1
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Karvelis E, Swanson C, Tidor B. Substrate Turnover Dynamics Guide Ketol-Acid Reductoisomerase Redesign for Increased Specific Activity. ACS Catal 2024; 14:10491-10509. [PMID: 39050899 PMCID: PMC11264209 DOI: 10.1021/acscatal.4c01446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/16/2024] [Accepted: 06/12/2024] [Indexed: 07/27/2024]
Abstract
The task of adapting enzymes for specific applications is often hampered by our incomplete ability to tune and tailor catalytic functions, particularly when seeking increased activity. Here, we develop and demonstrate a rational approach to address this challenge, applied to ketol-acid reductoisomerase (KARI), which has uses in industrial-scale isobutanol production. While traditional structure-based computational enzyme redesign strategies typically focus on the enzyme-bound ground state (GS) and transition state (TS), we postulated that additionally treating the underlying dynamics of complete turnover events that connect and pass through both states could further elucidate the structural properties affecting catalysis and help identify mutations that lead to increased catalytic activity. To examine the dynamics of substrate conversion with atomistic detail, we adapted and applied computational methods based on path sampling techniques to gather thousands of QM/MM simulations of attempted substrate turnover events by KARI: both productive (reactive) and unproductive (nonreactive) attempts. From these data, machine learning models were constructed and used to identify specific conformational features (interatomic distances, angles, and torsions) associated with successful, productive catalysis. Multistate protein redesign techniques were then used to select mutations that stabilized reactive-like structures over nonreactive-like ones while also meeting additional criteria consistent with enhanced specific activity. This procedure resulted in eight high-confidence enzyme mutants with a significant improvement in calculated specific activity relative to wild type (WT), with the fastest variant's increase in calculated k cat being (2 ± 1) × 104-fold. Collectively, these results suggest that introducing mutations designed to increase the population of reaction-promoting conformations of the enzyme-substrate complex before it reaches the barrier can provide an effective approach to engineering improved enzyme catalysts.
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Affiliation(s)
- Elijah Karvelis
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chloe Swanson
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bruce Tidor
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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2
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Pu Z, Cao J, Wu W, Song Z, Yang L, Wu J, Yu H. Reconstructing dynamics correlation network to simultaneously improve activity and stability of 2,3-butanediol dehydrogenase by design of distal interchain disulfide bonds. Int J Biol Macromol 2024; 267:131415. [PMID: 38582485 DOI: 10.1016/j.ijbiomac.2024.131415] [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: 01/18/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
The complete enzyme catalytic cycle includes substrate binding, chemical reaction and product release, in which different dynamic conformations are adopted. Due to the complex relationship among enzyme activity, stability and dynamics, the directed evolution of enzymes for improved activity or stability commonly leads to a trade-off in stability or activity. It hence remains a challenge to engineer an enzyme to have both enhanced activity and stability. Here, we have attempted to reconstruct the dynamics correlation network involved with active center to improve both activity and stability of a 2,3-butanediol dehydrogenase (2,3-BDH) by introducing inter-chain disulfide bonds. A computational strategy was first applied to evaluate the effect of introducing inter-chain disulfide bond on activity and stability of three 2,3-BDHs, and the N258C mutation of 2,3-BDH from Corynebacterium glutamicum (CgBDH) was proved to be effective in improving both activity and stability. In the results, CgBDH-N258C showed a different unfolding curve from the wild type, with two melting temperatures (Tm) of 68.3 °C and 50.8 °C, 19.7 °C and 2 °C higher than 48.6 °C of the wild type. Its half-life was also improved by 14.8-fold compared to the wild type. Catalytic efficiency (kcat/Km) of the mutant was increased by 7.9-fold toward native substrate diacetyl and 8.8-fold toward non-native substrate 2,5-hexanedione compared to the wild type. Molecular dynamics simulations revealed that an interaction network formed by Cys258, Arg162, Ala144 and the catalytic residues was reconstructed in the mutant and the dynamics change caused by the disulfide bond could be propagated through the interactions network. This improved the enzyme stability and activity by decreasing the flexibility and locking more "reactive" pose, respectively. Further construction of mutations including A144G showing a 44-fold improvement in catalytic efficiency toward meso-2,3-BD confirmed the role of modifying dynamics correlation network in tunning enzyme activity and selectivity. This study provided important insights into the relationship among dynamics, enzyme catalysis and stability, and will be useful in the designing new enzymes with co-evolution of stability, activity and selectivity.
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Affiliation(s)
- Zhongji Pu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China; Xianghu Laboratory, Hangzhou 311231, China
| | - Jiawen Cao
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Wenhui Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China
| | - Zhongdi Song
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China.
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3
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Kuca K, Valle da Silva JA, Nepovimova E, Pham NL, Wu W, Valis M, Wu Q, França TCC. Pralidoxime-like reactivator with increased lipophilicity - Molecular modeling and in vitro study. Chem Biol Interact 2023; 385:110734. [PMID: 37788753 DOI: 10.1016/j.cbi.2023.110734] [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: 07/09/2023] [Revised: 08/23/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023]
Abstract
Acetylcholinesterase (AChE, EC 3.1.1.7) reactivators (2-PAM, trimedoxime, obidoxime, asoxime) have become an integral part of antidotal treatment in cases of nerve agent and organophosphorus (OP) pesticide poisonings. They are often referred to as specific antidotes due to their ability to restore AChE function when it has been covalently inhibited by an OP compound. Currently available commercial reactivators exhibit limited ability to penetrate the blood-brain barrier, where reactivation of inhibited AChE is crucial. Consequently, there have been numerous efforts to discover more brain-penetrating AChE reactivators. In this study, we examined a derivative of 2-PAM designed to possess increased lipophilicity. This enhanced lipophilicity was achieved through the incorporation of a benzyl group into its molecular structure. Initially, a molecular modeling study was conducted, followed by a comparison of its reactivation efficacy with that of 2-PAM against 10 different AChE inhibitors in vitro. Unfortunately, this relatively significant structural modification of 2-PAM resulted in a decrease in its reactivation potency. Consequently, this derivative cannot be considered as a broad-spectrum AChE reactivator.
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Affiliation(s)
- Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic; Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic.
| | - Jorge Alberto Valle da Silva
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ngoc Lam Pham
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Wenda Wu
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic; School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China
| | - Martin Valis
- Department of Neurology, University Hospital Hradec Kralove, Hradec Kralove, 500 05, Czech Republic
| | - Qinghua Wu
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic; College of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Tanos Celmar Costa França
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic; Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic.
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4
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Wang L, Jiang Z, Zhang J, Chen K, Zhang M, Wang Z, Wang B, Ye M, Qiao X. Characterization and structure-based protein engineering of a regiospecific saponin acetyltransferase from Astragalus membranaceus. Nat Commun 2023; 14:5969. [PMID: 37749089 PMCID: PMC10519980 DOI: 10.1038/s41467-023-41599-7] [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: 05/05/2023] [Accepted: 09/12/2023] [Indexed: 09/27/2023] Open
Abstract
Acetylation contributes to the bioactivity of numerous medicinally important natural products. However, little is known about the acetylation on sugar moieties. Here we report a saponin acetyltransferase from Astragalus membranaceus. AmAT7-3 is discovered through a stepwise gene mining approach and characterized as the xylose C3'/C4'-O-acetyltransferse of astragaloside IV (1). To elucidate its catalytic mechanism, complex crystal structures of AmAT7-3/1 and AmAT7-3A310G/1 are obtained, which reveal a large active pocket decided by a specific sequence AADAG. Combining with QM/MM computation, the regiospecificity of AmAT7-3 is determined by sugar positioning modulated by surrounding amino acids including #A310 and #L290. Furthermore, a small mutant library is built using semi-rational design, where variants A310G and A310W are found to catalyze specific C3'-O and C4'-O acetylation, respectively. AmAT7-3 and its variants are also employed to acetylate other bioactive saponins. This work expands the understanding of saponin acetyltransferases, and provide efficient catalytic tools for saponin acetylation.
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Affiliation(s)
- Linlin Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Zhihui Jiang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China
| | - Jiahe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Kuan Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Meng Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Zilong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China.
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.
- Peking University-Yunnan Baiyao International Medical Research Center, 38 Xueyuan Road, Beijing, 100191, China.
| | - Xue Qiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.
- Peking University-Yunnan Baiyao International Medical Research Center, 38 Xueyuan Road, Beijing, 100191, China.
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5
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França TCC, Valle da Silva JA, Dos Santos MC, Cavalcante SFDA, Kuca K. Applications of the Near Attack Conformation (NAC) approach in the search for Acetylcholinesterase reactivators. Chem Biol Interact 2023; 382:110619. [PMID: 37406983 DOI: 10.1016/j.cbi.2023.110619] [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: 04/27/2023] [Revised: 06/25/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
The Near Attack Conformation (NAC) approach states that the efficiency of an enzyme-catalyzed reaction depends on the prior attainment of optimal conditions for substrate atom organization and positioning for bond formation. These conditions are prerequisites for the transition state (TS) in which the involved atoms are within the van der Waals range of contact and positioned at an angle similar to that achieved after bond formation. The successful application of this approach to investigate the reactivation mechanism of acetylcholinesterase inhibited by nerve agents has contributed to a better understanding of this mechanism and demonstrated consistent corroboration with experimental data. In this article, we summarize the accomplishments achieved thus far and outline future perspectives.
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Affiliation(s)
- Tanos Celmar Costa França
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil; Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003, Hradec Kralove, Czech Republic.
| | - Jorge Alberto Valle da Silva
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Marcelo Carneiro Dos Santos
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Samir Frontino de Almeida Cavalcante
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003, Hradec Kralove, Czech Republic; Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, RJ, Brazil
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003, Hradec Kralove, Czech Republic
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6
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Pirillo V, Orlando M, Battaglia C, Pollegioni L, Molla G. Efficient polyethylene terephthalate degradation at moderate temperature: a protein engineering study of LC-cutinase highlights the key role of residue 243. FEBS J 2023. [PMID: 36695006 DOI: 10.1111/febs.16736] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/31/2022] [Accepted: 01/23/2023] [Indexed: 01/26/2023]
Abstract
Enzymatic degradation of poly(ethylene terephthalate) (PET) is becoming a reality because of the identification of novel PET-hydrolysing enzymes (PHEs) and the engineering of evolved enzyme variants. Here, improved variants of leaf-branch compost cutinase (LCC), a thermostable enzyme isolated by a metagenomic approach, were generated by a semi-rational protein engineering approach. Starting from a deleted LCC form lacking the secretion signal (ΔLCC), single and double variants possessing a higher activity on PET were isolated. The single-point F243T ΔLCC variant partially (~ 67%) depolymerized amorphous PET film producing ~ 21.9 mm of products after 27 h of reaction at 72 °C. The S101N/F243T ΔLCC double variant reached a further increase in activity on PET. Notably, for both single and double variants the highest conversion yield was obtained at 55 °C. Kinetics studies and molecular dynamics simulations support that a slight decreased affinity for PET is responsible for the superior degradation performance of the S101N/F243T variant and that this stems from a slightly higher flexibility of the active site region close to position 243. Furthermore, our findings question the need for a high reaction temperature for PET degradation, at least for LCC: at ≥ 70 °C, the conversion of amorphous PET into a more crystalline polymer, resistant to enzymatic hydrolysis, is favoured. The evolved S101N/F243T ΔLCC variant is able to depolymerize fully 1.3 g of untreated postconsumer PET waste in ≤ 3 days at 55 °C (using 1.25 mg of enzyme only), this making PET enzymatic degradation by engineering LCC a more ecofriendly and sustainable process.
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Affiliation(s)
- Valentina Pirillo
- "The Protein Factory 2.0", Department of Biotechnology and Life Sciences (DBSV), University of Insubria, Varese, Italy
| | - Marco Orlando
- "The Protein Factory 2.0", Department of Biotechnology and Life Sciences (DBSV), University of Insubria, Varese, Italy
| | - Caren Battaglia
- "The Protein Factory 2.0", Department of Biotechnology and Life Sciences (DBSV), University of Insubria, Varese, Italy
| | - Loredano Pollegioni
- "The Protein Factory 2.0", Department of Biotechnology and Life Sciences (DBSV), University of Insubria, Varese, Italy
| | - Gianluca Molla
- "The Protein Factory 2.0", Department of Biotechnology and Life Sciences (DBSV), University of Insubria, Varese, Italy
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7
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Pirillo V, Orlando M, Tessaro D, Pollegioni L, Molla G. An Efficient Protein Evolution Workflow for the Improvement of Bacterial PET Hydrolyzing Enzymes. Int J Mol Sci 2021; 23:ijms23010264. [PMID: 35008691 PMCID: PMC8745736 DOI: 10.3390/ijms23010264] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 12/23/2022] Open
Abstract
Enzymatic degradation is a promising green approach to bioremediation and recycling of the polymer poly(ethylene terephthalate) (PET). In the past few years, several PET-hydrolysing enzymes (PHEs) have been discovered, and new variants have been evolved by protein engineering. Here, we report on a straightforward workflow employing semi-rational protein engineering combined to a high-throughput screening of variant libraries for their activity on PET nanoparticles. Using this approach, starting from the double variant W159H/S238F of Ideonella sakaiensis 201-F6 PETase, the W159H/F238A-ΔIsPET variant, possessing a higher hydrolytic activity on PET, was identified. This variant was stabilized by introducing two additional known substitutions (S121E and D186H) generating the TS-ΔIsPET variant. By using 0.1 mg mL−1 of TS-ΔIsPET, ~10.6 mM of degradation products were produced in 2 days from 9 mg mL−1 PET microparticles (~26% depolymerization yield). Indeed, TS-ΔIsPET allowed a massive degradation of PET nanoparticles (>80% depolymerization yield) in 1.5 h using only 20 μg of enzyme mL−1. The rationale underlying the effect on the catalytic parameters due to the F238A substitution was studied by enzymatic investigation and molecular dynamics/docking analysis. The present workflow is a well-suited protocol for the evolution of PHEs to help generate an efficient enzymatic toolbox for polyester degradation.
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Affiliation(s)
- Valentina Pirillo
- “The Protein Factory 2.0”, Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (V.P.); (M.O.)
| | - Marco Orlando
- “The Protein Factory 2.0”, Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (V.P.); (M.O.)
| | - Davide Tessaro
- Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, p.za L. da Vinci 32, 20133 Milano, Italy;
| | - Loredano Pollegioni
- “The Protein Factory 2.0”, Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (V.P.); (M.O.)
- Correspondence: (L.P.); (G.M.)
| | - Gianluca Molla
- “The Protein Factory 2.0”, Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (V.P.); (M.O.)
- Correspondence: (L.P.); (G.M.)
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8
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Diharce J, Bignon E, Fiorucci S, Antonczak S. Exploring Dihydroflavonol-4-Reductase Reactivity and Selectivity by QM/MM-MD Simulations. Chembiochem 2021; 23:e202100553. [PMID: 34859558 DOI: 10.1002/cbic.202100553] [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: 10/14/2021] [Revised: 11/29/2021] [Indexed: 11/12/2022]
Abstract
Flavonoids are secondary metabolites ubiquitously found in plants. Their antioxidant properties make them highly interesting natural compounds for use in pharmacology. Therefore, unravelling the mechanisms of flavonoid biosynthesis is an important challenge. Among all the enzymes involved in this biosynthetic pathway, dihydroflavonol-4-reductase (DFR) plays a key role in the production of anthocyanins and proanthocyanidins. Here, we provide new information on the mechanism of action of this enzyme by using QM/MM-MD simulations applied to both dihydroquercetin (DHQ) and dihydrokaempferol (DHK) substrates. The consideration of these very similar compounds shed light on the major role played by the enzyme on the stabilization of the transition state but also on the activation of the substrate before the reaction through near-attack conformer effects.
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Affiliation(s)
- Julien Diharce
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France.,Université de Paris, INSERM, Biologie Intégrée du Globule Rouge, UMR_S1134, 75015, Paris, France.,Laboratoire d'Excellence GR-Ex, 75015, Paris, France
| | - Emmanuelle Bignon
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
| | - Sébastien Fiorucci
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
| | - Serge Antonczak
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
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9
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Ramírez-Palacios C, Wijma HJ, Thallmair S, Marrink SJ, Janssen DB. Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations. J Chem Inf Model 2021; 61:5569-5580. [PMID: 34653331 PMCID: PMC8611723 DOI: 10.1021/acs.jcim.1c00617] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ω-Transaminases (ω-TAs) catalyze the conversion of ketones to chiral amines, often with high enantioselectivity and specificity, which makes them attractive for industrial production of chiral amines. Tailoring ω-TAs to accept non-natural substrates is necessary because of their limited substrate range. We present a computational protocol for predicting the enantioselectivity and catalytic selectivity of an ω-TA from Vibrio fluvialis with different substrates and benchmark it against 62 compounds gathered from the literature. Rosetta-generated complexes containing an external aldimine intermediate of the transamination reaction are used as starting conformations for multiple short independent molecular dynamics (MD) simulations. The combination of molecular docking and MD simulations ensures sufficient and accurate sampling of the relevant conformational space. Based on the frequency of near-attack conformations observed during the MD trajectories, enantioselectivities can be quantitatively predicted. The predicted enantioselectivities are in agreement with a benchmark dataset of experimentally determined ee% values. The substrate-range predictions can be based on the docking score of the external aldimine intermediate. The low computational cost required to run the presented framework makes it feasible for use in enzyme design to screen thousands of enzyme variants.
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Affiliation(s)
- Carlos Ramírez-Palacios
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Hein J Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sebastian Thallmair
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.,Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, 60438 Frankfurt am Main, Germany
| | - Siewert J Marrink
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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10
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Lyonnais S, Sadiq SK, Lorca-Oró C, Dufau L, Nieto-Marquez S, Escribà T, Gabrielli N, Tan X, Ouizougun-Oubari M, Okoronkwo J, Reboud-Ravaux M, Gatell JM, Marquet R, Paillart JC, Meyerhans A, Tisné C, Gorelick RJ, Mirambeau G. The HIV-1 Nucleocapsid Regulates Its Own Condensation by Phase-Separated Activity-Enhancing Sequestration of the Viral Protease during Maturation. Viruses 2021; 13:v13112312. [PMID: 34835118 PMCID: PMC8625067 DOI: 10.3390/v13112312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023] Open
Abstract
A growing number of studies indicate that mRNAs and long ncRNAs can affect protein populations by assembling dynamic ribonucleoprotein (RNP) granules. These phase-separated molecular ‘sponges’, stabilized by quinary (transient and weak) interactions, control proteins involved in numerous biological functions. Retroviruses such as HIV-1 form by self-assembly when their genomic RNA (gRNA) traps Gag and GagPol polyprotein precursors. Infectivity requires extracellular budding of the particle followed by maturation, an ordered processing of ∼2400 Gag and ∼120 GagPol by the viral protease (PR). This leads to a condensed gRNA-NCp7 nucleocapsid and a CAp24-self-assembled capsid surrounding the RNP. The choreography by which all of these components dynamically interact during virus maturation is one of the missing milestones to fully depict the HIV life cycle. Here, we describe how HIV-1 has evolved a dynamic RNP granule with successive weak–strong–moderate quinary NC-gRNA networks during the sequential processing of the GagNC domain. We also reveal two palindromic RNA-binding triads on NC, KxxFxxQ and QxxFxxK, that provide quinary NC-gRNA interactions. Consequently, the nucleocapsid complex appears properly aggregated for capsid reassembly and reverse transcription, mandatory processes for viral infectivity. We show that PR is sequestered within this RNP and drives its maturation/condensation within minutes, this process being most effective at the end of budding. We anticipate such findings will stimulate further investigations of quinary interactions and emergent mechanisms in crowded environments throughout the wide and growing array of RNP granules.
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Affiliation(s)
- Sébastien Lyonnais
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Centre d’Etudes des Maladies Infectieuses et Pharmacologie Anti-Infectieuse (CEMIPAI), CNRS UAR 3725, Université de Montpellier, 1919 Route de Mende, CEDEX 05, 34293 Montpellier, France
- Correspondence: (S.L.); (S.K.S.); (G.M.)
| | - S. Kashif Sadiq
- Infection Biology Laboratory, Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra, Carrer Doctor Aiguader 88, 08003 Barcelona, Spain;
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence: (S.L.); (S.K.S.); (G.M.)
| | - Cristina Lorca-Oró
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Laure Dufau
- Biological Adaptation and Ageing (B2A), CNRS UMR 8256 & INSERM ERL U1164, Institut de Biologie Paris-Seine (IBPS), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 7 Quai St Bernard, CEDEX 05, 75252 Paris, France; (L.D.); (M.R.-R.)
| | - Sara Nieto-Marquez
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Tuixent Escribà
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Natalia Gabrielli
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Xiao Tan
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Biological Adaptation and Ageing (B2A), CNRS UMR 8256 & INSERM ERL U1164, Institut de Biologie Paris-Seine (IBPS), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 7 Quai St Bernard, CEDEX 05, 75252 Paris, France; (L.D.); (M.R.-R.)
| | - Mohamed Ouizougun-Oubari
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Josephine Okoronkwo
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Michèle Reboud-Ravaux
- Biological Adaptation and Ageing (B2A), CNRS UMR 8256 & INSERM ERL U1164, Institut de Biologie Paris-Seine (IBPS), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 7 Quai St Bernard, CEDEX 05, 75252 Paris, France; (L.D.); (M.R.-R.)
| | - José Maria Gatell
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Facultat de Medicina y Ciencias de la Salud, Universitat de Barcelona, Carrer de Casanova 143, 08036 Barcelona, Spain
| | - Roland Marquet
- Architecture et Réactivité de l’ARN, CNRS UPR 9002, Université de Strasbourg, 2 Allée Conrad Roentgen, 67000 Strasbourg, France; (R.M.); (J.-C.P.)
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l’ARN, CNRS UPR 9002, Université de Strasbourg, 2 Allée Conrad Roentgen, 67000 Strasbourg, France; (R.M.); (J.-C.P.)
| | - Andreas Meyerhans
- Infection Biology Laboratory, Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra, Carrer Doctor Aiguader 88, 08003 Barcelona, Spain;
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys 23, 08010 Barcelona, Spain
| | - Carine Tisné
- Expression Génétique Microbienne, CNRS UMR 8261, Institut de Biologie Physico-Chimique (IBPC), Université de Paris, 13 Rue Pierre et Marie Curie, 75005 Paris, France;
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA;
| | - Gilles Mirambeau
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Biologie Intégrative des Organismes Marins (BIOM), CNRS UMR 7232, Observatoire Océanologique de Banyuls (OOB), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 1 Avenue Pierre Fabre, 66650 Banyuls-sur-Mer, France
- Correspondence: (S.L.); (S.K.S.); (G.M.)
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11
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Sadiq SK, Muñiz Chicharro A, Friedrich P, Wade RC. Multiscale Approach for Computing Gated Ligand Binding from Molecular Dynamics and Brownian Dynamics Simulations. J Chem Theory Comput 2021; 17:7912-7929. [PMID: 34739248 DOI: 10.1021/acs.jctc.1c00673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We develop an approach to characterize the effects of gating by a multiconformation protein consisting of macrostate conformations that are either accessible or inaccessible to ligand binding. We first construct a Markov state model of the apo-protein from atomistic molecular dynamics simulations from which we identify macrostates and their conformations, compute their relative macrostate populations and interchange kinetics, and structurally characterize them in terms of ligand accessibility. We insert the calculated first-order rate constants for conformational transitions into a multistate gating theory from which we derive a gating factor γ that quantifies the degree of conformational gating. Applied to HIV-1 protease, our approach yields a kinetic network of three accessible (semi-open, open, and wide-open) and two inaccessible (closed and a newly identified, "parted") macrostate conformations. The parted conformation sterically partitions the active site, suggesting a possible role in product release. We find that the binding kinetics of drugs and drug-like inhibitors to HIV-1 protease falls in the slow gating regime. However, because γ = 0.75, conformational gating only modestly slows ligand binding. Brownian dynamics simulations of the diffusional association of eight inhibitors to the protease─having a wide range of experimental association constants (∼104-1010 M-1 s-1)─yields gated rate constants in the range of ∼0.5-5.7 × 108 M-1 s-1. This indicates that, whereas the association rate of some inhibitors could be described by the model, for many inhibitors either subsequent conformational transitions or alternate binding mechanisms may be rate-limiting. For systems known to be modulated by conformational gating, the approach could be scaled computationally efficiently to screen association kinetics for a large number of ligands.
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Affiliation(s)
- S Kashif Sadiq
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Infection Biology Unit, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C/Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Abraham Muñiz Chicharro
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Patrick Friedrich
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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12
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Chen Q, Zhang W, Mu W. Molecular Dynamics Simulation for Food Enzyme Engineering: Why This Technique Should Be Encouraged To Learn. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:4-6. [PMID: 33382602 DOI: 10.1021/acs.jafc.0c07681] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Qiuming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
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13
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Liu Y, Xu G, Zhou J, Ni J, Zhang L, Hou X, Yin D, Rao Y, Zhao YL, Ni Y. Structure-Guided Engineering of d-Carbamoylase Reveals a Key Loop at Substrate Entrance Tunnel. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02942] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yafei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Jieyu Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Jie Ni
- Warshel Institute for Computational Biology, School of Life and Health Science, Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
| | - Lu Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Xiaodong Hou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Dejing Yin
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
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14
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Zhou J, Xu G, Ni Y. Stereochemistry in Asymmetric Reduction of Bulky–Bulky Ketones by Alcohol Dehydrogenases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02646] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jieyu Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu, China
| | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu, China
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu, China
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15
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Fine-Tuning of Sequence Specificity by Near Attack Conformations in Enzyme-Catalyzed Peptide Hydrolysis. Catalysts 2020. [DOI: 10.3390/catal10060684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The catalytic role of near attack conformations (NACs), molecular states that lie on the pathway between the ground state (GS) and transition state (TS) of a chemical reaction, is not understood completely. Using a computational approach that combines Bürgi–Dunitz theory with all-atom molecular dynamics simulations, the role of NACs in catalyzing the first stages of HIV-1 protease peptide hydrolysis was previously investigated using a substrate that represents the recognized SP1-NC cleavage site of the HIV-1 Gag polyprotein. NACs were found to confer no catalytic effect over the uncatalyzed reaction there ( Δ Δ G N ‡ ∼ 0 kcal/mol). Here, using the same approach, the role of NACs across multiple substrates that each represent a further recognized cleavage site is investigated. Overall rate enhancement varies by | Δ Δ G ‡ | ∼ 12–15 kcal/mol across this set, and although NACs contribute a small and approximately constant barrier to the uncatalyzed reaction (< Δ G N ‡ u > = 4.3 ± 0.3 kcal/mol), they are found to contribute little significant catalytic effect ( | Δ Δ G N ‡ | ∼ 0–2 kcal/mol). Furthermore, no correlation is exhibited between NAC contributions and the overall energy barrier ( R 2 = 0.01). However, these small differences in catalyzed NAC contributions enable rates to match those required for the kinetic order of processing. Therefore, NACs may offer an alternative and subtle mode compared to non-NAC contributions for fine-tuning reaction rates during complex evolutionary sequence selection processes—in this case across cleavable polyproteins whose constituents exhibit multiple functions during the virus life-cycle.
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16
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Kumar M, Mandal K, Blakeley MP, Wymore T, Kent SBH, Louis JM, Das A, Kovalevsky A. Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design. ACS OMEGA 2020; 5:11605-11617. [PMID: 32478251 PMCID: PMC7254801 DOI: 10.1021/acsomega.0c00835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
HIV-1 protease is indispensable for virus propagation and an important therapeutic target for antiviral inhibitors to treat AIDS. As such inhibitors are transition-state mimics, a detailed understanding of the enzyme mechanism is crucial for the development of better anti-HIV drugs. Here, we used room-temperature joint X-ray/neutron crystallography to directly visualize hydrogen atoms and map hydrogen bonding interactions in a protease complex with peptidomimetic inhibitor KVS-1 containing a reactive nonhydrolyzable ketomethylene isostere, which, upon reacting with the catalytic water molecule, is converted into a tetrahedral intermediate state, KVS-1TI. We unambiguously determined that the resulting tetrahedral intermediate is an oxyanion, rather than the gem-diol, and both catalytic aspartic acid residues are protonated. The oxyanion tetrahedral intermediate appears to be unstable, even though the negative charge on the oxyanion is delocalized through a strong n → π* hyperconjugative interaction into the nearby peptidic carbonyl group of the inhibitor. To better understand the influence of the ketomethylene isostere as a protease inhibitor, we have also examined the protease structure and binding affinity with keto-darunavir (keto-DRV), which similar to KVS-1 includes the ketomethylene isostere. We show that keto-DRV is a significantly less potent protease inhibitor than DRV. These findings shed light on the reaction mechanism of peptide hydrolysis catalyzed by HIV-1 protease and provide valuable insights into further improvements in the design of protease inhibitors.
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Affiliation(s)
- Mukesh Kumar
- Protein Crystallography
Section, Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Kalyaneswar Mandal
- Departments of Chemistry, and Biochemistry and Molecular Biology,
Institute for Biophysical Dynamics, University
of Chicago, Chicago, Illinois 60637, United States
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue−Langevin, 38000 Grenoble, France
| | - Troy Wymore
- Department of Chemistry, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Stephen B. H. Kent
- Departments of Chemistry, and Biochemistry and Molecular Biology,
Institute for Biophysical Dynamics, University
of Chicago, Chicago, Illinois 60637, United States
| | - John M. Louis
- Laboratory of Chemical Physics, National
Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, United States
| | - Amit Das
- Protein Crystallography
Section, Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Andrey Kovalevsky
- Neutron Scattering
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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17
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Reactivation of VX-Inhibited Human Acetylcholinesterase by Deprotonated Pralidoxime. A Complementary Quantum Mechanical Study. Biomolecules 2020; 10:biom10020192. [PMID: 32012780 PMCID: PMC7072650 DOI: 10.3390/biom10020192] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 01/25/2023] Open
Abstract
In the present work, we performed a complementary quantum mechanical (QM) study to describe the mechanism by which deprotonated pralidoxime (2-PAM) could reactivate human (Homo sapiens sapiens) acetylcholinesterase (HssAChE) inhibited by the nerve agent VX. Such a reaction is proposed to occur in subsequent addition-elimination steps, starting with a nucleophile bimolecular substitution (SN2) mechanism through the formation of a trigonal bipyramidal transition state (TS). A near attack conformation (NAC), obtained in a former study using molecular mechanics (MM) calculations, was taken as a starting point for this project, where we described the possible formation of the TS. Together, this combined QM/MM study on AChE reactivation shows the feasibility of the reactivation occurring via attack of the deprotonated form of 2-PAM against the Ser203-VX adduct of HssAChE.
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18
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von der Esch B, Dietschreit JCB, Peters LDM, Ochsenfeld C. Finding Reactive Configurations: A Machine Learning Approach for Estimating Energy Barriers Applied to Sirtuin 5. J Chem Theory Comput 2019; 15:6660-6667. [PMID: 31765138 DOI: 10.1021/acs.jctc.9b00876] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sirtuin 5 is a class III histone deacetylase that, unlike its classification, mainly catalyzes desuccinylation and demanoylation reactions. It is an interesting drug target that we use here to test new ideas for calculating reaction pathways of large molecular systems such as enzymes. A major issue with most schemes (e.g., adiabatic mapping) is that the resulting activation barrier height heavily depends on the chosen educt conformation. This makes the selection of the initial structure decisive for the success of the characterization. Here, we apply machine learning to a large number of molecular dynamics frames and potential energy barriers obtained by quantum mechanics/molecular mechanics calculations in order to identify (1) suitable start-conformations for reaction path calculations and (2) structural features relevant for the first step of the desuccinylation reaction catalyzed by Sirtuin 5. The latter generally aids the understanding of reaction mechanisms and important interactions in active centers. Using our novel approach, we found eleven key features that govern the reactivity. We were able to estimate reaction barriers with a mean absolute error of 3.6 kcal/mol and identified reactive configurations.
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Affiliation(s)
- Beatriz von der Esch
- Chair of Theoretical Chemistry, Department of Chemistry , University of Munich (LMU) , Butenandtstr. 7 , D-81377 München , Germany
| | - Johannes C B Dietschreit
- Chair of Theoretical Chemistry, Department of Chemistry , University of Munich (LMU) , Butenandtstr. 7 , D-81377 München , Germany
| | - Laurens D M Peters
- Chair of Theoretical Chemistry, Department of Chemistry , University of Munich (LMU) , Butenandtstr. 7 , D-81377 München , Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry , University of Munich (LMU) , Butenandtstr. 7 , D-81377 München , Germany
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19
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Bag S, Maiti PK. Tuning molecular fluctuation to boost the conductance in DNA based molecular wires. Phys Chem Chem Phys 2019; 21:23514-23520. [PMID: 31617554 DOI: 10.1039/c9cp03589c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Inherent molecular fluctuations are known to have a significant influence on the charge transport properties of biomolecules like DNA, PNA and proteins. In this work, we show ways to control these fluctuations and further demonstrate their use to enhance the conductance of two widely studied molecular wires, namely dsDNA (DNA) and G4 Quadruplex (G4-Quad). We quantify the molecular fluctuation in terms of the root mean square deviation (RMSD) of the molecule. In the case of DNA, we use temperature to control the fluctuations, while in the case of G4-Quad the fluctuations are tuned by the ions inside the pore. The electronic coupling between the bases of dsDNA and G4-Quad, which measures the conductance of these molecular wires, shows a non-monotonic behaviour with the increase in fluctuation. We find values of fluctuation which give rise to maximum electronic coupling and hence high conductivity for both the cases. In the case of DNA, these optimal fluctuations (∼2.5 Å) are achieved at a temperature of 210 K, which gives rise to an electronic coupling of 0.135 eV between the DNA bases. The optimal fluctuations in G4-Quad are achieved (∼7 Å) in a 4 base pair long system with 2 Na+ ions inside the pore, giving rise to an electronic coupling of 0.09 eV.
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Affiliation(s)
- Saientan Bag
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, Karnataka, India.
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20
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Ferrario V, Fischer M, Zhu Y, Pleiss J. Modelling of substrate access and substrate binding to cephalosporin acylases. Sci Rep 2019; 9:12402. [PMID: 31455800 PMCID: PMC6712217 DOI: 10.1038/s41598-019-48849-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/14/2019] [Indexed: 01/16/2023] Open
Abstract
Semisynthetic cephalosporins are widely used antibiotics currently produced by different chemical steps under harsh conditions, which results in a considerable amount of toxic waste. Biocatalytic synthesis by the cephalosporin acylase from Pseudomonas sp. strain N176 is a promising alternative. Despite intensive engineering of the enzyme, the catalytic activity is still too low for a commercially viable process. To identify the bottlenecks which limit the success of protein engineering efforts, a series of MD simulations was performed to study for two acylase variants (WT, M6) the access of the substrate cephalosporin C from the bulk to the active site and the stability of the enzyme-substrate complex. In both variants, cephalosporin C was binding to a non-productive substrate binding site (E86α, S369β, S460β) at the entrance to the binding pocket, preventing substrate access. A second non-productive binding site (G372β, W376β, L457β) was identified within the binding pocket, which competes with the active site for substrate binding. Noteworthy, substrate binding to the protein surface followed a Langmuir model resulting in binding constants K = 7.4 and 9.2 mM for WT and M6, respectively, which were similar to the experimentally determined Michaelis constants KM = 11.0 and 8.1 mM, respectively.
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Affiliation(s)
- Valerio Ferrario
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Mona Fischer
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Yushan Zhu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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21
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da Silva JAV, Nepovimova E, Ramalho TC, Kuca K, Costa França TC. Molecular modelling studies on the interactions of 7-methoxytacrine-4-pyridinealdoxime with VX-inhibited human acetylcholinesterase. A near attack approach to assess different spacer-lengths. Chem Biol Interact 2019; 307:195-205. [DOI: 10.1016/j.cbi.2019.05.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/18/2019] [Accepted: 05/13/2019] [Indexed: 10/26/2022]
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22
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da Silva JAV, Nepovimova E, Ramalho TC, Kuca K, Celmar Costa França T. Molecular modeling studies on the interactions of 7-methoxytacrine-4-pyridinealdoxime, 4-PA, 2-PAM, and obidoxime with VX-inhibited human acetylcholinesterase: a near attack conformation approach. J Enzyme Inhib Med Chem 2019; 34:1018-1029. [PMID: 31074292 PMCID: PMC6522925 DOI: 10.1080/14756366.2019.1609953] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
7-methoxytacrine-4-pyridinealdoxime (7-MEOTA-4-PA, named hybrid 5C) is a compound formerly synthesized and evaluated in vitro, together with 4-pyridine aldoxime (4-PA) and commercial reactivators of acetylcholinesterase (AChE). This compound was designed with the purpose of being a prophylactic reactivator, capable of interacting with different subdomains of the active site of AChE. To investigate these interactions, theoretical results from docking were first compared with experimental data of hybrid 5C, 4-PA, and two commercial oximes, on the reactivation of human AChE (HssAChE) inhibited by VX. Then, further docking studies, molecular dynamics simulations, and molecular mechanics Poisson–Boltzmann surface area calculations, were carried out to investigate reactivation performances, considering the near attack conformation (NAC) approach, prior to the nucleophilic substitution mechanism. Our results helped to elucidate the interactions of such molecules with the different subdomains of the active site of HssAChE. Additionally, NAC poses of each oxime were suggested for further theoretical studies on the reactivation reaction.
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Affiliation(s)
- Jorge Alberto Valle da Silva
- a Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Department of Chemical Engineering , Military Institute of Engineering , Rio de Janeiro/RJ , Brazil
| | - Eugenie Nepovimova
- b Faculty of Science, Department of Chemistry , University of Hradec Kralove , Hradec Kralove , Czech Republic
| | - Teodorico Castro Ramalho
- b Faculty of Science, Department of Chemistry , University of Hradec Kralove , Hradec Kralove , Czech Republic.,c Laboratory of Molecular Modeling, Chemistry Department , Federal University of Lavras , Lavras , Brazil
| | - Kamil Kuca
- b Faculty of Science, Department of Chemistry , University of Hradec Kralove , Hradec Kralove , Czech Republic
| | - Tanos Celmar Costa França
- a Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Department of Chemical Engineering , Military Institute of Engineering , Rio de Janeiro/RJ , Brazil.,b Faculty of Science, Department of Chemistry , University of Hradec Kralove , Hradec Kralove , Czech Republic
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23
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Bonk B, Weis JW, Tidor B. Machine Learning Identifies Chemical Characteristics That Promote Enzyme Catalysis. J Am Chem Soc 2019; 141:4108-4118. [PMID: 30761897 PMCID: PMC6407039 DOI: 10.1021/jacs.8b13879] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Indexed: 11/28/2022]
Abstract
Despite tremendous progress in understanding and engineering enzymes, knowledge of how enzyme structures and their dynamics induce observed catalytic properties is incomplete, and capabilities to engineer enzymes fall far short of industrial needs. Here, we investigate the structural and dynamic drivers of enzyme catalysis for the rate-limiting step of the industrially important enzyme ketol-acid reductoisomerase (KARI) and identify a region of the conformational space of the bound enzyme-substrate complex that, when populated, leads to large increases in reactivity. We apply computational statistical mechanical methods that implement transition interface sampling to simulate the kinetics of the reaction and combine this with machine learning techniques from artificial intelligence to select features relevant to reactivity and to build predictive models for reactive trajectories. We find that conformational descriptors alone, without the need for dynamic ones, are sufficient to predict reactivity with greater than 85% accuracy (90% AUC). Key descriptors distinguishing reactive from almost-reactive trajectories quantify substrate conformation, substrate bond polarization, and metal coordination geometry and suggest their role in promoting substrate reactivity. Moreover, trajectories constrained to visit a region of the reactant well, separated from the rest by a simple hyperplane defined by ten conformational parameters, show increases in computed reactivity by many orders of magnitude. This study provides evidence for the existence of reactivity promoting regions within the conformational space of the enzyme-substrate complex and develops methodology for identifying and validating these particularly reactive regions of phase space. We suggest that identification of reactivity promoting regions and re-engineering enzymes to preferentially populate them may lead to significant rate enhancements.
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Affiliation(s)
- Brian
M. Bonk
- Department
of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - James W. Weis
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computational
and Systems Biology, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bruce Tidor
- Department
of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computational
and Systems Biology, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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24
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Freindorf M, Tao Y, Sethio D, Cremer D, Kraka E. New mechanistic insights into the Claisen rearrangement of chorismate – a Unified Reaction Valley Approach study. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1530464] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Daniel Sethio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
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25
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Xiong J, Zhang C, Xu D. Catalytic mechanism of type C sialidase from Streptococcus pneumoniae: from covalent intermediate to final product. J Mol Model 2018; 24:297. [PMID: 30259133 DOI: 10.1007/s00894-018-3822-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/04/2018] [Indexed: 12/24/2022]
Abstract
Streptococcus pneumoniae is a Gram-positive human pathogenic bacterium, which is the main cause of pneumonia and meningitis in children and the elderly. Three sialidases (or neuraminidases) encoded from Streptococcus pneumoniae could catalyze the cleavage of sialic acid linkages. This mechanism is directly connected with infection, apoptosis, and signaling, and usually considered to be one of the critical virulence factors. Type C neuraminidase (NanC) is unique because its primary product of Neu5Ac2en is considered to be an inhibitor to the other two sialidases. Experimentally, there are two different pathways for the formation mechanism of Neu5Ac2en catalyzed by NanC. In this work, a combined quantum mechanical and molecular mechanical approach was employed in all calculations. Starting from the covalent sialylated intermediate, we first examined the reaction to Neu5Ac2en and found the reaction prefers a direct proton abstraction mechanism rather than the water mediated proton abstraction mechanism. Free energy profiles can confirm that Neu5Ac2en is the major product of NanC. Functional roles of some important residues were also investigated, e.g., D315 acts as the proton acceptor during the formation of Neu5Ac2en, while the general base for the hydrolytic reaction to Neu5Ac. This study can facilitate the understanding of the catalytic mechanism of NanC and has the potential to aid in future inhibitor design studies.
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Affiliation(s)
- Jing Xiong
- MOE Key Laboratory of Green Chemistry & Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China
- School of Pharmacy, Chengdu Medical College, Chengdu, Sichuan, 610500, People's Republic of China
| | - Chunchun Zhang
- Analytical&Testing Center, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China.
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry & Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China.
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26
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Maurer D, Enugala TR, Hamnevik E, Bauer P, Lüking M, Petrović D, Hillier H, Kamerlin SCL, Dobritzsch D, Widersten M. Stereo- and Regioselectivity in Catalyzed Transformation of a 1,2-Disubstituted Vicinal Diol and the Corresponding Diketone by Wild Type and Laboratory Evolved Alcohol Dehydrogenases. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01762] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Dirk Maurer
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Thilak Reddy Enugala
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Emil Hamnevik
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Paul Bauer
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
- Biophysics, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden
| | - Malin Lüking
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Dušan Petrović
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Heidi Hillier
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Doreen Dobritzsch
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Mikael Widersten
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
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27
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Abstract
Synthetic polymers are ubiquitous in the modern world but pose a global environmental problem. While plastics such as poly(ethylene terephthalate) (PET) are highly versatile, their resistance to natural degradation presents a serious, growing risk to fauna and flora, particularly in marine environments. Here, we have characterized the 3D structure of a newly discovered enzyme that can digest highly crystalline PET, the primary material used in the manufacture of single-use plastic beverage bottles, in some clothing, and in carpets. We engineer this enzyme for improved PET degradation capacity and further demonstrate that it can also degrade an important PET replacement, polyethylene-2,5-furandicarboxylate, providing new opportunities for biobased plastics recycling. Poly(ethylene terephthalate) (PET) is one of the most abundantly produced synthetic polymers and is accumulating in the environment at a staggering rate as discarded packaging and textiles. The properties that make PET so useful also endow it with an alarming resistance to biodegradation, likely lasting centuries in the environment. Our collective reliance on PET and other plastics means that this buildup will continue unless solutions are found. Recently, a newly discovered bacterium, Ideonella sakaiensis 201-F6, was shown to exhibit the rare ability to grow on PET as a major carbon and energy source. Central to its PET biodegradation capability is a secreted PETase (PET-digesting enzyme). Here, we present a 0.92 Å resolution X-ray crystal structure of PETase, which reveals features common to both cutinases and lipases. PETase retains the ancestral α/β-hydrolase fold but exhibits a more open active-site cleft than homologous cutinases. By narrowing the binding cleft via mutation of two active-site residues to conserved amino acids in cutinases, we surprisingly observe improved PET degradation, suggesting that PETase is not fully optimized for crystalline PET degradation, despite presumably evolving in a PET-rich environment. Additionally, we show that PETase degrades another semiaromatic polyester, polyethylene-2,5-furandicarboxylate (PEF), which is an emerging, bioderived PET replacement with improved barrier properties. In contrast, PETase does not degrade aliphatic polyesters, suggesting that it is generally an aromatic polyesterase. These findings suggest that additional protein engineering to increase PETase performance is realistic and highlight the need for further developments of structure/activity relationships for biodegradation of synthetic polyesters.
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28
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Santos-Martins D, Calixto AR, Fernandes PA, Ramos MJ. A Buried Water Molecule Influences Reactivity in α-Amylase on a Subnanosecond Time Scale. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04400] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Diogo Santos-Martins
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Ana R. Calixto
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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29
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Cáceres TB, Thakur A, Price OM, Ippolito N, Li J, Qu J, Acevedo O, Hevel JM. Phe71 in Type III Trypanosomal Protein Arginine Methyltransferase 7 (TbPRMT7) Restricts the Enzyme to Monomethylation. Biochemistry 2018; 57:1349-1359. [PMID: 29378138 DOI: 10.1021/acs.biochem.7b01265] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein arginine methyltransferase 7 (PRMT7) is unique within the PRMT family as it is the only isoform known to exclusively make monomethylarginine (MMA). Given its role in epigenetics, the mechanistic basis for the strict monomethylation activity is under investigation. It is thought that PRMT7 enzymes are unable to add a second methyl group because of steric hindrance in the active site that restricts them to monomethylation. To test this, we probed the active site of trypanosomal PRMT7 (TbPRMT7) using accelerated molecular dynamics, site-directed mutagenesis, kinetic, binding, and product analyses. Both the dynamics simulations and experimental results show that the mutation of Phe71 to Ile converts the enzyme from a type III methyltransferase into a mixed type I/II, that is, an enzyme that can now perform dimethylation. In contrast, the serine and alanine mutants of Phe71 preserve the type III behavior of the native enzyme. These results are inconsistent with a sterics-only model to explain product specificity. Instead, molecular dynamics simulations of these variants bound to peptides show hydrogen bonding between would-be substrates and Glu172 of TbPRMT7. Only in the case of the Phe71 to Ile mutation is this interaction between MMA and the enzyme maintained, and the geometry for optimal SN2 methyl transfer is obtained. The results of these studies highlight the benefit of combined computational and experimental methods in providing a better understanding for how product specificity is dictated by PRMTs.
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Affiliation(s)
- Tamar B Cáceres
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Abhishek Thakur
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Owen M Price
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Nicole Ippolito
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Jun Li
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York , Kapoor 318, North Campus, Buffalo, New York 14260, United States.,New York State Center of Excellence in Bioinformatics and Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York , Kapoor 318, North Campus, Buffalo, New York 14260, United States.,New York State Center of Excellence in Bioinformatics and Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Orlando Acevedo
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Joan M Hevel
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
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30
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Miranda-Rojas S, Fernández I, Kästner J, Toro-Labbé A, Mendizábal F. Unraveling the Nature of the Catalytic Power of Fluoroacetate Dehalogenase. ChemCatChem 2018. [DOI: 10.1002/cctc.201701517] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sebastián Miranda-Rojas
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas; Universidad Andres Bello; Av. República 275 Santiago Chile
| | - Israel Fernández
- Departamento de Química Orgánica I and Centro de Innovación en, Química Avanzada (ORFEO-CINQA); Facultad de Ciencias Químicas; Universidad Complutense de Madrid; 28040- Madrid Spain
| | - Johannes Kästner
- Institut für Theoretische Chemie; Universität Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional; Facultad de Química; Pontifica Universidad Católica de Chile; Av. Vicuña Mackenna 4860, Macul Santiago Chile
| | - Fernando Mendizábal
- Departamento de Química; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425, Ñuñoa Santiago Chile
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31
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Ortiz-Soto ME, Possiel C, Görl J, Vogel A, Schmiedel R, Seibel J. Impaired coordination of nucleophile and increased hydrophobicity in the +1 subsite shift levansucrase activity towards transfructosylation. Glycobiology 2017; 27:755-765. [PMID: 28575294 PMCID: PMC5881714 DOI: 10.1093/glycob/cwx050] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 12/26/2022] Open
Abstract
Bacterial levansucrases produce β(2,6)-linked levan-type polysaccharides using sucrose or sucrose analogs as donor/acceptor substrates. However, the dominant reaction of Bacillus megaterium levansucrase (Bm-LS) is hydrolysis. Single domain levansucrases from Gram-positive bacteria display a wide substrate-binding pocket with open access to water, challenging engineering for transfructosylation-efficient enzymes. We pursued a shift in reaction specificity by either modifying the water distribution in the active site or the coordination of the catalytic acid/base (E352) and the nucleophile (D95), thus affecting the fructosyl-transfer rate and allowing acceptors other than water to occupy the active site. Two serine (173/422) and two water-binding tyrosine (421/439) residues located in the first shell of the catalytic pocket were modified. Library variants of S173, Y421 and S422, which coordinate the position of D95 and E352, show increased transfructosylation (30–200%) and modified product spectra. Substitutions at position 422 have a higher impact on sucrose affinity, while changes at position 173 and 421 have a strong effect on the overall catalytic rate. As most retaining glycoside hydrolases (GHs) Bm-LS catalyzes hydrolysis and transglycosylation via a double displacement reaction involving two-transition states (TS1 and TS2). Hydrogen bonds of D95 with the side chains of S173 and S422 contribute a total of 2.4 kcal mol−1 to TS1 stabilization, while hydrogen bonds between invariant Y421, E352 and the glucosyl C-2 hydroxyl-group of sucrose contribute 2.15 kcal mol−1 stabilization. Changes at Y439 render predominantly hydrolytic variants synthesizing shorter oligosaccharides.
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Affiliation(s)
- Maria Elena Ortiz-Soto
- Institute of Organic Chemistry, University of Würzburg, Würzburg, Am Hubland 97074, Germany
| | - Christian Possiel
- Institute of Organic Chemistry, University of Würzburg, Würzburg, Am Hubland 97074, Germany
| | - Julian Görl
- Institute of Organic Chemistry, University of Würzburg, Würzburg, Am Hubland 97074, Germany
| | - Andreas Vogel
- c-LEcta GmbH, Leipzig, Perlickstr. 5, 04103, Germany
| | | | - Jürgen Seibel
- Institute of Organic Chemistry, University of Würzburg, Würzburg, Am Hubland 97074, Germany
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32
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Gathiaka S, Boykin B, Cáceres T, Hevel JM, Acevedo O. Understanding protein arginine methyltransferase 1 (PRMT1) product specificity from molecular dynamics. Bioorg Med Chem 2016; 24:4949-4960. [DOI: 10.1016/j.bmc.2016.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/04/2016] [Accepted: 08/06/2016] [Indexed: 10/21/2022]
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33
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Guo P, Lei X, Gao Y. Conformational flexibility of PPII-helix: A density functional theory study. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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34
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Ribeiro AJM, Santos-Martins D, Russo N, Ramos MJ, Fernandes PA. Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00759] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- António J. M. Ribeiro
- UCBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Dipartimento
di Chimica, Università della Calabria, 87036 Arcavacata
di Rende, Italia
| | - Diogo Santos-Martins
- UCBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Nino Russo
- Dipartimento
di Chimica, Università della Calabria, 87036 Arcavacata
di Rende, Italia
| | - Maria J. Ramos
- UCBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
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