title: A Model for the Molecular Mechanism of an Engineered Light-Driven Protein Machine.
abstract: Controllable protein-based machines and materials are of considerable interest for diverse biotechnological applications. We previously re-engineered an ATP-driven protein machine, a group II chaperonin, to function as a light-gated nanocage. Here we develop and test a model for the molecular mechanism of the re-engineered chaperonin, which undergoes a large-scale closed to open conformational change triggered by reversible photo-isomerization of a site-specifically attached azobenzene crosslinker. In silico experiments using all-atom simulations suggest that rigid body motions of protein subdomains couple the length changes of the crosslinker to rearrangements of the nucleotide-binding pocket, leading to cage opening. We tested this model by designing a mutant for which the orientation of the two protein subdomains forming the nucleotide-binding pocket is directly controlled by the crosslinker, and confirmed successful reversible photoswitching in vitro. The model probes the conformational cycle of group II chaperonins and offers a design principle for engineering other light-driven protein-based molecular machines.
authors.affiliation: Department of Physics, Freie Universität Berlin, Berlin 14195, Germany; Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: daniel.hoersch@fu-berlin.de.
authors.forename: Daniel
authors.initials: D
authors.lastname: Hoersch
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Kortemme
mesh_terms: D001391:Azo Compounds / Q000378:metabolism*; D001665:Binding Sites; D003198:Computer Simulation; D003432:Cross-Linking Reagents; D020285:Cryoelectron Microscopy; D056385:Group II Chaperonins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D008027:Light; D008958:Models, Molecular; D009154:Mutation; D011485:Protein Binding; D011487:Protein Conformation; D015202:Protein Engineering
chemical_list: D001391:Azo Compounds; D003432:Cross-Linking Reagents; D056385:Group II Chaperonins; C009850:azobenzene