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Miglioli F, Joel S, Tegoni M, Neira-Pelén P, Günther S, Carcelli M, Fisicaro E, Brancale A, Fernández-García Y, Rogolino D. Inhibitory interactions of the 2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-one scaffold with Bunyavirales cap-snatching endonucleases expose relevant drug design features. Eur J Med Chem 2024; 272:116467. [PMID: 38735150 DOI: 10.1016/j.ejmech.2024.116467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/19/2024] [Accepted: 04/28/2024] [Indexed: 05/14/2024]
Abstract
The World Health Organization (WHO) identifies several bunyaviruses as significant threats to global public health security. Developing effective therapies against these viruses is crucial to combat future outbreaks and mitigate their impact on patient outcomes. Here, we report the synthesis of some isoindol-1-one derivatives and explore their inhibitory properties over an indispensable metal-dependent cap-snatching endonuclease (Cap-ENDO) shared among evolutionary divergent bunyaviruses. The compounds suppressed RNA hydrolysis by Cap-ENDOs, with IC50 values predominantly in the lower μM range. Molecular docking studies revealed the interactions with metal ions to be essential for the 2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-one scaffold activity. Calorimetric analysis uncovered Mn2+ ions to have the highest affinity for sites within the targets, irrespective of aminoacidic variations influencing metal cofactor preferences. Interestingly, spectrophotometric findings unveiled sole dinuclear species formation between the scaffold and Mn2+. Moreover, the complexation of two Mn2+ ions within the viral enzymes appears to be favourable, as indicated by the binding of compound 11 to TOSV Cap-ENDO (Kd = 28 ± 3 μM). Additionally, the tendency of compound 11 to stabilize His+ more than His- Cap-ENDOs suggests exploitable differences in their catalytic pockets relevant to improving specificity. Collectively, our results underscore the isoindolinone scaffold's potential as a strategic starting point for the design of pan-antibunyavirus drugs.
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Affiliation(s)
- Francesca Miglioli
- Department of Chemistry, Life Sciences, Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy
| | - Shindhuja Joel
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Matteo Tegoni
- Department of Chemistry, Life Sciences, Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy
| | - Pedro Neira-Pelén
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Stephan Günther
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Mauro Carcelli
- Department of Chemistry, Life Sciences, Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy
| | - Emilia Fisicaro
- Department of Food and Drug, University of Parma, Viale delle Scienze 27/A, 43124, Parma, Italy
| | - Andrea Brancale
- Department of Organic Chemistry, University of Chemistry and Technology, 16628, Prague, Czech Republic
| | - Yaiza Fernández-García
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany.
| | - Dominga Rogolino
- Department of Chemistry, Life Sciences, Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy.
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2
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Nag S, Banerjee C, Goyal M, Siddiqui AA, Saha D, Mazumder S, Debsharma S, Pramanik S, Saha SJ, De R, Bandyopadhyay U. Plasmodium falciparum Alba6 exhibits DNase activity and participates in stress response. iScience 2024; 27:109467. [PMID: 38558939 PMCID: PMC10981135 DOI: 10.1016/j.isci.2024.109467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/12/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Alba domain proteins, owing to their functional plasticity, play a significant role in organisms. Here, we report an intrinsic DNase activity of PfAlba6 from Plasmodium falciparum, an etiological agent responsible for human malignant malaria. We identified that tyrosine28 plays a critical role in the Mg2+ driven 5'-3' DNase activity of PfAlba6. PfAlba6 cleaves both dsDNA as well as ssDNA. We also characterized PfAlba6-DNA interaction and observed concentration-dependent oligomerization in the presence of DNA, which is evident from size exclusion chromatography and single molecule AFM-imaging. PfAlba6 mRNA expression level is up-regulated several folds following heat stress and treatment with artemisinin, indicating a possible role in stress response. PfAlba6 has no human orthologs and is expressed in all intra-erythrocytic stages; thus, this protein can potentially be a new anti-malarial drug target.
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Affiliation(s)
- Shiladitya Nag
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Chinmoy Banerjee
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Manish Goyal
- Department of Molecular & Cell Biology, School of Dental Medicine, Boston University Medical Campus, Boston, MA, USA
| | - Asim Azhar Siddiqui
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Debanjan Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Somnath Mazumder
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
- Department of Zoology, Raja Peary Mohan College, 1 Acharya Dhruba Pal Road, Uttarpara, West Bengal 712258, India
| | - Subhashis Debsharma
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Saikat Pramanik
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Shubhra Jyoti Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Rudranil De
- Amity Institute of Biotechnology, Amity University, Kolkata, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, West Bengal 700135, India
| | - Uday Bandyopadhyay
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
- Division of Molecular Medicine, Bose Institute, Unified Academic Campus, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal 700091, India
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3
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Schuck B, Brenk R. On the hunt for metalloenzyme inhibitors: Investigating the presence of metal-coordinating compounds in screening libraries and chemical spaces. Arch Pharm (Weinheim) 2024; 357:e2300648. [PMID: 38279543 DOI: 10.1002/ardp.202300648] [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: 11/08/2023] [Revised: 12/20/2023] [Accepted: 12/27/2023] [Indexed: 01/28/2024]
Abstract
Metalloenzymes play vital roles in various biological processes, requiring the search for inhibitors to develop treatment options for diverse diseases. While compound library screening is a conventional approach, the exploration of virtual chemical spaces housing trillions of compounds has emerged as an alternative strategy. In this study, we investigated the suitability of selected screening libraries and chemical spaces for discovering inhibitors of metalloenzymes featuring common ions (Mg2+, Mn2+, and Zn2+). First, metal-coordinating groups from ligands interacting with ions in the Protein Data Bank were extracted. Subsequently, the prevalence of these groups in two focused screening libraries (Life Chemicals' chelator library, comprising 6,428 compounds, and Otava's chelator fragment library, with 1,784 fragments) as well as two chemical spaces (GalaXi and REAL space, containing billions of virtual products) was investigated. In total, 1,223 metal-coordinating groups were identified, with about a quarter of these groups found within the examined libraries and spaces. Our results indicate that these can serve as valuable starting points for drug discovery targeting metalloenzymes. In addition, this study suggests ways to improve libraries and spaces for better success in finding potential inhibitors for metalloenzymes.
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Affiliation(s)
- Bruna Schuck
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ruth Brenk
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
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4
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Aparecida Martins R, de Almeida Assunção AS, Cavalcante Souza Vieira J, Campos Rocha L, Michelin Groff Urayama P, Afonso Rabelo Buzalaf M, Roberto Sartori J, de Magalhães Padilha P. Metalloproteomic analysis of liver proteins isolated from broilers fed with different sources and levels of copper and manganese. Sci Rep 2024; 14:4883. [PMID: 38418503 PMCID: PMC10902370 DOI: 10.1038/s41598-024-55478-8] [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: 09/13/2023] [Accepted: 02/23/2024] [Indexed: 03/01/2024] Open
Abstract
Supplementing minerals beyond dietary requirements can increase the risk of toxicity and mineral excretion, making the selection of more bioavailable sources crucial. Thus, this work aimed to use metalloproteomics tools to investigate possible alterations in the hepatic proteome of broilers fed with diets containing two sources (sulfate and hydroxychloride) and two levels of copper (15 and 150 ppm) and manganese (80 and 120 ppm), totaling four treatments: low Cu/Mn SO4, high Cu/Mn SO4, low Cu/Mn (OH)Cl and high Cu/Mn (OH)Cl. The difference in abundance of protein spots and copper and manganese concentrations in liver and protein pellets were analyzed by analysis of variance with significance level of 5%. The Cu and Mn concentrations determined in liver and protein pellets suggested greater bioavailability of hydroxychloride sources. We identified 19 Cu-associated proteins spots, 10 Mn-associated protein spots, and 5 Cu and/or Mn-associated protein spots simultaneously. The analysis also indicated the induction of heat shock proteins and detoxification proteins in broilers fed with high levels of copper and manganese, suggesting the involvement of these proteins in metal tolerance and stress.
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Affiliation(s)
- Renata Aparecida Martins
- School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | | | | | - Leone Campos Rocha
- School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | | | | | - José Roberto Sartori
- School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
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5
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Brown HA, DeVeaux AL, Juliano BR, Photenhauer AL, Boulinguiez M, Bornschein RE, Wawrzak Z, Ruotolo BT, Terrapon N, Koropatkin NM. BoGH13A Sus from Bacteroides ovatus represents a novel α-amylase used for Bacteroides starch breakdown in the human gut. Cell Mol Life Sci 2023; 80:232. [PMID: 37500984 PMCID: PMC10540511 DOI: 10.1007/s00018-023-04812-w] [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: 04/10/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 07/29/2023]
Abstract
Members of the Bacteroidetes phylum in the human colon deploy an extensive number of proteins to capture and degrade polysaccharides. Operons devoted to glycan breakdown and uptake are termed polysaccharide utilization loci or PUL. The starch utilization system (Sus) is one such PUL and was initially described in Bacteroides thetaiotaomicron (Bt). BtSus is highly conserved across many species, except for its extracellular α-amylase, SusG. In this work, we show that the Bacteroides ovatus (Bo) extracellular α-amylase, BoGH13ASus, is distinguished from SusG in its evolutionary origin and its domain architecture and by being the most prevalent form in Bacteroidetes Sus. BoGH13ASus is the founding member of both a novel subfamily in the glycoside hydrolase family 13, GH13_47, and a novel carbohydrate-binding module, CBM98. The BoGH13ASus CBM98-CBM48-GH13_47 architecture differs from the CBM58 embedded within the GH13_36 of SusG. These domains adopt a distinct spatial orientation and invoke a different association with the outer membrane. The BoCBM98 binding site is required for Bo growth on polysaccharides and optimal enzymatic degradation thereof. Finally, the BoGH13ASus structure features bound Ca2+ and Mn2+ ions, the latter of which is novel for an α-amylase. Little is known about the impact of Mn2+ on gut bacterial function, much less on polysaccharide consumption, but Mn2+ addition to Bt expressing BoGH13ASus specifically enhances growth on starch. Further understanding of bacterial starch degradation signatures will enable more tailored prebiotic and pharmaceutical approaches that increase starch flux to the gut.
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Affiliation(s)
- Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Anna L DeVeaux
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Brock R Juliano
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Amanda L Photenhauer
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Matthieu Boulinguiez
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, CNRS AMU; USC1408 INRAE, 13288, Marseille, France
| | | | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Lemont, IL, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, CNRS AMU; USC1408 INRAE, 13288, Marseille, France
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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6
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Dixit H, Kulharia M, Verma SK. Metalloproteome of human-infective RNA viruses: a study towards understanding the role of metal ions in virology. Pathog Dis 2023; 81:ftad020. [PMID: 37653445 DOI: 10.1093/femspd/ftad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/07/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023] Open
Abstract
Metalloproteins and metal-based inhibitors have been shown to effectively combat infectious diseases, particularly those caused by RNA viruses. In this study, a diverse set of bioinformatics methods was employed to identify metal-binding proteins of human RNA viruses. Seventy-three viral proteins with a high probability of being metal-binding proteins were identified. These proteins included 40 zinc-, 47 magnesium- and 14 manganese-binding proteins belonging to 29 viral species and eight significant viral families, including Coronaviridae, Flaviviridae and Retroviridae. Further functional characterization has revealed that these proteins play a critical role in several viral processes, including viral replication, fusion and host viral entry. They fall under the essential categories of viral proteins, including polymerase and protease enzymes. Magnesium ion is abundantly predicted to interact with these viral enzymes, followed by zinc. In addition, this study also examined the evolutionary aspects of predicted viral metalloproteins, offering essential insights into the metal utilization patterns among different viral species. The analysis indicates that the metal utilization patterns are conserved within the functional classes of the proteins. In conclusion, the findings of this study provide significant knowledge on viral metalloproteins that can serve as a valuable foundation for future research in this area.
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Affiliation(s)
- Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
| | - Mahesh Kulharia
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
| | - Shailender Kumar Verma
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
- Department of Environmental Studies, University of Delhi 110007, Delhi, India
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7
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Insights into divalent cation regulation and G 13-coupling of orphan receptor GPR35. Cell Discov 2022; 8:135. [PMID: 36543774 PMCID: PMC9772185 DOI: 10.1038/s41421-022-00499-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/28/2022] [Indexed: 12/24/2022] Open
Abstract
Endogenous ions play important roles in the function and pharmacology of G protein-coupled receptors (GPCRs) with limited atomic evidence. In addition, compared with G protein subtypes Gs, Gi/o, and Gq/11, insufficient structural evidence is accessible to understand the coupling mechanism of G12/13 protein by GPCRs. Orphan receptor GPR35, which is predominantly expressed in the gastrointestinal tract and is closely related to inflammatory bowel diseases (IBDs), stands out as a prototypical receptor for investigating ionic modulation and G13 coupling. Here we report a cryo-electron microscopy structure of G13-coupled GPR35 bound to an anti-allergic drug, lodoxamide. This structure reveals a novel divalent cation coordination site and a unique ionic regulatory mode of GPR35 and also presents a highly positively charged binding pocket and the complementary electrostatic ligand recognition mode, which explain the promiscuity of acidic ligand binding by GPR35. Structural comparison of the GPR35-G13 complex with other G protein subtypes-coupled GPCRs reveals a notable movement of the C-terminus of α5 helix of the Gα13 subunit towards the receptor core and the least outward displacement of the cytoplasmic end of GPR35 TM6. A featured 'methionine pocket' contributes to the G13 coupling by GPR35. Together, our findings provide a structural basis for divalent cation modulation, ligand recognition, and subsequent G13 protein coupling of GPR35 and offer a new opportunity for designing GPR35-targeted drugs for the treatment of IBDs.
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8
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Characterization of novel nuclease and protease activities among Leptospiral immunoglobulin-like proteins. Arch Biochem Biophys 2022; 727:109349. [PMID: 35820644 DOI: 10.1016/j.abb.2022.109349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/01/2022] [Accepted: 07/03/2022] [Indexed: 11/24/2022]
Abstract
Bacterial immunoglobulin-like (BIg) domain containing proteins play a variety of biological functions. Leptospiral Immunoglobulin-like (Lig) proteins are well-known virulence factors located on the surface of the pathogenic Leptospira that act during adhesion, invasion, and immune evasion. The Lig proteins have many roles and have been designated as multifaceted proteins. However, the hydrolyzing function of Lig proteins is not yet investigated in detail. Here, we report novel in-vitro nuclease and protease activities in the Ig-like domain of LigA protein. All Ig-like domains were able to cleave DNA in the presence of a divalent ion, but not RNA. Site-directed mutagenesis revealed Mg+2 binding residues in the Ig-like domain of LigA7. The basis of novel nuclease activity may be associated with protein adopting different conformation in the presence of divalent ions and substrate as investigated by change of intrinsic fluorescence. The docking of a stretch of double-strand DNA shows the binding on the positive surface of the protein. In addition, the protein is also observed to cleave a general protease substrate, β-casein, in our experimental condition. Our results proposed that the novel functions may be associated with neutrophil extracellular Trap (NET) evasion. Overall this study enhances the basic knowledge of non-nuclease proteins involved in the DNA cleavage activity and makes the foundation to explore its in-vivo activity in pathogenic Leptospira and other pathogens as well. Moreover, this information may be utilized to develop preventive strategies to interfere with Leptospira immune evasion.
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9
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The Activity of the Durum Wheat (Triticum durum L.) Catalase 1 (TdCAT1) Is Modulated by Calmodulin. Antioxidants (Basel) 2022; 11:antiox11081483. [PMID: 36009202 PMCID: PMC9404813 DOI: 10.3390/antiox11081483] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/30/2022] [Accepted: 07/27/2022] [Indexed: 01/14/2023] Open
Abstract
Plant catalases (CAT) are involved in the cellular scavenging of the reactive oxygen species during developmental processes and in response to abiotic and biotic stresses. However, little is known about the regulation of the CAT activity to ensure efficient antioxidant function. Using bioinformatic analyses, we showed that durum wheat catalase 1 (TdCAT1) harbors highly conserved cation-binding and calmodulin binding (CaMBD) domains which are localized at different positions of the protein. As a result, the catalytic activity of TdCAT1 is enhanced in vitro by the divalent cations Mn2+ and Fe2+ and to a lesser extent by Cu2+, Zn2+, and Mg2+. Moreover, the GST-pull down assays performed here revealed that TdCAT1 bind to the wheat CaM (TdCaM1.3) in a Ca2+-independent manner. Furthermore, the TdCaM1.3/Ca2+ complex is stimulated in a CaM-dose-dependent manner by the catalytic activity of TdCAT1, which is further increased in the presence of Mn2+ cations. The catalase activity of TdCAT1 is enhanced by various divalent cations and TdCaM1.3 in a Ca-dependent manner. Such effects are not reported so far and raise a possible role of CaM and cations in the function of CATs during cellular response to oxidative stress.
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10
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Smethurst DGJ, Shcherbik N. Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules. J Biol Chem 2021; 297:101374. [PMID: 34732319 PMCID: PMC8633580 DOI: 10.1016/j.jbc.2021.101374] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 02/08/2023] Open
Abstract
Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain the activity they facilitate. While ancient earth's atmosphere was rich in iron and manganese and low in oxygen, periods of atmospheric oxygenation significantly altered the availability of certain metal ions, resulting in ion replacement within biomolecules. This adaptation mechanism has given rise to the phenomenon of metal cofactor interchangeability, whereby contemporary proteins and nucleic acids interact with multiple metal ions interchangeably, with different coordinated metals influencing biological activity, stability, and toxic potential. The ability of extant organisms to adapt to fluctuating metal availability remains relevant in a number of crucial biomolecules, including the superoxide dismutases of the antioxidant defense systems and ribonucleotide reductases. These well-studied and ancient enzymes illustrate the potential for metal interchangeability and adaptive utilization. More recently, the ribosome has also been demonstrated to exhibit interchangeable interactions with metal ions with impacts on function, stability, and stress adaptation. Using these and other examples, here we review the biological significance of interchangeable metal ions from a new angle that combines both biochemical and evolutionary viewpoints. The geochemical pressures and chemical properties that underlie biological metal utilization are discussed in the context of their impact on modern disease states and treatments.
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Affiliation(s)
- Daniel G J Smethurst
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
| | - Natalia Shcherbik
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
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11
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12
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Zhang Y, Zheng J. Bioinformatics of Metalloproteins and Metalloproteomes. Molecules 2020; 25:molecules25153366. [PMID: 32722260 PMCID: PMC7435645 DOI: 10.3390/molecules25153366] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/14/2022] Open
Abstract
Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and their functions, the application of bioinformatics in the research of metalloproteins and metalloproteomes is still limited. In the last few years, computational prediction and comparative genomics of metalloprotein genes have arisen, which provide significant insights into their distribution, function, and evolution in nature. This review aims to offer an overview of recent advances in bioinformatic analysis of metalloproteins, mainly focusing on metalloprotein prediction and the use of different metals across the tree of life. We describe current computational approaches for the identification of metalloprotein genes and metal-binding sites/patterns in proteins, and then introduce a set of related databases. Furthermore, we discuss the latest research progress in comparative genomics of several important metals in both prokaryotes and eukaryotes, which demonstrates divergent and dynamic evolutionary patterns of different metalloprotein families and metalloproteomes. Overall, bioinformatic studies of metalloproteins provide a foundation for systematic understanding of trace metal utilization in all three domains of life.
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Affiliation(s)
- Yan Zhang
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
- Correspondence: ; Tel.: +86-755-2692-2024
| | - Junge Zheng
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
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13
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Hinz SC, Elter A, Rammo O, Schwämmle A, Ali A, Zielonka S, Herget T, Kolmar H. A Generic Procedure for the Isolation of pH- and Magnesium-Responsive Chicken scFvs for Downstream Purification of Human Antibodies. Front Bioeng Biotechnol 2020; 8:688. [PMID: 32656201 PMCID: PMC7324474 DOI: 10.3389/fbioe.2020.00688] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
Affinity chromatography provides an excellent platform for protein purification, which is a key step in the large scale downstream processing of therapeutic monoclonal antibodies (Mabs). Protein A chromatography constitutes the gold standard for Mab purification. However, the required acidic conditions (2.8–3.5) for elution from the affinity matrix limit their applicability, particularly for next generation antibodies and antibody fusion proteins, since denaturation and irreversible aggregation can occur due to the acidic buffer conditions. Here we describe a generic procedure for the generation of antigen-specific chromatography ligands with tailor-made elution conditions. To this end, we generated a scFv-library based on mRNA from a chicken immunized with human Fc. The antibody repertoire was displayed on yeast Saccharomyces cerevisiae screened via FACS toward pH- and magnesium-responsive scFvs which specifically recognize human IgG antibodies. Isolated scFvs were reformatted, produced in Escherichia coli and immobilized on NHS-agarose columns. Several scFvs were identified that mediated antibody binding at neutral pH and antibody recovery at pH values of 4.5 and higher or even at neutral pH upon MgCl2 exposure. The iterative screening methodology established here is generally amenable to the straightforward isolation of stimulus-responsive antibodies that may become valuable tools for a variety of applications.
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Affiliation(s)
- Steffen C Hinz
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.,Merck Lab @ Technische Universität Darmstadt, Darmstadt, Germany
| | - Adrian Elter
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.,Merck Lab @ Technische Universität Darmstadt, Darmstadt, Germany
| | - Oliver Rammo
- Life Science Division, Merck KGaA, Darmstadt, Germany
| | | | - Ataurehman Ali
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Thomas Herget
- Strategy und Transformation, Merck KGaA, Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.,Merck Lab @ Technische Universität Darmstadt, Darmstadt, Germany
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14
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Shin M, Park J, Jin Y, Payne SM, Kim KH, Kim KH. Biochemical characterization of bacterial FeoBs: A perspective on nucleotide specificity. Arch Biochem Biophys 2020; 685:108350. [PMID: 32220566 PMCID: PMC9841765 DOI: 10.1016/j.abb.2020.108350] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 01/18/2023]
Abstract
Iron is an essential requirement for the survival and virulence of most bacteria. The bacterial ferrous iron transporter protein FeoB functions as a major reduced iron transporter in prokaryotes, but its biochemical mechanism has not been fully elucidated. In the present study, we compared enzymatic properties of the cytosolic portions of pathogenic bacterial FeoBs to elucidate each bacterial strain-specific characteristic of the Feo system. We show that bacterial FeoBs are classified into two distinct groups that possess either a sole GTPase or an NTPase with a substrate promiscuity. This difference in nucleotide preference alters cellular requirements for monovalent and divalent cations. While the hydrolytic activity of the GTP-dependent FeoBs was stimulated by potassium, the action of the NTP-dependent FeoBs was not significantly affected by the presence of monovalent cations. Mutation of Asn11, having a role in potassium-dependent GTP hydrolysis, changed nucleotide specificity of the NTP-dependent FeoB, resulting in loss of ATPase activity. Sequence analysis suggested a possible association of alanine in the G5 motif for the NTP-dependent activity in FeoBs. This demonstration of the distinct enzymatic properties of bacterial FeoBs provides important insights into mechanistic details of Feo iron transport processes, as well as offers a promising species-specific anti-virulence target.
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Affiliation(s)
- Minhye Shin
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Republic of Korea
| | - Jinsub Park
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Republic of Korea
| | - Yerin Jin
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Republic of Korea
| | - Shelley M. Payne
- Department of Molecular Biosciences, College of Natural Science, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Republic of Korea,Corresponding author: Kyoung Heon Kim, Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea, , Tel: +82-2-3290-3028
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, Republic of Korea.
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15
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Whey peptide-encapsulated silver nanoparticles as a colorimetric and spectrophotometric probe for palladium(II). Mikrochim Acta 2019; 186:763. [PMID: 31712977 DOI: 10.1007/s00604-019-3877-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/29/2019] [Indexed: 10/25/2022]
Abstract
Silver nanoparticles (AgNPs) coated with whey peptides are shown to be a useful optical nanoprobe for the highly sensitive determination of Pd(II). The peptidic surface of the AgNPs works as a molecular receptor for the rapid detection of Pd(II) via a color change from dark yellow to orange/red along with a spectral red-shift with a gap about 120 nm. The effect is caused by the formation of a coordination complex between Pd(II) and the peptide ligands. This results in the aggregation of AgNPs and an absorbance spectral shift from 410 to 530 nm. The absorbance response is linear in the range 0.1 to 1.3 μM Pd(II) with a low detection limit of 115 nM. The nanoprobe responds within a few minutes and is not interfered by other metal ions except for Mg(II). The probe potentially can be applied to the determination of Pd(II) contamination in the products of Pd(II)-catalyzed organic reactions and in pharmaceutical settings. Graphical abstractSchematic representation of the nanoprobe for Pd(II). (a) Synthesis of whey peptide-coated silver nanoparticles (AgNPs), (b) the nanoprobe design for Pd(II) detection, (c) HR-TEM imaging and elemental mapping, (d) quantitative determination of Pd(II) (Inset shows colorimetric results).
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16
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Roskamp KW, Kozlyuk N, Sengupta S, Bierma JC, Martin RW. Divalent Cations and the Divergence of βγ-Crystallin Function. Biochemistry 2019; 58:4505-4518. [PMID: 31647219 DOI: 10.1021/acs.biochem.9b00507] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The βγ-crystallin superfamily contains both β- and γ-crystallins of the vertebrate eye lens and the microbial calcium-binding proteins, all of which are characterized by a common double-Greek key domain structure. The vertebrate βγ-crystallins are long-lived structural proteins that refract light onto the retina. In contrast, the microbial βγ-crystallins bind calcium ions. The βγ-crystallin from the tunicate Ciona intestinalis (Ci-βγ) provides a potential link between these two functions. It binds calcium with high affinity and is found in a light-sensitive sensory organ that is highly enriched in metal ions. Thus, Ci-βγ is valuable for investigating the evolution of the βγ-crystallin fold away from calcium binding and toward stability in the apo form as part of the vertebrate lens. Here, we investigate the effect of Ca2+ and other divalent cations on the stability and aggregation propensity of Ci-βγ and human γS-crystallin (HγS). Beyond Ca2+, Ci-βγ is capable of coordinating Mg2+, Sr2+, Co2+, Mn2+, Ni2+, and Zn2+, although only Sr2+ is bound with comparable affinity to its preferred metal ion. The extent to which the tested divalent cations stabilize Ci-βγ structure correlates strongly with ionic radius. In contrast, none of the tested divalent cations improved the stability of HγS, and some of them induced aggregation. Zn2+, Ni2+, and Co2+ induce aggregation by interacting with cysteine residues, whereas Cu2+-mediated aggregation proceeds via a different binding site.
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Affiliation(s)
- Kyle W Roskamp
- Department of Chemistry , University of California , Irvine , California 92697-2025 , United States
| | - Natalia Kozlyuk
- Department of Chemistry , University of California , Irvine , California 92697-2025 , United States
| | - Suvrajit Sengupta
- Department of Chemistry , University of California , Irvine , California 92697-2025 , United States
| | - Jan C Bierma
- Department of Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3900 , United States
| | - Rachel W Martin
- Department of Chemistry , University of California , Irvine , California 92697-2025 , United States.,Department of Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3900 , United States
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17
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The Biochemical Properties of Manganese in Plants. PLANTS 2019; 8:plants8100381. [PMID: 31569811 PMCID: PMC6843630 DOI: 10.3390/plants8100381] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 01/12/2023]
Abstract
Manganese (Mn) is an essential micronutrient with many functional roles in plant metabolism. Manganese acts as an activator and co-factor of hundreds of metalloenzymes in plants. Because of its ability to readily change oxidation state in biological systems, Mn plays and important role in a broad range of enzyme-catalyzed reactions, including redox reactions, phosphorylation, decarboxylation, and hydrolysis. Manganese(II) is the prevalent oxidation state of Mn in plants and exhibits fast ligand exchange kinetics, which means that Mn can often be substituted by other metal ions, such as Mg(II), which has similar ion characteristics and requirements to the ligand environment of the metal binding sites. Knowledge of the molecular mechanisms catalyzed by Mn and regulation of Mn insertion into the active site of Mn-dependent enzymes, in the presence of other metals, is gradually evolving. This review presents an overview of the chemistry and biochemistry of Mn in plants, including an updated list of known Mn-dependent enzymes, together with enzymes where Mn has been shown to exchange with other metal ions. Furthermore, the current knowledge of the structure and functional role of the three most well characterized Mn-containing metalloenzymes in plants; the oxygen evolving complex of photosystem II, Mn superoxide dismutase, and oxalate oxidase is summarized.
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18
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Ghorbel M, Zaidi I, Ebel C, Hanin M. Differential regulation of the durum wheat MAPK phosphatase 1 by calmodulin, bivalent cations and possibly mitogen activated protein kinase 3. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 135:242-252. [PMID: 30584966 DOI: 10.1016/j.plaphy.2018.12.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
MAPK phosphatases (MKPs) are relevant negative regulators of MAPKs in eukaryotes as they mediate the feedback control of MAPK cascades in multiple cellular processes. Despite their relevance, our knowledge on the role of cereal MKPs in stress tolerance is scarce and TMKP1 remains today the only studied MKP in wheat. TMKP1 was previously reported to be involved in plant salt stress tolerance. Moreover, TMKP1 was shown to interact with calmodulin (CaM), 14-3-3 and TMPK3/TMPK6 proteins, which regulate its catalytic activity. To further understand the functional properties of TMKP1, we investigate here the contribution of its phosphorylation status, and of TMPK3 together with CaM and bivalent cations on the catalytic activity. In-gel kinase assays revealed that TMKP1 can be phosphorylated by similar wheat and Arabidopsis MAPKs, including most likely MPK3 and MPK6. In addition, we provide evidence for the capacity of wheat TMPK3 to bind to TMKP1 via a conserved Kinase Interacting Domain (KID) located on its C-terminal part. This interaction leads to a stimulation of TMKP1 activity in the presence of Mn2+ or Mg2+ ions, but to its inhibition in the presence of Ca2+ ions. However, the phosphorylation status of TMKP1 seems to be dispensable for TMKP1 activation by TMPK3. Remarkably, in assays combining TMPK3 with CaM/Ca2+ complex, we registered rather an inhibition of TMKP1 activity which however can be suppressed by Mn2+ cations. Our data are in favor of complex differential regulation of TMKP1 by its MPK substrates, metallic cations that might help in fine-tuning the plant cellular responses to various stresses.
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Affiliation(s)
- Mouna Ghorbel
- Laboratoire de Biotechnologie et Amélioration des Plantes, Centre de Biotechnologie de Sfax, BP "1177", 3018, Sfax, Tunisia; Unité de Génomique Fonctionnelle et Physiologie des Plantes, Institut Supérieur de Biotechnologie, Université de Sfax, BP "1175", 3038, Sfax, Tunisia
| | - Ikram Zaidi
- Laboratoire de Biotechnologie et Amélioration des Plantes, Centre de Biotechnologie de Sfax, BP "1177", 3018, Sfax, Tunisia
| | - Chantal Ebel
- Unité de Génomique Fonctionnelle et Physiologie des Plantes, Institut Supérieur de Biotechnologie, Université de Sfax, BP "1175", 3038, Sfax, Tunisia
| | - Moez Hanin
- Unité de Génomique Fonctionnelle et Physiologie des Plantes, Institut Supérieur de Biotechnologie, Université de Sfax, BP "1175", 3038, Sfax, Tunisia.
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19
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Singh R, Goyal VD, Kumar A, Sabharwal NS, Makde RD. Crystal structures and biochemical analyses of intermediate cleavage peptidase: role of dynamics in enzymatic function. FEBS Lett 2019; 593:443-454. [PMID: 30582634 DOI: 10.1002/1873-3468.13321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/19/2018] [Accepted: 12/19/2018] [Indexed: 01/20/2023]
Abstract
Intermediate cleavage peptidase (Icp55) processes a subset of mitochondrial matrix proteins by removing a bulky residue at their N termini, leaving behind smaller N-terminal residues (icp activity). This contributes towards the stability of the mitochondrial proteome. We report crystal structures of yeast Icp55 including one bound to the apstatin inhibitor. Apart from icp activity, the enzyme was found to exhibit Xaa-Pro aminopeptidase activity in vitro. Structural and biochemical data suggest that the enzyme exists in a rapid equilibrium between monomer and dimer. Furthermore, the dimer, and not the monomer, was found to be the active species with loop dynamics at the dimer interface playing an important role in activity. Based on the new evidence, we propose a model for binding and processing of cellular targets by Icp55. DATABASE: The atomic coordinates and structure factors for the structures of Icp55 (code 6A9T, 6A9U, 6A9V) have been deposited in the Protein Data Bank (PDB) (http://www.pdb.org/).
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Affiliation(s)
- Rahul Singh
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Venuka Durani Goyal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Naripjeet Singh Sabharwal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
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20
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Khrustalev VV, Khrustaleva TA, Poboinev VV, Karchevskaya CI, Shablovskaya EA, Terechova TG. Cobalt(ii) cation binding by proteins. Metallomics 2019; 11:1743-1752. [DOI: 10.1039/c9mt00205g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, a set of non-homologous proteins (238) that could bind the cobalt(ii) cations was selected from all the available Protein Data Bank structures with Co2+ cations.
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Affiliation(s)
| | - Tatyana Aleksandrovna Khrustaleva
- Biochemical Group of the Multidisciplinary Diagnostic Laboratory
- Institute of Physiology of the National Academy of Sciences of Belarus
- Minsk, Academicheskaya, 28
- Belarus
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21
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Khrustalev VV, Khrustaleva TA, Kordyukova LV. Selection and structural analysis of the NY25 peptide – A vaccine candidate from hemagglutinin of swine-origin Influenza H1N1. Microb Pathog 2018; 125:72-83. [DOI: 10.1016/j.micpath.2018.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 01/09/2023]
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22
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Oke M, Agbalajobi R, Osifeso M, Muhammad B, Lawal H, Mai M, Adegunle Q. Design and implementation of structural bioinformatics projects for biological sciences undergraduate students. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 46:547-554. [PMID: 30369034 DOI: 10.1002/bmb.21169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/21/2018] [Accepted: 09/03/2018] [Indexed: 06/08/2023]
Abstract
Contemporary biology is currently undergoing a revolution, driven by the availability of high-throughput technologies and a wide variety of bioinformatics tools. However, bioinformatics education and practice is still in its infancy in most of the African continent. Consequently, concerted efforts have been made in recent years to incorporate bioinformatics modules into biological sciences curriculum of African Universities. Despite this, one aspect of bioinformatics that is yet to be incorporated is structural bioinformatics. In this article, we report on a structural bioinformatics project carried out by final year project students in a Nigerian university. The target protein was the thermoacidophilic Sulfolobus islandicus rod-shaped virus 1 (SIRV1) Rep protein, which was further characterized using various free, user-friendly and online sequence-based and structure-based bioinformatics tools. This exercise gave students the opportunity to generate new data, interpret the data, and acquire collaborative research skills. In this report, emphasis is placed on analysis of the data generated to further encourage analytical skills. By sharing this experience, it is anticipated that other similar institutions would adopt parallel strategies to expose undergraduate students to structural biology, and increase awareness of freely available bioinformatics tools for tackling pertinent biological questions. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):547-554, 2018.
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Affiliation(s)
- Muse Oke
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| | - Ramon Agbalajobi
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| | | | - Babagana Muhammad
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| | - Halimat Lawal
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| | - Muhammad Mai
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| | - Quadri Adegunle
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
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23
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Khrustalev VV, Khrustaleva TA, Poboinev VV. Amino acid content of beta strands and alpha helices depends on their flanking secondary structure elements. Biosystems 2018; 168:45-54. [DOI: 10.1016/j.biosystems.2018.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 04/21/2018] [Accepted: 04/23/2018] [Indexed: 12/17/2022]
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24
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TM0416, a Hyperthermophilic Promiscuous Nonphosphorylated Sugar Isomerase, Catalyzes Various C 5 and C 6 Epimerization Reactions. Appl Environ Microbiol 2017; 83:AEM.03291-16. [PMID: 28258150 DOI: 10.1128/aem.03291-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 02/26/2017] [Indexed: 01/11/2023] Open
Abstract
There is currently little information on nonphosphorylated sugar epimerases, which are of potential interest for producing rare sugars. We found a gene (the TM0416 gene) encoding a putative d-tagatose-3-epimerase-related protein from the hyperthermophilic bacterium Thermotoga maritima We overexpressed the TM0416 gene in Escherichia coli and purified the resulting recombinant protein for detailed characterization. Amino acid sequence alignment and a structural similarity search revealed that TM0416 is a putative nonphosphorylated sugar epimerase. The recombinant enzyme exhibited maximal C-3 epimerization of l-ribulose to l-xylulose at ∼80°C and pH 7 in the presence of 1 mM Mn2+ In addition, this enzyme showed unusually high activity for the epimerization of d-tagatose to d-sorbose, with a conversion yield of 20% after 6 h at 80°C. Remarkably, the enzyme catalyzed the isomerization of d-erythrose or d-threose to d-erythrulose significantly, with conversion yields of 71% and 54.5%, respectively, after 6 h at 80°C at pH 7. To further investigate the substrate specificity of TM0416, we determined its crystal structures in complex with divalent metal ions and l-erythrulose at resolutions of 1.5 and 1.6 Å. Detailed inspection of the structural features and biochemical data clearly demonstrated that this metalloenzyme, with a freely accessible substrate-binding site and neighboring hydrophobic residues, exhibits different and promiscuous substrate preferences, compared with its mesophilic counterparts. Therefore, this study suggests that TM0416 can be functionally classified as a novel type of l-ribulose 3-epimerase (R3E) with d-erythrose isomerase activity.IMPORTANCE Rare sugars, which occur naturally in small amounts, have attracted considerable attention in the food and drug industries. However, there is little information on nonphosphorylated sugar epimerases, which might potentially be applied for the production of rare sugars. This study describes the characterization and functional annotation of a putative nonphosphorylated sugar 3-epimerase from a hyperthermophilic bacterium. Furthermore, we determined its crystal structures in complex with divalent metal ions and l-erythrulose, highlighting its metal-dependent, bifunctional, sugar-isomerizing activity. This hyperthermophilic R3E exhibited d-erythrose/d-threose isomerase activity, with structural features near the substrate-binding site distinct from those of its mesophilic counterparts. Moreover, this metalloenzyme showed unusually high activity for the epimerization of d-tagatose to d-sorbose at 70°C. Therefore, TM0416 can be functionally classified as a novel type of promiscuous R3E with a potential for the production of rare sugars for the food and pharmaceutical industries.
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