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Abstract
This Perspective presents a review of our work and that of others in the highly controversial topic of the coupling of protein dynamics to reaction in enzymes. We have been involved in studying this topic for many years. Thus, this perspective will naturally present our own views, but it also is designed to present an overview of the variety of viewpoints of this topic, both experimental and theoretical. This is obviously a large and contentious topic.
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Affiliation(s)
- Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
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2
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Abstract
This Perspective reviews the use of Transition Path Sampling methods to study enzymatically catalyzed chemical reactions. First applied by our group to an enzymatic reaction over 15 years ago, the method has uncovered basic principles in enzymatic catalysis such as the protein promoting vibration, and it has also helped harmonize such ideas as electrostatic preorganization with dynamic views of enzyme function. It is now being used to help uncover principles of protein design necessary to artificial enzyme creation.
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Affiliation(s)
- Steven D Schwartz
- Department of Chemistry and Biochemistry University of Arizona Tucson, Arizona 85721, United States
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3
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Lawal MM, Vaissier Welborn V. Structural dynamics support electrostatic interactions in the active site of Adenylate Kinase. Chembiochem 2022; 23:e202200097. [PMID: 35303385 DOI: 10.1002/cbic.202200097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Indexed: 11/12/2022]
Abstract
Electrostatic preorganization as well as structural and dynamic heterogeneity are often used to rationalize the remarkable catalytic efficiency of enzymes. However, they are often presented as incompatible because the generation of permanent electrostatic effects implies that the protein structure remains rigid. Here, we use a metric, electric fields, that can treat electrostatic contributions and dynamics effects on equal footing, for a unique perspective on enzymatic catalysis. We find that the residues that contribute the most to electrostatic interactions with the substrate in the active site of Adenylate Kinase (our working example) are also the most flexible residues. Further, entropy-tuning mutations raise flexibility at the picosecond timescale where more conformations can be visited on short time periods, thereby softening the sharp heterogeneity normally visible at the microsecond timescale.
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Affiliation(s)
| | - Valerie Vaissier Welborn
- Virginia Polytechnic Institute and State University, Chemistry, Davidson 421A, 1040 Drillfield Drive, 24073, Blacksburg, UNITED STATES
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4
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Lemay-St-Denis C, Doucet N, Pelletier JN. Integrating dynamics into enzyme engineering. Protein Eng Des Sel 2022; 35:6842866. [PMID: 36416215 DOI: 10.1093/protein/gzac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/02/2022] [Accepted: 11/06/2022] [Indexed: 11/24/2022] Open
Abstract
Enzyme engineering has become a widely adopted practice in research labs and industry. In parallel, the past decades have seen tremendous strides in characterizing the dynamics of proteins, using a growing array of methodologies. Importantly, links have been established between the dynamics of proteins and their function. Characterizing the dynamics of an enzyme prior to, and following, its engineering is beginning to inform on the potential of 'dynamic engineering', i.e. the rational modification of protein dynamics to alter enzyme function. Here we examine the state of knowledge at the intersection of enzyme engineering and protein dynamics, describe current challenges and highlight pioneering work in the nascent area of dynamic engineering.
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Affiliation(s)
- Claudèle Lemay-St-Denis
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Nicolas Doucet
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, QC, Canada
| | - Joelle N Pelletier
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
- Chemistry Department, Université de Montréal, Montreal, QC, Canada
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5
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Schafer JW, Chen X, Schwartz SD. Engineered Tryptophan Synthase Balances Equilibrium Effects and Fast Dynamic Effects. ACS Catal 2022; 12:913-922. [PMID: 35719741 PMCID: PMC9202816 DOI: 10.1021/acscatal.1c03913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Creating efficient and stable enzymes for catalysis in pharmaceutical and industrial laboratories is an important research goal. Arnold et al. used directed evolution to engineer a natural tryptophan synthase to create a mutant that is operable under laboratory conditions without the need for a natural allosteric effector. The use of directed evolution allows researchers to improve enzymes without understanding the structure-activity relationship. Here, we present a transition path sampling study of a key chemical transformation in the tryptophan synthase catalytic cycle. We observed that while directed evolution does mimic the natural allosteric effect from a stability perspective, fast protein dynamics associated with chemistry has been dramatically altered. This work provides further evidence of the role of protein dynamics in catalysis and clearly demonstrates the multifaceted complexity of mutations associated with protein engineering. This study also demonstrates a fascinating contrast between allosteric and stand-alone functions at the femtosecond time scale.
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Affiliation(s)
- Joseph W Schafer
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Xi Chen
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Steven D Schwartz
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
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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: 39] [Impact Index Per Article: 13.0] [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.
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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.
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Chalopin Y. The physical origin of rate promoting vibrations in enzymes revealed by structural rigidity. Sci Rep 2020; 10:17465. [PMID: 33060716 PMCID: PMC7566648 DOI: 10.1038/s41598-020-74439-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
Enzymes are the most efficient catalysts known to date. However, decades of research have failed to fully explain the catalytic power of enzymes, and most of the current attempts to uncloak the details of atomic motions at active sites remain incomplete. Here, a straightforward manner for understanding the interplay between the complex or irregular enzyme topology and dynamical effects at catalytic sites is introduced, by revealing how fast localized vibrations form spontaneously in the stiffest parts of the scaffold. While shedding light on a physical mechanism that allowed the selection of the picosecond (ps) timescale to increase the catalytic proficiency, this approach exposes the functional importance of localized motions as a by-product of the stability-function tradeoff in enzyme evolution. From this framework of analysis—directly accessible from available diffraction data—experimental strategies for engineering the catalytic rate in enzymatic proteins are proposed.
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Affiliation(s)
- Yann Chalopin
- Laboratoire EM2C, CNRS & CentraleSupelec, University of Paris-Saclay, 91190, Gif-sur-Yvette, France.
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Chalopin Y, Piazza F, Mayboroda S, Weisbuch C, Filoche M. Universality of fold-encoded localized vibrations in enzymes. Sci Rep 2019; 9:12835. [PMID: 31492876 PMCID: PMC6731342 DOI: 10.1038/s41598-019-48905-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023] Open
Abstract
Enzymes speed up biochemical reactions at the core of life by as much as 15 orders of magnitude. Yet, despite considerable advances, the fine dynamical determinants at the microscopic level of their catalytic proficiency are still elusive. In this work, we use a powerful mathematical approach to show that rate-promoting vibrations in the picosecond range, specifically encoded in the 3D protein structure, are localized vibrations optimally coupled to the chemical reaction coordinates at the active site. Remarkably, our theory also exposes an hithertho unknown deep connection between the unique localization fingerprint and a distinct partition of the 3D fold into independent, foldspanning subdomains that govern long-range communication. The universality of these features is demonstrated on a pool of more than 900 enzyme structures, comprising a total of more than 10,000 experimentally annotated catalytic sites. Our theory provides a unified microscopic rationale for the subtle structure-dynamics-function link in proteins.
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Affiliation(s)
- Yann Chalopin
- Laboratoire d'Energétique Macroscopique et Moléculaire, Combustion (EM2C), CentraleSupélec, CNRS, 91190, Gif-sur-Yvette, France.
| | - Francesco Piazza
- Centre de Biophysique Moléculaire (CBM) CNRS UPR4301 & Université d'Orléans, Orléans, 45071, France
| | - Svitlana Mayboroda
- School of Mathematics, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Claude Weisbuch
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, 91128, Palaiseau, France.,Materials Department, University of California, Santa Barbara, California, 93106, USA
| | - Marcel Filoche
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, 91128, Palaiseau, France
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Schafer JW, Zoi I, Antoniou D, Schwartz SD. Optimization of the Turnover in Artificial Enzymes via Directed Evolution Results in the Coupling of Protein Dynamics to Chemistry. J Am Chem Soc 2019; 141:10431-10439. [PMID: 31199129 DOI: 10.1021/jacs.9b04515] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The design of artificial enzymes is an emerging field of research. Although progress has been made, the catalytic proficiency of many designed enzymes is low compared to natural enzymes. Nevertheless, recently Hilvert et al. ( Nat. Chem. 2017, 9, 50-56) created a series of five artificial retro-aldolase enzymes via directed evolution, with the final variant exhibiting a rate comparable to the naturally occurring enzyme fructose 1,6 bisphosphate aldolase. We present a study of this system in atomistic detail that elucidates the effects of mutational changes on the chemical step. Transition path sampling is used to create ensembles of reactive trajectories, and committor analysis is used to identify the stochastic separatrix of each ensemble. The application of committor distribution analysis to constrained trajectories allows the identification of changes in important protein motions coupled to reaction across the generated series of the artificial retro-aldolases. We observed two different reaction mechanisms and analyzed the role of the residues participating in the reaction coordinate of each enzyme. However, only in the most evolved variant we identified a fast motion that promotes catalysis, suggesting that this rate promoting vibration was introduced during directed evolution. This study provides further evidence that protein dynamics must be taken into account in designing efficient artificial enzymes.
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Affiliation(s)
- Joseph W Schafer
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Ioanna Zoi
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Dimitri Antoniou
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
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10
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Affiliation(s)
- Valerie Vaissier Welborn
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, California 94720, United States
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