title: Visualizing chaperone-assisted protein folding.
abstract: Challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein folding. Obtaining structural ensembles of chaperone-substrate complexes would ultimately reveal how chaperones help proteins fold into their native state. To address this problem, we devised a new structural biology approach based on X-ray crystallography, termed residual electron and anomalous density (READ). READ enabled us to visualize even sparsely populated conformations of the substrate protein immunity protein 7 (Im7) in complex with the Escherichia coli chaperone Spy, and to capture a series of snapshots depicting the various folding states of Im7 bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded to native-like states and reveals how a substrate can explore its folding landscape while being bound to a chaperone.
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.|Howard Hughes Medical Institute, Ann Arbor, Michigan, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Horowitz
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.|Howard Hughes Medical Institute, Ann Arbor, Michigan, USA.
authors.forename: Loïc
authors.initials: L
authors.lastname: Salmon
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.|Howard Hughes Medical Institute, Ann Arbor, Michigan, USA.
authors.forename: Philipp
authors.initials: P
authors.lastname: Koldewey
authors.affiliation: Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan, USA.
authors.forename: Logan S
authors.initials: LS
authors.lastname: Ahlstrom
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.|Howard Hughes Medical Institute, Ann Arbor, Michigan, USA.
authors.forename: Raoul
authors.initials: R
authors.lastname: Martin
authors.affiliation: State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China.
authors.forename: Shu
authors.initials: S
authors.lastname: Quan
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Afonine
authors.affiliation: Division of Biosciences, SLAC National Accelerator Laboratory, Stanford University, Stanford, California, USA.
authors.forename: Henry
authors.identifier: 0000-0003-2358-841X
authors.initials: H
authors.lastname: van den Bedem
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.|Howard Hughes Medical Institute, Ann Arbor, Michigan, USA.
authors.forename: Lili
authors.initials: L
authors.lastname: Wang
authors.affiliation: Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Laboratory, Menlo Park, California, USA.
authors.forename: Qingping
authors.initials: Q
authors.lastname: Xu
authors.affiliation: Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
authors.forename: Raymond C
authors.initials: RC
authors.lastname: Trievel
authors.affiliation: Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan, USA.
authors.forename: Charles L
authors.initials: CL
authors.lastname: Brooks
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.|Howard Hughes Medical Institute, Ann Arbor, Michigan, USA.
authors.forename: James C A
authors.initials: JC
authors.lastname: Bardwell
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D002352:Carrier Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D018360:Crystallography, X-Ray / Q000379:methods; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D033903:Periplasmic Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D002352:Carrier Proteins; C509253:E colicin-binding immunity protein Im7, E coli; D029968:Escherichia coli Proteins; D033903:Periplasmic Proteins; D011994:Recombinant Proteins; C104888:Spy protein, E coli