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Mandal N, Surpeta B, Brezovsky J. Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics. J Chem Inf Model 2024. [PMID: 39143923 DOI: 10.1021/acs.jcim.4c00966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Tunnels are structural conduits in biomolecules responsible for transporting chemical compounds and solvent molecules from the active site. They have been shown to be present in a wide variety of enzymes across all functional and structural classes. However, the study of such pathways is experimentally challenging, because they are typically transient. Computational methods, such as molecular dynamics (MD) simulations, have been successfully proposed to explore tunnels. Conventional MD (cMD) provides structural details to characterize tunnels but suffers from sampling limitations to capture rare tunnel openings on longer time scales. Therefore, in this study, we explored the potential of Gaussian accelerated MD (GaMD) simulations to improve the exploration of complex tunnel networks in enzymes. We used the haloalkane dehalogenase LinB and its two variants with engineered transport pathways, which are not only well-known for their application potential but have also been extensively studied experimentally and computationally regarding their tunnel networks and their importance in multistep catalytic reactions. Our study demonstrates that GaMD efficiently improves tunnel sampling and allows the identification of all known tunnels for LinB and its two mutants. Furthermore, the improved sampling provided insight into a previously unknown transient side tunnel (ST). The extensive conformational landscape explored by GaMD simulations allowed us to investigate in detail the mechanism of ST opening. We determined variant-specific dynamic properties of ST opening, which were previously inaccessible due to limited sampling of cMD. Our comprehensive analysis supports multiple indicators of the functional relevance of the ST, emphasizing its potential significance beyond structural considerations. In conclusion, our research proves that the GaMD method can overcome the sampling limitations of cMD for the effective study of tunnels in enzymes, providing further means for identifying rare tunnels in enzymes with the potential for drug development, precision medicine, and rational protein engineering.
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Affiliation(s)
- Nishita Mandal
- 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, Poznan 61-614, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, Warsaw 02-109, Poland
| | - Bartlomiej 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, Poznan 61-614, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, Warsaw 02-109, 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, Poznan 61-614, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, Warsaw 02-109, Poland
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2
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Sequeiros-Borja C, Surpeta B, Thirunavukarasu AS, Dongmo Foumthuim CJ, Marchlewski I, Brezovsky J. Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases. J Chem Inf Model 2024; 64:6014-6025. [PMID: 38669675 PMCID: PMC11323245 DOI: 10.1021/acs.jcim.4c00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
An aqueous environment is vital for life as we know it, and water is essential for nearly all biochemical processes at the molecular level. Proteins utilize water molecules in various ways. Consequently, proteins must transport water molecules across their internal network of tunnels to reach the desired action sites, either within them or by functioning as molecular pipes to control cellular osmotic pressure. Despite water playing a crucial role in enzymatic activity and stability, its transport has been largely overlooked, with studies primarily focusing on water transport across membrane proteins. The transport of molecules through a protein's tunnel network is challenging to study experimentally, making molecular dynamics simulations the most popular approach for investigating such events. In this study, we focused on the transport of water molecules across three different α/β-hydrolases: haloalkane dehalogenase, epoxide hydrolase, and lipase. Using a 5 μs adaptive simulation per system, we observed that only a few tunnels were responsible for the majority of water transport in dehalogenase, in contrast to a higher diversity of tunnels in other enzymes. Interestingly, water molecules could traverse narrow tunnels with subangstrom bottlenecks, which is surprising given the commonly accepted water molecule radius of 1.4 Å. Our analysis of the transport events in such narrow tunnels revealed a markedly increased number of hydrogen bonds formed between the water molecules and protein, likely compensating for the steric penalty of the process. Overall, these commonly disregarded narrow tunnels accounted for ∼20% of the total water transport observed, emphasizing the need to surpass the standard geometrical limits on the functional tunnels to properly account for the relevant transport processes. Finally, we demonstrated how the obtained insights could be applied to explain the differences in a mutant of the human soluble epoxide hydrolase associated with a higher incidence of ischemic stroke.
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Affiliation(s)
- Carlos Sequeiros-Borja
- International
Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland
| | - Bartlomiej Surpeta
- International
Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland
| | - Aravind Selvaram Thirunavukarasu
- International
Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland
| | | | - Igor Marchlewski
- International
Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland
| | - Jan Brezovsky
- International
Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland
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3
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Krishna NB, Roopa L, Pravin Kumar R, S GT. Computational studies on the catalytic potential of the double active site for enzyme engineering. Sci Rep 2024; 14:17892. [PMID: 39095391 PMCID: PMC11297320 DOI: 10.1038/s41598-024-60824-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/27/2024] [Indexed: 08/04/2024] Open
Abstract
Proteins possessing double active sites have the potential to revolutionise enzyme design strategies. This study extensively explored an enzyme that contains both a natural active site (NAS) and an engineered active site (EAS), focusing on understanding its structural and functional properties. Metadynamics simulations were employed to investigate how substrates interacted with their respective active sites. The results revealed that both the NAS and EAS exhibited similar minimum energy states, indicating comparable binding affinities. However, it became apparent that the EAS had a weaker binding site for the substrate due to its smaller pocket and constrained conformation. Interestingly, the EAS also displayed dynamic behaviour, with the substrate observed to move outside the pocket, suggesting the possibility of substrate translocation. To gain further insights, steered molecular dynamics (SMD) simulations were conducted to study the conformational changes of the substrate and its interactions with catalytic residues. Notably, the substrate adopted distinct conformations, including near-attack conformations, in both the EAS and NAS. Nevertheless, the NAS demonstrated superior binding minima for the substrate compared to the EAS, reinforcing the observation that the engineered active site was less favourable for substrate binding due to its limitations. The QM/MM (Quantum mechanics and molecular mechanics) analyses highlight the energy disparity between NAS and EAS. Specifically, EAS exhibited elevated energy levels due to its engineered active site being located on the surface. This positioning exposes the substrate to solvents and water molecules, adding to the energy challenge. Consequently, the engineered enzyme did not provide a significant advantage in substrate binding over the single active site protein. Further, the investigation of internal channels and tunnels within the protein shed light on the pathways facilitating transport between the two active sites. By unravelling the complex dynamics and functional characteristics of this double-active site protein, this study offers valuable insights into novel strategies of enzyme engineering. These findings establish a solid foundation for future research endeavours aimed at harnessing the potential of double-active site proteins in diverse biotechnological applications.
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Affiliation(s)
- Naveen Banchallihundi Krishna
- Department of Computational Biology and AI, Kcat Enzymatic Private Limited, #16, Ramakrishnappa Road, Cox Town, Bangalore, 560005, India
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, 570015, India
| | - Lalitha Roopa
- Department of Computational Biology and AI, Kcat Enzymatic Private Limited, #16, Ramakrishnappa Road, Cox Town, Bangalore, 560005, India
| | - R Pravin Kumar
- Department of Computational Biology and AI, Kcat Enzymatic Private Limited, #16, Ramakrishnappa Road, Cox Town, Bangalore, 560005, India.
| | - Gopenath T S
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, 570015, India
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4
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Fernandes DC, Eto SF, Baldassi AC, Balbuena TS, Charlie-Silva I, de Andrade Belo MA, Pizauro JM. Meningitis caused by Aeromonas hydrophila in Oreochromis niloticus: Proteomics and druggability of virulence factors. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109687. [PMID: 38866348 DOI: 10.1016/j.fsi.2024.109687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/30/2024] [Accepted: 06/08/2024] [Indexed: 06/14/2024]
Abstract
Meningitis caused by Gram-negative bacteria is a serious public health problem, causing morbidity and mortality in both children and adults. Here, we propose a novel experimental model using Nile tilapia (Oreochromis niloticus) to study neuroinflammation. The fish were infected with Aeromonas hydrophila, and the course of infection was monitored in the peripheral blood. Septicemia was obvious in the blood, while in the brain tissue, infection of the meninges was present. The histopathological examination showed suppurative meningitis, and the cellular immune response in the brain tissue during infection was mediated by microglia. These cells were morphologically characterized and phenotyped by MHC class II markers and CD68. The increased production of TNF-α, IL-1β and iNOS supported the infiltration of these cells during the neuroinflammatory process. In the proteomic analysis of A. hydrophila isolated from brain tissue, we found chemotactic and transport proteins, proteolytic enzymes and enzymes associated with the dismutation of nitric oxide (NO), as well as motor proteins and those responsible for cell division. After characterizing the most abundant proteins during the course of infection, we investigated the druggability index of these proteins and identified promising peptide sequences as molecular targets that are similar among bacteria. Thus, these findings deepened the understanding of the pathophysiology of meningitis caused by A. hydrophila. Moreover, through the proteomics analysis, important mechanisms and pathways used by the pathogen to subvert the host response were revealed, providing insights for the development of novel antibiotics and vaccines.
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Affiliation(s)
- Dayanne Carla Fernandes
- Institute of Chemistry, São Paulo State University (Unesp), Araraquara, Sao Paulo, SP, Brazil.
| | - Silas Fernandes Eto
- Laboratory Center of Excellence in New Target Discovery (CENTD) Special Laboratory, Butantan Institute, São Paulo, SP, Brazil
| | - Amanda Cristina Baldassi
- Department of Technology, School of Agrarian and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, Sao Paulo, SP, Brazil
| | - Thiago Santana Balbuena
- Department of Technology, School of Agrarian and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, Sao Paulo, SP, Brazil
| | - Ives Charlie-Silva
- Institute of Chemistry, São Paulo State University (Unesp), Araraquara, Sao Paulo, SP, Brazil
| | | | - João Martins Pizauro
- Department of Technology, School of Agrarian and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, Sao Paulo, SP, Brazil
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5
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Dali A, Gabler T, Sebastiani F, Furtmüller PG, Becucci M, Hofbauer S, Smulevich G. Entrance channels to coproheme in coproporphyrin ferrochelatase probed by exogenous imidazole binding. J Inorg Biochem 2024; 260:112681. [PMID: 39146673 DOI: 10.1016/j.jinorgbio.2024.112681] [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: 05/17/2024] [Revised: 07/25/2024] [Accepted: 07/27/2024] [Indexed: 08/17/2024]
Abstract
Iron insertion into porphyrins is an essential step in heme biosynthesis. In the coproporphyrin-dependent pathway, specific to monoderm bacteria, this reaction is catalyzed by the monomeric enzyme coproporphyrin ferrochelatase. In addition to the mechanistic details of the metalation of the porphyrin, the identification of the substrate access channel for ferrous iron to the active site is important to fully understand this enzymatic system. In fact, whether the iron reaches the active site from the distal or the proximal porphyrin side is still under debate. In this study we have thoroughly addressed this question in Listeria monocytogenes coproporphyrin ferrochelatase by X-ray crystallography, steady-state and pre-steady-state imidazole ligand binding studies, together with a detailed spectroscopic characterization using resonance Raman and UV-vis absorption spectroscopies in solution. Analysis of the X-ray structures of coproporphyrin ferrochelatase-coproporphyrin III crystals soaked with ferrous iron shows that iron is present on both sides of the porphyrin. The kinetic and spectroscopic study of imidazole binding to coproporphyrin ferrochelatase‑iron coproporphyrin III clearly indicates the presence of two possible binding sites in this monomeric enzyme that influence each other, which is confirmed by the observed cooperativity at steady-state and a biphasic behavior in the pre-steady-state experiments. The current results are discussed in the context of the entire heme biosynthetic pathway and pave the way for future studies focusing on protein-protein interactions.
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Affiliation(s)
- Andrea Dali
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Thomas Gabler
- BOKU University, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Federico Sebastiani
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Paul G Furtmüller
- BOKU University, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Maurizio Becucci
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy; The European Laboratory for Non-Linear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino (FI), Italy.
| | - Stefan Hofbauer
- BOKU University, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria.
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy; INSTM Research Unit of Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy.
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6
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Betts PC, Blakely SJ, Rutkowski BN, Bender B, Klingler C, Froese JT. Engineering of Rieske dioxygenase variants with improved cis-dihydroxylation activity for benzoates. Biotechnol Bioeng 2024. [PMID: 38951963 DOI: 10.1002/bit.28786] [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: 04/04/2024] [Revised: 06/13/2024] [Accepted: 06/16/2024] [Indexed: 07/03/2024]
Abstract
Rieske dioxygenases have a long history of being utilized as green chemical tools in the organic synthesis of high-value compounds, due to their capacity to perform the cis-dihydroxylation of a wide variety of aromatic substrates. The practical utility of these enzymes has been hampered however by steric and electronic constraints on their substrate scopes, resulting in limited reactivity with certain substrate classes. Herein, we report the engineering of a widely used member of the Rieske dioxygenase class of enzymes, toluene dioxygenase (TDO), to produce improved variants with greatly increased activity for the cis-dihydroxylation of benzoates. Through rational mutagenesis and screening, TDO variants with substantially improved activity over the wild-type enzyme were identified. Homology modeling, docking studies, molecular dynamics simulations, and substrate tunnel analysis were applied in an effort to elucidate how the identified mutations resulted in improved activity for this polar substrate class. These analyses revealed modification of the substrate tunnel as the likely cause of the improved activity observed with the best-performing enzyme variants.
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Affiliation(s)
- Phillip C Betts
- Department of Chemistry, Ball State University, Muncie, Indiana, USA
| | - Spencer J Blakely
- Department of Chemistry, Ball State University, Muncie, Indiana, USA
| | | | - Brandon Bender
- Department of Chemistry, Ball State University, Muncie, Indiana, USA
| | - Cole Klingler
- Department of Chemistry, Ball State University, Muncie, Indiana, USA
| | - Jordan T Froese
- Department of Chemistry, Ball State University, Muncie, Indiana, USA
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7
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Guo B, Xue Q, Zhang Z, Zhai J, Wang C, Zhao Y, Zhang J. Atomic Insight into the Enzymatic Selectivity of Acetyltransferase for Endogenous Polyamines. Chemphyschem 2024:e202400412. [PMID: 38772911 DOI: 10.1002/cphc.202400412] [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: 04/23/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 05/23/2024]
Abstract
The N1-Spermidine/spermine acetyltransferase (SSAT) serves as the rate-limiting enzyme in the polyamine metabolism pathway, specifically catalyzing the acetylation of spermidine, spermine, and other specific polyamines. The source of its enzymatic selectivity remains elusive. Here, we used quantum mechanics and molecular mechanics simulations combined with various technologies to explore the enzymatic mechanism of SSAT for endogenous polyamines from an atomic perspective. The static binding and chemical transformation were considered. The binding affinity was identified to be dependent on protonated state of polyamine. The order of the binding affinity for Spm, Spd, and Put is consistent with the experimental results, which is also verified by the dynamic separation of polyamine and SSAT. Hydrogen bond interactions and salt bridges contribute most, and the common hot residues were identified. In addition, the transfer of acetyl and proton between polyamine and AcCoA was discovered to follow a concert mechanism, and thermodynamic properties are responsible for the catalytic efficiency of SSAT. This work may be helpful for development of polyamine derivatives based on catalysis to regulate polyamine metabolism.
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Affiliation(s)
- Baolin Guo
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, State Key Laboratory of Antiviral Drugs, Henan University, Kaifeng, 475001, China
| | - Qian Xue
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, State Key Laboratory of Antiviral Drugs, Henan University, Kaifeng, 475001, China
| | - Zhiyang Zhang
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, State Key Laboratory of Antiviral Drugs, Henan University, Kaifeng, 475001, China
| | - Jihang Zhai
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, State Key Laboratory of Antiviral Drugs, Henan University, Kaifeng, 475001, China
| | - Chaojie Wang
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, State Key Laboratory of Antiviral Drugs, Henan University, Kaifeng, 475001, China
| | - Yuan Zhao
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, State Key Laboratory of Antiviral Drugs, Henan University, Kaifeng, 475001, China
| | - Jie Zhang
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, State Key Laboratory of Antiviral Drugs, Henan University, Kaifeng, 475001, China
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8
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Son Y, Kenny TC, Khan A, Birsoy K, Hite RK. Structural basis of lipid head group entry to the Kennedy pathway by FLVCR1. Nature 2024; 629:710-716. [PMID: 38693265 PMCID: PMC11188936 DOI: 10.1038/s41586-024-07374-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
Phosphatidylcholine and phosphatidylethanolamine, the two most abundant phospholipids in mammalian cells, are synthesized de novo by the Kennedy pathway from choline and ethanolamine, respectively1-6. Despite the essential roles of these lipids, the mechanisms that enable the cellular uptake of choline and ethanolamine remain unknown. Here we show that the protein encoded by FLVCR1, whose mutation leads to the neurodegenerative syndrome posterior column ataxia and retinitis pigmentosa7-9, transports extracellular choline and ethanolamine into cells for phosphorylation by downstream kinases to initiate the Kennedy pathway. Structures of FLVCR1 in the presence of choline and ethanolamine reveal that both metabolites bind to a common binding site comprising aromatic and polar residues. Despite binding to a common site, FLVCR1 interacts in different ways with the larger quaternary amine of choline in and with the primary amine of ethanolamine. Structure-guided mutagenesis identified residues that are crucial for the transport of ethanolamine, but dispensable for choline transport, enabling functional separation of the entry points into the two branches of the Kennedy pathway. Altogether, these studies reveal how FLVCR1 is a high-affinity metabolite transporter that serves as the common origin for phospholipid biosynthesis by two branches of the Kennedy pathway.
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Affiliation(s)
- Yeeun Son
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- BCMB Allied Program, Weill Cornell Graduate School, New York, NY, USA
| | - Timothy C Kenny
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Artem Khan
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Richard K Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Hwang J, Lee MJ, Lee SG, Do H, Lee JH. Structural insights into the distinct substrate preferences of two bacterial epoxide hydrolases. Int J Biol Macromol 2024; 264:130419. [PMID: 38423431 DOI: 10.1016/j.ijbiomac.2024.130419] [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: 11/20/2023] [Revised: 01/22/2024] [Accepted: 02/22/2024] [Indexed: 03/02/2024]
Abstract
Epoxide hydrolases (EHs), which catalyze the transformation of epoxides to diols, are present in many eukaryotic and prokaryotic organisms. They have recently drawn considerable attention from organic chemists owing to their application in the semisynthesis of enantiospecific diol compounds. Here, we report the crystal structures of BoEH from Bosea sp. PAMC 26642 and CaEH from Caballeronia sordidicola PAMC 26510 at 1.95 and 2.43 Å resolution, respectively. Structural analysis showed that the overall structures of BoEH and CaEH commonly possess typical α/β hydrolase fold with the same ring-opening residues (Tyr-Tyr) and conserved catalytic triad residues (Asp-Asp-His). However, the two enzymes were found to have significantly different sequence compositions in the cap domain region, which is involved in the formation of the substrate-binding site in both enzymes. Enzyme activity assay results showed that BoEH had the strongest activity toward the linear aliphatic substrates, whereas CaEH had a higher preference for aromatic- and cycloaliphatic substrates. Computational docking simulations and tunnel identification revealed important residues with different substrate-binding preferences. Collectively, structure comparison studies, together with ligand docking simulation results, suggested that the differences in substrate-binding site residues were highly correlated with substrate specificity.
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Affiliation(s)
- Jisub Hwang
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Min Ju Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Sung Gu Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Hackwon Do
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea.
| | - Jun Hyuck Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea.
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Shen F, Yang W, Luan G, Peng J, Li Z, Gao J, Hou Y, Bai G. Catalpolaglycone disrupts mitochondrial thermogenesis by specifically binding to a conserved lysine residue of UCP2 on the proton leak tunnel. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 125:155356. [PMID: 38241920 DOI: 10.1016/j.phymed.2024.155356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/03/2023] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
BACKGROUND Catalpol (CAT), a naturally occurring iridoid glycoside sourced from the root of Rehmannia glutinosa, affects mitochondrial metabolic functions. However, the mechanism of action of CAT against pyrexia and its plausible targets remain to be fully elucidated. PURPOSE This study aimed to identify the specific targets of CAT for blocking mitochondrial thermogenesis and to unveil the unique biological mechanism of action of the orthogonal binding mode between the hemiacetal group and lysine residue on the target protein in vivo. METHODS Lipopolysaccharide (LPS)/ carbonyl cyanide 3-chlorophenylhydrazone (CCCP)-induced fever models were established to evaluate the potential antipyretic effects of CAT. An alkenyl-modified CAT probe was designed to identify and capture potential targets. Binding capacity was tested using in-gel imaging and a cellular thermal shift assay. The underlying antipyretic mechanisms were explored using biochemical and molecular biological methods. Catalpolaglycone (CA) was coupled with protein profile identification and molecular docking analysis to evaluate and identify its binding mode to UCP2. RESULTS After deglycation of CAT in vivo, the hemiacetal group in CA covalently binds to Lys239 of UCP2 in the mitochondria of the liver via an ɛ-amine nucleophilic addition. This irreversible binding affects proton leakage and improves mitochondrial membrane potential and ADP/ATP transformation efficiency, leading to an antipyretic effect. CONCLUSION Our findings highlight the potential role of CA in modulating UCP2 activity or function within the mitochondria and open new avenues for investigating the therapeutic effects of CA on mitochondrial homeostasis.
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Affiliation(s)
- Fukui Shen
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Wen Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Guoqing Luan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Jiamin Peng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Zhenqiang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Jie Gao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China.
| | - Yuanyuan Hou
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China.
| | - Gang Bai
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
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11
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Martins NF, Viana MJA, Maigret B. Fungi Tryptophan Synthases: What Is the Role of the Linker Connecting the α and β Structural Domains in Hemileia vastatrix TRPS? A Molecular Dynamics Investigation. Molecules 2024; 29:756. [PMID: 38398508 PMCID: PMC10893352 DOI: 10.3390/molecules29040756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Tryptophan synthase (TRPS) is a complex enzyme responsible for tryptophan biosynthesis. It occurs in bacteria, plants, and fungi as an αββα heterotetramer. Although encoded by independent genes in bacteria and plants, in fungi, TRPS is generated by a single gene that concurrently expresses the α and β entities, which are linked by an elongated peculiar segment. We conducted 1 µs all-atom molecular dynamics simulations on Hemileia vastatrix TRPS to address two questions: (i) the role of the linker segment and (ii) the comparative mode of action. Since there is not an experimental structure, we started our simulations with homology modeling. Based on the results, it seems that TRPS makes use of an already-existing tunnel that can spontaneously move the indole moiety from the α catalytic pocket to the β one. Such behavior was completely disrupted in the simulation without the linker. In light of these results and the αβ dimer's low stability, the full-working TRPS single genes might be the result of a particular evolution. Considering the significant losses that Hemileia vastatrix causes to coffee plantations, our next course of action will be to use the TRPS to look for substances that can block tryptophan production and therefore control the disease.
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Affiliation(s)
- Natália F Martins
- EMBRAPA Agroindústria Tropical, Planalto do Pici, Fortaleza 60511-110, CE, Brazil
| | - Marcos J A Viana
- EMBRAPA Agroindústria Tropical, Planalto do Pici, Fortaleza 60511-110, CE, Brazil
| | - Bernard Maigret
- LORIA, UMR 7504 CNRS, Université de Lorraine, 54000 Vandoeuvre les Nancy, France
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12
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Mealka M, Sierra NA, Matteo DA, Albekioni E, Khoury R, Mai T, Conley BM, Coleman NJ, Sabo KA, Komives EA, Bobkov AA, Cooksy AL, Silletti S, Schiffer JM, Huxford T, Sohl CD. Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.574970. [PMID: 38260668 PMCID: PMC10802581 DOI: 10.1101/2024.01.10.574970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation in a variety of cancers by replacing its conventional activity with a neomorphic activity that generates an oncometabolite. Little is understood of the mechanistic differences among tumor-driving IDH1 mutants. We previously reported that the R132Q mutant uniquely preserves conventional activity while catalyzing robust oncometabolite production, allowing an opportunity to compare these reaction mechanisms within a single active site. Here, we employed static and dynamic structural methods and found that, compared to R132H, the R132Q active site adopted a conformation primed for catalysis with optimized substrate binding and hydride transfer to drive improved conventional and neomorphic activity over R132H. This active site remodeling revealed a possible mechanism of resistance to selective mutant IDH1 therapeutic inhibitors. This work enhances our understanding of fundamental IDH1 mechanisms while pinpointing regions for improving inhibitor selectivity.
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Affiliation(s)
- Matthew Mealka
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nicole A. Sierra
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | | | - Elene Albekioni
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Rachel Khoury
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Timothy Mai
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Brittany M. Conley
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nalani J. Coleman
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Kaitlyn A. Sabo
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Elizabeth A. Komives
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Andrey A. Bobkov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA USA
| | - Andrew L. Cooksy
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Steve Silletti
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | | | - Tom Huxford
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Christal D. Sohl
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
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13
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Dhar R, Bowman AM, Hatungimana B, Sg Slusky J. Evolutionary Engineering a Larger Porin Using a Loop-to-Hairpin Mechanism. J Mol Biol 2023; 435:168292. [PMID: 37769963 PMCID: PMC11215794 DOI: 10.1016/j.jmb.2023.168292] [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: 06/14/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023]
Abstract
In protein evolution, diversification is generally driven by genetic duplication. The hallmarks of this mechanism are visible in the repeating topology of various proteins. In outer membrane β-barrels, duplication is visible with β-hairpins as the repeating unit of the barrel. In contrast to the overall use of duplication in diversification, a computational study hypothesized evolutionary mechanisms other than hairpin duplications leading to increases in the number of strands in outer membrane β-barrels. Specifically, the topology of some 16- and 18-stranded β-barrels appear to have evolved through a loop to β-hairpin transition. Here we test this novel evolutionary mechanism by creating a chimeric protein from an 18-stranded β-barrel and an evolutionarily related 16-stranded β-barrel. The chimeric combination of the two was created by replacing loop L3 of the 16-stranded barrel with the sequentially matched transmembrane β-hairpin region of the 18-stranded barrel. We find the resulting chimeric protein is stable and has characteristics of increased strand number. This study provides the first experimental evidence supporting the evolution through a loop to β-hairpin transition.
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Affiliation(s)
- Rik Dhar
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA. https://twitter.com/Rik_Skywalker
| | - Alexander M Bowman
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
| | - Brunojoel Hatungimana
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
| | - Joanna Sg Slusky
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA; Computational Biology Program, The University of Kansas, Lawrence, KS 66047, USA.
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14
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Son Y, Kenny TC, Khan A, Birsoy K, Hite RK. Structural basis of lipid head group entry to the Kennedy pathway by FLVCR1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.560019. [PMID: 37808796 PMCID: PMC10557757 DOI: 10.1101/2023.09.28.560019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Phosphatidylcholine and phosphatidylethanolamine, the two most abundant phospholipids in mammalian cells, are synthesized de novo by the Kennedy pathway from choline and ethanolamine, respectively1-6. Despite the importance of these lipids, the mechanisms that enable the cellular uptake of choline and ethanolamine remain unknown. Here, we show that FLVCR1, whose mutation leads to the neurodegenerative syndrome PCARP7-9, transports extracellular choline and ethanolamine into cells for phosphorylation by downstream kinases to initiate the Kennedy pathway. Structures of FLVCR1 in the presence of choline and ethanolamine reveal that both metabolites bind to a common binding site comprised of aromatic and polar residues. Despite binding to a common site, the larger quaternary amine of choline interacts differently with FLVCR1 than does the primary amine of ethanolamine. Structure-guided mutagenesis identified residues that are critical for the transport of ethanolamine, while being dispensable for choline transport, enabling functional separation of the entry points into the two branches of the Kennedy pathway. Altogether, these studies reveal how FLCVR1 is a high-affinity metabolite transporter that serves as the common origin for phospholipid biosynthesis by two branches of the Kennedy pathway.
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Affiliation(s)
- Yeeun Son
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- BCMB Allied Program, Weill Cornell Graduate School, New York, NY, USA
| | - Timothy C. Kenny
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Artem Khan
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Kivanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Richard K. Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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15
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Chan AHY, Ho TCS, Leeper FJ. Open-chain thiamine analogues as potent inhibitors of thiamine pyrophosphate (TPP)-dependent enzymes. Org Biomol Chem 2023; 21:6531-6536. [PMID: 37522836 DOI: 10.1039/d3ob00884c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
A common approach to studying thiamine pyrophosphate (TPP)-dependent enzymes is by chemical inhibition with thiamine/TPP analogues which feature a neutral aromatic ring in place of the positive thiazolium ring of TPP. These are potent inhibitors but their preparation generally involves multiple synthetic steps to construct the central ring. We report efficient syntheses of novel, open-chain thiamine analogues which potently inhibit TPP-dependent enzymes and are predicted to share the same binding mode as TPP. We also report some open-chain analogues that inhibit pyruvate dehydrogenase E1-subunit (PDH E1) and are predicted to occupy additional pockets in the enzyme other than the TPP-binding pockets. This opens up new possibilities for increasing the affinity and selectivity of the analogues for PDH, which is an established anti-cancer target.
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Affiliation(s)
- Alex H Y Chan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Terence C S Ho
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Finian J Leeper
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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16
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Kato T, Okada U, Hung LW, Yamashita E, Kim HB, Kim CY, Terwilliger TC, Schweizer HP, Murakami S. Crystal structures of multidrug efflux transporters from Burkholderia pseudomallei suggest details of transport mechanism. Proc Natl Acad Sci U S A 2023; 120:e2215072120. [PMID: 37428905 PMCID: PMC10629574 DOI: 10.1073/pnas.2215072120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/24/2023] [Indexed: 07/12/2023] Open
Abstract
BpeB and BpeF are multidrug efflux transporters from Burkholderia pseudomallei that enable multidrug resistance. Here, we report the crystal structures of BpeB and BpeF at 2.94 Å and 3.0 Å resolution, respectively. BpeB was found as an asymmetric trimer, consistent with the widely-accepted functional rotation mechanism for this type of transporter. One of the monomers has a distinct structure that we interpret as an intermediate along this functional cycle. Additionally, a detergent molecule bound in a previously undescribed binding site provides insights into substrate translocation through the pathway. BpeF shares structural similarities with the crystal structure of OqxB from Klebsiella pneumoniae, where both are symmetric trimers composed of three "binding"-state monomers. The structures of BpeB and BpeF further our understanding of the functional mechanisms of transporters belonging to the HAE1-RND superfamily.
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Affiliation(s)
- Takaaki Kato
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama226-8501, Japan
| | - Ui Okada
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama226-8501, Japan
| | - Li-Wei Hung
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM87545
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, Osaka565-0871, Japan
| | - Heung-Bok Kim
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM87545
| | - Chang-Yub Kim
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM87545
| | - Thomas C. Terwilliger
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM87545
- New Mexico Consortium, Los Alamos, NM87544
| | - Herbert P. Schweizer
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ86011
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ86011
| | - Satoshi Murakami
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama226-8501, Japan
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17
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Richmond V, Falcone BN, Maier MS, Arroyo Máñez P. Putting the Puzzle Together To Get the Whole Picture: Molecular Basis of the Affinity of Two Steroid Derivatives to Acetylcholinesterase. ACS OMEGA 2023; 8:25610-25622. [PMID: 37483177 PMCID: PMC10357547 DOI: 10.1021/acsomega.3c03749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 06/14/2023] [Indexed: 07/25/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that has no cure because its etiology is still unknown, and its main treatment is the administration of acetylcholinesterase (AChE) inhibitors. The study of the mechanism of action of this family of compounds is critical for the design of new more potent and specific inhibitors. In this work, we study the molecular basis of an uncompetitive inhibitor (compound 1, 2β, 3α-dihydroxy-5α-cholestan-6-one disulfate), which we have proved to be a peripheral anionic site (PAS)-binding AChE inhibitor. The pipeline designed in this work is key to the development of other PAS inhibitors that not only inhibit the esterase action of the enzyme but could also modulate the non-cholinergic functions of AChE linked to the process of amylogenesis. Our studies showed that 1 inhibits the enzyme not simply by blocking the main gate but by an allosteric mechanism. A detailed and careful analysis of the ligand binding position and the protein dynamics, particularly regarding their secondary gates and active site, was necessary to conclude this. The same analysis was executed with an inactive analogue (compound 2, 2β, 3α-dihydroxy-5α-cholestan-6-one). Our first computational results showed no differences in affinity to AChE between both steroids, making further analysis necessary. This work highlights the variables to be considered and develops a refined methodology, for the successful design of new potent dual-action drugs for AD, particularly PAS inhibitors, an attractive strategy to combat AD.
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Affiliation(s)
- Victoria Richmond
- Facultad
de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad
de Microanálisis y Métodos Físicos aplicados
a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Pabellón 2 de Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Bruno N. Falcone
- Facultad
de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad
de Microanálisis y Métodos Físicos aplicados
a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Pabellón 2 de Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Marta S. Maier
- Facultad
de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad
de Microanálisis y Métodos Físicos aplicados
a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Pabellón 2 de Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Pau Arroyo Máñez
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Doctor Moliner 50, Burjassot, Valencia 46100, Spain
- Departamento
de Química Orgánica, Universitat
de València, Doctor Moliner 50, Burjassot, Valencia 46100, Spain
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18
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Ferreira P, Carro J, Balcells B, Martínez AT, Serrano A. Expanding the Physiological Role of Aryl-Alcohol Flavooxidases as Quinone Reductases. Appl Environ Microbiol 2023; 89:e0184422. [PMID: 37154753 DOI: 10.1128/aem.01844-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Aryl-alcohol oxidases (AAOs) are members of the glucose-methanol-choline oxidase/dehydrogenase (GMC) superfamily. These extracellular flavoproteins have been described as auxiliary enzymes in the degradation of lignin by several white-rot basidiomycetes. In this context, they oxidize fungal secondary metabolites and lignin-derived compounds using O2 as an electron acceptor, and supply H2O2 to ligninolytic peroxidases. Their substrate specificity, including mechanistic aspects of the oxidation reaction, has been characterized in Pleurotus eryngii AAO, taken as a model enzyme of this GMC superfamily. AAOs show broad reducing-substrate specificity in agreement with their role in lignin degradation, being able to oxidize both nonphenolic and phenolic aryl alcohols (and hydrated aldehydes). In the present work, the AAOs from Pleurotus ostreatus and Bjerkandera adusta were heterologously expressed in Escherichia coli, and their physicochemical properties and oxidizing abilities were compared with those of the well-known recombinant AAO from P. eryngii. In addition, electron acceptors different from O2, such as p-benzoquinone and the artificial redox dye 2,6-Dichlorophenolindophenol, were also studied. Differences in reducing-substrate specificity were found between the AAO enzymes from B. adusta and the two Pleurotus species. Moreover, the three AAOs oxidized aryl alcohols concomitantly with the reduction of p-benzoquinone, with similar or even higher efficiencies than when using their preferred oxidizing-substrate, O2. IMPORTANCE In this work, quinone reductase activity is analyzed in three AAO flavooxidases, whose preferred oxidizing-substrate is O2. The results presented, including reactions in the presence of both oxidizing substrates-benzoquinone and molecular oxygen-suggest that such aryl-alcohol dehydrogenase activity, although less important than its oxidase activity in terms of maximal turnover, may have a physiological role during fungal decay of lignocellulose by the reduction of quinones (and phenoxy radicals) from lignin degradation, preventing repolymerization. Moreover, the resulting hydroquinones would participate in redox-cycling reactions for the production of hydroxyl free radical involved in the oxidative attack of the plant cell-wall. Hydroquinones can also act as mediators for laccases and peroxidases in lignin degradation in the form of semiquinone radicals, as well as activators of lytic polysaccharide monooxygenases in the attack of crystalline cellulose. Moreover, reduction of these, and other phenoxy radicals produced by laccases and peroxidases, promotes lignin degradation by limiting repolymerization reactions. These findings expand the role of AAO in lignin biodegradation.
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Affiliation(s)
- Patricia Ferreira
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
| | - Juan Carro
- Centro de Investigaciones Biológicas "Margarita Salas", CSIC, Madrid, Spain
| | - Beatriz Balcells
- Centro de Investigaciones Biológicas "Margarita Salas", CSIC, Madrid, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas "Margarita Salas", CSIC, Madrid, Spain
| | - Ana Serrano
- Centro de Investigaciones Biológicas "Margarita Salas", CSIC, Madrid, Spain
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19
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Roda S, Terholsen H, Meyer JRH, Cañellas-Solé A, Guallar V, Bornscheuer U, Kazemi M. AsiteDesign: a Semirational Algorithm for an Automated Enzyme Design. J Phys Chem B 2023; 127:2661-2670. [PMID: 36944360 PMCID: PMC10068746 DOI: 10.1021/acs.jpcb.2c07091] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
With advances in protein structure predictions, the number of available high-quality structures has increased dramatically. In light of these advances, structure-based enzyme engineering is expected to become increasingly important for optimizing biocatalysts for industrial processes. Here, we present AsiteDesign, a Monte Carlo-based protocol for structure-based engineering of active sites. AsiteDesign provides a framework for introducing new catalytic residues in a given binding pocket to either create a new catalytic activity or alter the existing one. AsiteDesign is implemented using pyRosetta and incorporates enhanced sampling techniques to efficiently explore the search space. The protocol was tested by designing an alternative catalytic triad in the active site of Pseudomonas fluorescens esterase (PFE). The designed variant was experimentally verified to be active, demonstrating that AsiteDesign can find alternative catalytic triads. Additionally, the AsiteDesign protocol was employed to enhance the hydrolysis of a bulky chiral substrate (1-phenyl-2-pentyl acetate) by PFE. The experimental verification of the designed variants demonstrated that F158L/F198A and F125A/F158L mutations increased the hydrolysis of 1-phenyl-2-pentyl acetate from 8.9 to 66.7 and 23.4%, respectively, and reversed the enantioselectivity of the enzyme from (R) to (S)-enantiopreference, with 32 and 55% enantiomeric excess (ee), respectively.
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Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Plaça d'Eusebi Güell, 1-3, Barcelona 08034, Spain
| | - Henrik Terholsen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Jule Ruth Heike Meyer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Albert Cañellas-Solé
- Barcelona Supercomputing Center (BSC), Plaça d'Eusebi Güell, 1-3, Barcelona 08034, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Plaça d'Eusebi Güell, 1-3, Barcelona 08034, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys, 23, Barcelona 08010, Spain
| | - Uwe Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Masoud Kazemi
- Barcelona Supercomputing Center (BSC), Plaça d'Eusebi Güell, 1-3, Barcelona 08034, Spain
- Biomatter Designs, Žirmu̅n̨ g. 139A, Vilnius 09120, Lithuania
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20
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Marasco R, Fusi M, Coscolín C, Barozzi A, Almendral D, Bargiela R, Nutschel CGN, Pfleger C, Dittrich J, Gohlke H, Matesanz R, Sanchez-Carrillo S, Mapelli F, Chernikova TN, Golyshin PN, Ferrer M, Daffonchio D. Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes. Nat Commun 2023; 14:1045. [PMID: 36828822 PMCID: PMC9958047 DOI: 10.1038/s41467-023-36610-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 02/08/2023] [Indexed: 02/26/2023] Open
Abstract
Microbial communities respond to temperature with physiological adaptation and compositional turnover. Whether thermal selection of enzymes explains marine microbiome plasticity in response to temperature remains unresolved. By quantifying the thermal behaviour of seven functionally-independent enzyme classes (esterase, extradiol dioxygenase, phosphatase, beta-galactosidase, nuclease, transaminase, and aldo-keto reductase) in native proteomes of marine sediment microbiomes from the Irish Sea to the southern Red Sea, we record a significant effect of the mean annual temperature (MAT) on enzyme response in all cases. Activity and stability profiles of 228 esterases and 5 extradiol dioxygenases from sediment and seawater across 70 locations worldwide validate this thermal pattern. Modelling the esterase phase transition temperature as a measure of structural flexibility confirms the observed relationship with MAT. Furthermore, when considering temperature variability in sites with non-significantly different MATs, the broadest range of enzyme thermal behaviour and the highest growth plasticity of the enriched heterotrophic bacteria occur in samples with the widest annual thermal variability. These results indicate that temperature-driven enzyme selection shapes microbiome thermal plasticity and that thermal variability finely tunes such processes and should be considered alongside MAT in forecasting microbial community thermal response.
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Affiliation(s)
- Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Marco Fusi
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre for Conservation and Restoration Science, Edinburgh Napier University Sighthill Campus, Edinburgh, UK
| | | | - Alan Barozzi
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - David Almendral
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid, Spain
| | - Rafael Bargiela
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, UK
| | | | - Christopher Pfleger
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jonas Dittrich
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC) and Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ruth Matesanz
- Spectroscopy Laboratory, Centro de Investigaciones Biologicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Sergio Sanchez-Carrillo
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid, Spain
- Centro de Biologia Molecular Severo Ochoa (CBM), CSIC-UAM, Madrid, Spain
| | - Francesca Mapelli
- Department of Food Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Tatyana N Chernikova
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, UK
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, UK
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid, Spain.
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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21
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Maghsoud Y, Vázquez-Montelongo EA, Yang X, Liu C, Jing Z, Lee J, Harger M, Smith AK, Espinoza M, Guo HF, Kurie JM, Dalby KN, Ren P, Cisneros GA. Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. J Chem Inf Model 2023; 63:986-1001. [PMID: 36779232 PMCID: PMC10233724 DOI: 10.1021/acs.jcim.2c01448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The catalytic function of lysyl hydroxylase-2 (LH2), a member of the Fe(II)/αKG-dependent oxygenase superfamily, is to catalyze the hydroxylation of lysine to hydroxylysine in collagen, resulting in stable hydroxylysine aldehyde-derived collagen cross-links (HLCCs). Reports show that high amounts of LH2 lead to the accumulation of HLCCs, causing fibrosis and specific types of cancer metastasis. Some members of the Fe(II)/αKG-dependent family have also been reported to have intramolecular O2 tunnels, which aid in transporting one of the required cosubstrates into the active site. While LH2 can be a promising target to combat these diseases, efficacious inhibitors are still lacking. We have used computational simulations to investigate a series of 44 small molecules as lead compounds for LH2 inhibition. Tunneling analyses indicate the existence of several intramolecular tunnels. The lengths of the calculated O2-transporting tunnels in holoenzymes are relatively longer than those in the apoenzyme, suggesting that the ligands may affect the enzyme's structure and possibly block (at least partially) the tunnels. The sequence alignment analysis between LH enzymes from different organisms shows that all of the amino acid residues with the highest occurrence rate in the oxygen tunnels are conserved. Our results suggest that the enolate form of diketone compounds establishes stronger interactions with the Fe(II) in the active site. Branching the enolate compounds with functional groups such as phenyl and pyridinyl enhances the interaction with various residues around the active site. Our results provide information about possible leads for further LH2 inhibition design and development.
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Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Erik Antonio Vázquez-Montelongo
- Department of Physical Medicine and Rehabilitation, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Xudong Yang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Juhoon Lee
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Matthew Harger
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ally K Smith
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Miguel Espinoza
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Hou-Fu Guo
- Department of Molecular and Cellular Biochemistry, College of Medicine, The University of Kentucky, Lexington, Kentucky 40536, United States
| | - Jonathan M Kurie
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77005, United States
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
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22
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Mitusińska K, Bzówka M, Magdziarz T, Góra A. Geometry-Based versus Small-Molecule Tracking Method for Tunnel Identification: Benefits and Pitfalls. J Chem Inf Model 2022; 62:6803-6811. [PMID: 36374085 PMCID: PMC9795556 DOI: 10.1021/acs.jcim.2c00985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Different methods for tunnel identification, geometry-based and small-molecule tracking approaches, were compared to provide their benefits and pitfalls. Results obtained for both crystal structures and molecular dynamics (MD) simulations were analyzed to investigate if a more computationally demanding method would be beneficial. Careful examination of the results is essential for the low-diameter tunnel description, and assessment of the tunnel functionality based only on their geometrical parameters is challenging. We showed that the small-molecule tracking approach can provide a detailed description of the system; however, it can also be the most computationally demanding.
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23
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Zhao Z, Rudman NA, He J, Dmochowski IJ. Programming xenon diffusion in maltose-binding protein. Biophys J 2022; 121:4635-4643. [PMID: 36271622 PMCID: PMC9748359 DOI: 10.1016/j.bpj.2022.10.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 12/15/2022] Open
Abstract
Protein interiors contain void space that can bind small gas molecules. Determination of gas pathways and kinetics in proteins has been an intriguing and challenging task. Here, we combined computational methods and the hyperpolarized xenon-129 chemical exchange saturation transfer (hyper-CEST) NMR technique to investigate xenon (Xe) exchange kinetics in maltose-binding protein (MBP). A salt bridge ∼9 Å from the Xe-binding site formed upon maltose binding and slowed the Xe exchange rate, leading to a hyper-CEST 129Xe signal from maltose-bound MBP. Xe dissociation occurred faster than dissociation of the salt bridge, as shown by 13C NMR spectroscopy and variable-B1 hyper-CEST experiments. "Xe flooding" molecular dynamics simulations identified a surface hydrophobic site, V23, that has good Xe binding affinity. Mutations at this site confirmed its role as a secondary exchange pathway in modulating Xe diffusion. This shows the possibility for site-specifically controlling xenon protein-solvent exchange. Analysis of the available MBP structures suggests a biological role of MBP's large hydrophobic cavity to accommodate structural changes associated with ligand binding and protein-protein interactions.
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Affiliation(s)
- Zhuangyu Zhao
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nathan A Rudman
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jiayi He
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania.
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24
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Ragavendran PV, Tripathi V, Gandotra S. Structure prediction-based insights into the patatin family of Mycobacterium tuberculosis. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748562 DOI: 10.1099/mic.0.001270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite its genome sequencing more than two decades ago, the majority of the genes of Mycobacterium tuberculosis remain functionally uncharacterized. Patatins are one such class of proteins that, despite undergoing an expansion in this pathogenic species compared to their non-pathogenic cousins, remain largely unstudied. Recent advances in protein structure prediction using machine learning tools such as AlphaFold2 have provided high-confidence predicted structures for all M. tuberculosis proteins. Here we present detailed analyses of the patatin family of M. tuberculosis using AlphaFold-predicted structures, providing insights into likely modes of regulation, membrane interaction and substrate binding. Regulatory domains within this family of proteins include cyclic nucleotide binding, lid-like domains and other helical domains. Using structural homologues, we identified the likely membrane localization mechanisms and substrate-binding sites. These analyses reveal diversity in their regulatory capacity, mechanisms of membrane binding and likely length of fatty acid substrates. Together, this analysis suggests unique roles for the eight predicted patatins of M. tuberculosis.
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Affiliation(s)
- P V Ragavendran
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh- 201 002, India.,Immunology and Infectious Disease, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India, New Delhi, India
| | - Vaishnavi Tripathi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh- 201 002, India.,Immunology and Infectious Disease, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India, New Delhi, India
| | - Sheetal Gandotra
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh- 201 002, India.,Immunology and Infectious Disease, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India, New Delhi, India
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25
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Ravera S, Nicola JP, Salazar-De Simone G, Sigworth FJ, Karakas E, Amzel LM, Bianchet MA, Carrasco N. Structural insights into the mechanism of the sodium/iodide symporter. Nature 2022; 612:795-801. [PMID: 36517601 PMCID: PMC10501339 DOI: 10.1038/s41586-022-05530-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/04/2022] [Indexed: 12/15/2022]
Abstract
The sodium/iodide symporter (NIS) is the essential plasma membrane protein that mediates active iodide (I-) transport into the thyroid gland, the first step in the biosynthesis of the thyroid hormones-the master regulators of intermediary metabolism. NIS couples the inward translocation of I- against its electrochemical gradient to the inward transport of Na+ down its electrochemical gradient1,2. For nearly 50 years before its molecular identification3, NIS was the molecule at the centre of the single most effective internal radiation cancer therapy: radioiodide (131I-) treatment for thyroid cancer2. Mutations in NIS cause congenital hypothyroidism, which must be treated immediately after birth to prevent stunted growth and cognitive deficiency2. Here we report three structures of rat NIS, determined by single-particle cryo-electron microscopy: one with no substrates bound; one with two Na+ and one I- bound; and one with one Na+ and the oxyanion perrhenate bound. Structural analyses, functional characterization and computational studies show the substrate-binding sites and key residues for transport activity. Our results yield insights into how NIS selects, couples and translocates anions-thereby establishing a framework for understanding NIS function-and how it transports different substrates with different stoichiometries and releases substrates from its substrate-binding cavity into the cytosol.
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Affiliation(s)
- Silvia Ravera
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Juan Pablo Nicola
- Department of Clinical Biochemistry, National University of Córdoba, Córdoba, Argentina
| | | | - Fred J Sigworth
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
| | - Erkan Karakas
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - L Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mario A Bianchet
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nancy Carrasco
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
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26
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Kaiser J, Gertzen CG, Bernauer T, Höfner G, Niessen KV, Seeger T, Paintner FF, Wanner KT, Worek F, Thiermann H, Gohlke H. A novel binding site in the nicotinic acetylcholine receptor for MB327 can explain its allosteric modulation relevant for organophosphorus-poisoning treatment. Toxicol Lett 2022; 373:160-171. [DOI: 10.1016/j.toxlet.2022.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/25/2022] [Indexed: 11/27/2022]
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27
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Sneha, Pandey JP, Pandey DM. Evaluating the role of trypsin in silk degumming: An in silico approach. J Biotechnol 2022; 359:35-47. [PMID: 36126805 DOI: 10.1016/j.jbiotec.2022.09.007] [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: 12/24/2021] [Revised: 08/30/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022]
Abstract
The trypsin being universal enzyme forming family of proteases catalyzes the hydrolysis of proteins into amino acids and regenerates the serine hydroxyl an active site. The trypsin enzyme from D. saccharalis, uses sericin as its preferred substrate. Presence of catalytic triad (serine, aspartic acid and histidine) at the substrate binding site of this enzyme is very important for the catalytic activity. In the current study, the interacting mechanism between the substrate sericin protein and enzyme trypsin protein were explored by integrating various computational approaches including physico-chemical properties, biophysical properties, dynamics, gene ontology, molecular docking, protein - protein interactions, binding free energy calculation and structural motifs were studied. The evolutionary study performed by MEGA X showed that trypsin protein sequence (ALE15212.1) is closely related to cocoonase protein sequence (ADG26770.1) from Antheraea pernyi. 3-D models of trypsin and sericin proteins were predicted using I-TASSER and further validated by PROCHECK, and ProSAweb softwares. The predicted trypsin structure model was assigned E.C. no. 3.4.21.4 which refers hydrolytic mechanism. Gene Ontology predicted by QuickGO showed that trypsin has serine hydrolase activity (GO: 00017171), and part of proteolysis (GO: 0006508) as well as protein metabolic process (GO:0019538) actvity. Molecular docking studies between trypsin and sericin proteins were conducted by the HADDOCK 2.4 having best docked protein complex with Z-score - 1.9. 2D and 3D protein-protein interaction was performed with LIGPLOT+ and HAWKDOCK, PDBsum, respectively. The amino acid residues interacting across proteins interface are sericin_chain A representing "Ser133, Tyr214, Thr188, Thr243, Ser225, Ser151, Ser156, His294, Arg293, Gly296″ and trypsin_chain B "Lys120, Tyr246, Asn119, Glu239, Ser62, Tyr194, Ile197, Ser171, Tyr169, Gly170″. Based on our results trypsin shows similarity with cocoonase and presumably trypsin can be used as an alternative source in cocoon degumming.
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Affiliation(s)
- Sneha
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India.
| | - Jay Prakash Pandey
- Central Tasar Research and Training Institute, Piska-Nagri, Ranchi, Jharkhand 835303, India.
| | - Dev Mani Pandey
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India.
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28
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Muellers SN, Nyitray MM, Reynarowych N, Saljanin E, Benzie AL, Schoenfeld AR, Stockman BJ, Allen KN. Structure-Guided Insight into the Specificity and Mechanism of a Parasitic Nucleoside Hydrolase. Biochemistry 2022; 61:1853-1861. [PMID: 35994320 PMCID: PMC10845162 DOI: 10.1021/acs.biochem.2c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Trichomonas vaginalis is the causative parasitic protozoan of the disease trichomoniasis, the most prevalent, nonviral sexually transmitted disease in the world. T. vaginalis is a parasite that scavenges nucleosides from the host organism via catalysis by nucleoside hydrolase (NH) enzymes to yield purine and pyrimidine bases. One of the four NH enzymes identified within the genome of T. vaginalis displays unique specificity toward purine nucleosides, adenosine and guanosine, but not inosine, and atypically shares greater sequence similarity to the pyrimidine hydrolases. Bioinformatic analysis of this enzyme, adenosine/guanosine-preferring nucleoside ribohydrolase (AGNH), was incapable of identifying the residues responsible for this uncommon specificity, highlighting the need for structural information. Here, we report the X-ray crystal structures of holo, unliganded AGNH and three additional structures of the enzyme bound to fragment and small-molecule inhibitors. Taken together, these structures facilitated the identification of residue Asp231, which engages in substrate interactions in the absence of those residues that typically support the canonical purine-specific tryptophan-stacking specificity motif. An altered substrate-binding pose is mirrored by repositioning within the protein scaffold of the His80 general acid/base catalyst. The newly defined structure-determined sequence markers allowed the assignment of additional NH orthologs, which are proposed to exhibit the same specificity for adenosine and guanosine alone and further delineate specificity classes for these enzymes.
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Affiliation(s)
- Samantha N Muellers
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Mattias M Nyitray
- Department of Chemistry, Adelphi University, Garden City, New York 11530, United States
| | - Nicholas Reynarowych
- Department of Chemistry, Adelphi University, Garden City, New York 11530, United States
| | - Edina Saljanin
- Department of Chemistry, Adelphi University, Garden City, New York 11530, United States
| | - Annie Laurie Benzie
- Department of Biology, Adelphi University, Garden City, New York 11530, United States
| | - Alan R Schoenfeld
- Department of Biology, Adelphi University, Garden City, New York 11530, United States
| | - Brian J Stockman
- Department of Chemistry, Adelphi University, Garden City, New York 11530, United States
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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29
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Transgenic Expression of Haemonchus contortus Cytochrome P450 Hco-cyp-13A11 Decreases Susceptibility to Particular but Not All Macrocyclic Lactones in the Model Organism Caenorhabditis elegans. Int J Mol Sci 2022; 23:ijms23169155. [PMID: 36012413 PMCID: PMC9409383 DOI: 10.3390/ijms23169155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/24/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
The number of reported macrocyclic lactones (ML) resistance cases across all livestock hosts is steadily increasing. Different studies in the parasitic nematode Haemonchus contortus assume the participation of cytochrome P450s (Cyps) enzymes in ML resistance. Still, functional data about their individual contribution to resistance or substrate specificity is missing. Via microinjection, transgenic Caenorhabditis elegans expressing HCON_00141052 (transgene-Hco-cyp-13A11) from extrachromosomal arrays were generated. After 24 h of exposure to different concentrations of ivermectin (IVM), ivermectin aglycone (IVMa), selamectin (SEL), doramectin (DRM), eprinomectin (EPR), and moxidectin (MOX), motility assays were performed to determine the impact of the H. contortus Cyp to the susceptibility of the worms against each ML. While transgene-Hco-cyp-13A11 significantly decreased susceptibility to IVM (four-fold), IVMa (2-fold), and SEL (3-fold), a slight effect for DRM and no effect for MOX, and EPR was observed. This substrate specificity of Hco-cyp-13A11 could not be explained by molecular modeling and docking studies. Hco-Cyp-13A11 molecular models were obtained for alleles from isolates with different resistance statuses. Although 14 amino acid polymorphisms were detected, none was resistance specific. In conclusion, Hco-cyp-13A11 decreased IVM, IVMa, and SEL susceptibility to a different extent, but its potential impact on ML resistance is not driven by polymorphisms.
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30
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Vollheyde K, Kühnel K, Lambrecht F, Kawelke S, Herrfurth C, Feussner I. Crystal Structure of the Bifunctional Wax Synthase 1 from Acinetobacter baylyi Suggests a Conformational Change upon Substrate Binding and Formation of Additional Substrate Binding Sites. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katharina Vollheyde
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077 Goettingen, Germany
| | - Karin Kühnel
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, D-37077 Goettingen, Germany
| | - Felix Lambrecht
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077 Goettingen, Germany
| | - Steffen Kawelke
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077 Goettingen, Germany
| | - Cornelia Herrfurth
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077 Goettingen, Germany
- Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, D-37077 Goettingen, Germany
| | - Ivo Feussner
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077 Goettingen, Germany
- Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, D-37077 Goettingen, Germany
- International Center for Advanced Studies of Energy Conversion (ICASEC), University of Goettingen, D-37077 Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, D-37077 Goettingen, Germany
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31
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Rozenberg A, Kaczmarczyk I, Matzov D, Vierock J, Nagata T, Sugiura M, Katayama K, Kawasaki Y, Konno M, Nagasaka Y, Aoyama M, Das I, Pahima E, Church J, Adam S, Borin VA, Chazan A, Augustin S, Wietek J, Dine J, Peleg Y, Kawanabe A, Fujiwara Y, Yizhar O, Sheves M, Schapiro I, Furutani Y, Kandori H, Inoue K, Hegemann P, Béjà O, Shalev-Benami M. Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels. Nat Struct Mol Biol 2022; 29:592-603. [PMID: 35710843 DOI: 10.1038/s41594-022-00783-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/27/2022] [Indexed: 11/09/2022]
Abstract
Many organisms sense light using rhodopsins, photoreceptive proteins containing a retinal chromophore. Here we report the discovery, structure and biophysical characterization of bestrhodopsins, a microbial rhodopsin subfamily from marine unicellular algae, in which one rhodopsin domain of eight transmembrane helices or, more often, two such domains in tandem, are C-terminally fused to a bestrophin channel. Cryo-EM analysis of a rhodopsin-rhodopsin-bestrophin fusion revealed that it forms a pentameric megacomplex (~700 kDa) with five rhodopsin pseudodimers surrounding the channel in the center. Bestrhodopsins are metastable and undergo photoconversion between red- and green-absorbing or green- and UVA-absorbing forms in the different variants. The retinal chromophore, in a unique binding pocket, photoisomerizes from all-trans to 11-cis form. Heterologously expressed bestrhodopsin behaves as a light-modulated anion channel.
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Affiliation(s)
- Andrey Rozenberg
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Igor Kaczmarczyk
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Donna Matzov
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Johannes Vierock
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Masahiro Sugiura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan
| | - Kota Katayama
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.,Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Japan
| | - Yuma Kawasaki
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Yujiro Nagasaka
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Mako Aoyama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan
| | - Ishita Das
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Efrat Pahima
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan Church
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Suliman Adam
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Veniamin A Borin
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ariel Chazan
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Sandra Augustin
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jonas Wietek
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Julien Dine
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot, Israel
| | - Akira Kawanabe
- Laboratory of Molecular Physiology & Biophysics, Faculty of Medicine, Kagawa University, Miki-cho, Japan
| | - Yuichiro Fujiwara
- Laboratory of Molecular Physiology & Biophysics, Faculty of Medicine, Kagawa University, Miki-cho, Japan
| | - Ofer Yizhar
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
| | - Moran Shalev-Benami
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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32
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Tan FF, Zhu R, Xiong B, Zhang GM, Zhao W, Jia KZ. Engineering the Entrance of a Flavonoid Glycosyltransferase Promotes the Glycosylation of Etoposide Aglycone. ACS Synth Biol 2022; 11:1874-1880. [PMID: 35522995 DOI: 10.1021/acssynbio.2c00032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzyme entrances, which function as the first molecular filters, influence substrate selectivity and enzymatic activity. Because of low binding affinities, engineering enzyme entrances that recognize non-natural substrates is a major challenge for artificial biocatalyst design. Here, the entrance of flavonoid glycosyltransferase UGT78D2 was engineered to promote the recognition of the aglycone of etoposide, a chemotherapeutic agent. We found that Q258, S446, R444, and R450, the key residues surrounding the substrate entrance, specifically guide the flux of etoposide aglycone, which has a high steric hindrance, into the active site; this activity was inferred to be determined by the entrance size and hydrophobic and electrostatic interactions. Engineering the coordination of Q258 and S446 to increase the entrance size and hydrophobic interaction between UGT78D2 and etoposide aglycone increased the affinity by 10.10-fold and the conversion by 10%. The entrance-engineering strategy applied in this study can improve the design of artificial biocatalysts.
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Affiliation(s)
- Fei-Fan Tan
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan 430068, China
| | - Rui Zhu
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan 430068, China
| | - Bin Xiong
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan 430068, China
| | - Gui-Min Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Kai-Zhi Jia
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan 430068, China
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Surpeta B, Grulich M, Palyzová A, Marešová H, Brezovsky J. Common Dynamic Determinants Govern Quorum Quenching Activity in N-Terminal Serine Hydrolases. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bartlomiej 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
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, 02-109 Warsaw, Poland
| | - Michal Grulich
- Laboratory of Modulation of Gene Expression, Institute of Microbiology,v.v.i., Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Andrea Palyzová
- Laboratory of Molecular Structure Characterization, Institute of Microbiology,v.v.i., Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Helena Marešová
- Laboratory of Molecular Structure Characterization, Institute of Microbiology,v.v.i., Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - 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
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, 02-109 Warsaw, Poland
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Wieder C, Peres da Silva R, Witts J, Jäger CM, Geib E, Brock M. Characterisation of ascocorynin biosynthesis in the purple jellydisc fungus Ascocoryne sarcoides. Fungal Biol Biotechnol 2022; 9:8. [PMID: 35477441 PMCID: PMC9047271 DOI: 10.1186/s40694-022-00138-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/19/2022] [Indexed: 12/02/2022] Open
Abstract
Background Non-ribosomal peptide synthetase-like (NRPS-like) enzymes are highly enriched in fungal genomes and can be discriminated into reducing and non-reducing enzymes. Non-reducing NRPS-like enzymes possess a C-terminal thioesterase domain that catalyses the condensation of two identical aromatic α-keto acids under the formation of enzyme-specific substrate-interconnecting core structures such as terphenylquinones, furanones, butyrolactones or dioxolanones. Ascocoryne sarcoides produces large quantities of ascocorynin, which structurally resembles a terphenylquinone produced from the condensation of p-hydroxyphenylpyruvate and phenylpyruvate. Since the parallel use of two different substrates by a non-reducing NRPS-like enzyme appeared as highly unusual, we investigated the biosynthesis of ascocorynin in A. sarcoides. Results Here, we searched the genome of A. sarcoides for genes coding for non-reducing NRPS-like enzymes. A single candidate gene was identified that was termed acyN. Heterologous gene expression confirmed that AcyN is involved in ascocorynin production but only produces the non-hydroxylated precursor polyporic acid. Although acyN is embedded in an ascocorynin biosynthesis gene cluster, a gene encoding a monooxygenase required for the hydroxylation of polyporic acid was not present. Expression analyses of all monooxygenase-encoding genes from A. sarcoides identified a single candidate that showed the same expression pattern as acyN. Accordingly, heterologous co-expression of acyN and the monooxygenase gene resulted in the production of ascocorynin. Structural modelling of the monooxygenase suggests that the hydrophobic substrate polyporic acid enters the monooxygenase from a membrane facing entry site and is converted into the more hydrophilic product ascocorynin, which prevents its re-entry for a second round of hydroxylation. Conclusion This study characterises the first naturally occurring polyporic acid synthetase from an ascomycete. It confirms the high substrate and product specificity of this non-reducing NRPS-like enzyme and highlights the requirement of a monooxygenase to produce the terphenylquinone ascocorynin. Supplementary Information The online version contains supplementary material available at 10.1186/s40694-022-00138-7.
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Affiliation(s)
- Carsten Wieder
- Fungal Biology Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.,Institute of Molecular Physiology, Johannes-Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Roberta Peres da Silva
- Fungal Biology Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.,University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Jessica Witts
- Fungal Biology Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Christof Martin Jäger
- Sustainable Process Technologies Research Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Elena Geib
- Fungal Biology Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Matthias Brock
- Fungal Biology Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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Sauer RT, Fei X, Bell TA, Baker TA. Structure and function of ClpXP, a AAA+ proteolytic machine powered by probabilistic ATP hydrolysis. Crit Rev Biochem Mol Biol 2022; 57:188-204. [PMID: 34923891 PMCID: PMC9871882 DOI: 10.1080/10409238.2021.1979461] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
ClpXP is an archetypical AAA+ protease, consisting of ClpX and ClpP. ClpX is an ATP-dependent protein unfoldase and polypeptide translocase, whereas ClpP is a self-compartmentalized peptidase. ClpXP is currently the only AAA+ protease for which high-resolution structures exist, the molecular basis of recognition for a protein substrate is understood, extensive biochemical and genetic analysis have been performed, and single-molecule optical trapping has allowed direct visualization of the kinetics of substrate unfolding and translocation. In this review, we discuss our current understanding of ClpXP structure and function, evaluate competing sequential and probabilistic mechanisms of ATP hydrolysis, and highlight open questions for future exploration.
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Affiliation(s)
- Robert T. Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xue Fei
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tristan A. Bell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tania A. Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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Quirk S, Lieberman RL. Structure and activity of a thermally stable mutant of Acanthamoeba actophorin. Acta Crystallogr F Struct Biol Commun 2022; 78:150-160. [PMID: 35400667 PMCID: PMC8996146 DOI: 10.1107/s2053230x22002448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/02/2022] [Indexed: 11/10/2022] Open
Abstract
Actophorin, which was recently tested for crystallization under microgravity on the International Space Station, was subjected to mutagenesis to identify a construct with improved biophysical properties that were expected to improve the extent of diffraction. First, 20 mutations, including one C-terminal deletion of three residues, were introduced individually into actophorin, resulting in modest increases in thermal stability of between +0.5°C and +2.2°C. All but two of the stabilizing mutants increased both the rates of severing F-actin filaments and of spontaneous polymerization of pyrenyl G-actin in vitro. When the individual mutations were combined into a single actophorin variant, Acto-2, the overall thermal stability was 22°C higher than that of wild-type actophorin. When an inactivating S2P mutation in Acto-2 was restored, Acto-2/P2S was more stable by 20°C but was notably more active than the wild-type protein. The inactivating S2P mutation reaffirms the importance that Ser2 plays in the F-actin-severing reaction. The crystal structure of Acto-2 was solved to 1.7 Å resolution in a monoclinic space group, a first for actophorin. Surprisingly, despite the increase in thermal stability, the extended β-turn region, which is intimately involved in interactions with F-actin, is disordered in one copy of Acto-2 in the asymmetric unit. These observations emphasize the complex interplay among protein thermal stability, function and dynamics.
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Affiliation(s)
- Stephen Quirk
- Kimberly Clark, 1400 Holcomb Bridge Road, Roswell, GA 30076, USA
| | - Raquel L Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
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Yang S, Zhao D, Xu Z, Yu H, Zhou J. Molecular understanding of acetylcholinesterase adsorption on functionalized carbon nanotubes for enzymatic biosensors. Phys Chem Chem Phys 2022; 24:2866-2878. [PMID: 35060980 DOI: 10.1039/d1cp04997f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The immobilization of acetylcholinesterase on different nanomaterials has been widely used in the field of amperometric organophosphorus pesticide (OP) biosensors. However, the molecular adsorption mechanism of acetylcholinesterase on a nanomaterial's surface is still unclear. In this work, multiscale simulations were utilized to study the adsorption behavior of acetylcholinesterase from Torpedo californica (TcAChE) on amino-functionalized carbon nanotube (CNT) (NH2-CNT), carboxyl-functionalized CNT (COOH-CNT) and pristine CNT surfaces. The simulation results show that the active center and enzyme substrate tunnel of TcAChE are both close to and oriented toward the surface when adsorbed on the positively charged NH2-CNT, which is beneficial to the direct electron transfer (DET) and accessibility of the substrate molecule. Meanwhile, the NH2-CNT can also reduce the tunnel cost of the enzyme substrate of TcAChE, thereby further accelerating the transfer rate of the substrate from the surface or solution to the active center. However, for the cases of TcAChE adsorbed on COOH-CNT and pristine CNT, the active center and substrate tunnel are far away from the surface and face toward the solution, which is disadvantageous for the DET and transportation of enzyme substrate. These results indicate that NH2-CNT is more suitable for the immobilization of TcAChE. This work provides a better molecular understanding of the adsorption mechanism of TcAChE on functionalized CNT, and also provides theoretical guidance for the ordered immobilization of TcAChE and the design, development and improvement of TcAChE-OPs biosensors based on functionalized carbon nanomaterials.
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Affiliation(s)
- Shengjiang Yang
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China.
| | - Daohui Zhao
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, School of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P. R. China
| | - Zhiyong Xu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China.
| | - Hai Yu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China.
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China.
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García‐Marquina G, Núñez‐Franco R, Peccati F, Tang Y, Jiménez‐Osés G, López‐Gallego F. Deconvoluting the Directed Evolution Pathway of Engineered Acyltransferase LovD. ChemCatChem 2022. [DOI: 10.1002/cctc.202101349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Guillermo García‐Marquina
- Center for cooperative Research in Biomaterials (CIC biomaGUNE) - Basque Research and Technology Alliance (BRTA) Heterogeneous Biocatalysis laboratory Paseo de Miramón, 182 20014 Donostia-San Sebastián Spain
- Universidad de La Rioja Departamento de Química Centro de Investigación en Síntesis Química Madre de Dios, 53 E-26006 Logroño Spain
| | - Reyes Núñez‐Franco
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) Computational Chemistry Laboratory Bizkaia Technology Park Building 800 48160 Derio Spain
| | - Francesca Peccati
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) Computational Chemistry Laboratory Bizkaia Technology Park Building 800 48160 Derio Spain
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering University of California 607 Charles E. Young Drive East 90095 Los Angeles, CA USA
| | - Gonzalo Jiménez‐Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) Computational Chemistry Laboratory Bizkaia Technology Park Building 800 48160 Derio Spain
- lkerbasque Basque Foundation for Science Plaza Euskadi 5 48009 Bilbao Spain
| | - Fernando López‐Gallego
- Center for cooperative Research in Biomaterials (CIC biomaGUNE) - Basque Research and Technology Alliance (BRTA) Heterogeneous Biocatalysis laboratory Paseo de Miramón, 182 20014 Donostia-San Sebastián Spain
- lkerbasque Basque Foundation for Science Plaza Euskadi 5 48009 Bilbao Spain
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Qureshi R, Ghosh A, Yan H. Correlated Motions and Dynamics in Different Domains of Epidermal Growth Factor Receptor With L858R and T790M Mutations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:383-394. [PMID: 32750848 DOI: 10.1109/tcbb.2020.2995569] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Non-small cell lung cancer with an activating epidermal growth factor receptor (EGFR) mutation responds well to targeted drugs. In most cases, drug resistance appears after about a year. Several studies have been conducted on the kinase domain of EGFR to understand the drug resistance mechanism. Since EGFR is a multi-domain protein, mutation in the kinase domain may affect the other domains as well. In this study, we examine the complete structure of the multi-domain EGFR protein and its mutants. We performed molecular dynamics simulations for wildtype EGFR, EGFR with L858R mutation, and EGFR with L858R and T790M mutations. We applied normal mode analysis and complex network analysis to extract the correlated motions in the domains of EGFR. The normal modes are used to construct the dynamic cross-correlation map (DCCM). Simulation results show different patterns of correlated motions in each domain of EGFR mutants compared to the wildtype. In Domains 1 and 3 of the extracellular region, a small number of weak positively correlated motions are extracted. Domains 2 and 4 show large numbers of both positive and negative motions. However, the negatively correlated motions are stronger in mutant structures compared to the wildtype. In Domain 7, some residues showed a positive correlation around the main diagonal. We also identified different communities, nodes and crucial residues in the domains of the structures, which can be important for the function of EGFR. Moreover, hydrogen bond analysis is performed for the stability analysis. The mutant structures have fewer hydrogen bonds compared to the wildtype. Overall, these findings are useful for understanding the dynamics and communications in EGFR domains.
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Yu J, Liao PJ, Xu W, Jones JR, Everman DB, Flanagan-Steet H, Keller TH, Virshup DM. Structural model of human PORCN illuminates disease-associated variants and drug-binding sites. J Cell Sci 2021; 134:273795. [PMID: 34817055 DOI: 10.1242/jcs.259383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/11/2021] [Indexed: 12/20/2022] Open
Abstract
Wnt signaling is essential for normal development and is a therapeutic target in cancer. The enzyme PORCN, or porcupine, is a membrane-bound O-acyltransferase (MBOAT) that is required for the post-translational modification of all Wnts, adding an essential mono-unsaturated palmitoleic acid to a serine on the tip of Wnt hairpin 2. Inherited mutations in PORCN cause focal dermal hypoplasia, and therapeutic inhibition of PORCN slows the growth of Wnt-dependent cancers. Based on homology to mammalian MBOAT proteins, we developed and validated a structural model of human PORCN. The model accommodates palmitoleoyl-CoA and Wnt hairpin 2 in two tunnels in the conserved catalytic core, shedding light on the catalytic mechanism. The model predicts how previously uncharacterized human variants of uncertain significance can alter PORCN function. Drugs including ETC-159, IWP-L6 and LGK-974 dock in the PORCN catalytic site, providing insights into PORCN pharmacologic inhibition. This structural model enhances our mechanistic understanding of PORCN substrate recognition and catalysis, as well as the inhibition of its enzymatic activity, and can facilitate the development of improved inhibitors and the understanding of disease-relevant PORCN mutants. This article has an associated First Person interview with the joint first authors of the paper.
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Affiliation(s)
- Jia Yu
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore
| | - Pei-Ju Liao
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore
| | - Weijun Xu
- Discovery Chemistry, Experimental Drug Development Centre, 10 Biopolis Road, Chromos, 138670, Singapore
| | - Julie R Jones
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - David B Everman
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | - Thomas H Keller
- Discovery Chemistry, Experimental Drug Development Centre, 10 Biopolis Road, Chromos, 138670, Singapore
| | - David M Virshup
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore.,Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
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Eto SF, Fernandes DC, Baldassi AC, Balbuena TS, da Costa Alecrim JV, Almeida de Carvalho FC, Lima C, Lopes-Ferreira M, Pizauro JM. Proteomic analysis capsule synthesis and redox mechanisms in the intracellular survival of group B Streptococcus in fish microglia. FISH & SHELLFISH IMMUNOLOGY 2021; 118:34-50. [PMID: 34464686 DOI: 10.1016/j.fsi.2021.08.019] [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: 03/21/2021] [Revised: 06/20/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Group B Streptococcus (GBS) causes meningitis in neonates and Nile tilapia (Oreochromis niloticus). The molecular mechanisms regulating the intracellular survival of this pathogen in the host cell are complex and crucial for the progression of infection. Thus, we propose the use of GBS-infected Nile tilapia microglia as an in vitro model system simulating infection caused by homologous bacteria in humans. We used this model to evaluate the phagocytic activity, as well as the functional aspects of the capsular proteins A, B, C, and D and the major redox enzymes, and the synergistic role of mechanisms/proteins involved in blocking phagocytic process. We observed that in the intracellular phase, GBS showed enhanced synthesis of the polysaccharide capsule and used superoxide dismutase, thioredoxin, NADH oxidase, and alkyl hydroperoxide reductase to scavenge reactive oxygen species and reactive nitrogen species produced by the host cell. Furthermore, although these virulence mechanisms were effective during the initial hours of infection, they were not able to subvert microglial responses, which partially neutralized the infection. Altogether, our findings provided important information regarding the intracellular survival mechanisms of GBS and perspectives for the production of new drugs and vaccines, through the druggability analysis of specific proteins. In conclusion, tilapia microglia serve as a potent in vitro experimental model for the study of meningitis.
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Affiliation(s)
- Silas Fernandes Eto
- Department of Postgraduate in Health Sciences-PROCISA, Federal University of Roraima (UFRR), Boa Vista, 69310-000, Brazil.
| | - Dayanne Carla Fernandes
- Immunochemistry Laboratory, Butantan Institute, (CeTICs/FAPESP), Vital Brazil Avenue, 1500, Butantã, 05503-009, São Paulo, Brazil
| | - Amanda Cristina Baldassi
- Department of Technology, School of Agrarian and Veterinary Sciences, Sao Paulo State University (Unesp), Jaboticabal, 14884-900, Sao Paulo/ SP, Brazil
| | - Thiago Santana Balbuena
- Department of Technology, School of Agrarian and Veterinary Sciences, Sao Paulo State University (Unesp), Jaboticabal, 14884-900, Sao Paulo/ SP, Brazil
| | - João Victor da Costa Alecrim
- Department of Postgraduate in Health Sciences-PROCISA, Federal University of Roraima (UFRR), Boa Vista, 69310-000, Brazil
| | | | - Carla Lima
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CeTICs/FAPESP), Butantan Institute, Vital Brazil Avenue, 1500, Butantã, 05503-009, São Paulo, Brazil
| | - Monica Lopes-Ferreira
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CeTICs/FAPESP), Butantan Institute, Vital Brazil Avenue, 1500, Butantã, 05503-009, São Paulo, Brazil
| | - João Martins Pizauro
- Department of Technology, School of Agrarian and Veterinary Sciences, Sao Paulo State University (Unesp), Jaboticabal, 14884-900, Sao Paulo/ SP, Brazil
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Berger MB, Walker AR, Vázquez-Montelongo EA, Cisneros GA. Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families. Phys Chem Chem Phys 2021; 23:22227-22240. [PMID: 34586107 PMCID: PMC8516722 DOI: 10.1039/d1cp03800a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA alkylation is used as the key epigenetic mark in eukaryotes, however, most alkylation in DNA can result in deleterious effects. Therefore, this process needs to be tightly regulated. The enzymes of the AlkB and Ten-Eleven Translocation (TET) families are members of the Fe and alpha-ketoglutarate-dependent superfamily of enzymes that are tasked with dealkylating DNA and RNA in cells. Members of these families span all species and are an integral part of transcriptional regulation. While both families catalyze oxidative dealkylation of various bases, each has specific preference for alkylated base type as well as distinct catalytic mechanisms. This perspective aims to provide an overview of computational work carried out to investigate several members of these enzyme families including AlkB, ALKB Homolog 2, ALKB Homolog 3 and Ten-Eleven Translocate 2. Insights into structural details, mutagenesis studies, reaction path analysis, electronic structure features in the active site, and substrate preferences are presented and discussed.
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Affiliation(s)
- Madison B Berger
- Department of Chemistry, University of North Texas, Denton, Texas, 76201, USA.
| | - Alice R Walker
- Department of Chemistry, Wayne State University, Detroit, Michigan, 48202, USA
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas, 76201, USA.
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Marjanovic A, Rozeboom HJ, de Vries MS, Mayer C, Otzen M, Wijma HJ, Janssen DB. Catalytic and structural properties of ATP-dependent caprolactamase from Pseudomonas jessenii. Proteins 2021; 89:1079-1098. [PMID: 33826169 PMCID: PMC8453981 DOI: 10.1002/prot.26082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/04/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022]
Abstract
Caprolactamase is the first enzyme in the caprolactam degradation pathway of Pseudomonas jessenii. It is composed of two subunits (CapA and CapB) and sequence-related to other ATP-dependent enzymes involved in lactam hydrolysis, like 5-oxoprolinases and hydantoinases. Low sequence similarity also exists with ATP-dependent acetone- and acetophenone carboxylases. The caprolactamase was produced in Escherichia coli, isolated by His-tag affinity chromatography, and subjected to functional and structural studies. Activity toward caprolactam required ATP and was dependent on the presence of bicarbonate in the assay buffer. The hydrolysis product was identified as 6-aminocaproic acid. Quantum mechanical modeling indicated that the hydrolysis of caprolactam was highly disfavored (ΔG0 '= 23 kJ/mol), which explained the ATP dependence. A crystal structure showed that the enzyme exists as an (αβ)2 tetramer and revealed an ATP-binding site in CapA and a Zn-coordinating site in CapB. Mutations in the ATP-binding site of CapA (D11A and D295A) significantly reduced product formation. Mutants with substitutions in the metal binding site of CapB (D41A, H99A, D101A, and H124A) were inactive and less thermostable than the wild-type enzyme. These residues proved to be essential for activity and on basis of the experimental findings we propose possible mechanisms for ATP-dependent lactam hydrolysis.
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Affiliation(s)
- Antonija Marjanovic
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | - Henriëtte J. Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | - Meintje S. de Vries
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | - Clemens Mayer
- Biomolecular Chemistry and Catalysis, Stratingh Institute for ChemistryUniversity of GroningenGroningenThe Netherlands
| | - Marleen Otzen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | | | - Dick B. Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
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Rayevsky A, Sirokha D, Samofalova D, Lozhko D, Gorodna O, Prokopenko I, Livshits L. Functional Effects In Silico Prediction for Androgen Receptor Ligand-Binding Domain Novel I836S Mutation. Life (Basel) 2021; 11:659. [PMID: 34357031 PMCID: PMC8303243 DOI: 10.3390/life11070659] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022] Open
Abstract
Over 1000 mutations are described in the androgen receptor (AR) gene. Of those, about 600 were found in androgen insensitivity syndrome (AIS) patients, among which 400 mutations affect the ligand-binding domain (LBD) of the AR protein. Recently, we reported a novel missense mutation c.2507T>G I836S (ClinVarID: 974911) in a patient with complete AIS (CAIS) phenotype. In the present study, we applied a set of computational approaches for the structural analysis of the ligand-binding domains in a wild-type and mutant AR to evaluate the functional impact of the novel I836S mutation. We revealed that the novel I836S substitution leads to a shorter existence time of the ligand's gating tunnel and internal cavity, occurring only in the presence of S836 phosphorylation. Additionally, the analysis of phosphorylation of the 836 mutant residues explained the negative impact on AR homodimerization, since monomer surface changes indirectly impacted the binding site. Our analyses provide evidence that I836S causes disruptions of AR protein functionality and development of CAIS clinical features in patients.
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Affiliation(s)
- Alexey Rayevsky
- Laboratory of Bioinformatics and Structural Biology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine; (A.R.); (D.S.)
- Department of Molecular Modeling, Enamine Ltd., 02094 Kyiv, Ukraine
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine; (D.S.); (D.L.); (O.G.)
| | - Dmytro Sirokha
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine; (D.S.); (D.L.); (O.G.)
| | - Dariia Samofalova
- Laboratory of Bioinformatics and Structural Biology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine; (A.R.); (D.S.)
- R&D Department, Life Chemicals Inc., 1a DIXIE AVE, Niagara-on-the-Lake, ON L0S 1J0, Canada
| | - Dmytro Lozhko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine; (D.S.); (D.L.); (O.G.)
| | - Olexandra Gorodna
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine; (D.S.); (D.L.); (O.G.)
| | - Inga Prokopenko
- Department of Clinical & Experimental Medicine, School of Biosciences & Medicine, University of Surrey, Guildford GU2 7XH, UK
- UMR 8199-EGID, Institut Pasteur de Lille, CNRS, University of Lille, F-59000 Lille, France
| | - Liudmyla Livshits
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine; (D.S.); (D.L.); (O.G.)
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Gabdulkhakov A, Kolyadenko I, Oliveira P, Tamagnini P, Mikhaylina A, Tishchenko S. The role of positive charged residue in the proton-transfer mechanism of two-domain laccase from Streptomyces griseoflavus Ac-993. J Biomol Struct Dyn 2021; 40:8324-8331. [PMID: 33870857 DOI: 10.1080/07391102.2021.1911852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Multi-copper oxidases are capable of coupling the one-electron oxidation of four substrate equivalents to the four-electron reduction of dioxygen to two molecules of water. This process takes place at the trinuclear copper center of the enzymes. Previously, the main catalytic stages for three-domain (3D) laccases have been identified. However, for bacterial small two-domain (2D) laccases several questions remain to be answered. One of them is the nature of the protonation events upon the reductive cleavage of dioxygen to water. In 3D laccases, acidic residues play a key role in the protonation mechanisms. In this study, the role of the Arg240 residue, located within the T2 tunnel of 2D laccase from Streptomyces griseoflavus Ac-993, was investigated. X-ray structural analysis and kinetic characterization of two mutants, R240A and R240H, have provided support for a role of this residue in the protonation events. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Azat Gabdulkhakov
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Ilya Kolyadenko
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Paulo Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Paula Tamagnini
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Alisa Mikhaylina
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
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Dai Y, Ma H, Wu M, Welsch TA, Vora SR, Ren D, Nangia S. Development of the computational antibiotic screening platform (CLASP) to aid in the discovery of new antibiotics. SOFT MATTER 2021; 17:2725-2736. [PMID: 33533373 DOI: 10.1039/d0sm02035d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bacterial colonization of biotic and abiotic surfaces and antibiotic resistance are grand challenges with paramount societal impacts. However, in the face of increasing bacterial resistance to all known antibiotics, efforts to discover new classes of antibiotics have languished, creating an urgent need to accelerate the antibiotic discovery pipeline. A major deterrent in the discovering of new antibiotics is the limited permeability of molecules across the bacterial envelope. Notably, the Gram-negative bacteria have nutrient specific protein channels (or porins) that restrict the permeability of non-essential molecules, including antibiotics. Here, we have developed the Computational Antibiotic Screening Platform (CLASP) for screening of potential drug molecules through the porins. The CLASP takes advantage of coarse grain (CG) resolution, advanced sampling techniques, and a parallel computing environment to maximize its performance. The CLASP yields comprehensive thermodynamic and kinetic output data of a potential drug molecule within a few hours of wall-clock time. Its output includes the potential of mean force profile, energy barrier, the rate constant, and contact analysis of the molecule with the pore-lining residues, and the orientational analysis of the molecule in the porin channel. In our first CLASP application, we report the transport properties of six carbapenem antibiotics-biapenem, doripenem, ertapenem, imipenem, meropenem, and panipenem-through OccD3, a major channel for carbapenem uptake in Pseudomonas aeruginosa. The CLASP is designed to screen small molecule libraries with a fast turnaround time to yield structure-property relationships to discover antibiotics with high permeability. The CLASP will be freely distributed to enable accelerated antibiotic drug discovery.
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Affiliation(s)
- Yinghui Dai
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, NY 13244, USA.
| | - Huilin Ma
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, NY 13244, USA.
| | - Meishan Wu
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, NY 13244, USA.
| | - Tory Alane Welsch
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, NY 13244, USA.
| | - Soor Rajiv Vora
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, NY 13244, USA.
| | - Dacheng Ren
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, NY 13244, USA.
| | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, NY 13244, USA.
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Essential role of accessory subunit LYRM6 in the mechanism of mitochondrial complex I. Nat Commun 2020; 11:6008. [PMID: 33243981 PMCID: PMC7693276 DOI: 10.1038/s41467-020-19778-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/29/2020] [Indexed: 01/18/2023] Open
Abstract
Respiratory complex I catalyzes electron transfer from NADH to ubiquinone (Q) coupled to vectorial proton translocation across the inner mitochondrial membrane. Despite recent progress in structure determination of this very large membrane protein complex, the coupling mechanism is a matter of ongoing debate and the function of accessory subunits surrounding the canonical core subunits is essentially unknown. Concerted rearrangements within a cluster of conserved loops of central subunits NDUFS2 (β1-β2S2 loop), ND1 (TMH5-6ND1 loop) and ND3 (TMH1-2ND3 loop) were suggested to be critical for its proton pumping mechanism. Here, we show that stabilization of the TMH1-2ND3 loop by accessory subunit LYRM6 (NDUFA6) is pivotal for energy conversion by mitochondrial complex I. We determined the high-resolution structure of inactive mutant F89ALYRM6 of eukaryotic complex I from the yeast Yarrowia lipolytica and found long-range structural changes affecting the entire loop cluster. In atomistic molecular dynamics simulations of the mutant, we observed conformational transitions in the loop cluster that disrupted a putative pathway for delivery of substrate protons required in Q redox chemistry. Our results elucidate in detail the essential role of accessory subunit LYRM6 for the function of eukaryotic complex I and offer clues on its redox-linked proton pumping mechanism. Respiratory complex I plays a key role in energy metabolism. Cryo-EM structure of a mutant accessory subunit LYRM6 from the yeast Yarrowia lipolytica and molecular dynamics simulations reveal conformational changes at the interface between LYRM6 and subunit ND3, propagated further into the complex. These findings offer insight into the mechanism of proton pumping by respiratory complex I.
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Hernández-Rodríguez EW, Escorcia AM, van der Kamp MW, Montero-Alejo AL, Caballero J. Multi-scale simulation reveals that an amino acid substitution increases photosensitizing reaction inputs in Rhodopsins. J Comput Chem 2020; 41:2278-2295. [PMID: 32757375 DOI: 10.1002/jcc.26392] [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: 02/09/2020] [Revised: 06/27/2020] [Accepted: 07/04/2020] [Indexed: 11/11/2022]
Abstract
Evaluating the availability of molecular oxygen (O2 ) and energy of excited states in the retinal binding site of rhodopsin is a crucial challenging first step to understand photosensitizing reactions in wild-type (WT) and mutant rhodopsins by absorbing visible light. In the present work, energies of the ground and excited states related to 11-cis-retinal and the O2 accessibility to the β-ionone ring are evaluated inside WT and human M207R mutant rhodopsins. Putative O2 pathways within rhodopsins are identified by using molecular dynamics simulations, Voronoi-diagram analysis, and implicit ligand sampling while retinal energetic properties are investigated through density functional theory, and quantum mechanical/molecular mechanical methods. Here, the predictions reveal that an amino acid substitution can lead to enough energy and O2 accessibility in the core hosting retinal of mutant rhodopsins to favor the photosensitized singlet oxygen generation, which can be useful in understanding retinal degeneration mechanisms and in designing blue-lighting-absorbing proteic photosensitizers.
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Affiliation(s)
- Erix W Hernández-Rodríguez
- Laboratorio de Bioinformática y Química Computacional, Escuela de Química y Farmacia, Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
| | - Andrés M Escorcia
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK
| | | | - Ana L Montero-Alejo
- Departamento de Física, Facultad de Ciencias Naturales, Matemática y del Medio Ambiente (FCNMM), Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Julio Caballero
- Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
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50
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Feng S, Dang S, Han TW, Ye W, Jin P, Cheng T, Li J, Jan YN, Jan LY, Cheng Y. Cryo-EM Studies of TMEM16F Calcium-Activated Ion Channel Suggest Features Important for Lipid Scrambling. Cell Rep 2020; 28:567-579.e4. [PMID: 31291589 PMCID: PMC6684876 DOI: 10.1016/j.celrep.2019.06.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 05/03/2019] [Accepted: 06/05/2019] [Indexed: 12/25/2022] Open
Abstract
As a Ca2+-activated lipid scramblase and ion channel that mediates Ca2+ influx, TMEM16F relies on both functions to facilitate extracellular vesicle generation, blood coagulation, and bone formation. How a bona fide ion channel scrambles lipids remains elusive. Our structural analyses revealed the coexistence of an intact channel pore and PIP2-dependent protein conformation changes leading to membrane distortion. Correlated to the extent of membrane distortion, many tightly bound lipids are slanted. Structure-based mutagenesis studies further reveal that neutralization of some lipid-binding residues or those near membrane distortion specifically alters the onset of lipid scrambling, but not Ca2+ influx, thus identifying features outside of channel pore that are important for lipid scrambling. Together, our studies demonstrate that membrane distortion does not require open hydrophilic grooves facing the membrane interior and provide further evidence to suggest separate pathways for lipid scrambling and ion permeation. TMEM16F is a calcium-activated ion channel and lipid scramblase linked to the bleeding disorder Scott syndrome. Feng et al. examine cryo-EM structures of TMEM16F with or without Ca2+ ions and PIP2 nanodisc supplementation and identify structural features for lipid binding and membrane distortion critical for lipid scrambling activity.
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Affiliation(s)
- Shengjie Feng
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Shangyu Dang
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tina Wei Han
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Wenlei Ye
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Peng Jin
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tong Cheng
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Junrui Li
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuh Nung Jan
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lily Yeh Jan
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
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