title: Systematic evaluation of CS-Rosetta for membrane protein structure prediction with sparse NOE restraints.
abstract: We critically test and validate the CS-Rosetta methodology for de novo structure prediction of α-helical membrane proteins (MPs) from NMR data, such as chemical shifts and NOE distance restraints. By systematically reducing the number and types of NOE restraints, we focus on determining the regime in which MP structures can be reliably predicted and pinpoint the boundaries of the approach. Five MPs of known structure were used as test systems, phototaxis sensory rhodopsin II (pSRII), a subdomain of pSRII, disulfide binding protein B (DsbB), microsomal prostaglandin E2 synthase-1 (mPGES-1), and translocator protein (TSPO). For pSRII and DsbB, where NMR and X-ray structures are available, resolution-adapted structural recombination (RASREC) CS-Rosetta yields structures that are as close to the X-ray structure as the published NMR structures if all available NMR data are used to guide structure prediction. For mPGES-1 and Bacillus cereus TSPO, where only X-ray crystal structures are available, highly accurate structures are obtained using simulated NMR data. One main advantage of RASREC CS-Rosetta is its robustness with respect to even a drastic reduction of the number of NOEs. Close-to-native structures were obtained with one randomly picked long-range NOEs for every 14, 31, 38, and 8 residues for full-length pSRII, the pSRII subdomain, TSPO, and DsbB, respectively, in addition to using chemical shifts. For mPGES-1, atomically accurate structures could be predicted even from chemical shifts alone. Our results show that atomic level accuracy for helical membrane proteins is achievable with CS-Rosetta using very sparse NOE restraint sets to guide structure prediction. Proteins 2017; 85:812-826. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Center for Theoretical Chemistry, Ruhr-University Bochum, Bochum, 44780, Germany.|Max Planck Institute of Biophysics, 60438, Frankfurt am Main, Germany.
authors.forename: Katrin
authors.initials: K
authors.lastname: Reichel
authors.affiliation: Center for Theoretical Chemistry, Ruhr-University Bochum, Bochum, 44780, Germany.
authors.forename: Olivier
authors.initials: O
authors.lastname: Fisette
authors.affiliation: ICS-6 Structural Biochemistry, Institute of Complex Systems, Forschungszentrum Jülich, Jülich, 52425, Germany.
authors.forename: Tatjana
authors.initials: T
authors.lastname: Braun
authors.affiliation: Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie, Technische Universität München, Garching, 85747, Germany.
authors.forename: Oliver F
authors.initials: OF
authors.lastname: Lange
authors.affiliation: Max Planck Institute of Biophysics, 60438, Frankfurt am Main, Germany.|Institute of Biophysics, Goethe University, 60438, Frankfurt am Main, Germany.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Hummer
authors.affiliation: Center for Theoretical Chemistry, Ruhr-University Bochum, Bochum, 44780, Germany.
authors.forename: Lars V
authors.initials: LV
authors.lastname: Schäfer
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D019843:Archaeal Proteins / Q000737:chemistry*; D001409:Bacillus cereus / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry*; D002338:Carotenoids / Q000737:chemistry*; D002352:Carrier Proteins / Q000737:chemistry*; D016931:Halobacteriales / Q000737:chemistry*; D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D000071876:Prostaglandin-E Synthases / Q000737:chemistry*; D000072756:Protein Conformation, alpha-Helical; D054730:Protein Interaction Domains and Motifs; D013816:Thermodynamics
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D002352:Carrier Proteins; C079503:DsbB protein, Bacteria; D008565:Membrane Proteins; C434450:phototaxis receptor sensory rhodopsin II, Natronobacterium pharaonis; D002338:Carotenoids; C000605862:PTGES protein, human; D000071876:Prostaglandin-E Synthases
keywords: Rosetta; enhanced sampling; protein structure prediction; sparse NMR data