title: Pushing the size limit of de novo structure ensemble prediction guided by sparse SDSL-EPR restraints to 200 residues: The monomeric and homodimeric forms of BAX.
abstract: Structure determination remains a challenge for many biologically important proteins. In particular, proteins that adopt multiple conformations often evade crystallization in all biologically relevant states. Although computational de novo protein folding approaches often sample biologically relevant conformations, the selection of the most accurate model for different functional states remains a formidable challenge, in particular, for proteins with more than about 150 residues. Electron paramagnetic resonance (EPR) spectroscopy can obtain limited structural information for proteins in well-defined biological states and thereby assist in selecting biologically relevant conformations. The present study demonstrates that de novo folding methods are able to accurately sample the folds of 192-residue long soluble monomeric Bcl-2-associated X protein (BAX). The tertiary structures of the monomeric and homodimeric forms of BAX were predicted using the primary structure as well as 25 and 11 EPR distance restraints, respectively. The predicted models were subsequently compared to respective NMR/X-ray structures of BAX. EPR restraints improve the protein-size normalized root-mean-square-deviation (RMSD100) of the most accurate models with respect to the NMR/crystal structure from 5.9Å to 3.9Å and from 5.7Å to 3.3Å, respectively. Additionally, the model discrimination is improved, which is demonstrated by an improvement of the enrichment from 5% to 15% and from 13% to 21%, respectively.
authors.affiliation: Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Axel W
authors.initials: AW
authors.lastname: Fischer
authors.affiliation: Department of Physics, Freie Universität Berlin, Berlin 14195, Germany.
authors.forename: Enrica
authors.initials: E
authors.lastname: Bordignon
authors.affiliation: Interfaculty Institute of Biochemistry, Eberhard Karls University Tübingen, Tübingen 72074, Germany.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Bleicken
authors.affiliation: Interfaculty Institute of Biochemistry, Eberhard Karls University Tübingen, Tübingen 72074, Germany.
authors.forename: Ana J
authors.initials: AJ
authors.lastname: García-Sáez
authors.affiliation: Laboratory of Physical Chemistry, ETH Zürich, Zürich 8093, Switzerland.
authors.forename: Gunnar
authors.initials: G
authors.lastname: Jeschke
authors.affiliation: Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA. Electronic address: jens.meiler@vanderbilt.edu.
authors.forename: Jens
authors.initials: J
authors.lastname: Meiler
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D006801:Humans; D008958:Models, Molecular; D015394:Molecular Structure; D011487:Protein Conformation; D017510:Protein Folding; D055503:Protein Multimerization; D051028:bcl-2-Associated X Protein / Q000737:chemistry*
chemical_list: D051028:bcl-2-Associated X Protein
keywords: Ab initio; DEER; EPR; PELDOR; Protein structure; Protein structure prediction