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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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Abstract
Natural enzymes catalyze biochemical transformations in superior catalytic efficiency and remarkable substrate specificity. The excellent catalytic repertoire of enzymes is attributed to the sophisticated chemical structures of their active sites, as a result of billions-of-years natural evolution. However, large-scale practical applications of natural enzymes are restricted due to their poor stability, difficulty in modification, and high costs of production. One viable solution is to fabricate supramolecular catalysts with enzyme-mimetic active sites. In this review, we introduce the principles and strategies of designing peptide-based artificial enzymes which display catalytic activities similar to those of natural enzymes, such as aldolases, laccases, peroxidases, and hydrolases (mainly the esterases and phosphatases). We also discuss some multifunctional enzyme-mimicking systems which are capable of catalyzing orthogonal or cascade reactions. We highlight the relationship between structures of enzyme-like active sites and the catalytic properties, as well as the significance of these studies from an evolutionary point of view.
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3
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Catalytic Peptides: the Challenge between Simplicity and Functionality. Isr J Chem 2022. [DOI: 10.1002/ijch.202200029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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4
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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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5
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Liu S, Du P, Sun H, Yu HY, Wang ZG. Bioinspired Supramolecular Catalysts from Designed Self-Assembly of DNA or Peptides. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03753] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Siyuan Liu
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
- College of Chemistry and Materials Science, Anhui Normal University, 189 Jiuhua Nanlu, Wuhu, Anhui 241002, China
| | - Peidong Du
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
| | - Hao Sun
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
| | - Hai-Yin Yu
- College of Chemistry and Materials Science, Anhui Normal University, 189 Jiuhua Nanlu, Wuhu, Anhui 241002, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
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6
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Abstract
Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.
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Rivilla I, Odriozola-Gimeno M, Aires A, Gimeno A, Jiménez-Barbero J, Torrent-Sucarrat M, Cortajarena AL, Cossío FP. Discovering Biomolecules with Huisgenase Activity: Designed Repeat Proteins as Biocatalysts for (3 + 2) Cycloadditions. J Am Chem Soc 2019; 142:762-776. [DOI: 10.1021/jacs.9b06823] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Iván Rivilla
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
| | - Mikel Odriozola-Gimeno
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
| | - Antonio Aires
- Parque Tecnológico de San Sebastián, CIC biomaGUNE, Paseo Miramón 182, 20014 Donostia/San Sebastián, Spain
| | - Ana Gimeno
- Molecular Recognition & Host−Pathogen Interactions Unit, CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition & Host−Pathogen Interactions Unit, CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain
- Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, Leioa 48940, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Ma Diaz de Haro 3, Bilbao 48013, Spain
| | - Miquel Torrent-Sucarrat
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, Ma Diaz de Haro 3, Bilbao 48013, Spain
| | - Aitziber L. Cortajarena
- Parque Tecnológico de San Sebastián, CIC biomaGUNE, Paseo Miramón 182, 20014 Donostia/San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, Ma Diaz de Haro 3, Bilbao 48013, Spain
| | - Fernando P. Cossío
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
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8
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Marshall LR, Zozulia O, Lengyel-Zhand Z, Korendovych IV. Minimalist de novo Design of Protein Catalysts. ACS Catal 2019; 9:9265-9275. [PMID: 34094654 PMCID: PMC8174531 DOI: 10.1021/acscatal.9b02509] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The field of protein design has grown enormously in the past few decades. In this review we discuss the minimalist approach to design of artificial enzymes, in which protein sequences are created with the minimum number of elements for folding and function. This method relies on identifying starting points in catalytically inert scaffolds for active site installation. The progress of the field from the original helical assemblies of the 1980s to the more complex structures of the present day is discussed, highlighting the variety of catalytic reactions which have been achieved using these methods. We outline the strengths and weaknesses of the minimalist approaches, describe representative design cases and put it in the general context of the de novo design of proteins.
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Affiliation(s)
- Liam R. Marshall
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Oleksii Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Zsofia Lengyel-Zhand
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
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9
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Abstract
Self-assembly of molecules often results in new emerging properties. Even very short peptides can self-assemble into structures with a variety of physical and structural characteristics. Remarkably, many peptide assemblies show high catalytic activity in model reactions reaching efficiencies comparable to those found in natural enzymes by weight. In this review, we discuss different strategies used to rationally develop self-assembled peptide catalysts with natural and unnatural backbones as well as with metal-containing cofactors.
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Affiliation(s)
- O Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA.
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10
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Buyst D, Gheerardijn V, Fehér K, Van Gasse B, Van Den Begin J, Martins JC, Madder A. Identification of a pKa-regulating motif stabilizing imidazole-modified double-stranded DNA. Nucleic Acids Res 2014; 43:51-62. [PMID: 25520197 PMCID: PMC4288195 DOI: 10.1093/nar/gku1306] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The predictable 3D structure of double-stranded DNA renders it ideally suited as a template for the bottom-up design of functionalized nucleic acid-based active sites. We here explore the use of a 14mer DNA duplex as a scaffold for the precise and predictable positioning of catalytic functionalities. Given the ubiquitous participation of the histidine-based imidazole group in protein recognition and catalysis events, single histidine-like modified duplexes were investigated. Tethering histamine to the C5 of the thymine base via an amide bond, allows the flexible positioning of the imidazole function in the major groove. The mutual interactions between the imidazole and the duplex and its influence on the imidazolium pKaH are investigated by placing a single modified thymine at four different positions in the center of the 14mer double helix. Using NMR and unrestrained molecular dynamics, a structural motif involving the formation of a hydrogen bond between the imidazole and the Hoogsteen side of the guanine bases of two neighboring GC base pairs is established. The motif contributes to a stabilization against thermal melting of 6°C and is key in modulating the pKaH of the imidazolium group. The general features, prerequisites and generic character of the new pKaH-regulating motif are described.
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Affiliation(s)
- Dieter Buyst
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Unit, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Vicky Gheerardijn
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Krisztina Fehér
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Unit, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Bjorn Van Gasse
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Unit, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Jos Van Den Begin
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - José C Martins
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Unit, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
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11
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Nastri F, Lista L, Ringhieri P, Vitale R, Faiella M, Andreozzi C, Travascio P, Maglio O, Lombardi A, Pavone V. A Heme–Peptide Metalloenzyme Mimetic with Natural Peroxidase‐Like Activity. Chemistry 2011; 17:4444-53. [DOI: 10.1002/chem.201003485] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 11/08/2022]
Affiliation(s)
- Flavia Nastri
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Liliana Lista
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Paola Ringhieri
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Rosa Vitale
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Marina Faiella
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Concetta Andreozzi
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Paola Travascio
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Ornella Maglio
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
- Permanent address: IBB, CNR, Via Mezzocannone 16, 80134 Napoli (Italy)
| | - Angela Lombardi
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Vincenzo Pavone
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
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12
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Abstract
The rational design of artificial enzymes, either by applying physico-chemical intuition of protein structure and function or with the aid of computational methods, is a promising area of research with the potential to tremendously impact medicine, industrial chemistry and energy production. Designed proteins also provide a powerful platform for dissecting enzyme mechanisms of natural systems. Artificial enzymes have come a long way from simple α-helical peptide catalysts to proteins that facilitate multistep chemical reactions designed by state-of-the-art computational methods. Looking forward, we examine strategies employed by natural enzymes that could be used to improve the speed and selectivity of artificial catalysts.
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13
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Faiella M, Andreozzi C, de Rosales RTM, Pavone V, Maglio O, Nastri F, DeGrado WF, Lombardi A. An artificial di-iron oxo-protein with phenol oxidase activity. Nat Chem Biol 2009; 5:882-4. [PMID: 19915535 PMCID: PMC3808167 DOI: 10.1038/nchembio.257] [Citation(s) in RCA: 157] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 09/15/2009] [Indexed: 12/11/2022]
Abstract
Here we report the de novo design and NMR structure of a four-helical bundle di-iron protein with phenol oxidase activity. The introduction of the cofactor-binding and phenol-binding sites required the incorporation of residues that were detrimental to the free energy of folding of the protein. Sufficient stability was, however, obtained by optimizing the sequence of a loop distant from the active site.
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Affiliation(s)
- Marina Faiella
- Department of Chemistry, University Federico II of Napoli, Complesso Universitario Monte S. Angelo, Italy
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