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Zhou L, Tao C, Shen X, Sun X, Wang J, Yuan Q. Unlocking the potential of enzyme engineering via rational computational design strategies. Biotechnol Adv 2024; 73:108376. [PMID: 38740355 DOI: 10.1016/j.biotechadv.2024.108376] [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: 12/27/2023] [Revised: 04/27/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
Enzymes play a pivotal role in various industries by enabling efficient, eco-friendly, and sustainable chemical processes. However, the low turnover rates and poor substrate selectivity of enzymes limit their large-scale applications. Rational computational enzyme design, facilitated by computational algorithms, offers a more targeted and less labor-intensive approach. There has been notable advancement in employing rational computational protein engineering strategies to overcome these issues, it has not been comprehensively reviewed so far. This article reviews recent developments in rational computational enzyme design, categorizing them into three types: structure-based, sequence-based, and data-driven machine learning computational design. Case studies are presented to demonstrate successful enhancements in catalytic activity, stability, and substrate selectivity. Lastly, the article provides a thorough analysis of these approaches, highlights existing challenges and potential solutions, and offers insights into future development directions.
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Affiliation(s)
- Lei Zhou
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chunmeng Tao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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2
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Quiroga I, Hernández-González JA, Bautista-Rodríguez E, Benítez-Rojas AC. Exploring the Structurally Conserved Regions and Functional Significance in Bacterial N-Terminal Nucleophile (Ntn) Amide-Hydrolases. Int J Mol Sci 2024; 25:6850. [PMID: 38999960 PMCID: PMC11241749 DOI: 10.3390/ijms25136850] [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: 05/12/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 07/14/2024] Open
Abstract
The initial adoption of penicillin as an antibiotic marked the start of exploring other compounds essential for pharmaceuticals, yet resistance to penicillins and their side effects has compromised their efficacy. The N-terminal nucleophile (Ntn) amide-hydrolases S45 family plays a key role in catalyzing amide bond hydrolysis in various compounds, including antibiotics like penicillin and cephalosporin. This study comprehensively analyzes the structural and functional traits of the bacterial N-terminal nucleophile (Ntn) amide-hydrolases S45 family, covering penicillin G acylases, cephalosporin acylases, and D-succinylase. Utilizing structural bioinformatics tools and sequence analysis, the investigation delineates structurally conserved regions (SCRs) and substrate binding site variations among these enzymes. Notably, sixteen SCRs crucial for substrate interaction are identified solely through sequence analysis, emphasizing the significance of sequence data in characterizing functionally relevant regions. These findings introduce a novel approach for identifying targets to enhance the biocatalytic properties of N-terminal nucleophile (Ntn) amide-hydrolases, while facilitating the development of more accurate three-dimensional models, particularly for enzymes lacking structural data. Overall, this research advances our understanding of structure-function relationships in bacterial N-terminal nucleophile (Ntn) amide-hydrolases, providing insights into strategies for optimizing their enzymatic capabilities.
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Affiliation(s)
- Israel Quiroga
- Department of Life and Health Sciences, Universidad Popular Autónoma del Estado de Puebla, 13 Poniente No. 1927, Barrio de Santiago, Puebla 72410, Mexico
| | - Juan Andrés Hernández-González
- Department of Life and Health Sciences, Universidad Popular Autónoma del Estado de Puebla, 13 Poniente No. 1927, Barrio de Santiago, Puebla 72410, Mexico
| | - Elizabeth Bautista-Rodríguez
- Department of Life and Health Sciences, Universidad Popular Autónoma del Estado de Puebla, 13 Poniente No. 1927, Barrio de Santiago, Puebla 72410, Mexico
- Department of Health Sciences, Universidad Autónoma de Tlaxcala, Sur 11, Barrio de Guardia, Zacatelco 90070, Mexico
| | - Alfredo C Benítez-Rojas
- Department of Life and Health Sciences, Universidad Popular Autónoma del Estado de Puebla, 13 Poniente No. 1927, Barrio de Santiago, Puebla 72410, Mexico
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Świderek K, Martí S, Arafet K, Moliner V. Computational study of the mechanism of a polyurethane esterase A (PueA) from Pseudomonas chlororaphis. Faraday Discuss 2024. [PMID: 38836643 DOI: 10.1039/d4fd00022f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
The effective management of plastic waste has become a global imperative, given our reliance on a linear model in which plastics are manufactured, used once, and then discarded. This has led to the pervasive accumulation of plastic debris in landfills and environmental contamination. Recognizing this issue, numerous initiatives are underway to address the environmental repercussions associated with plastic disposal. In this study, we investigate the possible molecular mechanism of polyurethane esterase A (PueA), which has been previously identified as responsible for the degradation of a polyester polyurethane (PU) sample in Pseudomonas chlororaphis, as an effort to develop enzymatic biodegradation solutions. After generating the unsolved 3D structure of the protein by AlphaFold2 from its known genome, the enzymatic hydrolysis of the same model PU compound previously used in experiments has been explored employing QM/MM molecular dynamics simulations. This required a preliminary analysis of the 3D structure of the apo-enzyme, identifying the putative active site, and the search for the optimal protein-substrate binding site. Finally, the resulting free energy landscape indicates that wild-type PueA can degrade PU chains, although with low-level activity. The reaction takes place by a characteristic four-step path of the serine hydrolases, involving an acylation followed by a diacylation step. Energetics and structural analysis of the evolution of the active site along the reaction suggests that PueA can be considered a promising protein scaffold for further development to achieve efficient biodegradation of PU.
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Affiliation(s)
- Katarzyna Świderek
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain.
| | - Sergio Martí
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain.
| | - Kemel Arafet
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain.
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain.
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Ruiz-Pernía JJ, Świderek K, Bertran J, Moliner V, Tuñón I. Electrostatics as a Guiding Principle in Understanding and Designing Enzymes. J Chem Theory Comput 2024; 20:1783-1795. [PMID: 38410913 PMCID: PMC10938506 DOI: 10.1021/acs.jctc.3c01395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/28/2024]
Abstract
Enzyme design faces challenges related to the implementation of the basic principles that govern the catalytic activity in natural enzymes. In this work, we revisit basic electrostatic concepts that have been shown to explain the origin of enzymatic efficiency like preorganization and reorganization. Using magnitudes such as the electrostatic potential and the electric field generated by the protein, we explain how these concepts work in different enzymes and how they can be used to rationalize the consequences of point mutations. We also discuss examples of protein design in which electrostatic effects have been implemented. For the near future, molecular simulations, coupled with the use of machine learning methods, can be used to implement electrostatics as a guiding principle for enzyme designs.
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Affiliation(s)
| | - Katarzyna Świderek
- Biocomp
group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón Spain
| | - Joan Bertran
- Departament
de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra, Spain
| | - Vicent Moliner
- Biocomp
group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón Spain
| | - Iñaki Tuñón
- Departament
de Química Física, Universitat
de València, 46100 Burjassot, Spain
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Nam K, Shao Y, Major DT, Wolf-Watz M. Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development. ACS OMEGA 2024; 9:7393-7412. [PMID: 38405524 PMCID: PMC10883025 DOI: 10.1021/acsomega.3c09084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/27/2024]
Abstract
Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.
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Affiliation(s)
- Kwangho Nam
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yihan Shao
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Dan T. Major
- Department
of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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Pan X, Van R, Pu J, Nam K, Mao Y, Shao Y. Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions. J Chem Theory Comput 2023; 19:8234-8244. [PMID: 37943896 PMCID: PMC10835707 DOI: 10.1021/acs.jctc.3c00973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
In enzyme mechanistic studies and mutant design, it is highly desirable to know the individual residue contributions to the reaction free energy and barrier. In this work, we show that such free energy contributions from each residue can be readily obtained by postprocessing ab initio quantum mechanical molecular mechanical (ai-QM/MM) free energy simulation trajectories. Specifically, through a mean force integration along the minimum free energy pathway, one can obtain the electrostatic, polarization, and van der Waals contributions from each residue to the free energy barrier. Separately, a similar analysis procedure allows us to assess the contribution from different collective variables along the reaction coordinate. The chorismate mutase reaction is used to demonstrate the utilization of these two trajectory analysis tools.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Richard Van
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, United States
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yuezhi Mao
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182, United States
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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Świderek K, Velasco-Lozano S, Galmés MÀ, Olazabal I, Sardon H, López-Gallego F, Moliner V. Mechanistic studies of a lipase unveil effect of pH on hydrolysis products of small PET modules. Nat Commun 2023; 14:3556. [PMID: 37321996 PMCID: PMC10272158 DOI: 10.1038/s41467-023-39201-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
Biocatalysis is a key technology enabling plastic recycling. However, despite advances done in the development of plastic-degrading enzymes, the molecular mechanisms that govern their catalytic performance are poorly understood, hampering the engineering of more efficient enzyme-based technologies. In this work, we study the hydrolysis of PET-derived diesters and PET trimers catalyzed by the highly promiscuous lipase B from Candida antarctica (CALB) through QM/MM molecular dynamics simulations supported by experimental Michaelis-Menten kinetics. The computational studies reveal the role of the pH on the CALB regioselectivity toward the hydrolysis of bis-(hydroxyethyl) terephthalate (BHET). We exploit this insight to perform a pH-controlled biotransformation that selectively hydrolyzes BHET to either its corresponding diacid or monoesters using both soluble and immobilized CALB. The discoveries presented here can be exploited for the valorization of BHET resulting from the organocatalytic depolymerization of PET.
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Affiliation(s)
- Katarzyna Świderek
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castellón, Spain.
| | - Susana Velasco-Lozano
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón, 182, 20014 Donostia-San Sebastián, Spain
| | - Miquel À Galmés
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castellón, Spain
| | - Ion Olazabal
- POLYMAT, Department of Polymer Science and Technology, University of the Basque Country UPV/EHU, Manuel de Lardizabal, 3, 20018, Donostia-San Sebastián, Spain
| | - Haritz Sardon
- POLYMAT, Department of Polymer Science and Technology, University of the Basque Country UPV/EHU, Manuel de Lardizabal, 3, 20018, Donostia-San Sebastián, Spain
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón, 182, 20014 Donostia-San Sebastián, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castellón, Spain.
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Belyaeva J, Zlobin A, Maslova V, Golovin A. Modern non-polarizable force fields diverge in modeling the enzyme-substrate complex of a canonical serine protease. Phys Chem Chem Phys 2023; 25:6352-6361. [PMID: 36779321 DOI: 10.1039/d2cp05502c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Classical molecular dynamics simulation is a powerful and established method of modern computational chemistry. Being able to obtain accurate information on molecular behavior is crucial to get valuable insights into structure-function relationships that translate into fundamental findings and practical applications. Active sites of enzymes are known to be particularly intricate, therefore, simpler non-polarizable force fields may provide an inaccurate description. In this work, we addressed this hypothesis in a case of a canonical serine triad protease trypsin in its complex with a substrate-mimicking inhibitor. We tested six modern and popular force fields to find that significantly diverging results may be obtained. Amber FB-15 and OPLS-AA/M turned out to model the active site incorrectly. Amber ff19sb and ff15ipq demonstrated mixed performance. The best performing force fields were CHARMM36m and Amber ff99sb-ildn, therefore, they are recommended for use with this and related systems. We speculate that a similar lack of cross-force field convergence may be characteristic of other enzymatic systems. Therefore, we advocate for careful consideration of different force fields in any study within the field of computational enzymology.
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Affiliation(s)
- Julia Belyaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, Moscow, Russia. .,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - Alexander Zlobin
- Sirius University of Science and Technology, 354340, Sochi, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Valentina Maslova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, Moscow, Russia. .,Sirius University of Science and Technology, 354340, Sochi, Russia
| | - Andrey Golovin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, Moscow, Russia. .,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia.,Sirius University of Science and Technology, 354340, Sochi, Russia
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