Methods:

  • Conformations were represented as vectors of inter-residue distances.
  • Conformational similarity was quantified using vector projections, generating a distribution of pairwise dissimilarities.
  • The heterogeneity measure was normalized against a Flory random coil model to establish an upper bound for calibration.

Main Results:

  • A new parameter was developed to quantify intra-ensemble conformational heterogeneity.
  • This parameter is calibrated against a random coil model, allowing for comparisons across different sequences and temperatures.
  • The measure effectively distinguishes between different types of coil-to-globule transitions.

Conclusions:

  • The new measure provides a quantitative assessment of conformational heterogeneity in protein ensembles.
  • It will be valuable for studying coupled folding-binding in IDPs and for de novo protein design.
  • This tool aids in controlling the heterogeneity of unbound IDP forms.