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Courbet A, Hansen J, Hsia Y, Bethel N, Park YJ, Xu C, Moyer A, Boyken S, Ueda G, Nattermann U, Nagarajan D, Silva D, Sheffler W, Quispe J, Nord A, King N, Bradley P, Veesler D, Kollman J, Baker D. Computational design of mechanically coupled axle-rotor protein assemblies. Science 2022; 376:383-390. [PMID: 35446645 PMCID: PMC10712554 DOI: 10.1126/science.abm1183] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Natural molecular machines contain protein components that undergo motion relative to each other. Designing such mechanically constrained nanoscale protein architectures with internal degrees of freedom is an outstanding challenge for computational protein design. Here we explore the de novo construction of protein machinery from designed axle and rotor components with internal cyclic or dihedral symmetry. We find that the axle-rotor systems assemble in vitro and in vivo as designed. Using cryo-electron microscopy, we find that these systems populate conformationally variable relative orientations reflecting the symmetry of the coupled components and the computationally designed interface energy landscape. These mechanical systems with internal degrees of freedom are a step toward the design of genetically encodable nanomachines.
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Affiliation(s)
- A. Courbet
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, USA
| | - J. Hansen
- Department of Biochemistry, University of Washington, Seattle, USA
| | - Y. Hsia
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - N. Bethel
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, USA
| | - YJ. Park
- Department of Biochemistry, University of Washington, Seattle, USA
| | - C. Xu
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, USA
| | - A. Moyer
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - S.E. Boyken
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - G. Ueda
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - U. Nattermann
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - D. Nagarajan
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - D. Silva
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Monod Bio, Inc, Seattle, USA
| | - W. Sheffler
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - J. Quispe
- Department of Biochemistry, University of Washington, Seattle, USA
| | - A. Nord
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France
| | - N. King
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - P. Bradley
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - D. Veesler
- Department of Biochemistry, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, USA
| | - J. Kollman
- Department of Biochemistry, University of Washington, Seattle, USA
| | - D. Baker
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, USA
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Tseng TT, Gratwick KS, Kollman J, Park D, Nies DH, Goffeau A, Saier MH. The RND permease superfamily: an ancient, ubiquitous and diverse family that includes human disease and development proteins. J Mol Microbiol Biotechnol 1999; 1:107-25. [PMID: 10941792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
A previous report identified and classified a small family of gram-negative bacterial drug and heavy metal efflux permeases, now commonly referred to as the RND family (TC no. 2.6). We here show that this family is actually a ubiquitous superfamily with representation in all major kingdoms. We report phylogenetic analyses that define seven families within the RND superfamily as follows: (1) the heavy metal efflux (HME) family (gram negative bacteria), (2) the hydrophobe/amphiphile efflux-1 (HAE1) family (gram negative bacteria), (3) the nodulation factor exporter (NFE) family (gram negative bacteria), (4) the SecDF protein-secretion accessory protein (SecDF) family (gram negative and gram positive bacteria as well as archaea), (5) the hydrophobe/amphiphile efflux-2 (HAE2) family (gram positive bacteria), (6) the eukaryotic sterol homeostasis (ESH) family, and (7) the hydrophobe/amphiphile efflux-3 (HAE3) family (archaea and spirochetes). Functionally uncharacterized proteins were identified that are members of the RND superfamily but fall outside of these seven families. Some of the eukaryotic homologues function as enzymes and receptors instead of (or in addition to) transporters. The sizes and topological patterns exhibited by members of all seven families are shown to be strikingly similar, and statistical analyses establish common descent. Multiple alignments of proteins within each family allow derivation of family-specific signature sequences. Structural, functional, mechanistic and evolutionary implication of the reported results are discussed.
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Affiliation(s)
- T T Tseng
- Department of Biology, University of California at San Diego, La Jolla 92093-0116, USA
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