1
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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [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: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
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2
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Wen K, Tao Y, Jiang W, Jiang L, Zhu J, Li Q. (De)carboxylation mechanisms of heteroaromatic substrates catalyzed by prenylated FMN-dependent UbiD decarboxylases: An in-silico study. Int J Biol Macromol 2024; 260:129294. [PMID: 38211929 DOI: 10.1016/j.ijbiomac.2024.129294] [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: 10/21/2023] [Revised: 12/24/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
The UbiD enzymes are proposed to catalyze reversible (de)carboxylation reaction of unsaturated carboxylic acids using prenylated flavin mononucleotide (prFMN) as a cofactor. This positions UbiD enzymes as promising candidates for converting CO2 into valuable chemicals. However, their industrial-scale biotransformation is currently constrained by low conversion rates attributed to thermodynamic limitations. To enhance the carboxylation activity of UbiD enzymes, a molecular-level understanding of the (de)carboxylation mechanisms is necessary. In this study, we investigated the reaction mechanisms of heteroaromatic substrates catalyzed by PtHmfF, PaHudA, and AnlnD enzymes using molecular dynamics (MD) simulations and free energy calculations. Our extensive mechanistic study elucidates the mechanisms involved in the formation of the initial prFMN-substrate intermediate. Specifically, we observed nucleophilic attack during decarboxylation, while carboxylation reactions involving furoic acid, pyrrole, and indole tend to favor a 1,3-dipolar cycloaddition mechanism. Furthermore, we identified proton transfer as the rate-limiting step in the carboxylation reaction. In addition, we considered the perspectives of reaction energies and electron transfer to understand the distinct mechanisms underlying decarboxylation and carboxylation. Our calculated free energies are consistent with available experimental kinetics data. Finally, we explored how different rotamers of catalytic residues influence the efficiency of the initial intermediate formation.
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Affiliation(s)
- Kai Wen
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yu Tao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Wenyan Jiang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Liyan Jiang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Jingxuan Zhu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Quanshun Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China; Center for Supramolecular Chemical Biology, Jilin University, Changchun 130012, China.
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3
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Chaturvedi SS, Bím D, Christov CZ, Alexandrova AN. From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics. Chem Sci 2023; 14:10997-11011. [PMID: 37860658 PMCID: PMC10583697 DOI: 10.1039/d3sc02982d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023] Open
Abstract
Enzymes are versatile and efficient biological catalysts that drive numerous cellular processes, motivating the development of enzyme design approaches to tailor catalysts for diverse applications. In this perspective, we investigate the unique properties of natural, evolved, and designed enzymes, recognizing their strengths and shortcomings. We highlight the challenges and limitations of current enzyme design protocols, with a particular focus on their limited consideration of long-range electrostatic and dynamic effects. We then delve deeper into the impact of the protein environment on enzyme catalysis and explore the roles of preorganized electric fields, second coordination sphere interactions, and protein dynamics for enzyme function. Furthermore, we present several case studies illustrating successful enzyme-design efforts incorporating enzyme strategies mentioned above to achieve improved catalytic properties. Finally, we envision the future of enzyme design research, spotlighting the challenges yet to be overcome and the synergy of intrinsic electric fields, second coordination sphere interactions, and conformational dynamics to push the state-of-the-art boundaries.
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Affiliation(s)
- Shobhit S Chaturvedi
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095 USA
| | - Daniel Bím
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095 USA
| | - Christo Z Christov
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095 USA
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4
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Berta D, Gehrke S, Nyíri K, Vértessy BG, Rosta E. Mechanism-Based Redesign of GAP to Activate Oncogenic Ras. J Am Chem Soc 2023; 145:20302-20310. [PMID: 37682266 PMCID: PMC10515638 DOI: 10.1021/jacs.3c04330] [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: 04/26/2023] [Indexed: 09/09/2023]
Abstract
Ras GTPases play a crucial role in cell signaling pathways. Mutations of the Ras gene occur in about one third of cancerous cell lines and are often associated with detrimental clinical prognosis. Hot spot residues Gly12, Gly13, and Gln61 cover 97% of oncogenic mutations, which impair the enzymatic activity in Ras. Using QM/MM free energy calculations, we present a two-step mechanism for the GTP hydrolysis catalyzed by the wild-type Ras.GAP complex. We found that the deprotonation of the catalytic water takes place via the Gln61 as a transient Brønsted base. We also determined the reaction profiles for key oncogenic Ras mutants G12D and G12C using QM/MM minimizations, matching the experimentally observed loss of catalytic activity, thereby validating our reaction mechanism. Using the optimized reaction paths, we devised a fast and accurate procedure to design GAP mutants that activate G12D Ras. We replaced GAP residues near the active site and determined the activation barrier for 190 single mutants. We furthermore built a machine learning for ultrafast screening, by fast prediction of the barrier heights, tested both on the single and double mutations. This work demonstrates that fast and accurate screening can be accomplished via QM/MM reaction path optimizations to design protein sequences with increased catalytic activity. Several GAP mutations are predicted to re-enable catalysis in oncogenic G12D, offering a promising avenue to overcome aberrant Ras-driven signal transduction by activating enzymatic activity instead of inhibition. The outlined computational screening protocol is readily applicable for designing ligands and cofactors analogously.
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Affiliation(s)
- Dénes Berta
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E
6BT, United Kingdom
| | - Sascha Gehrke
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E
6BT, United Kingdom
| | - Kinga Nyíri
- Institute
of Enzymology, Research Centre for Natural Sciences, Magyar tudósok körútja
2, Budapest 1117, Hungary
- Department
of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budafoki út 6-8, Budapest 1111, Hungary
| | - Beáta G. Vértessy
- Institute
of Enzymology, Research Centre for Natural Sciences, Magyar tudósok körútja
2, Budapest 1117, Hungary
- Department
of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budafoki út 6-8, Budapest 1111, Hungary
| | - Edina Rosta
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E
6BT, United Kingdom
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5
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Zheng Y, Vaissier Welborn V. Tuning the Catalytic Activity of Synthetic Enzyme KE15 with DNA. J Phys Chem B 2022; 126:3407-3413. [PMID: 35483007 DOI: 10.1021/acs.jpcb.2c00765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficiency improvement of synthetic enzymes through scaffold modifications suffers from limitations in terms of effectiveness, cost, and potential devastating consequences for protein structural stability. Here, we propose an alternative to scaffold modification, within electrostatic preorganization theory, where the enzyme's greater environment is designed to support the evolution of the reaction in the active site. We demonstrate the feasibility of such an approach by placing a (polar) DNA fragment in the surroundings of the Kemp eliminase enzyme KE15 (structure from Houk's group) and computing the resulting change in catalytic activity. We find that the introduction of a DNA fragment magnifies the contribution of protein residues to the stabilization of the transition state, estimated from electric field calculations with polarizable molecular dynamics. Our randomly generated test systems reveal a 2.0 kcal/mol reduction in activation energy, suggesting that even more significant catalytic improvements could be made by optimizing DNA size, sequence, and orientation with respect to the enzyme, validating our approach.
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Affiliation(s)
- Yi Zheng
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
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6
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Dong Y, Li T, Zhang S, Sanchis J, Yin H, Ren J, Sheng X, Li G, Reetz MT. Biocatalytic Baeyer–Villiger Reactions: Uncovering the Source of Regioselectivity at Each Evolutionary Stage of a Mutant with Scrutiny of Fleeting Chiral Intermediates. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00415] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yijie Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
- Key Laboratory of Agricultural Microbiomics and Precision Application − Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Tang Li
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, PR China
| | - Shiqing Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P.R. China
| | - Joaquin Sanchis
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Heng Yin
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, PR China
| | - Jie Ren
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P.R. China
| | - Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim 45470, Germany
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7
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QM and QM/MM study on inhibition mechanism of polyphenolic compounds as non-classical inhibitors of α-human carbonic anhydrase (II). Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02839-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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8
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Ghiasi M, Shahabi P, Supuran CT. Quantum mechanical study on the activation mechanism of human carbonic anhydrase VII cluster model with bis-histamine schiff bases and bis-spinaceamine derivatives. Bioorg Med Chem 2021; 44:116276. [PMID: 34225168 DOI: 10.1016/j.bmc.2021.116276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/10/2021] [Accepted: 06/10/2021] [Indexed: 02/05/2023]
Abstract
The activation mechanism of human carbonic anhydrase (hCA) isoform VII, hCA VII, with histamine, histamine bis-Schiff bases and bis-spinaceamine derivatives has been investigated using quantum mechanical calculations. The DFT-D3 method has been employed to calculate in detail the electronic structure and electronic energy of different compounds and complexes throughout the reaction pathway. The model system of hCA VII included the core catalytic center, the Zn2+ ion, its three histidine ligands and a hydroxide ion or water molecule coordinated to it. Furthermore, Thr199, Glu106 and the deep water molecule were considered in the model. Five activators of this enzyme, including histamine as standard, in complex with the cluster model of hCA VII were investigated. Thermodynamic functions for the overall reaction and for the complexation between activators and hCA VII were evaluated. Our results demonstrate that the protonatable moiety of these activators participates in proton transfer reactions from the zinc-bound water molecule to the reaction medium, promoting the formation of the catalytically active zinc hydroxide species of the enzyme. The QM analysis revealed that the electrostatic interactions between activators and hCA VII are the driving force of the enzyme-activator complex formation.
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Affiliation(s)
- Mina Ghiasi
- Department of Chemistry, Faculty of Physics and Chemistry, Alzahra University, Tehran, Iran.
| | - Parisa Shahabi
- Department of Chemistry, Faculty of Physics and Chemistry, Alzahra University, Tehran, Iran
| | - Claudiu T Supuran
- Dipartimento Neurofarba, Sezione di, Scienze Farmaceutiche e Nutraceutiche, Universita degli Studi di Firenze, Sesto Fiorentino, Italy
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9
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Veit-Acosta M, de Azevedo Junior WF. Computational Prediction of Binding Affinity for CDK2-ligand Complexes. A Protein Target for Cancer Drug Discovery. Curr Med Chem 2021; 29:2438-2455. [PMID: 34365938 DOI: 10.2174/0929867328666210806105810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND CDK2 participates in the control of eukaryotic cell-cycle progression. Due to the great interest in CDK2 for drug development and the relative easiness in crystallizing this enzyme, we have over 400 structural studies focused on this protein target. This structural data is the basis for the development of computational models to estimate CDK2-ligand binding affinity. OBJECTIVE This work focuses on the recent developments in the application of supervised machine learning modeling to develop scoring functions to predict the binding affinity of CDK2. METHOD We employed the structures available at the protein data bank and the ligand information accessed from the BindingDB, Binding MOAD, and PDBbind to evaluate the predictive performance of machine learning techniques combined with physical modeling used to calculate binding affinity. We compared this hybrid methodology with classical scoring functions available in docking programs. RESULTS Our comparative analysis of previously published models indicated that a model created using a combination of a mass-spring system and cross-validated Elastic Net to predict the binding affinity of CDK2-inhibitor complexes outperformed classical scoring functions available in AutoDock4 and AutoDock Vina. CONCLUSION All studies reviewed here suggest that targeted machine learning models are superior to classical scoring functions to calculate binding affinities. Specifically for CDK2, we see that the combination of physical modeling with supervised machine learning techniques exhibits improved predictive performance to calculate the protein-ligand binding affinity. These results find theoretical support in the application of the concept of scoring function space.
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Affiliation(s)
- Martina Veit-Acosta
- Western Michigan University, 1903 Western, Michigan Ave, Kalamazoo, MI 49008. United States
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10
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Abstract
QM/MM simulations have become an indispensable tool in many chemical and biochemical investigations. Considering the tremendous degree of success, including recognition by a 2013 Nobel Prize in Chemistry, are there still "burning challenges" in QM/MM methods, especially for biomolecular systems? In this short Perspective, we discuss several issues that we believe greatly impact the robustness and quantitative applicability of QM/MM simulations to many, if not all, biomolecules. We highlight these issues with observations and relevant advances from recent studies in our group and others in the field. Despite such limited scope, we hope the discussions are of general interest and will stimulate additional developments that help push the field forward in meaningful directions.
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Affiliation(s)
- Qiang Cui
- Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Tanmoy Pal
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Luke Xie
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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11
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Planas-Iglesias J, Marques SM, Pinto GP, Musil M, Stourac J, Damborsky J, Bednar D. Computational design of enzymes for biotechnological applications. Biotechnol Adv 2021; 47:107696. [PMID: 33513434 DOI: 10.1016/j.biotechadv.2021.107696] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/14/2022]
Abstract
Enzymes are the natural catalysts that execute biochemical reactions upholding life. Their natural effectiveness has been fine-tuned as a result of millions of years of natural evolution. Such catalytic effectiveness has prompted the use of biocatalysts from multiple sources on different applications, including the industrial production of goods (food and beverages, detergents, textile, and pharmaceutics), environmental protection, and biomedical applications. Natural enzymes often need to be improved by protein engineering to optimize their function in non-native environments. Recent technological advances have greatly facilitated this process by providing the experimental approaches of directed evolution or by enabling computer-assisted applications. Directed evolution mimics the natural selection process in a highly accelerated fashion at the expense of arduous laboratory work and economic resources. Theoretical methods provide predictions and represent an attractive complement to such experiments by waiving their inherent costs. Computational techniques can be used to engineer enzymatic reactivity, substrate specificity and ligand binding, access pathways and ligand transport, and global properties like protein stability, solubility, and flexibility. Theoretical approaches can also identify hotspots on the protein sequence for mutagenesis and predict suitable alternatives for selected positions with expected outcomes. This review covers the latest advances in computational methods for enzyme engineering and presents many successful case studies.
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Affiliation(s)
- Joan Planas-Iglesias
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Sérgio M Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Gaspar P Pinto
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Milos Musil
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic; IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, 61266 Brno, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic.
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
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12
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Ghattas W, Mahy JP, Réglier M, Simaan AJ. Artificial Enzymes for Diels-Alder Reactions. Chembiochem 2020; 22:443-459. [PMID: 32852088 DOI: 10.1002/cbic.202000316] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/17/2020] [Indexed: 12/13/2022]
Abstract
The Diels-Alder (DA) reaction is a cycloaddition of a conjugated diene and an alkene (dienophile) leading to the formation of a cyclohexene derivative through a concerted mechanism. As DA reactions generally proceed with a high degree of regio- and stereoselectivity, they are widely used in synthetic organic chemistry. Considering eco-conscious public and governmental movements, efforts are now directed towards the development of synthetic processes that meet environmental concerns. Artificial enzymes, which can be developed to catalyze abiotic reactions, appear to be important synthetic tools in the synthetic biology field. This review describes the different strategies used to develop protein-based artificial enzymes for DA reactions, including for in cellulo approaches.
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Affiliation(s)
- Wadih Ghattas
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Université Paris Sud, Université Paris-Saclay, Orsay, 91405 Cedex 8, France
| | - Jean-Pierre Mahy
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Université Paris Sud, Université Paris-Saclay, Orsay, 91405 Cedex 8, France
| | - Marius Réglier
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Avenue Escadrille Normandie Niemen, Service 342, Marseille, 13397, France
| | - A Jalila Simaan
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Avenue Escadrille Normandie Niemen, Service 342, Marseille, 13397, France
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13
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Martí S, Tuñón I, Moliner V, Bertran J. Are Heme-Dependent Enzymes Always Using a Redox Mechanism? A Theoretical Study of the Kemp Elimination Catalyzed by a Promiscuous Aldoxime Dehydratase. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02215] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sergio Martí
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Joan Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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14
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Multiscale computation delivers organophosphorus reactivity and stereoselectivity to immunoglobulin scavengers. Proc Natl Acad Sci U S A 2020; 117:22841-22848. [PMID: 32859757 PMCID: PMC7502716 DOI: 10.1073/pnas.2010317117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Developed quantum mechanics/molecular mechanics (QM/MM) supercomputation is used to identify maturation of immunoglobulin (Ig) reactivity through optimization of amino acids in the catalytic core, focused on enhanced nucleophilic attack on phosphorus. A computationally optimized variant, l-Leu47Lys, delivers 340-fold reactivity enhancement for paraoxon relative to wild-type Ig-paraoxonase resulting from substrate-induced ionization of the Tyr37 nucleophile. Variant antibody stereoselectivity toward a P-chiral phenylphosphonate toxin results from starkly contrasting solvent-assisted or general base catalytic mechanisms relative to the parent Ig-paraoxonase. These mechanisms are defined by crystallographic and QM/MM analyses as resulting from changed substrate orientation and participating amino acid conformations within the catalytic site. Quantum mechanics/molecular mechanics (QM/MM) maturation of an immunoglobulin (Ig) powered by supercomputation delivers novel functionality to this catalytic template and facilitates artificial evolution of biocatalysts. We here employ density functional theory-based (DFT-b) tight binding and funnel metadynamics to advance our earlier QM/MM maturation of A17 Ig-paraoxonase (WTIgP) as a reactibody for organophosphorus toxins. It enables regulation of biocatalytic activity for tyrosine nucleophilic attack on phosphorus. The single amino acid substitution l-Leu47Lys results in 340-fold enhanced reactivity for paraoxon. The computed ground-state complex shows substrate-induced ionization of the nucleophilic l-Tyr37, now H-bonded to l-Lys47, resulting from repositioning of l-Lys47. Multiple antibody structural homologs, selected by phenylphosphonate covalent capture, show contrasting enantioselectivities for a P-chiral phenylphosphonate toxin. That is defined by crystallographic analysis of phenylphosphonylated reaction products for antibodies A5 and WTIgP. DFT-b analysis using QM regions based on these structures identifies transition states for the favored and disfavored reactions with surprising results. This stereoselection analysis is extended by funnel metadynamics to a range of WTIgP variants whose predicted stereoselectivity is endorsed by experimental analysis. The algorithms used here offer prospects for tailored design of highly evolved, genetically encoded organophosphorus scavengers and for broader functionalities of members of the Ig superfamily, including cell surface-exposed receptors.
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15
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Osuna S. The challenge of predicting distal active site mutations in computational enzyme design. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1502] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química Universitat de Girona Girona Spain
- ICREA Barcelona Spain
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16
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Cuevas-Zuviría B, Pacios LF. Analytical Model of Electron Density and Its Machine Learning Inference. J Chem Inf Model 2020; 60:3831-3842. [DOI: 10.1021/acs.jcim.0c00197] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Bruno Cuevas-Zuviría
- Centro de Biotecnologı́a y Genómica de Plantas (CBGP, UPM-INIA), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Campus de Montegancedo-UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Luis F. Pacios
- Centro de Biotecnologı́a y Genómica de Plantas (CBGP, UPM-INIA), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Campus de Montegancedo-UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
- Departamento de Biotecnologı́a-Biologı́a Vegetal, Escuela Técnica Superior de Ingenierı́a Agraria, Alimentaria y de Biosistemas (ETSIAAB), Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
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17
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De Raffele D, Martí S, Moliner V. Understanding the Directed Evolution of De Novo Retro-Aldolases from QM/MM Studies. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Daria De Raffele
- Departament de Química Física i Analítica; Universitat Jaume I., 12071 Castellón, Spain
| | - Sergio Martí
- Departament de Química Física i Analítica; Universitat Jaume I., 12071 Castellón, Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica; Universitat Jaume I., 12071 Castellón, Spain
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18
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Beker W, Sokalski WA. Bottom-Up Nonempirical Approach To Reducing Search Space in Enzyme Design Guided by Catalytic Fields. J Chem Theory Comput 2020; 16:3420-3429. [PMID: 32282205 PMCID: PMC7467639 DOI: 10.1021/acs.jctc.0c00139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Currently developed protocols of theozyme design still lead to biocatalysts with much lower catalytic activity than enzymes existing in nature, and, so far, the only avenue of improvement was the in vitro laboratory-directed evolution (LDE) experiments. In this paper, we propose a different strategy based on "reversed" methodology of mutation prediction. Instead of common "top-down" approach, requiring numerous assumptions and vast computational effort, we argue for a "bottom-up" approach that is based on the catalytic fields derived directly from transition state and reactant complex wave functions. This enables direct one-step determination of the general quantitative angular characteristics of optimal catalytic site and simultaneously encompasses both the transition-state stabilization (TSS) and ground-state destabilization (GSD) effects. We further extend the static catalytic field approach by introducing a library of atomic multipoles for amino acid side-chain rotamers, which, together with the catalytic field, allow one to determine the optimal side-chain orientations of charged amino acids constituting the elusive structure of a preorganized catalytic environment. Obtained qualitative agreement with experimental LDE data for Kemp eliminase KE07 mutants validates the proposed procedure, yielding, in addition, a detailed insight into possible dynamic and epistatic effects.
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Affiliation(s)
- Wiktor Beker
- Wroclaw University of Science and Technology, Wroclaw, Poland
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19
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Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Kemp Elimination Reaction Catalyzed by Electric Fields. Chemphyschem 2020; 21:295-306. [PMID: 31840917 DOI: 10.1002/cphc.201901155] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/12/2019] [Indexed: 12/20/2022]
Abstract
The Kemp elimination reaction is the most widely used in the de novo design of new enzymes. The effect of two different kinds of electric fields in the reactions of acetate as a base with benzisoxazole and 5-nitrobenzisoxazole as substrates have been theoretically studied. The effect of the solvent reaction field has been calculated using the SMD continuum model for several solvents; we have shown that solvents inhibit both reactions, the decrease of the reaction rate being larger as far as the dielectric constant is increased. The diminution of the reaction rate is especially remarkable between aprotic organic solvents and protic solvents as water, the electrostatic term of the hydrogen bonds being the main factor for the large inhibitory effect of water. The presence of an external electric field oriented in the direction of the charge transfer (z axis) increases it and, so, the reaction rate. In the reaction of the nitro compound, if the electric field is oriented in an orthogonal direction (x axis) the charge transfer to the NO2 group is favored and there is a subsequent increase of the reaction rate. However, this increase is smaller than the one produced by the field in the z axis. It is worthwhile mentioning that one of the main effects of external electric fields of intermediate intensity is the reorientation of the reactants. Finally, the implications of our results in the de novo design of enzymes are discussed.
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Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Joan Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Vicenç Branchadell
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Antoni Oliva
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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20
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Lodola A, Callegari D, Scalvini L, Rivara S, Mor M. Design and SAR Analysis of Covalent Inhibitors Driven by Hybrid QM/MM Simulations. Methods Mol Biol 2020; 2114:307-337. [PMID: 32016901 DOI: 10.1007/978-1-0716-0282-9_19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) hybrid technique is emerging as a reliable computational method to investigate and characterize chemical reactions occurring in enzymes. From a drug discovery perspective, a thorough understanding of enzyme catalysis appears pivotal to assist the design of inhibitors able to covalently bind one of the residues belonging to the enzyme catalytic machinery. Thanks to the current advances in computer power, and the availability of more efficient algorithms for QM-based simulations, the use of QM/MM methodology is becoming a viable option in the field of covalent inhibitor design. In the present review, we summarized our experience in the field of QM/MM simulations applied to drug design problems which involved the optimization of agents working on two well-known drug targets, namely fatty acid amide hydrolase (FAAH) and epidermal growth factor receptor (EGFR). In this context, QM/MM simulations gave valuable information in terms of geometry (i.e., of transition states and metastable intermediates) and reaction energetics that allowed to correctly predict inhibitor binding orientation and substituent effect on enzyme inhibition. What is more, enzyme reaction modelling with QM/MM provided insights that were translated into the synthesis of new covalent inhibitor featured by a unique combination of intrinsic reactivity, on-target activity, and selectivity.
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Affiliation(s)
- Alessio Lodola
- Drug Design and Discovery Group, Department of Food and Drug, University of Parma, Parma, Italy.
| | - Donatella Callegari
- Drug Design and Discovery Group, Department of Food and Drug, University of Parma, Parma, Italy
| | - Laura Scalvini
- Drug Design and Discovery Group, Department of Food and Drug, University of Parma, Parma, Italy
| | - Silvia Rivara
- Drug Design and Discovery Group, Department of Food and Drug, University of Parma, Parma, Italy
| | - Marco Mor
- Drug Design and Discovery Group, Department of Food and Drug, University of Parma, Parma, Italy
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21
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Abstract
Quantum mechanics (QM) methods provide a fine description of receptor-ligand interactions and of chemical reactions. Their use in drug design and drug discovery is increasing, especially for complex systems including metal ions in the binding sites, for the design of highly selective inhibitors, for the optimization of bi-specific compounds, to understand enzymatic reactions, and for the study of covalent ligands and prodrugs. They are also used for generating molecular descriptors for predictive QSAR/QSPR models and for the parameterization of force fields. Thanks to the continuous increase of computational power offered by GPUs and to the development of sophisticated algorithms, QM methods are becoming part of the standard tools used in computer-aided drug design (CADD). We present the most used QM methods and software packages, and we discuss recent representative applications in drug design and drug discovery.
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Affiliation(s)
- Martin Kotev
- Global Research Informatics/Cheminformatics and Drug Design, Evotec (France) SAS, Toulouse, France
| | - Laurie Sarrat
- Global Research Informatics/Cheminformatics and Drug Design, Evotec (France) SAS, Toulouse, France
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22
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Santos YLDL, Chew-Fajardo YL, Brault G, Doucet N. Dissecting the evolvability landscape of the CalB active site toward aromatic substrates. Sci Rep 2019; 9:15588. [PMID: 31666622 PMCID: PMC6821916 DOI: 10.1038/s41598-019-51940-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 10/07/2019] [Indexed: 01/17/2023] Open
Abstract
A key event in the directed evolution of enzymes is the systematic use of mutagenesis and selection, a process that can give rise to mutant libraries containing millions of protein variants. To this day, the functional analysis and identification of active variants among such high numbers of mutational possibilities is not a trivial task. Here, we describe a combinatorial semi-rational approach to partly overcome this challenge and help design smaller and smarter mutant libraries. By adapting a liquid medium transesterification assay in organic solvent conditions with a combination of virtual docking, iterative saturation mutagenesis, and residue interaction network (RIN) analysis, we engineered lipase B from P. antarctica (CalB) to improve enzyme recognition and activity against the bulky aromatic substrates and flavoring agents methyl cinnamate and methyl salicylate. Substrate-imprinted docking was used to target active-site positions involved in enzyme-substrate and enzyme-product complexes, in addition to identifying 'hot spots' most likely to yield active variants. This iterative semi-rational design strategy allowed selection of CalB variants exhibiting increased activity in just two rounds of site-saturation mutagenesis. Beneficial replacements were observed by screening only 0.308% of the theoretical library size, illustrating how semi-rational approaches with targeted diversity can quickly facilitate the discovery of improved activity variants relevant to a number of biotechnological applications.
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Affiliation(s)
- Yossef López de Los Santos
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Ying Lian Chew-Fajardo
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Guillaume Brault
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada.
- PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, 1045 Avenue de la Médecine, Université Laval, Quebec City, QC, G1V 0A6, Canada.
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23
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De Raffele D, Martí S, Moliner V. QM/MM Theoretical Studies of a de Novo Retro-Aldolase Design. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04457] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daria De Raffele
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Sergio Martí
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
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24
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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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25
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Huggins DJ, Biggin PC, Dämgen MA, Essex JW, Harris SA, Henchman RH, Khalid S, Kuzmanic A, Laughton CA, Michel J, Mulholland AJ, Rosta E, Sansom MSP, van der Kamp MW. Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1393] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- David J. Huggins
- TCM Group, Cavendish Laboratory University of Cambridge Cambridge UK
- Unilever Centre, Department of Chemistry University of Cambridge Cambridge UK
- Department of Physiology and Biophysics Weill Cornell Medical College New York NY
| | | | - Marc A. Dämgen
- Department of Biochemistry University of Oxford Oxford UK
| | - Jonathan W. Essex
- School of Chemistry University of Southampton Southampton UK
- Institute for Life Sciences University of Southampton Southampton UK
| | - Sarah A. Harris
- School of Physics and Astronomy University of Leeds Leeds UK
- Astbury Centre for Structural and Molecular Biology University of Leeds Leeds UK
| | - Richard H. Henchman
- Manchester Institute of Biotechnology The University of Manchester Manchester UK
- School of Chemistry The University of Manchester Oxford UK
| | - Syma Khalid
- School of Chemistry University of Southampton Southampton UK
- Institute for Life Sciences University of Southampton Southampton UK
| | | | - Charles A. Laughton
- School of Pharmacy University of Nottingham Nottingham UK
- Centre for Biomolecular Sciences University of Nottingham Nottingham UK
| | - Julien Michel
- EaStCHEM school of Chemistry University of Edinburgh Edinburgh UK
| | - Adrian J. Mulholland
- Centre of Computational Chemistry, School of Chemistry University of Bristol Bristol UK
| | - Edina Rosta
- Department of Chemistry King's College London London UK
| | | | - Marc W. van der Kamp
- Centre of Computational Chemistry, School of Chemistry University of Bristol Bristol UK
- School of Biochemistry, Biomedical Sciences Building University of Bristol Bristol UK
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26
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Piazzetta P, Marino T, Russo N, Salahub DR. The role of metal substitution in the promiscuity of natural and artificial carbonic anhydrases. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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27
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Świderek K, Tuñón I, Moliner V, Bertran J. Revealing the Origin of the Efficiency of the De Novo Designed Kemp Eliminase HG-3.17 by Comparison with the Former Developed HG-3. Chemistry 2017; 23:7582-7589. [DOI: 10.1002/chem.201700807] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Katarzyna Świderek
- Departament de Química Física i Analítica; Universitat Jaume I; 12071 Castellón Spain
- Institute of Applied Radiation Chemistry; Lodz University of Technology; 90-924 Lodz Poland
| | - Iñaki Tuñón
- Departament de Química Física; Universitat de València; 46100 Burjassot Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica; Universitat Jaume I; 12071 Castellón Spain
- Department of Chemistry; University of Bath; Bath BA2 7AY United Kingdom
| | - Joan Bertran
- Departament de Química; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
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28
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Biocatalysts for the pharmaceutical industry created by structure-guided directed evolution of stereoselective enzymes. Bioorg Med Chem 2017; 26:1241-1251. [PMID: 28693917 DOI: 10.1016/j.bmc.2017.05.021] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/11/2017] [Accepted: 05/09/2017] [Indexed: 01/01/2023]
Abstract
Enzymes have been used for a long time as catalysts in the asymmetric synthesis of chiral intermediates needed in the production of therapeutic drugs. However, this alternative to man-made catalysts has suffered traditionally from distinct limitations, namely the often observed wrong or insufficient enantio- and/or regioselectivity, low activity, narrow substrate range, and insufficient thermostability. With the advent of directed evolution, these problems can be generally solved. The challenge is to develop and apply the most efficient mutagenesis methods which lead to highest-quality mutant libraries requiring minimal screening. Structure-guided saturation mutagenesis and its iterative form have emerged as the method of choice for evolving stereo- and regioselective mutant enzymes needed in the asymmetric synthesis of chiral intermediates. The number of (industrial) applications in the preparation of chiral pharmaceuticals is rapidly increasing. This review features and analyzes typical case studies.
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29
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Amrein BA, Steffen-Munsberg F, Szeler I, Purg M, Kulkarni Y, Kamerlin SCL. CADEE: Computer-Aided Directed Evolution of Enzymes. IUCRJ 2017; 4:50-64. [PMID: 28250941 PMCID: PMC5331465 DOI: 10.1107/s2052252516018017] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/09/2016] [Indexed: 05/10/2023]
Abstract
The tremendous interest in enzymes as biocatalysts has led to extensive work in enzyme engineering, as well as associated methodology development. Here, a new framework for computer-aided directed evolution of enzymes (CADEE) is presented which allows a drastic reduction in the time necessary to prepare and analyze in silico semi-automated directed evolution of enzymes. A pedagogical example of the application of CADEE to a real biological system is also presented in order to illustrate the CADEE workflow.
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Affiliation(s)
- Beat Anton Amrein
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Fabian Steffen-Munsberg
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Ireneusz Szeler
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Miha Purg
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Yashraj Kulkarni
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
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30
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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.
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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.
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31
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Kravchuk VO, Savytskyi OV, Odynets KO, Mykuliak VV, Kornelyuk AI. Computational modeling and molecular dynamics simulations of mammalian cytoplasmic tyrosyl-tRNA synthetase and its complexes with substrates. J Biomol Struct Dyn 2016; 35:2772-2788. [PMID: 27615678 DOI: 10.1080/07391102.2016.1235512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Cytoplasmic tyrosyl-tRNA synthetase (TyrRS) is one of the key enzymes of protein biosynthesis. TyrRSs of pathogenic organisms have gained attention as potential targets for drug development. Identifying structural differences between various TyrRSs will facilitate the development of specific inhibitors for the TyrRSs of pathogenic organisms. However, there is a deficiency in structural data for mammalian cytoplasmic TyrRS in complexes with substrates. In this work, we constructed spatial structure of full-length Bos taurus TyrRS (BtTyrRS) and its complexes with substrates using the set of computational modeling techniques. Special attention was paid to BtTyrRS complexes with substrates [L-tyrosine, K+ and ATP:Mg2+] and intermediate products [tyrosyl-adenylate (Tyr-AMP), K+ and PPi:Mg2+] with the different catalytic loop conformations. In order to analyze their dynamical properties, we performed 100 ns of molecular dynamics (MD) simulations. MD simulations revealed new structural data concerning the tyrosine activation reaction in mammalian TyrRS. Formation of strong interaction between Lys154 and γ-phosphate suggests the additional role of CP1 insertion as an important factor for ATP binding. The presence of a potassium-binding pocket within the active site of mammalian TyrRS compensates the absence of the second lysine in the KMSKS motif. Our data provide new details concerning a role of K+ ions at different stages of the first step of the tyrosylation reaction, including the coordination of substrates and involvement in the PPi releasing. The results of this work suggest that differences between ATP-binding sites of mammalian and bacterial TyrRSs are meaningful and could be exploited in the drug design.
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Affiliation(s)
- Vladyslav O Kravchuk
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.,b Department of Biotechnology , National Aviation University , 1, Kosmonavta Komarova Str., Kyiv , 03058 , Ukraine
| | - Oleksandr V Savytskyi
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine
| | - Konstantin O Odynets
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine
| | - Vasyl V Mykuliak
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.,c Institute of High Technologies , Taras Shevchenko National University of Kyiv , 64, Volodymyrs'ka Str., Kyiv , 01601 , Ukraine
| | - Alexander I Kornelyuk
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.,c Institute of High Technologies , Taras Shevchenko National University of Kyiv , 64, Volodymyrs'ka Str., Kyiv , 01601 , Ukraine
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32
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Maeda Y, Makhlynets OV, Matsui H, Korendovych IV. Design of Catalytic Peptides and Proteins Through Rational and Combinatorial Approaches. Annu Rev Biomed Eng 2016; 18:311-28. [PMID: 27022702 PMCID: PMC6345664 DOI: 10.1146/annurev-bioeng-111215-024421] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This review focuses on recent progress in noncomputational methods to introduce catalytic function into proteins, peptides, and peptide assemblies. We discuss various approaches to creating catalytic activity and classification of noncomputational methods into rational and combinatorial classes. The section on rational design covers recent progress in the development of short peptides and oligomeric peptide assemblies for various natural and unnatural reactions. The section on combinatorial design describes recent advances in the discovery of catalytic peptides. We present the future prospects of these and other new approaches in a broader context, including implications for functional material design.
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Affiliation(s)
- Yoshiaki Maeda
- Department of Chemistry, City University of New York-Hunter College, New York, New York 10065;
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Olga V Makhlynets
- Department of Chemistry, Syracuse University, Syracuse, New York 13244;
| | - Hiroshi Matsui
- Department of Chemistry, City University of New York-Hunter College, New York, New York 10065;
- Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021
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33
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Zorn K, Oroz-Guinea I, Brundiek H, Bornscheuer UT. Engineering and application of enzymes for lipid modification, an update. Prog Lipid Res 2016; 63:153-64. [DOI: 10.1016/j.plipres.2016.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/30/2016] [Accepted: 06/10/2016] [Indexed: 12/21/2022]
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34
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Goyal B, Srivastava KR, Patel K, Durani S. Modulation of β-Hairpin Peptide Self-Assembly: A Twenty-Residue Poly-lβ-Hairpin Modified Rationally as a Mixed-l,dHydrolase. ChemistrySelect 2016. [DOI: 10.1002/slct.201600078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry; Indian Institute of Technology Bombay; Powai Mumbai- 400076 India
- Department of Chemistry; School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib- 140406 Punjab India
| | - Kinshuk Raj Srivastava
- Department of Chemistry; Indian Institute of Technology Bombay; Powai Mumbai- 400076 India
- Department of Physics and Astronomy; Michigan State University; East Lansing USA
| | - Kirti Patel
- Department of Chemistry; Indian Institute of Technology Bombay; Powai Mumbai- 400076 India
- Department of Chemistry; N. B. Mehta Science College, Bordi, Dahanu; Dist. Thane Maharashtra India
| | - Susheel Durani
- Department of Chemistry; Indian Institute of Technology Bombay; Powai Mumbai- 400076 India
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Kaushik M, Sinha P, Jaiswal P, Mahendru S, Roy K, Kukreti S. Protein engineering andde novodesigning of a biocatalyst. J Mol Recognit 2016; 29:499-503. [DOI: 10.1002/jmr.2546] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/16/2016] [Accepted: 04/01/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Mahima Kaushik
- Cluster Innovation Centre; University of Delhi; Delhi 110 007 India
- Nucleic Acids Research Laboratory, Department of Chemistry; University of Delhi; Delhi 110007 India
| | - Prashant Sinha
- Cluster Innovation Centre; University of Delhi; Delhi 110 007 India
| | - Pragya Jaiswal
- Cluster Innovation Centre; University of Delhi; Delhi 110 007 India
| | - Swati Mahendru
- Nucleic Acids Research Laboratory, Department of Chemistry; University of Delhi; Delhi 110007 India
| | - Kapil Roy
- Nucleic Acids Research Laboratory, Department of Chemistry; University of Delhi; Delhi 110007 India
| | - Shrikant Kukreti
- Nucleic Acids Research Laboratory, Department of Chemistry; University of Delhi; Delhi 110007 India
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Sun Z, Wikmark Y, Bäckvall JE, Reetz MT. New Concepts for Increasing the Efficiency in Directed Evolution of Stereoselective Enzymes. Chemistry 2016; 22:5046-54. [DOI: 10.1002/chem.201504406] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Indexed: 01/28/2023]
Affiliation(s)
- Zhoutong Sun
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Ylva Wikmark
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 106 91 Stockholm Sweden
| | - Jan-E. Bäckvall
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 106 91 Stockholm Sweden
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
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Świderek K, Moliner V. Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point To Redesign New Diels-Alderases. J Phys Chem B 2015; 120:2053-70. [PMID: 26624234 DOI: 10.1021/acs.jpcb.5b10527] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The design of new biocatalysts is a target that is receiving increasing attention. One of the most popular reactions in this regard is the Diels-Alder cycloaddition because of its applications in organic synthesis and the absence of efficient natural enzymes that catalyze it. In this paper, the possibilities of using the highly promiscuous Candida Antarctica lipase B as a protein scaffold to redesign a Diels-Alderase has been explored by means of theoretical quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. Free energy surfaces have been computed for two reactions in the wild-type and in several mutants with hybrid AM1/MM potentials with corrections at M06-2X/MM level. The study of the counterpart reactions in solution has allowed performing comparative analysis that render interesting conclusions. Since the dienophile anchors very well in the oxyanion hole of all tested protein variants, the slight electronic changes from reactant complex to the transition state suggest that mutations should be focused in favoring the formation of reactive conformations of a reactant complex that, in turn, would reduce the energy barrier.
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Affiliation(s)
- Katarzyna Świderek
- Institute of Applied Radiation Chemistry, Lodz University of Technology , 90-924 Lodz, Poland.,Departamento de Química Física y Analítica, Universitat Jaume I , 12071 Castellón, Spain
| | - Vicent Moliner
- Departamento de Química Física y Analítica, Universitat Jaume I , 12071 Castellón, Spain
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Goyal B, Patel K, Srivastava KR, Durani S. De novo design of stereochemically-bent sixteen-residue β-hairpin as a hydrolase mimic. RSC Adv 2015. [DOI: 10.1039/c5ra19015k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Stepwise design of sixteen-residue β-hairpin as a hydrolase mimic involving fold design by stereochemical mutation followed by inverse-design of sequence.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai–400076
- India
| | - Kirti Patel
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai–400076
- India
| | | | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai–400076
- India
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