1
|
Kipnis Y, Chaib AO, Vorobieva AA, Cai G, Reggiano G, Basanta B, Kumar E, Mittl PR, Hilvert D, Baker D. Design and optimization of enzymatic activity in a de novo β-barrel scaffold. Protein Sci 2022; 31:e4405. [PMID: 36305767 PMCID: PMC9601869 DOI: 10.1002/pro.4405] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/11/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022]
Abstract
While native scaffolds offer a large diversity of shapes and topologies for enzyme engineering, their often unpredictable behavior in response to sequence modification makes de novo generated scaffolds an exciting alternative. Here we explore the customization of the backbone and sequence of a de novo designed eight stranded β-barrel protein to create catalysts for a retro-aldolase model reaction. We show that active and specific catalysts can be designed in this fold and use directed evolution to further optimize activity and stereoselectivity. Our results support previous suggestions that different folds have different inherent amenability to evolution and this property could account, in part, for the distribution of natural enzymes among different folds.
Collapse
Affiliation(s)
- Yakov Kipnis
- Department of BiochemistryUniversity of WashingtonSeattleUSA
- Institute for Protein DesignUniversity of WashingtonSeattleUSA
- Howard Hughes Medical InstituteUniversity of WashingtonSeattleUSA
| | | | - Anastassia A. Vorobieva
- Department of BiochemistryUniversity of WashingtonSeattleUSA
- Institute for Protein DesignUniversity of WashingtonSeattleUSA
- Howard Hughes Medical InstituteUniversity of WashingtonSeattleUSA
- VIB‐VUB Center for Structural BiologyVlaams Instituut voor BiotechnologieBrusselsBelgium
- Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
| | - Guangyang Cai
- Department of BiochemistryUniversity of WashingtonSeattleUSA
- Institute for Protein DesignUniversity of WashingtonSeattleUSA
| | - Gabriella Reggiano
- Department of BiochemistryUniversity of WashingtonSeattleUSA
- Institute for Protein DesignUniversity of WashingtonSeattleUSA
| | - Benjamin Basanta
- Department of BiochemistryUniversity of WashingtonSeattleUSA
- Institute for Protein DesignUniversity of WashingtonSeattleUSA
| | - Eshan Kumar
- Department of BiochemistryUniversity of WashingtonSeattleUSA
- Institute for Protein DesignUniversity of WashingtonSeattleUSA
| | - Peer R.E. Mittl
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
| | - Donald Hilvert
- Laboratory of Organic ChemistryETH ZurichZurichSwitzerland
| | - David Baker
- Department of BiochemistryUniversity of WashingtonSeattleUSA
- Institute for Protein DesignUniversity of WashingtonSeattleUSA
- Howard Hughes Medical InstituteUniversity of WashingtonSeattleUSA
| |
Collapse
|
2
|
Reetz MT, Garcia-Borràs M. The Unexplored Importance of Fleeting Chiral Intermediates in Enzyme-Catalyzed Reactions. J Am Chem Soc 2021; 143:14939-14950. [PMID: 34491742 PMCID: PMC8461649 DOI: 10.1021/jacs.1c04551] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Indexed: 02/07/2023]
Abstract
Decades of extensive research efforts by biochemists, organic chemists, and protein engineers have led to an understanding of the basic mechanisms of essentially all known types of enzymes, but in a formidable number of cases an essential aspect has been overlooked. The occurrence of short-lived chiral intermediates formed by symmetry-breaking of prochiral precursors in enzyme catalyzed reactions has been systematically neglected. We designate these elusive species as fleeting chiral intermediates and analyze such crucial questions as "Do such intermediates occur in homochiral form?" If so, what is the absolute configuration, and why did Nature choose that particular stereoisomeric form, even when the isolable final product may be achiral? Does the absolute configuration of a chiral product depend in any way on the absolute configuration of the fleeting chiral precursor? How does this affect the catalytic proficiency of the enzyme? If these issues continue to be unexplored, then an understanding of the mechanisms of many enzyme types remains incomplete. We have systematized the occurrence of these chiral intermediates according to their structures and enzyme types. This is followed by critical analyses of selected case studies and by final conclusions and perspectives. We hope that the fascinating concept of fleeting chiral intermediates will attract the attention of scientists, thereby opening an exciting new research field.
Collapse
Affiliation(s)
- Manfred T. Reetz
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Marc Garcia-Borràs
- Institute
of Computational Chemistry and Catalysis (IQCC) and Departament de
Química, Universitat de Girona, Carrer Maria Aurèlia Capmany
69, 17003 Girona, Spain
| |
Collapse
|
3
|
Bunzel HA, Anderson JLR, Mulholland AJ. Designing better enzymes: Insights from directed evolution. Curr Opin Struct Biol 2021; 67:212-218. [PMID: 33517098 DOI: 10.1016/j.sbi.2020.12.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/03/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022]
Abstract
De novo enzymes can be created by computational design and directed evolution. Here, we review recent insights into the origins of catalytic power in evolved designer enzymes to pinpoint opportunities for next-generation designs: Evolution precisely organizes active sites, introduces catalytic H-bonding networks, invokes electrostatic catalysis, and creates dynamical networks embedding the active site in a reactive protein scaffold. Such insights foster our fundamental knowledge of enzyme catalysis and fuel the future design of tailor-made enzymes.
Collapse
Affiliation(s)
- H Adrian Bunzel
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | | | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
| |
Collapse
|
4
|
Basanta B, Bick MJ, Bera AK, Norn C, Chow CM, Carter LP, Goreshnik I, Dimaio F, Baker D. An enumerative algorithm for de novo design of proteins with diverse pocket structures. Proc Natl Acad Sci U S A 2020; 117:22135-22145. [PMID: 32839327 PMCID: PMC7486743 DOI: 10.1073/pnas.2005412117] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To create new enzymes and biosensors from scratch, precise control over the structure of small-molecule binding sites is of paramount importance, but systematically designing arbitrary protein pocket shapes and sizes remains an outstanding challenge. Using the NTF2-like structural superfamily as a model system, we developed an enumerative algorithm for creating a virtually unlimited number of de novo proteins supporting diverse pocket structures. The enumerative algorithm was tested and refined through feedback from two rounds of large-scale experimental testing, involving in total the assembly of synthetic genes encoding 7,896 designs and assessment of their stability on yeast cell surface, detailed biophysical characterization of 64 designs, and crystal structures of 5 designs. The refined algorithm generates proteins that remain folded at high temperatures and exhibit more pocket diversity than naturally occurring NTF2-like proteins. We expect this approach to transform the design of small-molecule sensors and enzymes by enabling the creation of binding and active site geometries much more optimal for specific design challenges than is accessible by repurposing the limited number of naturally occurring NTF2-like proteins.
Collapse
Affiliation(s)
- Benjamin Basanta
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Matthew J Bick
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Christoffer Norn
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Cameron M Chow
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Lauren P Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Inna Goreshnik
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Frank Dimaio
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA 98195;
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
| |
Collapse
|
5
|
Nödling AR, Santi N, Williams TL, Tsai YH, Luk LYP. Enabling protein-hosted organocatalytic transformations. RSC Adv 2020; 10:16147-16161. [PMID: 33184588 PMCID: PMC7654312 DOI: 10.1039/d0ra01526a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/25/2020] [Indexed: 12/30/2022] Open
Abstract
In this review, the development of organocatalytic artificial enzymes will be discussed. This area of protein engineering research has underlying importance, as it enhances the biocompatibility of organocatalysis for applications in chemical and synthetic biology research whilst expanding the catalytic repertoire of enzymes. The approaches towards the preparation of organocatalytic artificial enzymes, techniques used to improve their performance (selectivity and reactivity) as well as examples of their applications are presented. Challenges and opportunities are also discussed.
Collapse
Affiliation(s)
- Alexander R Nödling
- School of Chemistry, Cardiff University, Main Building, Cardiff, CF10 3AT, UK.
| | - Nicolò Santi
- School of Chemistry, Cardiff University, Main Building, Cardiff, CF10 3AT, UK.
| | - Thomas L Williams
- School of Chemistry, Cardiff University, Main Building, Cardiff, CF10 3AT, UK.
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Main Building, Cardiff, CF10 3AT, UK.
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Main Building, Cardiff, CF10 3AT, UK.
| |
Collapse
|
6
|
Maria-Solano MA, Serrano-Hervás E, Romero-Rivera A, Iglesias-Fernández J, Osuna S. Role of conformational dynamics in the evolution of novel enzyme function. Chem Commun (Camb) 2018; 54:6622-6634. [PMID: 29780987 PMCID: PMC6009289 DOI: 10.1039/c8cc02426j] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/10/2018] [Indexed: 12/26/2022]
Abstract
The free energy landscape concept that describes enzymes as an ensemble of differently populated conformational sub-states in dynamic equilibrium is key for evaluating enzyme activity, enantioselectivity, and specificity. Mutations introduced in the enzyme sequence can alter the populations of the pre-existing conformational states, thus strongly modifying the enzyme ability to accommodate alternative substrates, revert its enantiopreferences, and even increase the activity for some residual promiscuous reactions. In this feature article, we present an overview of the current experimental and computational strategies to explore the conformational free energy landscape of enzymes. We provide a series of recent publications that highlight the key role of conformational dynamics for the enzyme evolution towards new functions and substrates, and provide some perspectives on how conformational dynamism should be considered in future computational enzyme design protocols.
Collapse
Affiliation(s)
- Miguel A. Maria-Solano
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Eila Serrano-Hervás
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Adrian Romero-Rivera
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Javier Iglesias-Fernández
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Sílvia Osuna
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
- ICREA
,
Pg. Lluís Companys 23
, 08010 Barcelona
, Spain
| |
Collapse
|
7
|
Romero-Rivera A, Iglesias-Fernández J, Osuna S. Exploring the Conversion of ad-Sialic Acid Aldolase into al-KDO Aldolase. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química; Universitat de Girona; Carrer Maria Aurèlia Capmany 69 17003 Girona Spain
| | - Javier Iglesias-Fernández
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química; Universitat de Girona; Carrer Maria Aurèlia Capmany 69 17003 Girona Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química; Universitat de Girona; Carrer Maria Aurèlia Capmany 69 17003 Girona Spain
- ICREA; Passeig Lluís Companys, 23 08010 Barcelona Spain
| |
Collapse
|
8
|
Bunzel HA, Garrabou X, Pott M, Hilvert D. Speeding up enzyme discovery and engineering with ultrahigh-throughput methods. Curr Opin Struct Biol 2018; 48:149-156. [PMID: 29413955 DOI: 10.1016/j.sbi.2017.12.010] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/26/2017] [Indexed: 01/24/2023]
Abstract
Exploring the sequence space of enzyme catalysts is ultimately a numbers game. Ultrahigh-throughput screening methods for rapid analysis of millions of variants are therefore increasingly important for investigating sequence-function relationships, searching large metagenomic libraries for interesting activities, and accelerating enzyme evolution in the laboratory. Recent applications of such technologies are reviewed here, with a particular focus on the practical benefits of droplet-based microfluidics for the directed evolution of natural and artificial enzymes. Broader implementation of such rapid, cost-effective screening technologies is likely to redefine the way enzymes are studied and engineered for academic and industrial purposes.
Collapse
Affiliation(s)
- Hans Adrian Bunzel
- Laboratory of Organic Chemistry, ETH Zurich, Zurich CH-8093, Switzerland
| | - Xavier Garrabou
- Laboratory of Organic Chemistry, ETH Zurich, Zurich CH-8093, Switzerland
| | - Moritz Pott
- Laboratory of Organic Chemistry, ETH Zurich, Zurich CH-8093, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, Zurich CH-8093, Switzerland.
| |
Collapse
|
9
|
Romero-Rivera A, Garcia-Borràs M, Osuna S. Role of Conformational Dynamics in the Evolution of Retro-Aldolase Activity. ACS Catal 2017; 7:8524-8532. [PMID: 29226011 PMCID: PMC5716449 DOI: 10.1021/acscatal.7b02954] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/19/2017] [Indexed: 12/19/2022]
Abstract
![]()
Enzymes exist as
ensembles of conformations that are important
for function. Tuning these populations of conformational states through
mutation enables evolution toward additional activities. Here we computationally
evaluate the population shifts induced by distal and active site mutations
in a family of computationally designed and experimentally optimized
retro-aldolases. The conformational landscape of these enzymes was
significantly altered during evolution, as pre-existing catalytically
active conformational substates became major states in the most evolved
variants. We further demonstrate that key residues responsible for
these substate conversions can be predicted computationally. Significantly,
the identified residues coincide with those positions mutated in the
laboratory evolution experiments. This study establishes that distal
mutations that affect enzyme catalytic activity can be predicted computationally
and thus provides the enzyme (re)design field with a rational strategy
to determine promising sites for enhancing activity through mutation.
Collapse
Affiliation(s)
- Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), 607 Charles E. Young Drive, Los Angeles, California 90095, United States
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| |
Collapse
|
10
|
Otte KB, Maurer E, Kirtz M, Grabs D, Althoff E, Bartsch S, Vogel A, Nestl BM, Hauer B. Synthesis of Sebacic Acid Using a De Novo Designed Retro-Aldolase as a Key Catalyst. ChemCatChem 2017. [DOI: 10.1002/cctc.201601551] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Konrad B. Otte
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Elena Maurer
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Marko Kirtz
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | | | | | | | - Andreas Vogel
- c-LEcta GmbH; Perlickstrasse 5 04103 Leipzig Germany
| | - Bettina M. Nestl
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| |
Collapse
|
11
|
Roldán R, Sanchez-Moreno I, Scheidt T, Hélaine V, Lemaire M, Parella T, Clapés P, Fessner WD, Guérard-Hélaine C. Breaking the Dogma of Aldolase Specificity: Simple Aliphatic Ketones and Aldehydes are Nucleophiles for Fructose-6-phosphate Aldolase. Chemistry 2017; 23:5005-5009. [DOI: 10.1002/chem.201701020] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Raquel Roldán
- Departamento de Química Biológica y Modelización Molecular; Instituto de Química Avanzada de Cataluña IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Israel Sanchez-Moreno
- Université Clermont Auvergne; CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand; 63000 Clermont-Ferrand France
| | - Thomas Scheidt
- Institut für Organische Chemie und Biochemie; Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Virgil Hélaine
- Université Clermont Auvergne; CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand; 63000 Clermont-Ferrand France
| | - Marielle Lemaire
- Université Clermont Auvergne; CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand; 63000 Clermont-Ferrand France
| | - Teodor Parella
- Servei de Ressonancia Magnetica Nuclear; Universitat Autonoma de Barcelona; Bellaterra Spain
| | - Pere Clapés
- Departamento de Química Biológica y Modelización Molecular; Instituto de Química Avanzada de Cataluña IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie; Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Christine Guérard-Hélaine
- Université Clermont Auvergne; CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand; 63000 Clermont-Ferrand France
| |
Collapse
|
12
|
Romero-Rivera A, Garcia-Borràs M, Osuna S. Computational tools for the evaluation of laboratory-engineered biocatalysts. Chem Commun (Camb) 2016; 53:284-297. [PMID: 27812570 PMCID: PMC5310519 DOI: 10.1039/c6cc06055b] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/06/2016] [Indexed: 12/18/2022]
Abstract
Biocatalysis is based on the application of natural catalysts for new purposes, for which enzymes were not designed. Although the first examples of biocatalysis were reported more than a century ago, biocatalysis was revolutionized after the discovery of an in vitro version of Darwinian evolution called Directed Evolution (DE). Despite the recent advances in the field, major challenges remain to be addressed. Currently, the best experimental approach consists of creating multiple mutations simultaneously while limiting the choices using statistical methods. Still, tens of thousands of variants need to be tested experimentally, and little information is available on how these mutations lead to enhanced enzyme proficiency. This review aims to provide a brief description of the available computational techniques to unveil the molecular basis of improved catalysis achieved by DE. An overview of the strengths and weaknesses of current computational strategies is explored with some recent representative examples. The understanding of how this powerful technique is able to obtain highly active variants is important for the future development of more robust computational methods to predict amino-acid changes needed for activity.
Collapse
Affiliation(s)
- Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, 607 Charles E. Young Drive, Los Angeles, California 90095, USA
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.
| |
Collapse
|
13
|
Garrabou X, Wicky BIM, Hilvert D. Fast Knoevenagel Condensations Catalyzed by an Artificial Schiff-Base-Forming Enzyme. J Am Chem Soc 2016; 138:6972-4. [DOI: 10.1021/jacs.6b00816] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xavier Garrabou
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| |
Collapse
|
14
|
Hadadi N, Hatzimanikatis V. Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways. Curr Opin Chem Biol 2015; 28:99-104. [DOI: 10.1016/j.cbpa.2015.06.025] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/16/2015] [Accepted: 06/21/2015] [Indexed: 12/28/2022]
|
15
|
Świderek K, Tuñón I, Moliner V, Bertran J. Computational strategies for the design of new enzymatic functions. Arch Biochem Biophys 2015; 582:68-79. [PMID: 25797438 PMCID: PMC4554825 DOI: 10.1016/j.abb.2015.03.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/09/2015] [Accepted: 03/13/2015] [Indexed: 11/28/2022]
Abstract
In this contribution, recent developments in the design of biocatalysts are reviewed with particular emphasis in the de novo strategy. Studies based on three different reactions, Kemp elimination, Diels-Alder and Retro-Aldolase, are used to illustrate different success achieved during the last years. Finally, a section is devoted to the particular case of designed metalloenzymes. As a general conclusion, the interplay between new and more sophisticated engineering protocols and computational methods, based on molecular dynamics simulations with Quantum Mechanics/Molecular Mechanics potentials and fully flexible models, seems to constitute the bed rock for present and future successful design strategies.
Collapse
Affiliation(s)
- K Świderek
- Departament de Química Física, Universitat de València, 46100 Burjasot, Spain; Institute of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - I Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjasot, Spain
| | - V Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - J Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| |
Collapse
|
16
|
Garrabou X, Beck T, Hilvert D. A Promiscuous De Novo Retro-Aldolase Catalyzes Asymmetric Michael Additions via Schiff Base Intermediates. Angew Chem Int Ed Engl 2015; 54:5609-12. [PMID: 25777153 DOI: 10.1002/anie.201500217] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Indexed: 02/03/2023]
Abstract
Recent advances in computational design have enabled the development of primitive enzymes for a range of mechanistically distinct reactions. Here we show that the rudimentary active sites of these catalysts can give rise to useful chemical promiscuity. Specifically, RA95.5-8, designed and evolved as a retro-aldolase, also promotes asymmetric Michael additions of carbanions to unsaturated ketones with high rates and selectivities. The reactions proceed by amine catalysis, as indicated by mutagenesis and X-ray data. The inherent flexibility and tunability of this catalyst should make it a versatile platform for further optimization and/or mechanistic diversification by directed evolution.
Collapse
Affiliation(s)
- Xavier Garrabou
- Laboratory of Organic Chemistry, ETH Zürich, 8093 Zürich (Switzerland); Instituto de Química Avanzada de Cataluña-CSIC, Jordi Girona 18-26, 08034 Barcelona (Spain)
| | | | | |
Collapse
|
17
|
Garrabou X, Beck T, Hilvert D. A Promiscuous De Novo Retro-Aldolase Catalyzes Asymmetric Michael Additions via Schiff Base Intermediates. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500217] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
18
|
Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
Collapse
Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| |
Collapse
|
19
|
Panigrahi K, Applegate GA, Malik G, Berkowitz DB. Combining a Clostridial enzyme exhibiting unusual active site plasticity with a remarkably facile sigmatropic rearrangement: rapid, stereocontrolled entry into densely functionalized fluorinated phosphonates for chemical biology. J Am Chem Soc 2015; 137:3600-9. [PMID: 25719907 DOI: 10.1021/jacs.5b00022] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Described is an efficient stereocontrolled route into valuable, densely functionalized fluorinated phosphonates that takes advantage of (i) a Clostridial enzyme to set the absolute stereochemistry and (ii) a new [3,3]-sigmatropic rearrangement of the thiono-Claisen variety that is among the fastest sigmatropic rearrangements yet reported. Here, a pronounced rate enhancement is achieved by distal fluorination. This rearrangement is completely stereoretentive, parlaying the enzymatically established β-C-O stereochemistry in the substrate into the δ-C-S stereochemistry in the product. The final products are of interest to chemical biology, with a platform for Zn-aminopeptidase A inhibitors being constructed here. The enzyme, Clostridium acetobutylicum (CaADH), recently expressed by our group, reduces a spectrum of γ,δ-unsaturated β-keto-α,α-difluorophosphonate esters (93-99% ee; 10 examples). The resultant β-hydroxy-α,α-difluorophosphonates possess the "L"-stereochemistry, opposite to that previously observed for the CaADH-reduction of ω-keto carboxylate esters ("D"), indicating an unusual active site plasticity. For the thiono-Claisen rearrangement, a notable structure-reactivity relationship is observed. Measured rate constants vary by over 3 orders of magnitude, depending upon thiono-ester structure. Temperature-dependent kinetics reveal an unusually favorable entropy of activation (ΔS(‡) = 14.5 ± 0.6 e.u.). Most notably, a 400-fold rate enhancement is seen upon fluorination of the distal arene ring, arising from favorable enthalpic (ΔΔH(‡) = -2.3 kcal/mol) and entropic (ΔΔS(‡) = 4 e.u., i.e. 1.2 kcal/mol at rt) contributions. The unusual active site plasticity seen here is expected to drive structural biology studies on CaADH, while the exceptionally facile sigmatropic rearrangement is expected to drive computational studies to elucidate its underlying entropic and enthalpic basis.
Collapse
Affiliation(s)
- Kaushik Panigrahi
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Gregory A Applegate
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Guillaume Malik
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| |
Collapse
|