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Schnettler JD, Wang MS, Gantz M, Bunzel HA, Karas C, Hollfelder F, Hecht MH. Selection of a promiscuous minimalist cAMP phosphodiesterase from a library of de novo designed proteins. Nat Chem 2024; 16:1200-1208. [PMID: 38702405 PMCID: PMC11230910 DOI: 10.1038/s41557-024-01490-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/27/2024] [Indexed: 05/06/2024]
Abstract
The ability of unevolved amino acid sequences to become biological catalysts was key to the emergence of life on Earth. However, billions of years of evolution separate complex modern enzymes from their simpler early ancestors. To probe how unevolved sequences can develop new functions, we use ultrahigh-throughput droplet microfluidics to screen for phosphoesterase activity amidst a library of more than one million sequences based on a de novo designed 4-helix bundle. Characterization of hits revealed that acquisition of function involved a large jump in sequence space enriching for truncations that removed >40% of the protein chain. Biophysical characterization of a catalytically active truncated protein revealed that it dimerizes into an α-helical structure, with the gain of function accompanied by increased structural dynamics. The identified phosphodiesterase is a manganese-dependent metalloenzyme that hydrolyses a range of phosphodiesters. It is most active towards cyclic AMP, with a rate acceleration of ~109 and a catalytic proficiency of >1014 M-1, comparable to larger enzymes shaped by billions of years of evolution.
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Affiliation(s)
| | - Michael S Wang
- Department of Chemistry, Princeton University, Princeton, USA
| | - Maximilian Gantz
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - H Adrian Bunzel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Christina Karas
- Department of Molecular Biology, Princeton University, Princeton, USA
| | | | - Michael H Hecht
- Department of Chemistry, Princeton University, Princeton, USA.
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2
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Frumkin I, Laub MT. Selection of a de novo gene that can promote survival of Escherichia coli by modulating protein homeostasis pathways. Nat Ecol Evol 2023; 7:2067-2079. [PMID: 37945946 PMCID: PMC10697842 DOI: 10.1038/s41559-023-02224-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 09/12/2023] [Indexed: 11/12/2023]
Abstract
Cellular novelty can emerge when non-functional loci become functional genes in a process termed de novo gene birth. But how proteins with random amino acid sequences beneficially integrate into existing cellular pathways remains poorly understood. We screened ~108 genes, generated from random nucleotide sequences and devoid of homology to natural genes, for their ability to rescue growth arrest of Escherichia coli cells producing the ribonuclease toxin MazF. We identified ~2,000 genes that could promote growth, probably by reducing transcription from the promoter driving toxin expression. Additionally, one random protein, named Random antitoxin of MazF (RamF), modulated protein homeostasis by interacting with chaperones, leading to MazF proteolysis and a consequent loss of its toxicity. Finally, we demonstrate that random proteins can improve during evolution by identifying beneficial mutations that turned RamF into a more efficient inhibitor. Our work provides a mechanistic basis for how de novo gene birth can produce functional proteins that effectively benefit cells evolving under stress.
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Affiliation(s)
- Idan Frumkin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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3
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Heames B, Buchel F, Aubel M, Tretyachenko V, Loginov D, Novák P, Lange A, Bornberg-Bauer E, Hlouchová K. Experimental characterization of de novo proteins and their unevolved random-sequence counterparts. Nat Ecol Evol 2023; 7:570-580. [PMID: 37024625 PMCID: PMC10089919 DOI: 10.1038/s41559-023-02010-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/10/2023] [Indexed: 04/08/2023]
Abstract
De novo gene emergence provides a route for new proteins to be formed from previously non-coding DNA. Proteins born in this way are considered random sequences and typically assumed to lack defined structure. While it remains unclear how likely a de novo protein is to assume a soluble and stable tertiary structure, intersecting evidence from random sequence and de novo-designed proteins suggests that native-like biophysical properties are abundant in sequence space. Taking putative de novo proteins identified in human and fly, we experimentally characterize a library of these sequences to assess their solubility and structure propensity. We compare this library to a set of synthetic random proteins with no evolutionary history. Bioinformatic prediction suggests that de novo proteins may have remarkably similar distributions of biophysical properties to unevolved random sequences of a given length and amino acid composition. However, upon expression in vitro, de novo proteins exhibit moderately higher solubility which is further induced by the DnaK chaperone system. We suggest that while synthetic random sequences are a useful proxy for de novo proteins in terms of structure propensity, de novo proteins may be better integrated in the cellular system than random expectation, given their higher solubility.
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Affiliation(s)
- Brennen Heames
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Filip Buchel
- Department of Cell Biology, Charles University, BIOCEV, Prague, Czech Republic
- Department of Biochemistry, Charles University, Prague, Czech Republic
| | - Margaux Aubel
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | | | - Dmitry Loginov
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Novák
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Andreas Lange
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
- Department of Protein Evolution, MPI for Developmental Biology, Tübingen, Germany.
| | - Klára Hlouchová
- Department of Cell Biology, Charles University, BIOCEV, Prague, Czech Republic.
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.
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4
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Siebenaller C, Schlösser L, Junglas B, Schmidt-Dengler M, Jacob D, Hellmann N, Sachse C, Helm M, Schneider D. Binding and/or hydrolysis of purine-based nucleotides is not required for IM30 ring formation. FEBS Lett 2021; 595:1876-1885. [PMID: 34060653 DOI: 10.1002/1873-3468.14140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/30/2021] [Accepted: 05/20/2021] [Indexed: 11/09/2022]
Abstract
IM30, the inner membrane-associated protein of 30 kDa, is conserved in cyanobacteria and chloroplasts. Although its exact physiological function is still mysterious, IM30 is clearly essential for thylakoid membrane biogenesis and/or dynamics. Recently, a cryptic IM30 GTPase activity has been reported, albeit thus far no physiological function has been attributed to this. Yet, it is still possible that GTP binding/hydrolysis affects formation of the prototypical large homo-oligomeric IM30 ring and rod structures. Here, we show that the Synechocystis sp. PCC 6803 IM30 protein in fact is an NTPase that hydrolyzes GTP and ATP, but not CTP or UTP, with about identical rates. While IM30 forms large oligomeric ring complexes, nucleotide binding and/or hydrolysis are clearly not required for ring formation.
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Affiliation(s)
- Carmen Siebenaller
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Germany
| | - Lukas Schlösser
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Germany
| | - Benedikt Junglas
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Germany.,Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Germany
| | - Martina Schmidt-Dengler
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Germany
| | - Dominik Jacob
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Germany
| | - Nadja Hellmann
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Germany
| | - Carsten Sachse
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Germany
| | - Mark Helm
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Germany
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Germany.,Institute of Molecular Physiology, Johannes Gutenberg University Mainz, Germany
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Roman BI. The Expanding Role of Chemistry in Optimizing Proteins for Human Health Applications. J Med Chem 2021; 64:7179-7188. [PMID: 34014084 DOI: 10.1021/acs.jmedchem.1c00294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the past decades, therapeutics based on biological macromolecules and cells have successfully entered the clinical arena and progressively occupied an increasing share of what once was almost exclusively small molecule territory. This perspective explores the opportunities for chemists at the interface between biologics and small molecule-based products. It provides concrete examples by zooming in on the area of post-translational protein modification. The conclusion is that, rather than diminishing the relevance of chemistry in the pharmaceutical enterprise, the advent of the biologics has provided an additional playing field for synthetic and medicinal chemists, where they can contribute to the efficacy and scope of applicability of biological entities in a collaborative effort to transformatively address unmet medical needs.
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Affiliation(s)
- Bart I Roman
- Research Group SynBioC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Universiteit Gent, Coupure Links 653, 9000 Gent, Belgium.,Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, 9000 Gent, Belgium
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Hamley IW. Biocatalysts Based on Peptide and Peptide Conjugate Nanostructures. Biomacromolecules 2021; 22:1835-1855. [PMID: 33843196 PMCID: PMC8154259 DOI: 10.1021/acs.biomac.1c00240] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/31/2021] [Indexed: 12/15/2022]
Abstract
Peptides and their conjugates (to lipids, bulky N-terminals, or other groups) can self-assemble into nanostructures such as fibrils, nanotubes, coiled coil bundles, and micelles, and these can be used as platforms to present functional residues in order to catalyze a diversity of reactions. Peptide structures can be used to template catalytic sites inspired by those present in natural enzymes as well as simpler constructs using individual catalytic amino acids, especially proline and histidine. The literature on the use of peptide (and peptide conjugate) α-helical and β-sheet structures as well as turn or disordered peptides in the biocatalysis of a range of organic reactions including hydrolysis and a variety of coupling reactions (e.g., aldol reactions) is reviewed. The simpler design rules for peptide structures compared to those of folded proteins permit ready ab initio design (minimalist approach) of effective catalytic structures that mimic the binding pockets of natural enzymes or which simply present catalytic motifs at high density on nanostructure scaffolds. Research on these topics is summarized, along with a discussion of metal nanoparticle catalysts templated by peptide nanostructures, especially fibrils. Research showing the high activities of different classes of peptides in catalyzing many reactions is highlighted. Advances in peptide design and synthesis methods mean they hold great potential for future developments of effective bioinspired and biocompatible catalysts.
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Affiliation(s)
- Ian W. Hamley
- Department of Chemistry, University of Reading, RG6 6AD Reading, United Kingdom
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7
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Affiliation(s)
- Dragana Despotovic
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
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Tong CL, Lee KH, Seelig B. De novo proteins from random sequences through in vitro evolution. Curr Opin Struct Biol 2021; 68:129-134. [PMID: 33517151 DOI: 10.1016/j.sbi.2020.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/29/2020] [Indexed: 11/29/2022]
Abstract
Natural proteins are the result of billions of years of evolution. The earliest predecessors of today's proteins are believed to have emerged from random polypeptides. While we have no means to determine how this process exactly happened, there is great interest in understanding how it reasonably could have happened. We are reviewing how researchers have utilized in vitro selection and molecular evolution methods to investigate plausible scenarios for the emergence of early functional proteins. The studies range from analyzing general properties and structural features of unevolved random polypeptides to isolating de novo proteins with specific functions from synthetic randomized sequence libraries or generating novel proteins by combining evolution with rational design. While the results are exciting, more work is needed to fully unravel the mechanisms that seeded protein-dominated biology.
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Affiliation(s)
- Cher Ling Tong
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Kun-Hwa Lee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA.
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