De novo design of buttressed loops for sculpting protein functions

Jiang, Hanlun; Jude, Kevin M.; Wu, Kejia; Fallas, Jorge; Ueda, George; Brunette, T. J.; Hicks, Derrick R.; Pyles, Harley; Yang, Aerin; Carter, Lauren; Lamb, Mila; Li, Xinting; Levine, Paul M.; Stewart, Lance; Garcia, K. Christopher; Baker, David

doi:10.1038/s41589-024-01632-2

De novo design of buttressed loops for sculpting protein functions

Journal Article · Thu May 30 00:00:00 EDT 2024 · Nature Chemical Biology

DOI:https://doi.org/10.1038/s41589-024-01632-2· OSTI ID:2403423

^[1]; ^[2]; Wu, Kejia ^[3]; Fallas, Jorge ^[3]; ^[3]; Brunette, T. J. ^[3]; Hicks, Derrick R. ^[3]; Pyles, Harley ^[3]; ^[2]; Carter, Lauren ^[3]; Lamb, Mila ^[3]; Li, Xinting ^[3]; Levine, Paul M. ^[3]; ^[3]; ^[2]; ^[3]

Univ. of Washington, Seattle, WA (United States); SLAC
Stanford Univ., CA (United States). School of Medicine
Univ. of Washington, Seattle, WA (United States)

In natural proteins, structured loops have central roles in molecular recognition, signal transduction and enzyme catalysis. However, because of the intrinsic flexibility and irregularity of loop regions, organizing multiple structured loops at protein functional sites has been very difficult to achieve by de novo protein design. Here we describe a solution to this problem that designs tandem repeat proteins with structured loops (9–14 residues) buttressed by extensive hydrogen bonding interactions. Experimental characterization shows that the designs are monodisperse, highly soluble, folded and thermally stable. Crystal structures are in close agreement with the design models, with the loops structured and buttressed as designed. We demonstrate the functionality afforded by loop buttressing by designing and characterizing binders for extended peptides in which the loops form one side of an extended binding pocket. The ability to design multiple structured loops should contribute generally to efforts to design new protein functions.

View Accepted Manuscript (DOE)

Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States); Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-76SF00515; AC02-06CH11357

OSTI ID:: 2403423

Journal Information:: Nature Chemical Biology, Journal Name: Nature Chemical Biology Vol. 20; ISSN 1552-4450

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (61)

Data for de novo design of buttressed loops for sculpting protein functions Jiang, Hanlun; Jude, Kevin M.; Kejia, Wu Zenodo https://doi.org/10.5281/zenodo.10999147	dataset	January 2024
Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units Venkatachalam, C. M. Biopolymers, Vol. 6, Issue 10 https://doi.org/10.1002/bip.1968.360061006	journal	October 1968
Roles of β-turns in protein folding: From peptide models to protein engineering Marcelino, Anna Marie C.; Gierasch, Lila M. Biopolymers, Vol. 89, Issue 5 https://doi.org/10.1002/bip.20960	journal	January 2008
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Kabsch, Wolfgang; Sander, Christian Biopolymers, Vol. 22, Issue 12 https://doi.org/10.1002/bip.360221211	journal	December 1983
Improved side-chain torsion potentials for the Amber ff99SB protein force field Lindorff-Larsen, Kresten; Piana, Stefano; Palmo, Kim Proteins: Structure, Function, and Bioinformatics https://doi.org/10.1002/prot.22711	journal	January 2010
In vitro-engineered non-antibody protein therapeutics Simeon, Rudo; Chen, Zhilei Protein & Cell, Vol. 9, Issue 1 https://doi.org/10.1007/s13238-017-0386-6	journal	March 2017
Beyond Antibodies: The DARPin® Drug Platform Stumpp, Michael T.; Dawson, Keith M.; Binz, H. Kaspar BioDrugs, Vol. 34, Issue 4 https://doi.org/10.1007/s40259-020-00429-8	journal	June 2020
Clustering to minimize the maximum intercluster distance Gonzalez, Teofilo F. Theoretical Computer Science, Vol. 38 https://doi.org/10.1016/0304-3975(85)90224-5	journal	January 1985
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules Leaver-Fay, Andrew; Tyka, Michael; Lewis, Steven M. Computer Methods, Part C https://doi.org/10.1016/B978-0-12-381270-4.00019-6	book	January 2011
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
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers Abraham, Mark James; Murtola, Teemu; Schulz, Roland SoftwareX, Vol. 1-2 https://doi.org/10.1016/j.softx.2015.06.001	journal	September 2015
Exploring the repeat protein universe through computational protein design Brunette, Tj; Parmeggiani, Fabio; Huang, Po-Ssu Nature, Vol. 528, Issue 7583 https://doi.org/10.1038/nature16162	journal	December 2015
Accurate de novo design of hyperstable constrained peptides Bhardwaj, Gaurav; Mulligan, Vikram Khipple; Bahl, Christopher D. Nature, Vol. 538, Issue 7625 https://doi.org/10.1038/nature19791	journal	September 2016
High-affinity binders selected from designed ankyrin repeat protein libraries Binz, H. Kaspar; Amstutz, Patrick; Kohl, Andreas Nature Biotechnology, Vol. 22, Issue 5, p. 575-582 https://doi.org/10.1038/nbt962	journal	April 2004
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
De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy Huang, Po-Ssu; Feldmeier, Kaspar; Parmeggiani, Fabio Nature Chemical Biology, Vol. 12, Issue 1 https://doi.org/10.1038/nchembio.1966	journal	November 2015
Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS) Hura, Greg L.; Menon, Angeli L.; Hammel, Michal Nature Methods, Vol. 6, Issue 8 https://doi.org/10.1038/nmeth.1353	journal	July 2009
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
Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander Nature https://doi.org/10.1038/s41586-021-03819-2	journal	July 2021
Design of protein-binding proteins from the target structure alone Cao, Longxing; Coventry, Brian; Goreshnik, Inna Nature, Vol. 605, Issue 7910 https://doi.org/10.1038/s41586-022-04654-9	journal	March 2022
De novo design of protein structure and function with RFdiffusion Watson, Joseph L.; Juergens, David; Bennett, Nathaniel R. Nature, Vol. 620, Issue 7976 https://doi.org/10.1038/s41586-023-06415-8	journal	July 2023
Large language models generate functional protein sequences across diverse families Madani, Ali; Krause, Ben; Greene, Eric R. Nature Biotechnology, Vol. 41, Issue 8 https://doi.org/10.1038/s41587-022-01618-2	journal	January 2023
Macromolecular modeling and design in Rosetta: recent methods and frameworks Leman, Julia Koehler; Weitzner, Brian D.; Lewis, Steven M. Nature Methods, Vol. 17, Issue 7 https://doi.org/10.1038/s41592-020-0848-2	journal	June 2020
Protein structure predictions to atomic accuracy with AlphaFold Jumper, John; Hassabis, Demis Nature Methods, Vol. 19, Issue 1 https://doi.org/10.1038/s41592-021-01362-6	journal	January 2022
Controllable protein design with language models Ferruz, Noelia; Höcker, Birte Nature Machine Intelligence, Vol. 4, Issue 6 https://doi.org/10.1038/s42256-022-00499-z	journal	June 2022
Score-based generative modeling for de novo protein design Lee, Jin Sub; Kim, Jisun; Kim, Philip M. Nature Computational Science, Vol. 3, Issue 5 https://doi.org/10.1038/s43588-023-00440-3	journal	May 2023
Canonical sampling through velocity rescaling Bussi, Giovanni; Donadio, Davide; Parrinello, Michele The Journal of Chemical Physics, Vol. 126, Issue 1 https://doi.org/10.1063/1.2408420	journal	January 2007
Polymorphic transitions in single crystals: A new molecular dynamics method Parrinello, M.; Rahman, A. Journal of Applied Physics, Vol. 52, Issue 12 https://doi.org/10.1063/1.328693	journal	December 1981
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems Darden, Tom; York, Darrin; Pedersen, Lee The Journal of Chemical Physics, Vol. 98, Issue 12 https://doi.org/10.1063/1.464397	journal	June 1993
Simulation of activation free energies in molecular systems Neria, Eyal; Fischer, Stefan; Karplus, Martin The Journal of Chemical Physics, Vol. 105, Issue 5 https://doi.org/10.1063/1.472061	journal	August 1996
An approach to crystallizing proteins by synthetic symmetrization Banatao, D. R.; Cascio, D.; Crowley, C. S. Proceedings of the National Academy of Sciences, Vol. 103, Issue 44 https://doi.org/10.1073/pnas.0607674103	journal	October 2006
Modular repeat protein sculpting using rigid helical junctions Brunette, Tj; Bick, Matthew J.; Hansen, Jesse M. Proceedings of the National Academy of Sciences, Vol. 117, Issue 16 https://doi.org/10.1073/pnas.1908768117	journal	April 2020
Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion Caldwell, Shane J.; Haydon, Ian C.; Piperidou, Nikoletta Proceedings of the National Academy of Sciences, Vol. 117, Issue 48 https://doi.org/10.1073/pnas.2008535117	journal	November 2020
Transferrin receptor targeting by de novo sheet extension Sahtoe, Danny D.; Coscia, Adrian; Mustafaoglu, Nur Proceedings of the National Academy of Sciences, Vol. 118, Issue 17 https://doi.org/10.1073/pnas.2021569118	journal	April 2021
Consensus-derived structural determinants of the ankyrin repeat motif Mosavi, L. K.; Minor, D. L.; Peng, Z. -y. Proceedings of the National Academy of Sciences, Vol. 99, Issue 25 https://doi.org/10.1073/pnas.252537899	journal	December 2002
PISCES: a protein sequence culling server Wang, G.; Dunbrack, R. L. Bioinformatics, Vol. 19, Issue 12 https://doi.org/10.1093/bioinformatics/btg224	journal	August 2003
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta Chaudhury, S.; Lyskov, S.; Gray, J. J. Bioinformatics, Vol. 26, Issue 5, p. 689-691 https://doi.org/10.1093/bioinformatics/btq007	journal	January 2010
TM-align: a protein structure alignment algorithm based on the TM-score Zhang, Y. Nucleic Acids Research, Vol. 33, Issue 7 https://doi.org/10.1093/nar/gki524	journal	April 2005
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Graphical tools for macromolecular crystallography in PHENIX Echols, Nathaniel; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. Journal of Applied Crystallography, Vol. 45, Issue 3 https://doi.org/10.1107/S0021889812017293	journal	May 2012
Optimal description of a protein structure in terms of multiple groups undergoing TLS motion Painter, Jay; Merritt, Ethan A. Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 4 https://doi.org/10.1107/S0907444906005270	journal	March 2006
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1 https://doi.org/10.1107/S090744490705024X	journal	December 2007
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Data processing and analysis with the autoPROC toolbox Vonrhein, Clemens; Flensburg, Claus; Keller, Peter Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911007773	journal	March 2011
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement Headd, Jeffrey J.; Echols, Nathaniel; Afonine, Pavel V. Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 5 https://doi.org/10.1107/S1399004714003277	journal	April 2014
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
Matplotlib: A 2D Graphics Environment Hunter, John D. Computing in Science & Engineering, Vol. 9, Issue 3 https://doi.org/10.1109/MCSE.2007.55	journal	January 2007
Accurate prediction of protein structures and interactions using a three-track neural network Baek, Minkyung; DiMaio, Frank; Anishchenko, Ivan Science, Vol. 373, Issue 6557 https://doi.org/10.1126/science.abj8754	journal	July 2021
Robust deep learning–based protein sequence design using ProteinMPNN Dauparas, J.; Anishchenko, I.; Bennett, N. Science, Vol. 378, Issue 6615 https://doi.org/10.1126/science.add2187	journal	October 2022
Sequence-Specific Recognition of a PxLPxI/L Motif by an Ankyrin Repeat Tumbler Lock Xu, Chao; Jin, Jing; Bian, Chuanbing Science Signaling, Vol. 5, Issue 226 https://doi.org/10.1126/scisignal.2002979	journal	May 2012
Beyond Antibodies as Binding Partners: The Role of Antibody Mimetics in Bioanalysis Yu, Xiaowen; Yang, Yu-Ping; Dikici, Emre Annual Review of Analytical Chemistry, Vol. 10, Issue 1 https://doi.org/10.1146/annurev-anchem-061516-045205	journal	June 2017
Designed Ankyrin Repeat Proteins (DARPins): Binding Proteins for Research, Diagnostics, and Therapy Plückthun, Andreas Annual Review of Pharmacology and Toxicology, Vol. 55, Issue 1 https://doi.org/10.1146/annurev-pharmtox-010611-134654	journal	January 2015
Computational design of structured loops for new protein functions Kundert, Kale; Kortemme, Tanja Biological Chemistry, Vol. 400, Issue 3 https://doi.org/10.1515/hsz-2018-0348	journal	January 2019
seaborn: statistical data visualization Waskom, Michael Journal of Open Source Software, Vol. 6, Issue 60 https://doi.org/10.21105/joss.03021	journal	April 2021
Data Structures for Statistical Computing in Python McKinney, Wes Proceedings of the Python in Science Conference https://doi.org/10.25080/Majora-92bf1922-00a	conference	January 2010
De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design Chu, Alexander E.; Fernandez, Daniel; Liu, Jingjia BioDesign Research, Vol. 2022 https://doi.org/10.34133/2022/9842315	journal	January 2022
pandas-dev/pandas: Pandas No authors listed https://doi.org/10.5281/zenodo.3509134	software	January 2024
Collaboration gets the most out of software Morin, Andrew; Eisenbraun, Ben; Key, Jason eLife, Vol. 2 https://doi.org/10.7554/eLife.01456	journal	September 2013

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