Computational design of mechanically coupled axle-rotor protein assemblies

Courbet, A.; Hansen, J.; Hsia, Y.; Bethel, N.; Park, Y. -J.; Xu, C.; Moyer, A.; Boyken, S. E.; Ueda, G.; Nattermann, U.; Nagarajan, D.; Silva, D.; Sheffler, W.; Quispe, J.; Nord, A.; King, N.; Bradley, P.; Veesler, D.; Kollman, J.; Baker, D.

doi:10.1126/science.abm1183

Computational design of mechanically coupled axle-rotor protein assemblies

Journal Article · 22 April 2022 · Science

DOI:https://doi.org/10.1126/science.abm1183· OSTI ID:1982956

^[1]; ^[2]; ^[3]; ^[1]; ^[2]; ^[1]; Moyer, A. ^[3]; ^[3]; ^[3]; ^[3]; ^[3]; ^[4]; ^[3]; ^[2]; ^[5]; ^[3]; ^[6]; ^[7]; ^[2]; ^[1]

Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.; Monod Bio, Inc., Seattle, WA, USA.
Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France.
Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.

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.

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC02-05CH11231

OSTI ID:: 1982956

Journal Information:: Science, Vol. 376, Issue 6591; ISSN 0036-8075

Publisher:: AAAS

Country of Publication:: United States

Language:: English

References (55)

ATP Synthase Junge, Wolfgang; Nelson, Nathan Annual Review of Biochemistry, Vol. 84, Issue 1 https://doi.org/10.1146/annurev-biochem-060614-034124	journal	June 2015
Rotation and structure of FoF1-ATP synthase Okuno, D.; Iino, R.; Noji, H. Journal of Biochemistry, Vol. 149, Issue 6 https://doi.org/10.1093/jb/mvr049	journal	April 2011
Structures of the stator complex that drives rotation of the bacterial flagellum Deme, Justin C.; Johnson, Steven; Vickery, Owen Nature Microbiology, Vol. 5, Issue 12 https://doi.org/10.1038/s41564-020-0788-8	journal	September 2020
Molecular machines with bio-inspired mechanisms Zhang, Liang; Marcos, Vanesa; Leigh, David A. Proceedings of the National Academy of Sciences, Vol. 115, Issue 38 https://doi.org/10.1073/pnas.1712788115	journal	February 2018
Building molecular machine systems Drexler, K. Trends in Biotechnology, Vol. 17, Issue 1 https://doi.org/10.1016/S0167-7799(98)01278-5	journal	January 1999
The Art of Building Small: From Molecular Switches to Molecular Motors Feringa, Ben L. The Journal of Organic Chemistry, Vol. 72, Issue 18 https://doi.org/10.1021/jo070394d	journal	August 2007
From Chemical Topology to Molecular Machines (Nobel Lecture) Sauvage, Jean-Pierre Angewandte Chemie International Edition, Vol. 56, Issue 37 https://doi.org/10.1002/anie.201702992	journal	June 2017
Wholly Synthetic Molecular Machines Cheng, Chuyang; Stoddart, J. Fraser ChemPhysChem, Vol. 17, Issue 12 https://doi.org/10.1002/cphc.201501155	journal	March 2016
Building machines with DNA molecules Ramezani, Hamid; Dietz, Hendrik Nature Reviews Genetics, Vol. 21, Issue 1 https://doi.org/10.1038/s41576-019-0175-6	journal	October 2019
What has de novo protein design taught us about protein folding and biophysics? Baker, David Protein Science, Vol. 28, Issue 4 https://doi.org/10.1002/pro.3588	journal	February 2019
Evolution of a designed protein assembly encapsulating its own RNA genome Butterfield, Gabriel L.; Lajoie, Marc J.; Gustafson, Heather H. Nature, Vol. 552, Issue 7685 https://doi.org/10.1038/nature25157	journal	December 2017
De novo design of protein logic gates Chen, Zibo; Kibler, Ryan D.; Hunt, Andrew Science, Vol. 368, Issue 6486 https://doi.org/10.1126/science.aay2790	journal	April 2020
Design of multi-scale protein complexes by hierarchical building block fusion Hsia, Yang; Mout, Rubul; Sheffler, William Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-22276-z	journal	April 2021
De novo design of bioactive protein switches Langan, Robert A.; Boyken, Scott E.; Ng, Andrew H. Nature, Vol. 572, Issue 7768 https://doi.org/10.1038/s41586-019-1432-8	journal	July 2019
Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens Ueda, George; Antanasijevic, Aleksandar; Fallas, Jorge A. eLife, Vol. 9 https://doi.org/10.7554/eLife.57659	journal	August 2020
Computational design of transmembrane pores Xu, Chunfu; Lu, Peilong; Gamal El-Din, Tamer M. Nature, Vol. 585, Issue 7823 https://doi.org/10.1038/s41586-020-2646-5	journal	August 2020
Designed proteins assemble antibodies into modular nanocages Divine, Robby; Dang, Ha V.; Ueda, George Science, Vol. 372, Issue 6537 https://doi.org/10.1126/science.abd9994	journal	April 2021
Design of biologically active binary protein 2D materials Ben-Sasson, Ariel J.; Watson, Joseph L.; Sheffler, William Nature, Vol. 589, Issue 7842 https://doi.org/10.1038/s41586-020-03120-8	journal	January 2021
Advances in protein structure prediction and design Kuhlman, Brian; Bradley, Philip Nature Reviews Molecular Cell Biology, Vol. 20, Issue 11 https://doi.org/10.1038/s41580-019-0163-x	journal	August 2019
Accurate design of megadalton-scale two-component icosahedral protein complexes Bale, J. B.; Gonen, S.; Liu, Y. Science, Vol. 353, Issue 6297 https://doi.org/10.1126/science.aaf8818	journal	July 2016
Simple mechanics of protein machines Flechsig, Holger; Mikhailov, Alexander S. Journal of The Royal Society Interface, Vol. 16, Issue 155 https://doi.org/10.1098/rsif.2019.0244	journal	June 2019
Rational design of α-helical tandem repeat proteins with closed architectures Doyle, Lindsey; Hallinan, Jazmine; Bolduc, Jill Nature, Vol. 528, Issue 7583 https://doi.org/10.1038/nature16191	journal	December 2015
High-Throughput SAXS for the Characterization of Biomolecules in Solution: A Practical Approach Dyer, Kevin N.; Hammel, Michal; Rambo, Robert P. Structural Genomics https://doi.org/10.1007/978-1-62703-691-7_18	book	October 2013
Comprehensive macromolecular conformations mapped by quantitative SAXS analyses Hura, Greg L.; Budworth, Helen; Dyer, Kevin N. Nature Methods, Vol. 10, Issue 6 https://doi.org/10.1038/nmeth.2453	journal	April 2013
De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity Boyken, S. E.; Chen, Z.; Groves, B. Science, Vol. 352, Issue 6286 https://doi.org/10.1126/science.aad8865	journal	May 2016
Perturbing the energy landscape for improved packing during computational protein design Maguire, Jack B.; Haddox, Hugh K.; Strickland, Devin Proteins: Structure, Function, and Bioinformatics, Vol. 89, Issue 4 https://doi.org/10.1002/prot.26030	journal	December 2020
3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM Punjani, Ali; Fleet, David J. Journal of Structural Biology, Vol. 213, Issue 2 https://doi.org/10.1016/j.jsb.2021.107702	journal	June 2021
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination Punjani, Ali; Rubinstein, John L.; Fleet, David J. Nature Methods, Vol. 14, Issue 3 https://doi.org/10.1038/nmeth.4169	journal	February 2017
Cryo-EM structures provide insight into how E. coli F1Fo ATP synthase accommodates symmetry mismatch Sobti, Meghna; Walshe, James L.; Wu, Di Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-16387-2	journal	May 2020
Cryo-EM structure of the homohexameric T3SS ATPase-central stalk complex reveals rotary ATPase-like asymmetry Majewski, Dorothy D.; Worrall, Liam J.; Hong, Chuan Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-08477-7	journal	February 2019
Reconfigurable asymmetric protein assemblies through implicit negative design Sahtoe, Danny D.; Praetorius, Florian; Courbet, Alexis Science, Vol. 375, Issue 6578 https://doi.org/10.1126/science.abj7662	journal	January 2022
The Fourier transform of a coiled-coil Crick, F. H. C. Acta Crystallographica, Vol. 6, Issue 8 https://doi.org/10.1107/S0365110X53001952	journal	September 1953
Probing Designability via a Generalized Model of Helical Bundle Geometry Grigoryan, Gevorg; DeGrado, William F. Journal of Molecular Biology, Vol. 405, Issue 4 https://doi.org/10.1016/j.jmb.2010.08.058	journal	January 2011
Computational design of self-assembling cyclic protein homo-oligomers Fallas, Jorge A.; Ueda, George; Sheffler, William Nature Chemistry, Vol. 9, Issue 4 https://doi.org/10.1038/nchem.2673	journal	December 2016
RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design Huang, Po-Ssu; Ban, Yih-En Andrew; Richter, Florian PLoS ONE, Vol. 6, Issue 8 https://doi.org/10.1371/journal.pone.0024109	journal	August 2011
Engineering and functionalization of large circular tandem repeat protein nanoparticles Correnti, Colin E.; Hallinan, Jazmine P.; Doyle, Lindsey A. Nature Structural & Molecular Biology, Vol. 27, Issue 4 https://doi.org/10.1038/s41594-020-0397-5	journal	March 2020
ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution Tian, Chuan; Kasavajhala, Koushik; Belfon, Kellon A. A. Journal of Chemical Theory and Computation, Vol. 16, Issue 1 https://doi.org/10.1021/acs.jctc.9b00591	journal	November 2019
A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations Roe, Daniel R.; Brooks, Bernard R. The Journal of Chemical Physics, Vol. 153, Issue 5 https://doi.org/10.1063/5.0013849	journal	August 2020
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data Roe, Daniel R.; Cheatham, Thomas E. Journal of Chemical Theory and Computation, Vol. 9, Issue 7 https://doi.org/10.1021/ct400341p	journal	June 2013
SciPy 1.0: fundamental algorithms for scientific computing in Python Virtanen, Pauli; Gommers, Ralf; Oliphant, Travis E. Nature Methods https://doi.org/10.1038/s41592-019-0686-2	journal	February 2020
Protein production by auto-induction in high-density shaking cultures Studier, F. William Protein Expression and Purification, Vol. 41, Issue 1, p. 207-234 https://doi.org/10.1016/j.pep.2005.01.016	journal	May 2005
Scatter : software for the analysis of nano- and mesoscale small-angle scattering Förster, S.; Apostol, L.; Bras, W. Journal of Applied Crystallography, Vol. 43, Issue 3 https://doi.org/10.1107/S0021889810008289	journal	April 2010
Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments Schneidman-Duhovny, Dina; Hammel, Michal; Tainer, John A. Biophysical Journal, Vol. 105, Issue 4 https://doi.org/10.1016/j.bpj.2013.07.020	journal	August 2013
SAXSMoW 2.0: Online calculator of the molecular weight of proteins in dilute solution from experimental SAXS data measured on a relative scale Piiadov, Vassili; Ares de Araújo, Evandro; Oliveira Neto, Mario Protein Science, Vol. 28, Issue 2 https://doi.org/10.1002/pro.3528	journal	December 2018
Overview of Electron Crystallography of Membrane Proteins: Crystallization and Screening Strategies Using Negative Stain Electron Microscopy Nannenga, Brent L.; Iadanza, Matthew G.; Vollmar, Breanna S. Current Protocols in Protein Science, Vol. 72, Issue 1 https://doi.org/10.1002/0471140864.ps1715s72	journal	April 2013
cisTEM, user-friendly software for single-particle image processing Grant, Timothy; Rohou, Alexis; Grigorieff, Nikolaus eLife, Vol. 7 https://doi.org/10.7554/eLife.35383	journal	March 2018
Leginon: An Automated System for Acquisition of Images from Vitreous Ice Specimens Carragher, Bridget; Kisseberth, Nick; Kriegman, David Journal of Structural Biology, Vol. 132, Issue 1 https://doi.org/10.1006/jsbi.2000.4314	journal	October 2000
EMAN2: An extensible image processing suite for electron microscopy Tang, Guang; Peng, Liwei; Baldwin, Philip R. Journal of Structural Biology, Vol. 157, Issue 1 https://doi.org/10.1016/j.jsb.2006.05.009	journal	January 2007
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy Zheng, Shawn Q.; Palovcak, Eugene; Armache, Jean-Paul Nature Methods, Vol. 14, Issue 4 https://doi.org/10.1038/nmeth.4193	journal	February 2017
CTFFIND4: Fast and accurate defocus estimation from electron micrographs Rohou, Alexis; Grigorieff, Nikolaus Journal of Structural Biology, Vol. 192, Issue 2 https://doi.org/10.1016/j.jsb.2015.08.008	journal	November 2015
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Real-space refinement in PHENIX for cryo-EM and crystallography Afonine, Pavel V.; Poon, Billy K.; Read, Randy J. Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 6 https://doi.org/10.1107/S2059798318006551	journal	May 2018
Evaluating Local and Directional Resolution of Cryo-EM Density Maps Aiyer, Sriram; Zhang, Cheng; Baldwin, Philp R. cryoEM https://doi.org/10.1007/978-1-0716-0966-8_8	book	December 2020
Rapid online buffer exchange for screening of proteins, protein complexes and cell lysates by native mass spectrometry VanAernum, Zachary L.; Busch, Florian; Jones, Benjamin J. Nature Protocols, Vol. 15, Issue 3 https://doi.org/10.1038/s41596-019-0281-0	journal	January 2020
Surface-Induced Dissociation of Noncovalent Protein Complexes in an Extended Mass Range Orbitrap Mass Spectrometer VanAernum, Zachary L.; Gilbert, Joshua D.; Belov, Mikhail E. Analytical Chemistry, Vol. 91, Issue 5 https://doi.org/10.1021/acs.analchem.8b05605	journal	January 2019

Similar Records

Design of multi-scale protein complexes by hierarchical building block fusion

Journal Article · 2021 · Nature Communications · OSTI ID:1780612

Hsia, Yang; Mout, Rubul; Sheffler, William; +17 more

Unconstrained peptoid tetramer exhibits a predominant conformation in aqueous solution

Journal Article · 2019 · Biopolymers · OSTI ID:1498163

Roe, Leah T.; Pelton, Jeffrey G.; Edison, John R.; +6 more

Polyalkylene Glycol (PAG) Based Lubricant for Light & Medium Duty Axles

Technical Report · 2018 · OSTI ID:1460541

Gangopadhyay, Arup; Ved, Chintan

Related Subjects

Science & Technology - Other Topics

Computational design of mechanically coupled axle-rotor protein assemblies

Citation Formats

References (55)

Similar Records

Related Subjects