Pseudocontact Shift-Driven Iterative Resampling for 3D Structure Determinations of Large Proteins

Journal of Molecular Biology
Kala Bharath PillaThomas Huber

Abstract

Pseudocontact shifts (PCSs) induced by paramagnetic lanthanides produce pronounced effects in nuclear magnetic resonance spectra, which are easily measured and which deliver valuable long-range structure restraints. Even sparse PCS data greatly enhance the success rate of 3D (3-dimensional) structure predictions of proteins by the modeling program Rosetta. The present work extends this approach to 3D structures of larger proteins, comprising more than 200 residues, which are difficult to model by Rosetta without additional experimental restraints. The new algorithm improves the fragment assembly method of Rosetta by utilizing PCSs generated from paramagnetic lanthanide ions attached at four different sites as the only experimental restraints. The sparse PCS data are utilized at multiple stages, to identify native-like local structures, to rank the best structural models and to rebuild the fragment libraries. The fragment libraries are refined iteratively until convergence. The PCS-driven iterative resampling algorithm is strictly data dependent and shown to generate accurate models for a benchmark set of eight different proteins, ranging from 100 to 220 residues, using solely PCSs of backbone amide protons.

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Citations

Mar 3, 2017·IUCrJ·Enrico Luchinat, Lucia Banci
Jun 3, 2016·Chemical Communications : Chem Comm·Michael D LeeBim Graham
Jul 30, 2016·Chemical Communications : Chem Comm·Bin-Bin PanXun-Cheng Su
Apr 24, 2017·Journal of Biomolecular NMR·Benjamin J G PearceGottfried Otting
Jun 3, 2020·Nature Methods·Julia Koehler LemanRichard Bonneau
Apr 20, 2018·Emerging Topics in Life Sciences·Enrico Luchinat, Lucia Banci
Apr 1, 2019·Biochimica Et Biophysica Acta. General Subjects·Tomohide Saio, Koichiro Ishimori
Mar 12, 2017·Progress in Nuclear Magnetic Resonance Spectroscopy·Christoph Nitsche, Gottfried Otting
Nov 30, 2019·Progress in Nuclear Magnetic Resonance Spectroscopy·Daniel Joss, Daniel Häussinger
Aug 3, 2021·Journal of Biomolecular NMR·Stefano CucuzzaOliver Zerbe

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