1
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Jacquet P, Billot R, Shimon A, Hoekstra N, Bergonzi C, Jenks A, Chabrière E, Daudé D, Elias MH. Changes in Active Site Loop Conformation Relate to the Transition toward a Novel Enzymatic Activity. JACS AU 2024; 4:1941-1953. [PMID: 38818068 PMCID: PMC11134384 DOI: 10.1021/jacsau.4c00179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 06/01/2024]
Abstract
Enzymatic promiscuity, the ability of enzymes to catalyze multiple, distinct chemical reactions, has been well documented and is hypothesized to be a major driver of the emergence of new enzymatic functions. Yet, the molecular mechanisms involved in the transition from one activity to another remain debated and elusive. Here, we evaluated the redesign of the active site binding cleft of lactonase SsoPox using structure-based design and combinatorial libraries. We created variants with largely improved catalytic abilities against phosphotriesters, the best ones being >1000-fold better compared to the wild-type enzyme. The observed shifts in activity specificity are large, and some variants completely lost their initial activity. The selected combinations of mutations have considerably reshaped the active site cavity via side chain changes but mostly through large rearrangements of the active site loops and changes to their conformations, as revealed by a suite of crystal structures. This suggests that a specific active site loop configuration is critical to the lactonase activity. Interestingly, analysis of high-resolution structures hints at the potential role of conformational sampling and its directionality in defining the enzyme activity profile.
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Affiliation(s)
| | - Raphaël Billot
- Gene&GreenTK, 19-21 Bd Jean Moulin, Marseille 13005, France
| | - Amir Shimon
- Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Nathan Hoekstra
- Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Céline Bergonzi
- Gene&GreenTK, 19-21 Bd Jean Moulin, Marseille 13005, France
- Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Anthony Jenks
- Department
of Biochemistry, Molecular Biology and Biophysics & Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Eric Chabrière
- Gene&GreenTK, 19-21 Bd Jean Moulin, Marseille 13005, France
- Aix
Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille 13005, France
| | - David Daudé
- Gene&GreenTK, 19-21 Bd Jean Moulin, Marseille 13005, France
| | - Mikael H. Elias
- Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
- Department
of Biochemistry, Molecular Biology and Biophysics & Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
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2
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Brissos V, Borges PT, Sancho F, Lucas MF, Frazão C, Conzuelo F, Martins LO. Flexible active-site loops fine-tune substrate specificity of hyperthermophilic metallo-oxidases. J Biol Inorg Chem 2024; 29:339-351. [PMID: 38227199 PMCID: PMC11111587 DOI: 10.1007/s00775-023-02040-y] [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: 06/12/2023] [Accepted: 11/21/2023] [Indexed: 01/17/2024]
Abstract
Hyperthermophilic ('superheat-loving') archaea found in high-temperature environments such as Pyrobaculum aerophilum contain multicopper oxidases (MCOs) with remarkable efficiency for oxidizing cuprous and ferrous ions. In this work, directed evolution was used to expand the substrate specificity of P. aerophilum McoP for organic substrates. Six rounds of error-prone PCR and DNA shuffling followed by high-throughput screening lead to the identification of a hit variant with a 220-fold increased efficiency (kcat/Km) than the wild-type for 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) without compromising its intrinsic activity for metal ions. The analysis of the X-ray crystal structure reveals four proximal mutations close to the T1Cu active site. One of these mutations is within the 23-residues loop that occludes this site, a distinctive feature of prokaryotic MCOs. The increased flexibility of this loop results in an enlarged tunnel and one additional pocket that facilitates bulky substrate-enzyme interactions. These findings underscore the synergy between mutations that modulate the dynamics of the active-site loop enabling enhanced catalytic function. This study highlights the potential of targeting loops close to the T1Cu for engineering improvements suitable for biotechnological applications.
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Affiliation(s)
- Vânia Brissos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Ferran Sancho
- Zymvol Biomodeling, C/ Pau Claris, 94, 3B, 08010, Barcelona, Spain
| | | | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Felipe Conzuelo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Lígia O Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal.
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3
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Lavrinenko IA, Vashanov GA, Hernández Cáceres JL, Nechipurenko YD. Mathematical models describing oxygen binding by hemoglobin. Biophys Rev 2023; 15:1269-1278. [PMID: 37974982 PMCID: PMC10643423 DOI: 10.1007/s12551-023-01110-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/03/2023] [Indexed: 11/19/2023] Open
Abstract
Despite the fact that the investigation of the structural and functional properties of hemoglobin dates back more than 150 years, the topic has not lost its relevance today. The most important component of these studies is the development of mathematical models that formalize and generalize the mechanisms determining the cooperative binding of ligands based on data on the structural and functional state of the protein. In this work, we review the mathematical relationships describing oxygen binding by hemoglobin, ranging from the classical Hüfner, Hill, and Adair equations to the Szabo-Karplus and tertiary two-state mathematical models based on the Monod-Wyman-Changeux and Koshland-Némethy-Filmer concepts. The generality of the considered equations as mathematical functions, bearing in their basis a power dependence, is demonstrated. The problems and possible solutions related to approximation of experimental data by the oxygenation equations with correlated fitting parameters are noted. Attention is paid to empirical equations, extended versions of the Hill equation, where the coefficient of cooperation is modulated by Gauss and Lorentz distributions as functions of partial oxygen pressure.
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Affiliation(s)
- Igor A. Lavrinenko
- Department of Human and Animal Physiology, Voronezh State University, Voronezh, 394018 Russia
| | - Gennady A. Vashanov
- Department of Human and Animal Physiology, Voronezh State University, Voronezh, 394018 Russia
| | | | - Yury D. Nechipurenko
- Laboratory of DNA-Protein Interactions, Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991 Russia
- Laboratory of Molecular and Cellular Biophysics, Sevastopol State University, Sevastopol, 299053 Russia
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4
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Yamaguchi H, Takahashi K, Tatsumi M, Tagami U, Mizukoshi T, Miyano H, Sugiki M. Development of a novel single-chain l-glutamate oxidase from Streptomyces sp. X-119-6 by inserting flexible linkers. Enzyme Microb Technol 2023; 170:110287. [PMID: 37487431 DOI: 10.1016/j.enzmictec.2023.110287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/26/2023]
Abstract
L-glutamate oxidase (LGOX, EC: 1.4.3.11) is an oxidoreductase that catalyzes L-glutamate deamination. LGOX from Streptomyces sp. X-119-6 is used widely for L-glutamate quantification in research and industrial applications. This enzyme encoded as a single precursor chain that undergoes post-translational cleavage to four fragments by an endogenous protease to become highly active. Efficient preparation of active LGOX by heterologous expression without proteolysis process should be indispensable for wide application of this enzyme. Thus, developing an LGOX that requires no protease treatment should expand the potential applications of recombinant LGOX. In this report, we succeeded in obtaining an active single-chain LGOX by connecting the four fragments of the mature form with insertion of flexible linkers. The most active single-chain mutant showed the similar activity to that of the mature form from Streptomyces sp. X-119-6. The structure of this mutant was determined at 2.9 Å resolution by X-ray crystallography. It was revealed that this single-stranded mutant had the similar conformation to that of mature form. This single-chain LGOX can be produced efficiently and should expand LGOX applications.
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Affiliation(s)
- Hiroki Yamaguchi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan.
| | - Kazutoshi Takahashi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan
| | - Moemi Tatsumi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan
| | - Uno Tagami
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan
| | - Toshimi Mizukoshi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan
| | - Hiroshi Miyano
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan
| | - Masayuki Sugiki
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan.
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5
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Smerkolj J, Stojan J, Bavec A, Goličnik M. Substrate-dependent inactivation of recombinant paraoxonase 1 during catalytic dihydrocoumarin turnover and the protective properties of surfactants. Chem Biol Interact 2023; 382:110563. [PMID: 37286155 DOI: 10.1016/j.cbi.2023.110563] [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: 03/30/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 06/09/2023]
Abstract
Human paraoxonase-1 (PON1) is the most studied member of the paraoxonases (PONs) family and catalyzes the hydrolysis of various substrates (lactones, aryl esters, and paraoxon). Numerous studies link PON1 to oxidative stress-related diseases such as cardiovascular disease, diabetes, HIV infection, autism, Parkinson's, and Alzheimer's, where the kinetic behavior of an enzyme is characterized by initial rates or by modern methods that obtain enzyme kinetic parameters by fitting the computed curves over the entire time-courses of product formation (progress curves). In the analysis of progress curves, the behavior of PON1 during hydrolytically catalyzed turnover cycles is unknown. Hence, progress curves for enzyme-catalyzed hydrolysis of the lactone substrate dihydrocoumarin (DHC) by recombinant PON1 (rePON1) were analyzed to investigate the effect of catalytic DHC turnover on the stability of rePON1. Although rePON1 was significantly inactivated during the catalytic DHC turnover, its activity was not lost due to the product inhibition or spontaneous inactivation of rePON1 in the sample buffers. Examination of the progress curves of DHC hydrolysis by rePON1 led to the conclusion that rePON1 inactivates itself during catalytic DHC turnover hydrolysis. Moreover, human serum albumin or surfactants protected rePON1 from inactivation during this catalytic process, which is significant because the activity of PON1 in clinical samples is measured in the presence of albumin.
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Affiliation(s)
- Janez Smerkolj
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI 1000, Ljubljana, Slovenia
| | - Jure Stojan
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI 1000, Ljubljana, Slovenia
| | - Aljoša Bavec
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI 1000, Ljubljana, Slovenia
| | - Marko Goličnik
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI 1000, Ljubljana, Slovenia.
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6
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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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7
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Corbella M, Pinto GP, Kamerlin SCL. Loop dynamics and the evolution of enzyme activity. Nat Rev Chem 2023; 7:536-547. [PMID: 37225920 DOI: 10.1038/s41570-023-00495-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2023] [Indexed: 05/26/2023]
Abstract
In the early 2000s, Tawfik presented his 'New View' on enzyme evolution, highlighting the role of conformational plasticity in expanding the functional diversity of limited repertoires of sequences. This view is gaining increasing traction with increasing evidence of the importance of conformational dynamics in both natural and laboratory evolution of enzymes. The past years have seen several elegant examples of harnessing conformational (particularly loop) dynamics to successfully manipulate protein function. This Review revisits flexible loops as critical participants in regulating enzyme activity. We showcase several systems of particular interest: triosephosphate isomerase barrel proteins, protein tyrosine phosphatases and β-lactamases, while briefly discussing other systems in which loop dynamics are important for selectivity and turnover. We then discuss the implications for engineering, presenting examples of successful loop manipulation in either improving catalytic efficiency, or changing selectivity completely. Overall, it is becoming clearer that mimicking nature by manipulating the conformational dynamics of key protein loops is a powerful method of tailoring enzyme activity, without needing to target active-site residues.
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Affiliation(s)
- Marina Corbella
- Department of Chemistry, Uppsala University, Uppsala, Sweden
| | - Gaspar P Pinto
- Department of Chemistry, Uppsala University, Uppsala, Sweden
- Cortex Discovery GmbH, Regensburg, Germany
| | - Shina C L Kamerlin
- Department of Chemistry, Uppsala University, Uppsala, Sweden.
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
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8
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Maatouk M, Merhej V, Pontarotti P, Ibrahim A, Rolain JM, Bittar F. Metallo-Beta-Lactamase-like Encoding Genes in Candidate Phyla Radiation: Widespread and Highly Divergent Proteins with Potential Multifunctionality. Microorganisms 2023; 11:1933. [PMID: 37630493 PMCID: PMC10459063 DOI: 10.3390/microorganisms11081933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/22/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
The Candidate Phyla Radiation (CPR) was found to harbor a vast repertoire of genes encoding for enzymes with potential antibiotic resistance activity. Among these, as many as 3349 genes were predicted in silico to contain a metallo-beta-lactamase-like (MBL-like) fold. These proteins were subject to an in silico functional characterization by comparing their protein profiles (presence/absence of conserved protein domains) to other MBLs, including 24 already expressed in vitro, along with those of the beta-lactamase database (BLDB) (n = 761). The sequence similarity network (SSN) was then used to predict the functional clusters of CPR MBL-like sequences. Our findings showed that CPR MBL-like sequences were longer and more diverse than bacterial MBL sequences, with a high content of functional domains. Most CPR MBL-like sequences did not show any SSN connectivity with expressed MBLs, indicating the presence of many potential, yet unidentified, functions in CPR. In conclusion, CPR was shown to have many protein functions and a large sequence variability of MBL-like folds, exceeding all known MBLs. Further experimental and evolutionary studies of this superfamily of hydrolyzing enzymes are necessary to illustrate their functional annotation, origin, and expansion for adaptation or specialization within a given niche or compared to a specific substrate.
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Affiliation(s)
- Mohamad Maatouk
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Vicky Merhej
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Pierre Pontarotti
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
- Centre National de la Recherche Scientifique (CNRS-SNC5039), 13009 Marseille, France
| | - Ahmad Ibrahim
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Jean-Marc Rolain
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Fadi Bittar
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
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9
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Liang K, Dong W, Gao J, Liu Z, Zhou R, Shu Z, Duan M. The Conformational Transitions and Dynamics of Burkholderia cepacia Lipase Regulated by Water-Oil Interfaces. J Chem Inf Model 2023. [PMID: 37307245 DOI: 10.1021/acs.jcim.3c00194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Structural dynamics and conformational transitions are crucial for the activities of enzymes. As one of the most widely used industrial biocatalysts, lipase could be activated by the water-oil interfaces. The interface activations were believed to be dominated by the close-to-open transitions of the lid subdomains. However, the detailed mechanism and the roles of structure transitions are still under debate. In this study, the dynamic structures and conformational transitions of Burkholderia cepacia lipase (LipA) were investigated by combining all-atom molecular dynamics simulations, enhanced sampling simulation, and spectrophotometric assay experiments. The conformational transitions between the lid-open and lid-closed states of LipA in aqueous solution are directly observed by the computational simulation methods. The interactions between the hydrophobic residues on the two lid-subdomains are the driven forces for the LipA closing. Meanwhile, the hydrophobic environment provided by the oil interfaces would separate the interactions between the lid-subdomains and promote the structure opening of LipA. Moreover, our studies demonstrate the opening of the lids structure is insufficient to initiate the interfacial activation, providing explanations for the inability of interfacial activation of many lipases with lid structures.
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Affiliation(s)
- Kuan Liang
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technoloy, College of Life Sciences, Fujian Normal University (Qishan campus), Fuzhou, 350117 Fujian China
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071 Hubei China
| | - Wanqian Dong
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technoloy, College of Life Sciences, Fujian Normal University (Qishan campus), Fuzhou, 350117 Fujian China
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071 Hubei China
| | - Jiamin Gao
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technoloy, College of Life Sciences, Fujian Normal University (Qishan campus), Fuzhou, 350117 Fujian China
| | - Zhenhao Liu
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071 Hubei China
| | - Rui Zhou
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071 Hubei China
| | - Zhengyu Shu
- National & Local United Engineering Research Center of Industrial Microbiology and Fermentation Technoloy, College of Life Sciences, Fujian Normal University (Qishan campus), Fuzhou, 350117 Fujian China
| | - Mojie Duan
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071 Hubei China
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10
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Jacquet P, Billot R, Shimon A, Hoekstra N, Bergonzi C, Jenks A, Chabrière E, Daudé D, Elias MH. Changes in Active Site Loop Conformation Relate to the Transition toward a Novel Enzymatic Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541809. [PMID: 37292757 PMCID: PMC10245850 DOI: 10.1101/2023.05.22.541809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Enzymatic promiscuity, the ability of enzymes to catalyze multiple, distinct chemical reactions, has been well documented and is hypothesized to be a major driver for the emergence of new enzymatic functions. Yet, the molecular mechanisms involved in the transition from one activity to another remain debated and elusive. Here, we evaluated the redesign of the active site binding cleft of the lactonase SsoPox using structure-based design and combinatorial libraries. We created variants with largely improved catalytic abilities against phosphotriesters, the best ones being > 1,000-fold better compared to the wild-type enzyme. The observed shifts in activity specificity are large, ~1,000,000-fold and beyond, since some variants completely lost their initial activity. The selected combinations of mutations have considerably reshaped the active site cavity via side chain changes but mostly through large rearrangements of the active site loops, as revealed by a suite of crystal structures. This suggests that specific active site loop configuration is critical to the lactonase activity. Interestingly, analysis of high-resolution structures hints at the potential role of conformational sampling and its directionality in defining an enzyme activity profile.
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Affiliation(s)
- Pauline Jacquet
- Gene&GreenTK, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Raphaël Billot
- Gene&GreenTK, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Amir Shimon
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Nathan Hoekstra
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Céline Bergonzi
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Anthony Jenks
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Eric Chabrière
- Gene&GreenTK, 19-21 Bd Jean Moulin, 13005, Marseille, France
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille 13005, France
| | - David Daudé
- Gene&GreenTK, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Mikael H. Elias
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
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11
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Sánchez-Moguel I, Costa-Silva TA, Pillaca-Pullo OS, Flores-Santos JC, Freire RKB, Carretero G, da Luz Bueno J, Camacho-Córdova DI, Santos JH, Sette LD, Pessoa-Jr A. Antarctic yeasts as a source of L-asparaginase: characterization of a glutaminase-activity free L-asparaginase from psychrotolerant yeast Leucosporidium scottii L115. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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12
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Blazeck J, Karamitros CS, Ford K, Somody C, Qerqez A, Murray K, Burkholder NT, Marshall N, Sivakumar A, Lu WC, Tan B, Lamb C, Tanno Y, Siddiqui MY, Ashoura N, Coma S, Zhang XM, McGovern K, Kumada Y, Zhang YJ, Manfredi M, Johnson KA, D’Arcy S, Stone E, Georgiou G. Bypassing evolutionary dead ends and switching the rate-limiting step of a human immunotherapeutic enzyme. Nat Catal 2022; 5:952-967. [PMID: 36465553 PMCID: PMC9717613 DOI: 10.1038/s41929-022-00856-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 09/09/2022] [Indexed: 11/08/2022]
Abstract
The Trp metabolite kynurenine (KYN) accumulates in numerous solid tumours and mediates potent immunosuppression. Bacterial kynureninases (KYNases), which preferentially degrade kynurenine, can relieve immunosuppression in multiple cancer models, but immunogenicity concerns preclude their clinical use, while the human enzyme (HsKYNase) has very low activity for kynurenine and shows no therapeutic effect. Using fitness selections, we evolved a HsKYNase variant with 27-fold higher activity, beyond which exploration of >30 evolutionary trajectories involving the interrogation of >109 variants led to no further improvements. Introduction of two amino acid substitutions conserved in bacterial KYNases reduced enzyme fitness but potentiated rapid evolution of variants with ~500-fold improved activity and reversed substrate specificity, resulting in an enzyme capable of mediating strong anti-tumour effects in mice. Pre-steady-state kinetics revealed a switch in rate-determining step attributable to changes in both enzyme structure and conformational dynamics. Apart from its clinical significance, our work highlights how rationally designed substitutions can potentiate trajectories that overcome barriers in protein evolution.
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Affiliation(s)
- John Blazeck
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Christos S. Karamitros
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Kyle Ford
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Catrina Somody
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Ahlam Qerqez
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Kyle Murray
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas, USA
| | - Nathaniel T. Burkholder
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Nicholas Marshall
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Anirudh Sivakumar
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Wei-Cheng Lu
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Bing Tan
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Candice Lamb
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Yuri Tanno
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Menna Y. Siddiqui
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Norah Ashoura
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Silvia Coma
- Ikena Oncology, Cambridge, Massachusetts, USA
| | | | | | - Yoichi Kumada
- Department of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Kyoto, Japan
| | - Yan Jessie Zhang
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin (UT Austin), Austin, Texas, USA
| | | | - Kenneth A. Johnson
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Sheena D’Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas, USA
| | - Everett Stone
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin (UT Austin), Austin, Texas, USA
- Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, Texas, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin (UT Austin), Austin, Texas, USA
- Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, Texas, USA
- Department of Biomedical Engineering, University of Texas at Austin (UT Austin), Austin, TX, USA
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13
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Lavrinenko IA, Vashanov GA, Hernández Cáceres JL, Buchelnikov AS, Nechipurenko YD. A New Model of Hemoglobin Oxygenation. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1214. [PMID: 36141103 PMCID: PMC9498255 DOI: 10.3390/e24091214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 06/16/2023]
Abstract
The study of hemoglobin oxygenation, starting from the classical works of Hill, has laid the foundation for molecular biophysics. The cooperative nature of oxygen binding to hemoglobin has been variously described in different models. In the Adair model, which better fits the experimental data, the constants of oxygen binding at various stages differ. However, the physical meaning of the parameters in this model remains unclear. In this work, we applied Hill's approach, extending its interpretation; we obtained a good agreement between the theory and the experiment. The equation in which the Hill coefficient is modulated by the Lorentz distribution for oxygen partial pressure approximates the experimental data better than not only the classical Hill equation, but also the Adair equation.
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Affiliation(s)
- Igor A. Lavrinenko
- Department of Human and Animal Physiology, Voronezh State University, Universitetskaya Sq. 1, 394018 Voronezh, Russia
| | - Gennady A. Vashanov
- Department of Human and Animal Physiology, Voronezh State University, Universitetskaya Sq. 1, 394018 Voronezh, Russia
| | | | - Anatoly S. Buchelnikov
- Laboratory of Molecular and Cellular Biophysics, Sevastopol State University, Universitetskaya Str. 33, 299053 Sevastopol, Russia
| | - Yury D. Nechipurenko
- Laboratory of DNA-Protein Interactions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, 119991 Moscow, Russia
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14
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Gutierrez-Rus LI, Alcalde M, Risso VA, Sanchez-Ruiz JM. Efficient Base-Catalyzed Kemp Elimination in an Engineered Ancestral Enzyme. Int J Mol Sci 2022; 23:ijms23168934. [PMID: 36012203 PMCID: PMC9408544 DOI: 10.3390/ijms23168934] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/25/2022] Open
Abstract
The routine generation of enzymes with completely new active sites is a major unsolved problem in protein engineering. Advances in this field have thus far been modest, perhaps due, at least in part, to the widespread use of modern natural proteins as scaffolds for de novo engineering. Most modern proteins are highly evolved and specialized and, consequently, difficult to repurpose for completely new functionalities. Conceivably, resurrected ancestral proteins with the biophysical properties that promote evolvability, such as high stability and conformational diversity, could provide better scaffolds for de novo enzyme generation. Kemp elimination, a non-natural reaction that provides a simple model of proton abstraction from carbon, has been extensively used as a benchmark in de novo enzyme engineering. Here, we present an engineered ancestral β-lactamase with a new active site that is capable of efficiently catalyzing Kemp elimination. The engineering of our Kemp eliminase involved minimalist design based on a single function-generating mutation, inclusion of an extra polypeptide segment at a position close to the de novo active site, and sharply focused, low-throughput library screening. Nevertheless, its catalytic parameters (kcat/KM~2·105 M−1 s−1, kcat~635 s−1) compare favorably with the average modern natural enzyme and match the best proton-abstraction de novo Kemp eliminases that are reported in the literature. The general implications of our results for de novo enzyme engineering are discussed.
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Affiliation(s)
- Luis I. Gutierrez-Rus
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Valeria A. Risso
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
- Correspondence: (V.A.R.); (J.M.S.-R.)
| | - Jose M. Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
- Correspondence: (V.A.R.); (J.M.S.-R.)
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15
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Dušeková E, Garajová K, Yavaşer R, Tomková M, Sedláková D, Dzurillová V, Kulik N, Fadaei F, Shaposhnikova A, Minofar B, Sedlák E. Modulation of global stability, ligand binding and catalytic properties of trypsin by anions. Biophys Chem 2022; 288:106856. [PMID: 35872468 DOI: 10.1016/j.bpc.2022.106856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/02/2022] [Accepted: 07/13/2022] [Indexed: 12/01/2022]
Abstract
Specific salts effect is well-known on stability and solubility of proteins, however, relatively limited knowledge is known regarding the effect on catalytic properties of enzymes. Here, we examined the effect of four sodium anions on thermal stability and catalytic properties of trypsin and binding of the fluorescent probe, p-aminobenzamidine (PAB), to the enzyme. We show that the specific anions effect on trypsin properties agrees with the localization of the anions in the Hofmeister series. Thermal stability of trypsin, Tm, the affinity of the fluorescent probe to the binding site, Kd, and the rate constant, kcat, of trypsin-catalyzed hydrolysis of the substrate N-benzoyl-L-arginine ethyl ester (BAEE) increase with increasing kosmotropic character of anions in the order: perchlorate<bromide<chloride<sulfate, while the value of Michaelis constant, KM, decreases. Correlations between the values of Tm, Kd for PAB, kcat, and KM for BAEE in the presence of 1 M studied salts suggest interrelation among these parameters of the enzyme. Global stabilization as well as increased rigidity of trypsin is accompanied by strengthening of interaction with fluorescent probe PAB and in accordance with decreasing values of KM for the substrate BAEE. Strong correlations between parameters characterizing the trypsin properties with the charge densities of anions clearly indicate direct electrostatic interaction as a basis of the specific anion effect on the conformational and functional properties of the enzyme.
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Affiliation(s)
- Eva Dušeková
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Katarína Garajová
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Moyzesova 11, 04154 Košice, Slovakia
| | - Rukiye Yavaşer
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Moyzesova 11, 04154 Košice, Slovakia; Chemistry Department, Faculty of Arts and Science, Aydın Adnan Menderes University, 09010 Aydın, Turkey
| | - Mária Tomková
- Center for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Dagmar Sedláková
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Košice, Slovakia
| | - Veronika Dzurillová
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Natalia Kulik
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic
| | - Fatemeh Fadaei
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic; Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic
| | - Anastasiia Shaposhnikova
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic; Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic
| | - Babak Minofar
- Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic.
| | - Erik Sedlák
- Center for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia.
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16
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Lemay-St-Denis C, Doucet N, Pelletier JN. Integrating dynamics into enzyme engineering. Protein Eng Des Sel 2022; 35:6842866. [PMID: 36416215 DOI: 10.1093/protein/gzac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/02/2022] [Accepted: 11/06/2022] [Indexed: 11/24/2022] Open
Abstract
Enzyme engineering has become a widely adopted practice in research labs and industry. In parallel, the past decades have seen tremendous strides in characterizing the dynamics of proteins, using a growing array of methodologies. Importantly, links have been established between the dynamics of proteins and their function. Characterizing the dynamics of an enzyme prior to, and following, its engineering is beginning to inform on the potential of 'dynamic engineering', i.e. the rational modification of protein dynamics to alter enzyme function. Here we examine the state of knowledge at the intersection of enzyme engineering and protein dynamics, describe current challenges and highlight pioneering work in the nascent area of dynamic engineering.
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Affiliation(s)
- Claudèle Lemay-St-Denis
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Nicolas Doucet
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, QC, Canada
| | - Joelle N Pelletier
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
- Chemistry Department, Université de Montréal, Montreal, QC, Canada
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17
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Hot spots-making directed evolution easier. Biotechnol Adv 2022; 56:107926. [DOI: 10.1016/j.biotechadv.2022.107926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/04/2022] [Accepted: 02/07/2022] [Indexed: 01/20/2023]
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18
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Aristov VV, Buchelnikov AS, Nechipurenko YD. The Use of the Statistical Entropy in Some New Approaches for the Description of Biosystems. ENTROPY (BASEL, SWITZERLAND) 2022; 24:172. [PMID: 35205467 PMCID: PMC8871276 DOI: 10.3390/e24020172] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 01/13/2023]
Abstract
Some problems of describing biological systems with the use of entropy as a measure of the complexity of these systems are considered. Entropy is studied both for the organism as a whole and for its parts down to the molecular level. Correlation of actions of various parts of the whole organism, intercellular interactions and control, as well as cooperativity on the microlevel lead to a more complex structure and lower statistical entropy. For a multicellular organism, entropy is much lower than entropy for the same mass of a colony of unicellular organisms. Cooperativity always reduces the entropy of the system; a simple example of ligand binding to a macromolecule carrying two reaction centers shows how entropy is consistent with the ambiguity of the result in the Bernoulli test scheme. Particular attention is paid to the qualitative and quantitative relationship between the entropy of the system and the cooperativity of ligand binding to macromolecules. A kinetic model of metabolism. corresponding to Schrödinger's concept of the maintenance biosystems by "negentropy feeding", is proposed. This model allows calculating the nonequilibrium local entropy and comparing it with the local equilibrium entropy inherent in non-living matter.
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Affiliation(s)
- Vladimir V. Aristov
- Dorodnicyn Computing Centre, Federal Research Center “Computer Science and Control” of Russian Academy of Sciences, Vavilova Str. 40, 119333 Moscow, Russia
| | - Anatoly S. Buchelnikov
- Laboratory of Molecular and Cellular Biophysics, Sevastopol State University, Universitetskaya Str. 33, 299053 Sevastopol, Russia;
| | - Yury D. Nechipurenko
- Laboratory of DNA–Protein Recognition, Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Vavilova Str. 32, 119991 Moscow, Russia;
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19
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Qu G, Bi Y, Liu B, Li J, Han X, Liu W, Jiang Y, Qin Z, Sun Z. Unlocking the Stereoselectivity and Substrate Acceptance of Enzymes: Proline‐Induced Loop Engineering Test. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202110793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- National Technology Innovation Center of Synthetic Biology Tianjin 300308 China
| | - Yuexin Bi
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- University of Science and Technology of China Hefei 230027 China
| | - Beibei Liu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
| | - Junkuan Li
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- Department of Chemistry School of Science Tianjin University Tianjin 300072 China
| | - Xu Han
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- National Technology Innovation Center of Synthetic Biology Tianjin 300308 China
| | - Weidong Liu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- National Technology Innovation Center of Synthetic Biology Tianjin 300308 China
| | - Yingying Jiang
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zongmin Qin
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
- National Technology Innovation Center of Synthetic Biology Tianjin 300308 China
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20
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Winter SD, Jones HBL, Răsădean DM, Crean RM, Danson MJ, Pantoş GD, Katona G, Prentice E, Arcus VL, van der Kamp MW, Pudney CR. Chemical Mapping Exposes the Importance of Active Site Interactions in Governing the Temperature Dependence of Enzyme Turnover. ACS Catal 2021; 11:14854-14863. [PMID: 34956689 PMCID: PMC8689651 DOI: 10.1021/acscatal.1c04679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/16/2021] [Indexed: 12/26/2022]
Abstract
Uncovering the role of global protein dynamics in enzyme turnover is needed to fully understand enzyme catalysis. Recently, we have demonstrated that the heat capacity of catalysis, ΔC P ‡, can reveal links between the protein free energy landscape, global protein dynamics, and enzyme turnover, suggesting that subtle changes in molecular interactions at the active site can affect long-range protein dynamics and link to enzyme temperature activity. Here, we use a model promiscuous enzyme (glucose dehydrogenase from Sulfolobus solfataricus) to chemically map how individual substrate interactions affect the temperature dependence of enzyme activity and the network of motions throughout the protein. Utilizing a combination of kinetics, red edge excitation shift (REES) spectroscopy, and computational simulation, we explore the complex relationship between enzyme-substrate interactions and the global dynamics of the protein. We find that changes in ΔC P ‡ and protein dynamics can be mapped to specific substrate-enzyme interactions. Our study reveals how subtle changes in substrate binding affect global changes in motion and flexibility extending throughout the protein.
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Affiliation(s)
- Samuel D. Winter
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, U.K
| | - Hannah B. L. Jones
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, U.K
| | | | - Rory M. Crean
- Science for Life Laboratory, Department of Chemistry − BMC, Uppsala University, Uppsala 752 37, Sweden
| | - Michael J. Danson
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, U.K
| | - G. Dan Pantoş
- Department of Chemistry, University of Bath, Bath BA2 7AY, U.K
| | - Gergely Katona
- Department of Chemistry and Biology, University of Gothenburg, Göteborg 412 96, Sweden
| | - Erica Prentice
- School of Science, University of Waikato, Hamilton 3216, New Zealand
| | - Vickery L. Arcus
- School of Science, University of Waikato, Hamilton 3216, New Zealand
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21
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Qu G, Bi Y, Liu B, Li J, Han X, Liu W, Jiang Y, Qin Z, Sun Z. Unlocking the Stereoselectivity and Substrate Acceptance of Enzymes: Proline-Induced Loop Engineering Test. Angew Chem Int Ed Engl 2021; 61:e202110793. [PMID: 34658118 DOI: 10.1002/anie.202110793] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/25/2021] [Indexed: 12/12/2022]
Abstract
Protein stability and evolvability influence each other. Although protein dynamics play essential roles in various catalytically important properties, their high flexibility and diversity makes it difficult to incorporate such properties into rational engineering. Therefore, how to unlock the potential evolvability in a user-friendly rational design process remains a challenge. In this endeavor, we describe a method for engineering an enantioselective alcohol dehydrogenase. It enables synthetically important substrate acceptance for 4-chlorophenyl pyridine-2-yl ketone, and perfect stereocontrol of both (S)- and (R)-configured products. Thermodynamic analysis unveiled the subtle interaction between enzyme stability and evolvability, while computational studies provided insights into the origin of selectivity and substrate recognition. Preparative-scale synthesis of the (S)-product (73 % yield; >99 % ee) was performed on a gram-scale. This proof-of-principle study demonstrates that interfaced proline residues can be rationally engineered to unlock evolvability and thus provide access to new biocatalysts with highly improved catalytic performance.
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Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Yuexin Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Science and Technology of China, Hefei, 230027, China
| | - Beibei Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Junkuan Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Department of Chemistry, School of Science, Tianjin University, Tianjin, 300072, China
| | - Xu Han
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Weidong Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Yingying Jiang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zongmin Qin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
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22
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Rodrigues CF, Borges PT, Scocozza MF, Silva D, Taborda A, Brissos V, Frazão C, Martins LO. Loops around the Heme Pocket Have a Critical Role in the Function and Stability of BsDyP from Bacillus subtilis. Int J Mol Sci 2021; 22:ijms221910862. [PMID: 34639208 PMCID: PMC8509576 DOI: 10.3390/ijms221910862] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 11/27/2022] Open
Abstract
Bacillus subtilis BsDyP belongs to class I of the dye-decolorizing peroxidase (DyP) family of enzymes and is an interesting biocatalyst due to its high redox potential, broad substrate spectrum and thermostability. This work reports the optimization of BsDyP using directed evolution for improved oxidation of 2,6-dimethoxyphenol, a model lignin-derived phenolic. After three rounds of evolution, one variant was identified displaying 7-fold higher catalytic rates and higher production yields as compared to the wild-type enzyme. The analysis of X-ray structures of the wild type and the evolved variant showed that the heme pocket is delimited by three long conserved loop regions and a small α helix where, incidentally, the mutations were inserted in the course of evolution. One loop in the proximal side of the heme pocket becomes more flexible in the evolved variant and the size of the active site cavity is increased, as well as the width of its mouth, resulting in an enhanced exposure of the heme to solvent. These conformational changes have a positive functional role in facilitating electron transfer from the substrate to the enzyme. However, they concomitantly resulted in decreasing the enzyme’s overall stability by 2 kcal mol−1, indicating a trade-off between functionality and stability. Furthermore, the evolved variant exhibited slightly reduced thermal stability compared to the wild type. The obtained data indicate that understanding the role of loops close to the heme pocket in the catalysis and stability of DyPs is critical for the development of new and more powerful biocatalysts: loops can be modulated for tuning important DyP properties such as activity, specificity and stability.
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Affiliation(s)
- Carolina F. Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Patrícia T. Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Magali F. Scocozza
- Instituto de Química Física de los Materiales, Medio Ambiente y Energia (INQUIMAE), CONICET—Universidad de Buenos Aires, Buenos Aires 148EHA, Argentina;
| | - Diogo Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - André Taborda
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Vânia Brissos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
- Correspondence:
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23
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Elings W, Chikunova A, van Zanten DB, Drenth R, Ahmad MUD, Blok AJ, Timmer M, Perrakis A, Ubbink M. Two β-Lactamase Variants with Reduced Clavulanic Acid Inhibition Display Different Millisecond Dynamics. Antimicrob Agents Chemother 2021; 65:e0262820. [PMID: 34031049 PMCID: PMC8284444 DOI: 10.1128/aac.02628-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 05/07/2021] [Indexed: 11/20/2022] Open
Abstract
The β-lactamase of Mycobacterium tuberculosis, BlaC, is susceptible to inhibition by clavulanic acid. The ability of this enzyme to escape inhibition through mutation was probed using error-prone PCR combined with functional screening in Escherichia coli. The variant that was found to confer the most inhibitor resistance, K234R, as well as variant G132N that was found previously were characterized using X-ray crystallography and nuclear magnetic resonance (NMR) relaxation experiments to probe structural and dynamic properties. The G132N mutant exists in solution in two almost equally populated conformations that exchange with a rate of ca. 88 s-1. The conformational change affects a broad region of the enzyme. The crystal structure reveals that the Asn132 side chain forces the peptide bond between Ser104 and Ile105 in a cis-conformation. The crystal structure suggests multiple conformations for several side chains (e.g., Ser104 and Ser130) and a short loop (positions 214 to 216). In the K234R mutant, the active-site dynamics are significantly diminished with respect to the wild-type enzyme. These results show that multiple evolutionary routes are available to increase inhibitor resistance in BlaC and that active-site dynamics on the millisecond time scale are not required for catalytic function.
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Affiliation(s)
- Wouter Elings
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | | | - Ralphe Drenth
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Misbha Ud Din Ahmad
- Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Anneloes J. Blok
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Monika Timmer
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Anastassis Perrakis
- Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
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24
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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25
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Zhang H, Wen B, Liu Y, Du G, Wei X, Imam KMSU, Zhou H, Fan S, Wang F, Wang Y, Xin F. A reverse catalytic triad Asp containing loop shaping a wide substrate binding pocket of a feruloyl esterase from Lactobacillus plantarum. Int J Biol Macromol 2021; 184:92-100. [PMID: 34116094 DOI: 10.1016/j.ijbiomac.2021.06.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/08/2021] [Accepted: 06/06/2021] [Indexed: 11/18/2022]
Abstract
Feruloyl esterase is an indispensable biocatalyst in food processing, pesticide and pharmaceutical industries, catalyzing the cleavage of the ester bond cross-linked between the polysaccharide side chain of hemicellulose and ferulic acid in plant cell walls. LP_0796 from Lactobacillus plantarum was identified as a feruloyl esterase that may have potential applications in the food industry, but the lack of the substrate recognition and catalytic mechanisms limits its application. Here, LP_0796 showed the highest activity towards methyl caffeate at pH 6.6 and 40 °C. The crystal structure of LP_0796 was determined at 2.5 Å resolution and featured a catalytic triad Asp195-containing loop facing the opposite direction, thus forming a wider substrate binding pocket. Molecular docking simulation and site-directed mutagenesis studies further demonstrated that in addition to the catalytic triad (Ser94, Asp195, His225), Arg125 and Val128 played essential roles in the function of the active site. Our data also showed that Asp mutation of Ala23 and Ile198 increased the catalytic efficiency to 4- and 5-fold, respectively. Collectively, this work provided a better understanding of the substrate recognition and catalytic mechanisms of LP_0796 and may facilitate the future protein design of this important feruloyl esterase.
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Affiliation(s)
- Haowen Zhang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Boting Wen
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yusi Liu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guoming Du
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xue Wei
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Khandaker Md Sharif Uddin Imam
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huan Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Shilong Fan
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fengzhong Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yulu Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Fengjiao Xin
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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26
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Zalloum WA, Zalloum N. Comparative QM/MM Molecular Dynamics and Umbrella Sampling Simulations: Interaction of the Zinc-Bound Intermediate Gem-Diolate Trapoxin A Inhibitor and Acetyl-l-lysine Substrate with Histone Deacetylase 8. J Phys Chem B 2021; 125:5321-5337. [PMID: 33998791 DOI: 10.1021/acs.jpcb.1c01696] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Targeting the genetic material without destruction is a priority to develop safe anticancer drugs. Histone deacetylase 8 (HDAC8), which is proved to be involved in carcinogenesis, is an enzyme associated with the chromatin for post-translational deacetylation of acetylated lysine. In this study, HDAC8 co-crystallized with the intermediate state tetrapeptide Trapoxin A (TA) inhibitor and the holoenzyme are utilized to find their conformational ensembles. Furthermore, the co-crystallized intermediate gem-diolate TA was used to find optimum interactions with the active site residues by conventional molecular dynamics (MD) simulation and QM/MM umbrella sampling. Finally, the intermediate state of the acetyl-l-lysine substrate was explored by QM/MM steered MD and compared to the binding of the intermediate state of the inhibitor. This research showed that HDAC8 is flexible and exists in conformational ensembles in its holoenzyme state. Binding of the intermediate state TA stabilizes its conformation. The optimum binding to the active site of HDAC8 for structures of gem-diolate TA (intermediate state) and acetyl-l-lysine (intermediate state) was determined according to the corresponding energy profiles. The use of these models will aid in the design of potentially reversible, potent, and selective inhibitors of HDAC8 for cancer treatment.
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Affiliation(s)
- Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O. Box 2882, Amman 11821, Jordan
| | - Needa Zalloum
- Department of Biopharmaceutics and Clinical Pharmacy, Faculty of Pharmacy, University of Jordan, Amman 11942, Jordan
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27
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Modi T, Risso VA, Martinez-Rodriguez S, Gavira JA, Mebrat MD, Van Horn WD, Sanchez-Ruiz JM, Banu Ozkan S. Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity. Nat Commun 2021; 12:1852. [PMID: 33767175 PMCID: PMC7994827 DOI: 10.1038/s41467-021-22089-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/01/2021] [Indexed: 01/31/2023] Open
Abstract
TEM-1 β-lactamase degrades β-lactam antibiotics with a strong preference for penicillins. Sequence reconstruction studies indicate that it evolved from ancestral enzymes that degraded a variety of β-lactam antibiotics with moderate efficiency. This generalist to specialist conversion involved more than 100 mutational changes, but conserved fold and catalytic residues, suggesting a role for dynamics in enzyme evolution. Here, we develop a conformational dynamics computational approach to rationally mold a protein flexibility profile on the basis of a hinge-shift mechanism. By deliberately weighting and altering the conformational dynamics of a putative Precambrian β-lactamase, we engineer enzyme specificity that mimics the modern TEM-1 β-lactamase with only 21 amino acid replacements. Our conformational dynamics design thus re-enacts the evolutionary process and provides a rational allosteric approach for manipulating function while conserving the enzyme active site.
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Affiliation(s)
- Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Valeria A Risso
- Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
- Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain
| | - Sergio Martinez-Rodriguez
- Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
- Departamento de Bioquimica, Biologia Molecular III e Inmunologia, Universidad de Granada, Granada, Spain
| | - Jose A Gavira
- Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain
- Laboratorio de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC, Universidad de Granada, Granada, Armilla, Spain
| | - Mubark D Mebrat
- The Biodesign Institute Virginia G. Piper Center for Personalized Diagnostics, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Wade D Van Horn
- The Biodesign Institute Virginia G. Piper Center for Personalized Diagnostics, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
- Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain.
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA.
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28
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Pervasive cooperative mutational effects on multiple catalytic enzyme traits emerge via long-range conformational dynamics. Nat Commun 2021; 12:1621. [PMID: 33712579 PMCID: PMC7955134 DOI: 10.1038/s41467-021-21833-w] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 01/29/2021] [Indexed: 12/11/2022] Open
Abstract
Multidimensional fitness landscapes provide insights into the molecular basis of laboratory and natural evolution. To date, such efforts usually focus on limited protein families and a single enzyme trait, with little concern about the relationship between protein epistasis and conformational dynamics. Here, we report a multiparametric fitness landscape for a cytochrome P450 monooxygenase that was engineered for the regio- and stereoselective hydroxylation of a steroid. We develop a computational program to automatically quantify non-additive effects among all possible mutational pathways, finding pervasive cooperative signs and magnitude epistasis on multiple catalytic traits. By using quantum mechanics and molecular dynamics simulations, we show that these effects are modulated by long-range interactions in loops, helices and β-strands that gate the substrate access channel allowing for optimal catalysis. Our work highlights the importance of conformational dynamics on epistasis in an enzyme involved in secondary metabolism and offers insights for engineering P450s. Connecting conformational dynamics and epistasis has so far been limited to a few proteins and a single fitness trait. Here, the authors provide evidence of positive epistasis on multiple catalytic traits in the evolution and dynamics of engineered cytochrome P450 monooxygenase, offering insights for in silico protein design.
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29
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Iyer A, Reis RAG, Gannavaram S, Momin M, Spring-Connell AM, Orozco-Gonzalez Y, Agniswamy J, Hamelberg D, Weber IT, Gozem S, Wang S, Germann MW, Gadda G. A Single-Point Mutation in d-Arginine Dehydrogenase Unlocks a Transient Conformational State Resulting in Altered Cofactor Reactivity. Biochemistry 2021; 60:711-724. [PMID: 33630571 DOI: 10.1021/acs.biochem.1c00054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Proteins are inherently dynamic, and proper enzyme function relies on conformational flexibility. In this study, we demonstrated how an active site residue changes an enzyme's reactivity by modulating fluctuations between conformational states. Replacement of tyrosine 249 (Y249) with phenylalanine in the active site of the flavin-dependent d-arginine dehydrogenase yielded an enzyme with both an active yellow FAD (Y249F-y) and an inactive chemically modified green FAD, identified as 6-OH-FAD (Y249F-g) through various spectroscopic techniques. Structural investigation of Y249F-g and Y249F-y variants by comparison to the wild-type enzyme showed no differences in the overall protein structure and fold. A closer observation of the active site of the Y249F-y enzyme revealed an alternative conformation for some active site residues and the flavin cofactor. Molecular dynamics simulations probed the alternate conformations observed in the Y249F-y enzyme structure and showed that the enzyme variant with FAD samples a metastable conformational state, not available to the wild-type enzyme. Hybrid quantum/molecular mechanical calculations identified differences in flavin electronics between the wild type and the alternate conformation of the Y249F-y enzyme. The computational studies further indicated that the alternate conformation in the Y249F-y enzyme is responsible for the higher spin density at the C6 atom of flavin, which is consistent with the formation of 6-OH-FAD in the variant enzyme. The observations in this study are consistent with an alternate conformational space that results in fine-tuning the microenvironment around a versatile cofactor playing a critical role in enzyme function.
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Affiliation(s)
- Archana Iyer
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Swathi Gannavaram
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Mohamed Momin
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | | | | | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Irene T Weber
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Siming Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States
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30
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Wang CK, Craik DJ. Linking molecular evolution to molecular grafting. J Biol Chem 2021; 296:100425. [PMID: 33600801 PMCID: PMC8005815 DOI: 10.1016/j.jbc.2021.100425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/01/2022] Open
Abstract
Molecular grafting is a strategy for the engineering of molecular scaffolds into new functional agents, such as next-generation therapeutics. Despite its wide use, studies so far have focused almost exclusively on demonstrating its utility rather than understanding the factors that lead to either poor or successful grafting outcomes. Here, we examine protein evolution and identify parallels between the natural process of protein functional diversification and the artificial process of molecular grafting. We discuss features of natural proteins that are correlated to innovability-the capacity to acquire new functions-and describe their implications to molecular grafting scaffolds. Disulfide-rich peptides are used as exemplars because they are particularly promising scaffolds onto which new functions can be grafted. This article provides a perspective on why some scaffolds are more suitable for grafting than others, identifying opportunities on how molecular grafting might be improved.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
| | - David J Craik
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
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31
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Mhashal AR, Major DT. Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations. J Phys Chem B 2021; 125:1369-1377. [PMID: 33522797 PMCID: PMC7883348 DOI: 10.1021/acs.jpcb.0c10318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/05/2021] [Indexed: 11/28/2022]
Abstract
Calculation of temperature-dependent kinetic isotope effects (KIE) in enzymes presents a significant theoretical challenge. Additionally, it is not trivial to identify enzymes with available experimental accurate intrinsic KIEs in a range of temperatures. In the current work, we present a theoretical study of KIEs in the primitive R67 dihydrofolate reductase (DHFR) enzyme and compare with experimental work. The advantage of R67 DHFR is its significantly lower kinetic complexity compared to more evolved DHFR isoforms. We employ mass-perturbation-based path-integral simulations in conjunction with umbrella sampling and a hybrid quantum mechanics-molecular mechanics Hamiltonian. We obtain temperature-dependent KIEs in good agreement with experiments and ascribe the temperature-dependent KIEs primarily to zero-point energy effects. The active site in the primitive enzyme is found to be poorly preorganized, which allows excessive water access to the active site and results in loosely bound reacting ligands.
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Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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32
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Gamiz-Arco G, Gutierrez-Rus LI, Risso VA, Ibarra-Molero B, Hoshino Y, Petrović D, Justicia J, Cuerva JM, Romero-Rivera A, Seelig B, Gavira JA, Kamerlin SCL, Gaucher EA, Sanchez-Ruiz JM. Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase. Nat Commun 2021; 12:380. [PMID: 33452262 PMCID: PMC7810902 DOI: 10.1038/s41467-020-20630-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022] Open
Abstract
Glycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ∼5500 reported crystallographic structures of ∼1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when sampling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed. Family 1 glycosidases (GH1) are present in the three domains of life and share classical TIM-barrel fold. Structural and biochemical analyses of a resurrected ancestral GH1 enzyme reveal heme binding, not known in its modern descendants. Heme rigidifies the TIM-barrel and allosterically enhances catalysis.
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Affiliation(s)
- Gloria Gamiz-Arco
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Luis I Gutierrez-Rus
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Valeria A Risso
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Beatriz Ibarra-Molero
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Yosuke Hoshino
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Dušan Petrović
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23, Uppsala, Sweden.,Hit Discovery, Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, 431 50, Gothenburg, Sweden
| | - Jose Justicia
- Departamento de Quimica Organica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Juan Manuel Cuerva
- Departamento de Quimica Organica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Adrian Romero-Rivera
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23, Uppsala, Sweden
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America, & BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Jose A Gavira
- Laboratorio de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Avenida de las Palmeras 4, Granada, 18100, Armilla, Spain
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23, Uppsala, Sweden.
| | - Eric A Gaucher
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA.
| | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain.
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Karamitros CS, Murray K, Sugiyama Y, Kumada Y, Johnson KA, Georgiou G, D'Arcy S, Stone EM. Conformational Dynamics Contribute to Substrate Selectivity and Catalysis in Human Kynureninase. ACS Chem Biol 2020; 15:3159-3166. [PMID: 33275413 PMCID: PMC11104311 DOI: 10.1021/acschembio.0c00676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Kynureninases (KYNases) are enzymes that play a key role in tryptophan catabolism through the degradation of intermediate kynurenine and 3'-hydroxy-kynurenine metabolites (KYN and OH-KYN, respectively). Bacterial KYNases exhibit high catalytic efficiency toward KYN and moderate activity toward OH-KYN, whereas animal KYNases are highly selective for OH-KYN, exhibiting only minimal activity toward the smaller KYN substrate. These differences reflect divergent pathways for KYN and OH-KYN utilization in the respective kingdoms. We examined the Homo sapiens and Pseudomonas fluorescens KYNases (HsKYNase and PfKYNase respectively) using pre-steady-state and hydrogen-deuterium exchange mass spectrometry (HDX-MS) methodologies. We discovered that the activity of HsKYNase critically depends on formation of hydrogen bonds with the hydroxyl group of OH-KYN to stabilize the entire active site and allow productive substrate turnover. With the preferred OH-KYN substrate, stabilization is observed at the substrate-binding site and the region surrounding the PLP cofactor. With the nonpreferred KYN substrate, less stabilization occurs, revealing a direct correlation with activity. This correlation holds true for PfKYNases; however there is only a modest stabilization at the substrate-binding site, suggesting that substrate discrimination is simply achieved by steric hindrance. We speculate that eukaryotic KYNases use dynamic mobility as a mechanism of substrate specificity to commit OH-KYN to nicotinamide synthesis and avoid futile hydrolysis of KYN. These findings have important ramifications for the engineering of HsKynase with high KYN activity as required for clinical applications in cancer immunotherapy. Our study shows how homologous enzymes with conserved active sites can use dynamics to discriminate between two highly similar substrates.
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Affiliation(s)
- Christos S Karamitros
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kyle Murray
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Yusuke Sugiyama
- Department of Molecular Chemistry and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Yoichi Kumada
- Department of Molecular Chemistry and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Kenneth A Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - George Georgiou
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, Texas 78712, United States
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Everett M Stone
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, Texas 78712, United States
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De Luca V, Mandrich L. Enzyme Promiscuous Activity: How to Define it and its Evolutionary Aspects. Protein Pept Lett 2020; 27:400-410. [PMID: 31868141 DOI: 10.2174/0929866527666191223141205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 10/30/2019] [Accepted: 11/07/2019] [Indexed: 11/22/2022]
Abstract
Enzymes are among the most studied biological molecules because better understanding enzymes structure and activity will shed more light on their biological processes and regulation; from a biotechnological point of view there are many examples of enzymes used with the aim to obtain new products and/or to make industrial processes less invasive towards the environment. Enzymes are known for their high specificity in the recognition of a substrate but considering the particular features of an increasing number of enzymes this is not completely true, in fact, many enzymes are active on different substrates: this ability is called enzyme promiscuity. Usually, promiscuous activities have significantly lower kinetic parameters than to that of primary activity, but they have a crucial role in gene evolution. It is accepted that gene duplication followed by sequence divergence is considered a key evolutionary mechanism to generate new enzyme functions. In this way, promiscuous activities are the starting point to increase a secondary activity in the main activity and then get a new enzyme. The primary activity can be lost or reduced to a promiscuous activity. In this review we describe the differences between substrate and enzyme promiscuity, and its rule in gene evolution. From a practical point of view the knowledge of promiscuity can facilitate the in vitro progress of proteins engineering, both for biomedical and industrial applications. In particular, we report cases regarding esterases, phosphotriesterases and cytochrome P450.
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Affiliation(s)
- Valentina De Luca
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 111, 80131, Naples, Italy
| | - Luigi Mandrich
- Research Institute on Terrestrial Ecosystems, National Research Council, Via Pietro Castellino, 111, 80131, Naples, Italy
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35
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Ambrus V, Hoffka G, Fuxreiter M. Asymmetric dynamic coupling promotes alternative evolutionary pathways in an enzyme dimer. Sci Rep 2020; 10:18866. [PMID: 33139795 PMCID: PMC7608688 DOI: 10.1038/s41598-020-75772-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 10/16/2020] [Indexed: 11/09/2022] Open
Abstract
The importance of dynamic factors in enzyme evolution is gaining recognition. Here we study how the evolution of a new enzymatic activity exploits conformational tinkering and demonstrate that conversion of a dimeric phosphotriesterase to an arylesterase in Pseudomonas diminuta is accompanied by structural divergence between the two subunits. Deviations in loop conformations increase with promiscuity, leading to functionally distinct states, while they decrease during specialisation for the new function. We show that opposite loop movements in the two subunits are due to a dynamic coupling with the dimer interface, the importance of which is also corroborated by the co-evolution of the loop and interface residues. These results illuminate how protein dynamics promotes conformational heterogeneity in a dimeric enzyme, leading to alternative evolutionary pathways for the emergence of a new function.
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Affiliation(s)
- V Ambrus
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Gy Hoffka
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - M Fuxreiter
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary. .,Department of Biomedical Sciences, University of Padova, Padua, Italy.
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36
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Wingert B, Krieger J, Li H, Bahar I. Adaptability and specificity: how do proteins balance opposing needs to achieve function? Curr Opin Struct Biol 2020; 67:25-32. [PMID: 33053463 DOI: 10.1016/j.sbi.2020.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 08/30/2020] [Accepted: 08/30/2020] [Indexed: 12/14/2022]
Abstract
Many proteins select from a small repertoire of 3-dimensional folds retained over evolutional timescales and recruited for different functions, with changes in local structure and sequence to enable specificity. Recent studies have revealed the evolutionary constraints on protein dynamics to achieve function. The significance of protein dynamics in simultaneously satisfying conformational flexibility/malleability and stability/precision requirements becomes clear upon dissecting the spectrum of equilibrium motions accessible to fold families. Accessibility to highly conserved global modes of motions shared by family members, to low-to-intermediate-frequency modes that distinguish subfamilies and confer specificity, and to conserved high-frequency modes ensuring chemical precision and core stability underlies functional specialization while exploiting highly versatile folds. These design principles are illustrated for the family of PDZ domains.
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Affiliation(s)
- Bentley Wingert
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA 15213 USA
| | - James Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA 15213 USA
| | - Hongchun Li
- Research Center for Computer-Aided Drug Discovery at Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA 15213 USA.
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37
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Meemongkolkiat T, Allison J, Seebacher F, Lim J, Chanchao C, Oldroyd BP. Thermal adaptation in the honeybee ( Apis mellifera) via changes to the structure of malate dehydrogenase. ACTA ACUST UNITED AC 2020; 223:jeb.228239. [PMID: 32680901 DOI: 10.1242/jeb.228239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/14/2020] [Indexed: 11/20/2022]
Abstract
In honeybees there are three alleles of cytosolic malate dehydrogenase gene: F, M and S. Allele frequencies are correlated with environmental temperature, suggesting that the alleles have temperature-dependent fitness benefits. We determined the enzyme activity of each allele across a range of temperatures in vitro The F and S alleles have higher activity and are less sensitive to high temperatures than the M allele, which loses activity after incubation at temperatures found in the thorax of foraging bees in hot climates. Next, we predicted the protein structure of each allele and used molecular dynamics simulations to investigate their molecular flexibility. The M allozyme is more flexible than the S and F allozymes at 50°C, suggesting a plausible explanation for its loss of activity at high temperatures, and has the greatest structural flexibility at 15°C, suggesting that it can retain some enzyme activity at cooler temperatures. MM bees recovered from 2 h of cold narcosis significantly better than all other genotypes. Combined, these results explain clinal variation in malate dehydrogenase allele frequencies in the honeybee at the molecular level.
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Affiliation(s)
- Thitipan Meemongkolkiat
- Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.,Macleay Building A12, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jane Allison
- Digital Life Institute and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Private Bag, 92019 Auckland, New Zealand
| | - Frank Seebacher
- Heyden Laurence Building, The University of Sydney, Sydney, NSW 2006, Australia
| | - Julianne Lim
- Macleay Building A12, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chanpen Chanchao
- Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Benjamin P Oldroyd
- Macleay Building A12, The University of Sydney, Sydney, NSW 2006, Australia
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38
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Ding F, Peng W, Peng YK, Liu BQ. Elucidating the potential neurotoxicity of chiral phenthoate: Molecular insight from experimental and computational studies. CHEMOSPHERE 2020; 255:127007. [PMID: 32416396 DOI: 10.1016/j.chemosphere.2020.127007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
Chiral organophosphorus pollutants are existed ubiquitously in the ecological environment, but the enantioselective toxicities of these nerve agents to humans and their molecular bases have not been fully elucidated. Using experimental and computational approaches, this story was to explore the neurotoxic response process of the target acetylcholinesterase (AChE) to chiral phenthoate and further decipher the microscopic mechanism of such toxicological effect at the enantiomeric level. The results showed that the toxic reaction of AChE with chiral phenthoate exhibited significant enantioselectivity, and (R)-phenthoate (K=1.486 × 105 M-1) has a bioaffinity for the nerve enzyme nearly three times that of (S)-phenthoate (K=4.503 × 104 M-1). Dynamic research outcomes interpreted the wet experiments, and the inherent conformational flexibility of the target enzyme has a great influence on the enantioselective neurotoxicological action processes, especially reflected in the conformational changes of the three key loop regions (i.e. residues His-447, Gly-448, and Tyr-449; residues Gly-122, Phe-123, and Tyr-124; and residues Thr-75, Leu-76, and Tyr-77) around the reaction patch. This was supported by the quantitative results of conformational studies derived from circular dichroism spectroscopy (α-helix: 34.7%→30.2%/31.6%; β-sheet: 23.6%→19.5%/20.7%; turn: 19.2%→22.4%/21.9%; and random coil: 22.5%→27.9%/25.8%). Meanwhile, via analyzing the modes of toxic action and free energies, we can find that (R)-phenthoate has a strong inhibitory effect on the enzymatic activity of AChE, as compared with (S)-phenthoate, and electrostatic energy (-23.79/-17.77 kJ mol-1) played a critical role in toxicological reactions. These points were the underlying causes of chiral phenthoate displaying different degrees of enantioselective neurotoxicity.
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Affiliation(s)
- Fei Ding
- Department of Environmental Science and Engineering, School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, No. 126 Yanta Road, Yanta District, Xi'an, 710054, China
| | - Wei Peng
- 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, Xiamen, 361005, China.
| | - Yu-Kui Peng
- Center for Food Quality Supervision, Inspection & Testing, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, 712100, China
| | - Bing-Qi Liu
- Department of Agricultural Chemistry, Qingdao Agricultural University, Qingdao, 266109, China
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Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity. Biochem J 2020; 476:3475-3492. [PMID: 31675069 PMCID: PMC6874516 DOI: 10.1042/bcj20190625] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/30/2019] [Accepted: 11/01/2019] [Indexed: 12/18/2022]
Abstract
Apoptotic caspases evolved with metazoans more than 950 million years ago (MYA), and a series of gene duplications resulted in two subfamilies consisting of initiator and effector caspases. The effector caspase genes (caspases-3, -6, and -7) were subsequently fixed into the Chordata phylum more than 650 MYA when the gene for a common ancestor (CA) duplicated, and the three effector caspases have persisted throughout mammalian evolution. All caspases prefer an aspartate residue at the P1 position of substrates, so each caspase evolved discrete cellular roles through changes in substrate recognition at the P4 position combined with allosteric regulation. We examined the evolution of substrate specificity in caspase-6, which prefers valine at the P4 residue, compared with caspases-3 and -7, which prefer aspartate, by reconstructing the CA of effector caspases (AncCP-Ef1) and the CA of caspase-6 (AncCP-6An). We show that AncCP-Ef1 is a promiscuous enzyme with little distinction between Asp, Val, or Leu at P4. The specificity of caspase-6 was defined early in its evolution, where AncCP-6An demonstrates a preference for Val over Asp at P4. Structures of AncCP-Ef1 and of AncCP-6An show a network of charged amino acids near the S4 pocket that, when combined with repositioning a flexible active site loop, resulted in a more hydrophobic binding pocket in AncCP-6An. The ancestral protein reconstructions show that the caspase-hemoglobinase fold has been conserved for over 650 million years and that only three substitutions in the scaffold are necessary to shift substrate selection toward Val over Asp.
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40
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Crean RM, Gardner JM, Kamerlin SCL. Harnessing Conformational Plasticity to Generate Designer Enzymes. J Am Chem Soc 2020; 142:11324-11342. [PMID: 32496764 PMCID: PMC7467679 DOI: 10.1021/jacs.0c04924] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Indexed: 02/08/2023]
Abstract
Recent years have witnessed an explosion of interest in understanding the role of conformational dynamics both in the evolution of new enzymatic activities from existing enzymes and in facilitating the emergence of enzymatic activity de novo on scaffolds that were previously non-catalytic. There are also an increasing number of examples in the literature of targeted engineering of conformational dynamics being successfully used to alter enzyme selectivity and activity. Despite the obvious importance of conformational dynamics to both enzyme function and evolvability, many (although not all) computational design approaches still focus either on pure sequence-based approaches or on using structures with limited flexibility to guide the design. However, there exist a wide variety of computational approaches that can be (re)purposed to introduce conformational dynamics as a key consideration in the design process. Coupled with laboratory evolution and more conventional existing sequence- and structure-based approaches, these techniques provide powerful tools for greatly expanding the protein engineering toolkit. This Perspective provides an overview of evolutionary studies that have dissected the role of conformational dynamics in facilitating the emergence of novel enzymes, as well as advances in computational approaches that allow one to target conformational dynamics as part of enzyme design. Harnessing conformational dynamics in engineering studies is a powerful paradigm with which to engineer the next generation of designer biocatalysts.
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Affiliation(s)
- Rory M. Crean
- Department of Chemistry -
BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Jasmine M. Gardner
- Department of Chemistry -
BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Department of Chemistry -
BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
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41
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Gupta P, Liang Z, Freed JH. Microsecond dynamics in proteins by two-dimensional ESR: Predictions. J Chem Phys 2020; 152:214112. [PMID: 32505151 PMCID: PMC7863697 DOI: 10.1063/5.0008094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/14/2020] [Indexed: 01/04/2023] Open
Abstract
Two-dimensional electron-electron double resonance (2D-ELDOR) provides extensive insight into molecular motions. Recent developments permitting experiments at higher frequencies (95 GHz) provide molecular orientational resolution, enabling a clearer description of the nature of the motions. In this work, simulations are provided for the example of domain motions within proteins that are themselves slowly tumbling in solution. These show the nature of the exchange cross-peaks that are predicted to develop in real time from such domain motions. However, we find that the existing theoretical methods for computing 2D-ELDOR experiments over a wide motional range begin to fail seriously when applied to very slow motions characteristic of proteins in solution. One reason is the failure to obtain accurate eigenvectors and eigenvalues of the complex symmetric stochastic Liouville matrices describing the experiment when computed by the efficient Lanczos algorithm in the range of very slow motion. Another, perhaps more serious, issue is that these matrices are "non-normal," such that for the very slow motional range even rigorous diagonalization algorithms do not yield the correct eigenvalues and eigenvectors. We have employed algorithms that overcome both these issues and lead to valid 2D-ELDOR predictions even for motions approaching the rigid limit. They are utilized to describe the development of cross-peaks in 2D-ELDOR at 95 GHz for a particular case of domain motion.
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Affiliation(s)
- Pranav Gupta
- Department of Chemistry and Chemical Biology, National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York 14853, USA
| | - Zhichun Liang
- Department of Chemistry and Chemical Biology, National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York 14853, USA
| | - Jack H. Freed
- Department of Chemistry and Chemical Biology, National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York 14853, USA
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42
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Borges PT, Brissos V, Hernandez G, Masgrau L, Lucas MF, Monza E, Frazão C, Cordeiro TN, Martins LO. Methionine-Rich Loop of Multicopper Oxidase McoA Follows Open-to-Close Transitions with a Role in Enzyme Catalysis. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01623] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Patrícia T. Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Vânia Brissos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Guillem Hernandez
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Laura Masgrau
- Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain
- Department of Chemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | | | - Emanuele Monza
- Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Tiago N. Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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Abstract
We review the adaptations of enzyme activity to different temperatures. Psychrophilic (cold-adapted) enzymes show significantly different activation parameters (lower activation enthalpies and entropies) from their mesophilic counterparts. Furthermore, there is increasing evidence that the temperature dependence of many enzyme-catalyzed reactions is more complex than is widely believed. Many enzymes show curvature in plots of activity versus temperature that is not accounted for by denaturation or unfolding. This is explained by macromolecular rate theory: A negative activation heat capacity for the rate-limiting chemical step leads directly to predictions of temperature optima; both entropy and enthalpy are temperature dependent. Fluctuations in the transition state ensemble are reduced compared to the ground state. We show how investigations combining experiment with molecular simulation are revealing fundamental details of enzyme thermoadaptation that are relevant for understanding aspects of enzyme evolution. Simulations can calculate relevant thermodynamic properties (such as activation enthalpies, entropies, and heat capacities) and reveal the molecular mechanisms underlying experimentally observed behavior.
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Affiliation(s)
- Vickery L Arcus
- School of Science, University of Waikato, Hamilton 3240, New Zealand;
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
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44
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Surpeta B, Sequeiros-Borja CE, Brezovsky J. Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering. Int J Mol Sci 2020; 21:E2713. [PMID: 32295283 PMCID: PMC7215530 DOI: 10.3390/ijms21082713] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/10/2020] [Accepted: 04/12/2020] [Indexed: 12/13/2022] Open
Abstract
Computational prediction has become an indispensable aid in the processes of engineering and designing proteins for various biotechnological applications. With the tremendous progress in more powerful computer hardware and more efficient algorithms, some of in silico tools and methods have started to apply the more realistic description of proteins as their conformational ensembles, making protein dynamics an integral part of their prediction workflows. To help protein engineers to harness benefits of considering dynamics in their designs, we surveyed new tools developed for analyses of conformational ensembles in order to select engineering hotspots and design mutations. Next, we discussed the collective evolution towards more flexible protein design methods, including ensemble-based approaches, knowledge-assisted methods, and provable algorithms. Finally, we highlighted apparent challenges that current approaches are facing and provided our perspectives on their further development.
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Affiliation(s)
- Bartłomiej Surpeta
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (B.S.); (C.E.S.-B.)
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, 02-109 Warsaw, Poland
| | - Carlos Eduardo Sequeiros-Borja
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (B.S.); (C.E.S.-B.)
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, 02-109 Warsaw, Poland
| | - Jan Brezovsky
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (B.S.); (C.E.S.-B.)
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, 02-109 Warsaw, Poland
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45
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Gardner JM, Biler M, Risso VA, Sanchez-Ruiz JM, Kamerlin SCL. Manipulating Conformational Dynamics To Repurpose Ancient Proteins for Modern Catalytic Functions. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00722] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jasmine M. Gardner
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Michal Biler
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Valeria A. Risso
- Departamento de Quı́mica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quı́mica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Jose M. Sanchez-Ruiz
- Departamento de Quı́mica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quı́mica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Shina C. L. Kamerlin
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
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46
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Pollack JD, Gerard D, Makhatadze GI, Pearl DK. Evolutionary conservation and structural localizations suggest a physical trace of metabolism’s progressive geochronological emergence. J Biomol Struct Dyn 2019; 38:3700-3719. [DOI: 10.1080/07391102.2019.1679666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- J. Dennis Pollack
- Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - David Gerard
- Department of Mathematics and Statistics, American University, Washington, DC, USA
| | - George I. Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Dennis K. Pearl
- Department of Statistics, Penn State University, University Park, Pennsylvania, USA
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Abrusán G, Marsh JA. Ligand-Binding-Site Structure Shapes Allosteric Signal Transduction and the Evolution of Allostery in Protein Complexes. Mol Biol Evol 2019; 36:1711-1727. [PMID: 31004156 PMCID: PMC6657754 DOI: 10.1093/molbev/msz093] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The structure of ligand-binding sites has been shown to profoundly influence the evolution of function in homomeric protein complexes. Complexes with multichain binding sites (MBSs) have more conserved quaternary structure, more similar binding sites and ligands between homologs, and evolve new functions slower than homomers with single-chain binding sites (SBSs). Here, using in silico analyses of protein dynamics, we investigate whether ligand-binding-site structure shapes allosteric signal transduction pathways, and whether the structural similarity of binding sites influences the evolution of allostery. Our analyses show that: 1) allostery is more frequent among MBS complexes than in SBS complexes, particularly in homomers; 2) in MBS homomers, semirigid communities and critical residues frequently connect interfaces and thus they are characterized by signal transduction pathways that cross protein-protein interfaces, whereas SBS homomers usually not; 3) ligand binding alters community structure differently in MBS and SBS homomers; and 4) except MBS homomers, allosteric proteins are more likely to have homologs with similar binding site than nonallosteric proteins, suggesting that binding site similarity is an important factor driving the evolution of allostery.
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Affiliation(s)
- György Abrusán
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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Laciak AR, Korasick DA, Wyatt JW, Gates KS, Tanner JJ. Structural and biochemical consequences of pyridoxine-dependent epilepsy mutations that target the aldehyde binding site of aldehyde dehydrogenase ALDH7A1. FEBS J 2019; 287:173-189. [PMID: 31302938 DOI: 10.1111/febs.14997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/21/2019] [Accepted: 07/10/2019] [Indexed: 01/17/2023]
Abstract
In humans, certain mutations in the gene encoding aldehyde dehydrogenase 7A1 are associated with pyridoxine-dependent epilepsy (PDE). Understanding the impact of PDE-causing mutations on the structure and activity of ALDH7A1 could allow for the prediction of symptom-severity and aid the development of patient-specific medical treatments. Herein, we investigate the biochemical and structural consequences of PDE missense mutations targeting residues in the aldehyde substrate binding site: N167S, P169S, A171V, G174V, and W175G. All but G174V could be purified for biochemical and X-ray crystallographic analysis. W175G has a relatively mild kinetic defect, exhibiting a fivefold decrease in kcat with no change in Km . P169S and N167S have moderate defects, characterized by catalytic efficiencies of 20- and 100-times lower than wild-type, respectively. A171V has a profound functional defect, with catalytic efficiency 2000-times lower than wild-type. The crystal structures of the variants are the first for any PDE-associated mutant of ALDH7A1. The structures show that missense mutations that decrease the steric bulk of the side chain tend to create a cavity in the active site. The protein responds by relaxing into the vacant space, and this structural perturbation appears to cause misalignment of the aldehyde substrate in W175G and N167S. The P169S structure is nearly identical to that of the wild-type enzyme; however, analysis of B-factors suggests the catalytic defect may result from altered protein dynamics. The A171V structure suggests that the potential for steric clash with Val171 prevents Glu121 from ion pairing with the amino group of the aldehyde substrate. ENZYMES: Aldehyde dehydrogenase 7A1 (EC1.2.1.31). DATABASES: Coordinates have been deposited in the Protein Data Bank under the following accession codes: 6O4B, 6O4C, 6O4D, 6O4E, 6O4F, 6O4G, 6O4H.
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Affiliation(s)
- Adrian R Laciak
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Jesse W Wyatt
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Kent S Gates
- Department of Chemistry, University of Missouri, Columbia, MO, USA.,Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - John J Tanner
- Department of Chemistry, University of Missouri, Columbia, MO, USA.,Department of Biochemistry, University of Missouri, Columbia, MO, USA
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Tonin F, Otten LG, Arends IWCE. NAD + -Dependent Enzymatic Route for the Epimerization of Hydroxysteroids. CHEMSUSCHEM 2019; 12:3192-3203. [PMID: 30265441 PMCID: PMC6681466 DOI: 10.1002/cssc.201801862] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/28/2018] [Indexed: 05/12/2023]
Abstract
Epimerization of cholic and chenodeoxycholic acid (CA and CDCA, respectively) is a notable conversion for the production of ursodeoxycholic acid (UDCA). Two enantiocomplementary hydroxysteroid dehydrogenases (7α- and 7β-HSDHs) can carry out this transformation fully selectively by specific oxidation of the 7α-OH group of the substrate and subsequent reduction of the keto intermediate to the final product (7β-OH). With a view to developing robust and active biocatalysts, novel NADH-active 7β-HSDH species are necessary to enable a solely NAD+ -dependent redox-neutral cascade for UDCA production. A wild-type NADH-dependent 7β-HSDH from Lactobacillus spicheri (Ls7β-HSDH) was identified, recombinantly expressed, purified, and biochemically characterized. Using this novel NAD+ -dependent 7β-HSDH enzyme in combination with 7α-HSDH from Stenotrophomonas maltophilia permitted the biotransformations of CA and CDCA in the presence of catalytic amounts of NAD+ , resulting in high yields (>90 %) of UCA and UDCA.
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Affiliation(s)
- Fabio Tonin
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629HZDelftThe Netherlands
| | - Linda G. Otten
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629HZDelftThe Netherlands
| | - Isabel W. C. E. Arends
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629HZDelftThe Netherlands
- Present address: Faculty of ScienceUtrecht UniversityBudapestlaan 63584 CDUtrechtThe Netherlands
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Abstract
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The enormous rate accelerations observed
for many enzyme catalysts
are due to strong stabilizing interactions between the protein and
reaction transition state. The defining property of these catalysts
is their specificity for binding the transition state with a much
higher affinity than substrate. Experimental results are presented
which show that the phosphodianion-binding energy of phosphate monoester
substrates is used to drive conversion of their protein catalysts
from flexible and entropically rich ground states to stiff and catalytically
active Michaelis complexes. These results are generalized to other
enzyme-catalyzed reactions. The existence of many enzymes in flexible,
entropically rich, and inactive ground states provides a mechanism
for utilization of ligand-binding energy to mold these catalysts into
stiff and active forms. This reduces the substrate-binding energy
expressed at the Michaelis complex, while enabling the full and specific
expression of large transition-state binding energies. Evidence is
presented that the complexity of enzyme conformational changes increases
with increases in the enzymatic rate acceleration. The requirement
that a large fraction of the total substrate-binding energy be utilized
to drive conformational changes of floppy enzymes is proposed to favor
the selection and evolution of protein folds with multiple flexible
unstructured loops, such as the TIM-barrel fold. The effect of protein
motions on the kinetic parameters for enzymes that undergo ligand-driven
conformational changes is considered. The results of computational
studies to model the complex ligand-driven conformational change in
catalysis by triosephosphate isomerase are presented.
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Affiliation(s)
- John P Richard
- Department of Chemistry , SUNY, University at Buffalo , Buffalo , New York 14260-3000 , United States
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