1
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Tsuchiya K, Fujita S, Numata K. Ampholytic Peptides Consisting of an Alternating Lysine/Glutamic Acid Sequence for the Simultaneous Formation of Polyion Complex Vesicles. ACS POLYMERS AU 2024; 4:320-330. [PMID: 39156560 PMCID: PMC11328329 DOI: 10.1021/acspolymersau.4c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 08/20/2024]
Abstract
Nanoarchitectures such as micelles and vesicles that self-assemble via electrostatic interactions between their charged polymeric components have been widely used as material delivery platforms. In this work, ampholytic peptides with a sequence of alternating lysine and glutamic acid residues were designed and synthesized via chemoenzymatic polymerization. This alternating sequence was achieved by trypsin-catalyzed polymerization of a dipeptide monomer. Due to the electrostatic interaction between the anionic and cationic residues, the prepared ampholytic peptides spontaneously formed nanosized assemblies with a size of 100-200 nm in water. Modification with tetra(ethylene glycol) (TEG) at the N-terminus of these ampholytic alternating peptides resulted in the formation of stable nanosized assemblies, while peptides consisting of random sequences of lysine and glutamic acid formed large aggregates with deteriorated stability even with TEG modification. Morphological observations using a field-emission scanning electron microscope and an atomic force microscope revealed that the obtained assemblies were spherical and hollow, indicating the spontaneous formation of vesicles from the TEG-modified ampholytic alternating peptides. These vesicles were able to encapsulate a model fluorescent protein within their hollow structures without structural collapse causing loss of fluorescence, demonstrating the potential of these nanocarriers for use in material delivery systems.
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Affiliation(s)
- Kousuke Tsuchiya
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1
Hirosawa, Wako, Saitama 351-0198, Japan
| | - Seiya Fujita
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Keiji Numata
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1
Hirosawa, Wako, Saitama 351-0198, Japan
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2
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Fujii K, Izumi Y, Maita N, Matsuo K, Kato M. Observation of the Liquid-Liquid Phase Separation of FUS-LC Using Vacuum-Ultraviolet Circular Dichroism Spectroscopy. Chirality 2024; 36:e23707. [PMID: 39129227 DOI: 10.1002/chir.23707] [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: 01/30/2024] [Revised: 07/03/2024] [Accepted: 07/11/2024] [Indexed: 08/13/2024]
Abstract
To reveal the structural mechanism by which the low-complexity domain of the fused in sarcoma protein (FUS-LC) mediates liquid-liquid phase separation (LLPS), we conducted a vacuum-ultraviolet circular dichroism (VUV-CD) spectroscopic study, a technique to analyze the secondary structures of proteins. The VUV-CD measurements were performed at the BL12 VUV-CD station at the Hiroshima Synchrotron Radiation Center (HiSOR) in Japan. CD spectra were measured between 180 and 260 nm while controlling the temperature of samples from 37°C to 5°C to obtain the LLPS of FUS-LC. The CD spectrum obtained at 37°C exhibited a large negative peak at 195 nm and a small negative shoulder near 220 nm. The peak intensity around 195 nm decreased as the sample temperature decreased. The spectral changes originated from the LLPS formation.
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Affiliation(s)
- Kentaro Fujii
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yudai Izumi
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Nobuo Maita
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima, Japan
| | - Masato Kato
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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3
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Guérin M, Vandevenne M, Brans A, Matagne A, Marquant R, Prost E, Octave S, Avalle B, Maffucci I, Padiolleau-Lefèvre S. Production, purification, and quality assessment of borrelial proteins CspZ from Borrelia burgdorferi and FhbA from Borrelia hermsii. Appl Microbiol Biotechnol 2024; 108:425. [PMID: 39042328 PMCID: PMC11266248 DOI: 10.1007/s00253-024-13195-2] [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: 03/25/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 07/24/2024]
Abstract
Borrelia, spirochetes transmitted by ticks, are the etiological agents of numerous multisystemic diseases, such as Lyme borreliosis (LB) and tick-borne relapsing fever (TBRF). This study focuses on two surface proteins from two Borrelia subspecies involved in these diseases: CspZ, expressed by Borrelia burgdorferi sensu stricto (also named BbCRASP-2 for complement regulator-acquiring surface protein 2), and the factor H binding A (FhbA), expressed by Borrelia hermsii. Numerous subspecies of Borrelia, including these latter, are able to evade the immune defenses of a variety of potential vertebrate hosts in a number of ways. In this context, previous data suggested that both surface proteins play a role in the immune evasion of both Borrelia subspecies by interacting with key regulators of the alternative pathway of the human complement system, factor H (FH) and FH-like protein 1 (FHL-1). The recombinant proteins, CspZ and FhbA, were expressed in Escherichia coli and purified by one-step metal-affinity chromatography, with yields of 15 and 20 mg or pure protein for 1 L of cultured bacteria, respectively. The purity was evaluated by SDS-PAGE and HPLC and is close to about 95%. The mass of CspZ and FhbA was checked by mass spectrometry (MS). Proper folding of CspZ and FhbA was confirmed by circular dichroism (CD), and their biological activity, namely their interaction with purified FH from human serum (recombinant FH15-20 and recombinant FHL-1), was characterized by SPR. Such a study provides the basis for the biochemical characterization of the studied proteins and their biomolecular interactions which is a necessary prerequisite for the development of new approaches to improve the current diagnosis of LB and TBRF. KEY POINTS: • DLS, CD, SEC-MALS, NMR, HPLC, and MS are tools for protein quality assessment • Borrelia spp. possesses immune evasion mechanisms, including human host complement • CspZ and FhbA interact with high affinity (pM to nM) to human FH and rFHL-1.
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Affiliation(s)
- Mickaël Guérin
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, Compiègne, 60203, France
| | - Marylène Vandevenne
- Robotein®, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, Sart-Tilman, Liège, 4000, Belgium
- Centre for Protein Engineering, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, Liège, Sart- Tilman), 4000, Belgium
| | - Alain Brans
- Protein Factory, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, Sart-Tilman, Liège, 4000, Belgium
- Centre for Protein Engineering, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, Liège, Sart- Tilman), 4000, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, Sart-Tilman, Liège, 4000, Belgium
- Centre for Protein Engineering, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, Liège, Sart- Tilman), 4000, Belgium
| | - Rodrigue Marquant
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, Compiègne, 60203, France
| | - Elise Prost
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, Compiègne, 60203, France
| | - Stéphane Octave
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, Compiègne, 60203, France
| | - Bérangère Avalle
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, Compiègne, 60203, France
| | - Irene Maffucci
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, Compiègne, 60203, France
| | - Séverine Padiolleau-Lefèvre
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, Compiègne, 60203, France.
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4
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Guerreiro BM, Dionísio MM, Lima JC, Silva JC, Freitas F. Cryoprotective Polysaccharides with Ordered Gel Structures Induce Ice Growth Anticipation and Survival Enhancement during Cell Cryopreservation. Biomacromolecules 2024; 25:3384-3397. [PMID: 38739855 DOI: 10.1021/acs.biomac.4c00040] [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: 05/16/2024]
Abstract
This work cross-correlated rheological, thermodynamic, and conformational features of several natural polysaccharides to their cryoprotective performance. The basis of cryoprotection of FucoPol, pectin, and agar revealed a causal combination of (i) an emerging sol-gel transition (p = 0.014) at near-hypothermia (4 °C), (ii) noncolligative attenuated supercooling of the kinetic freezing point of water (p = 0.026) supporting ice growth anticipation, and (iii) increased conformational order (p < 0.0001), where helix-/sheet-like features boost cryoprotection. FucoPol, of highest cryoprotective performance, revealed a predominantly helical structure (α/β = 1.5) capable of forming a gel state at 4 °C and the highest degree of supercooling attenuation (TH = 6.2 °C). Ice growth anticipation with gel-like polysaccharides suggests that the gel matrix neutralizes elastic deformations and lethal cell volumetric fluctuations during freezing, thus preventing the loss of homeostasis and increasing post-thaw viability. Ultimately, structured gels capable of attenuated supercooling enable cryoprotective action at the polymer-cell interface, in addition to polymer-ice interactions. This rationale potentiates implementing alternative, biobased, noncytotoxic polymers in cryobiology.
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Affiliation(s)
- Bruno M Guerreiro
- UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica 2829-516, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica 2829-516, Portugal
| | - M Madalena Dionísio
- LAQV-REQUIMTE, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica 2829-516, Portugal
| | - João Carlos Lima
- LAQV-REQUIMTE, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica 2829-516, Portugal
| | - Jorge Carvalho Silva
- CENIMAT/I3N, Department of Physics, School of Science and Technology, NOVA University Lisbon, Caparica 2829-516, Portugal
| | - Filomena Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica 2829-516, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica 2829-516, Portugal
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5
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Freedman H, Tuszynski JA. Study of the Myosin Relay Helix Peptide by Molecular Dynamics Simulations, Pump-Probe and 2D Infrared Spectroscopy. Int J Mol Sci 2024; 25:6406. [PMID: 38928112 PMCID: PMC11203622 DOI: 10.3390/ijms25126406] [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: 03/25/2024] [Revised: 05/07/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
The Davydov model was conjectured to describe how an amide I excitation created during ATP hydrolysis in myosin might be significant in providing energy to drive myosin's chemomechanical cycle. The free energy surfaces of the myosin relay helix peptide dissolved in 2,2,2-trifluoroethanol (TFE), determined by metadynamics simulations, demonstrate local minima differing in free energy by only ~2 kT, corresponding to broken and stabilized hydrogen bonds, respectively. Experimental pump-probe and 2D infrared spectroscopy were performed on the peptide dissolved in TFE. The relative heights of two peaks seen in the pump-probe data and the corresponding relative volumes of diagonal peaks seen in the 2D-IR spectra at time delays between 0.5 ps and 1 ps differ noticeably from what is seen at earlier or later time delays or in the linear spectrum, indicating that a vibrational excitation may influence the conformational state of this helix. Thus, it is possible that the presence of an amide I excitation may be a direct factor in the conformational state taken on by the myosin relay helix following ATP hydrolysis in myosin.
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Affiliation(s)
- Holly Freedman
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, UT 84112, USA
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, AB T6G 2M9, Canada;
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, I-1029 Turin, Italy
- Department of Data Science and Engineering, The Silesian University of Technology, 44-100 Gliwice, Poland
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6
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Grifnée E, Kune C, Delvaux C, Tilmant T, Quinton L, Matagne A, Mazzucchelli G, Far J, De Pauw E. Investigation of Structure-Stabilizing Elements in Proteins by Ion Mobility Mass Spectrometry and Collision-Induced Unfolding. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1076-1088. [PMID: 38660944 DOI: 10.1021/jasms.3c00398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
A recently developed proteolytic reactor, designed for protein structural investigation, was coupled to ion mobility mass spectrometry to monitor collisional cross section (CCS) evolution of model proteins undergoing trypsin-mediated mono enzymatic digestion. As peptides are released during digestion, the CCS of the remaining protein structure may deviate from the classical 2/3 power of the CCS-mass relationship for spherical structures. The classical relationship between CCS and mass (CCS = A × M2/3) for spherical structures, assuming a globular shape in the gas phase, may deviate as stabilizing elements are lost during digestion. In addition, collision-induced unfolding (CIU) experiments on partially digested proteins provided insights into the CCS resilience in the gas phase to ion activation, potentially due to the presence of stabilizing elements. The study initially investigated a model peptide ModBea (3 kDa), assessing the impact of disulfide bridges on CCS resilience in both reduced and oxidized forms. Subsequently, β-lactoglobulin (2 disulfide bridges), calmodulin (Ca2+ coordination cation), and cytochrome c (heme) were selected to investigate the influence of common structuring elements on CCS resilience. CIU experiments probed the unfolding process, evaluating the effect of losing specific peptides on the energy landscapes of partially digested proteins. Comparisons of the TWCCSN2→He to trend curves describing the CCS/mass relationship revealed that proteins with structure-stabilizing elements consistently exhibit TWCCSN2→He and greater resilience toward CIU compared to proteins lacking these elements. The integration of online digestion, ion mobility, and CIU provides a valuable tool for identifying structuring elements in biopolymers in the gas phase.
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Affiliation(s)
- Elodie Grifnée
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Christopher Kune
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Cédric Delvaux
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Thomas Tilmant
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Center for Protein Engineering, InBioS Research Unit, University of Liège, B-4000 Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
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7
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Britton D, Katsara O, Mishkit O, Wang A, Pandya N, Liu C, Mao H, Legocki J, Jia S, Xiao Y, Aristizabal O, Paul D, Deng Y, Schneider R, Wadghiri YZ, Montclare JK. Engineered coiled-coil HIF1α protein domain mimic. Biomater Sci 2024; 12:2951-2959. [PMID: 38656316 PMCID: PMC11191652 DOI: 10.1039/d4bm00354c] [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: 04/26/2024]
Abstract
The development of targeted anti-cancer therapeutics offers the potential for increased efficacy of drugs and diagnostics. Utilizing modalities agnostic to tumor type, such as the hypoxic tumor microenvironment (TME), may assist in the development of universal tumor targeting agents. The hypoxia-inducible factor (HIF), in particular HIF1, plays a key role in tumor adaptation to hypoxia, and inhibiting its interaction with p300 has been shown to provide therapeutic potential. Using a multivalent assembled protein (MAP) approach based on the self-assembly of the cartilage oligomeric matrix protein coiled-coil (COMPcc) domain fused to the critical residues of the C-terminal transactivation domain (C-TAD) of the α subunit of HIF1 (HIF1α), we generate HIF1α-MAP (H-MAP). The resulting H-MAP demonstrates picomolar binding affinity to p300, the ability to downregulate hypoxia-inducible genes, and in vivo tumor targeting capability.
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Affiliation(s)
- Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Olga Katsara
- Department of Microbiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Orin Mishkit
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Andrew Wang
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
- Department of Biomedical Engineering, State University of New York Downstate Medical Center, Brooklyn, New York, 11203, USA
- College of Medicine, State University of New York Downstate Medical Center, Brooklyn, New York, 11203, USA
| | - Neelam Pandya
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Chengliang Liu
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Heather Mao
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Jakub Legocki
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Sihan Jia
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Yingxin Xiao
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Orlando Aristizabal
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Deven Paul
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Yan Deng
- Microscopy Laboratory, New York University Langone Health, New York, NY, 10016, USA
| | - Robert Schneider
- Department of Microbiology, New York University School of Medicine, New York, New York, 10016, USA
- Department of Radiation Oncology, New York University School of Medicine, New York, New York, 10016, USA
| | - Youssef Z Wadghiri
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Department of Chemistry, New York University, New York, New York, 10012, USA
- Department of Biomaterials, New York University College of Dentistry, New York, New York, 10010, USA
- Department of Biomedical Engineering, New York University, New York, NY, 11201, USA
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8
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Yamaguchi S, Sunagawa N, Samejima M, Igarashi K. Thermotolerance Mechanism of Fungal GH6 Cellobiohydrolase. Part I. Characterization of Thermotolerant Mutant from the Basidiomycete Phanerochaete chrysosporium. J Appl Glycosci (1999) 2024; 71:55-62. [PMID: 38863951 PMCID: PMC11163330 DOI: 10.5458/jag.jag.jag-2023_0017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/14/2024] [Indexed: 06/13/2024] Open
Abstract
Cellobiohydrolase (CBH), belonging to glycoside hydrolase family 6 (GH6), plays an essential role in cellulose saccharification, but its low thermotolerance presents a challenge in improving the reaction efficiency. Based on a report that chimeric CBH II (GH6) engineered to remove non-disulfide-bonded free Cys shows increased thermotolerance, we previously mutated the two free Cys residues to Ser in GH6 CBH from the basidiomycete Phanerochaete chrysosporium (PcCel6A) and obtained a thermotolerant double mutant, C240S/C393S (Yamaguchi et al., J. Appl. Glycosci. 2020; 67: 79-86). Here, characterization of the double mutant revealed that its activity towards both amorphous and crystalline cellulose was higher than that of the wild-type enzyme at elevated temperature, suggesting that the catalytic domain is the major contributor to the increased thermotolerance. To investigate the role of each free Cys residue, we prepared both single mutants, C240S and C393S, of the catalytic domain of PcCel6A and examined their residual activity at high temperature and the temperature-dependent changes of folding by means of circular dichroism measurements and thermal shift assay. The results indicate that the C393S mutation is the main contributor to both the increased thermotolerance of C240S/C393S and the increased activity of the catalytic domain at high temperature.
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Affiliation(s)
- Sora Yamaguchi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
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9
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Sharma S, Patel SN, Singh SP. A novel thermotolerant L-rhamnose isomerase variant for biocatalytic conversion of D-allulose to D-allose. Appl Microbiol Biotechnol 2024; 108:279. [PMID: 38564031 PMCID: PMC10987364 DOI: 10.1007/s00253-024-13074-w] [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: 08/29/2023] [Revised: 01/24/2024] [Accepted: 02/13/2024] [Indexed: 04/04/2024]
Abstract
A novel L-rhamnose isomerase was identified and cloned from an extreme-temperature aquatic habitat metagenome. The deduced amino acid sequence homology suggested the possible source of this metagenomic sequence to be Chloroflexus islandicus. The gene expression was performed in a heterologous host, Escherichia coli, and the recombinant protein L-rhamnose isomerase (L-RIM) was extracted and purified. The catalytic function of L-RIM was characterized for D-allulose to D-allose bioconversion. D-Allose is a sweet, rare sugar molecule with anti-tumour, anti-hypertensive, cryoprotective, and antioxidative properties. The characterization experiments showed L-RIM to be a Co++- or Mn++-dependent metalloenzyme. L-RIM was remarkably active (~ 80%) in a broad spectrum of pH (6.0 to 9.0) and temperature (70 to 80 °C) ranges. Optimal L-RIM activity with D-allulose as the substrate occurred at pH 7.0 and 75 °C. The enzyme was found to be excessively heat stable, displaying a half-life of about 12 days and 5 days at 65 °C and 70 °C, respectively. L-RIM catalysis conducted at slightly acidic pH of 6.0 and 70 °C achieved biosynthesis of about 30 g L-1 from 100 g L-1 D-allulose in 3 h. KEY POINTS: • The present study explored an extreme temperature metagenome to identify a novel gene that encodes a thermostable l-rhamnose isomerase (L-RIM) • L-RIM exhibits substantial (80% or more) activity in a broad spectrum of pH (6.0 to 9.0) and temperature (70 to 80 °C) ranges • L-RIM is excessively heat stable, displaying a half-life of about 12 days and 5 days at 65 °C and 70 °C, respectively.
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Affiliation(s)
- Sweety Sharma
- Center of Innovative and Applied Bioprocessing, Biotechnology Research and Innovation Council (Department of Biotechnology, Government of India), NABI Campus, SAS Nagar, Sector 81, Mohali, India, 140306
- Indian Institute of Science Education and Research Mohali, SAS Nagar, Sector 81, Mohali, India, 140306
| | - Satya Narayan Patel
- Center of Innovative and Applied Bioprocessing, Biotechnology Research and Innovation Council (Department of Biotechnology, Government of India), NABI Campus, SAS Nagar, Sector 81, Mohali, India, 140306
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, Biotechnology Research and Innovation Council (Department of Biotechnology, Government of India), NABI Campus, SAS Nagar, Sector 81, Mohali, India, 140306.
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10
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Heber S, McClintock MA, Simon B, Mehtab E, Lapouge K, Hennig J, Bullock SL, Ephrussi A. Tropomyosin 1-I/C coordinates kinesin-1 and dynein motors during oskar mRNA transport. Nat Struct Mol Biol 2024; 31:476-488. [PMID: 38297086 PMCID: PMC10948360 DOI: 10.1038/s41594-024-01212-x] [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: 03/16/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
Dynein and kinesin motors mediate long-range intracellular transport, translocating towards microtubule minus and plus ends, respectively. Cargoes often undergo bidirectional transport by binding to both motors simultaneously. However, it is not known how motor activities are coordinated in such circumstances. In the Drosophila female germline, sequential activities of the dynein-dynactin-BicD-Egalitarian (DDBE) complex and of kinesin-1 deliver oskar messenger RNA from nurse cells to the oocyte, and within the oocyte to the posterior pole. We show through in vitro reconstitution that Tm1-I/C, a tropomyosin-1 isoform, links kinesin-1 in a strongly inhibited state to DDBE-associated oskar mRNA. Nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and structural modeling indicate that Tm1-I/C suppresses kinesin-1 activity by stabilizing its autoinhibited conformation, thus preventing competition with dynein until kinesin-1 is activated in the oocyte. Our work reveals a new strategy for ensuring sequential activity of microtubule motors.
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Affiliation(s)
- Simone Heber
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mark A McClintock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Eve Mehtab
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Karine Lapouge
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Bayreuth, Germany
| | - Simon L Bullock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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11
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Almeida LHDO, Ramalho SR, Almeida CV, Gutierrez CDO, Sardi JDCO, Miranda AD, Oliveira RAD, Rezende SBD, Crusca E, Franco OL, Oliveira CFRD, Cardoso MH, Macedo MLR. A potent candicidal peptide designed based on an encrypted peptide from a proteinase inhibitor. Biochim Biophys Acta Gen Subj 2024; 1868:130583. [PMID: 38360076 DOI: 10.1016/j.bbagen.2024.130583] [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: 08/04/2023] [Revised: 01/23/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024]
Abstract
Antimicrobial peptides (AMP) represent an alternative in the treatment of fungal infections associated with countless deaths. Here, we report a new AMP, named KWI-19, which was designed based on a peptide encrypted in the sequence of an Inga laurina Kunitz-type inhibitor (ILTI). KWI-19 inhibited the growth of Candida species and acted as a fungicidal agent from 2.5 to 20 μmol L-1, also showing synergistic activity with amphotericin B. Kinetic assays showed that KWI-19 killed Candida tropicalis cells within 60 min. We also report the membrane-associated mechanisms of action of KWI-19 and its interaction with ergosterol. KWI-19 was also characterized as a potent antibiofilm peptide, with activity against C. tropicalis. Finally, non-toxicity was reported against Galleria mellonella larvae, thus strengthening the interest in all the bioactivities mentioned above. This study extends our knowledge on how AMPs can be engineered from peptides encrypted in larger proteins and their potential as candicidal agents.
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Affiliation(s)
- Luís Henrique de Oliveira Almeida
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Suellen Rodrigues Ramalho
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Claudiane Vilharroel Almeida
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Camila de Oliveira Gutierrez
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Janaína de Cassia Orlandi Sardi
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Antonio de Miranda
- Departamento de Biofísica da Universidade Federal de São Paulo - SP, Brazil
| | - Ricardo Abreu de Oliveira
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Samilla Beatriz de Rezende
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, MS, Brazil
| | - Edson Crusca
- Instituto de Química, Departamento de Bioquímica e Química Tecnológica, Universidade Estadual Paulista Júlio de Mesquita Filho, Araraquara, São Paulo, Brazil
| | - Octávio Luiz Franco
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, MS, Brazil; Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, DF, Brazil
| | - Caio Fernando Ramalho de Oliveira
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Marlon Henrique Cardoso
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil; S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, MS, Brazil; Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, DF, Brazil
| | - Maria Lígia Rodrigues Macedo
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil.
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12
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Cardoso FF, Salvador GHM, Cavalcante WLG, Dal-Pai M, Fontes MRDM. BthTX-I, a phospholipase A 2-like toxin, is inhibited by the plant cinnamic acid derivative: chlorogenic acid. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140988. [PMID: 38142025 DOI: 10.1016/j.bbapap.2023.140988] [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: 09/05/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
Snakebite is a significant health concern in tropical and subtropical regions, particularly in Africa, Asia, and Latin America, resulting in more than 2.7 million envenomations and an estimated one hundred thousand fatalities annually. The Bothrops genus is responsible for the majority of snakebite envenomings in Latin America and Caribbean countries. Accidents involving snakes from this genus are characterized by local symptoms that often lead to permanent sequelae and death. However, specific antivenoms exhibit limited effectiveness in inhibiting local tissue damage. Phospholipase A2-like (PLA2-like) toxins emerge as significant contributors to local myotoxicity in accidents involving Bothrops species. As a result, they represent a crucial target for prospective treatments. Some natural and synthetic compounds have shown the ability to reduce or abolish the myotoxic effects of PLA2-like proteins. In this study, we employed a combination approach involving myographic, morphological, biophysical and bioinformatic techniques to investigate the interaction between chlorogenic acid (CGA) and BthTX-I, a PLA2-like toxin. CGA provided a protection of 71.8% on muscle damage in a pre-incubation treatment. Microscale thermophoresis and circular dichroism experiments revealed that CGA interacted with the BthTX-I while preserving its secondary structure. CGA exhibited an affinity to the toxin that ranks among the highest observed for a natural compound. Bioinformatics simulations indicated that CGA inhibitor binds to the toxin's hydrophobic channel in a manner similar to other phenolic compounds previously investigated. These findings suggest that CGA interferes with the allosteric transition of the non-activated toxin, and the stability of the dimeric assembly of its activated state.
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Affiliation(s)
- Fábio Florença Cardoso
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | | | - Walter Luís Garrido Cavalcante
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil; Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Maeli Dal-Pai
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Marcos Roberto de Mattos Fontes
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil; Instituto de Estudos Avançados do Mar (IEAMar), Universidade Estadual Paulista (UNESP), São Vicente, SP, Brazil.
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13
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Walther FJ, Waring AJ. Structure and Function of Canine SP-C Mimic Proteins in Synthetic Surfactant Lipid Dispersions. Biomedicines 2024; 12:163. [PMID: 38255268 PMCID: PMC10813813 DOI: 10.3390/biomedicines12010163] [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: 11/21/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Lung surfactant is a mixture of lipids and proteins and is essential for air breathing in mammals. The hydrophobic surfactant proteins B and C (SP-B and SP-C) assist in reducing surface tension in the lung alveoli by organizing the surfactant lipids. SP-B deficiency is life-threatening, and a lack of SP-C can lead to progressive interstitial lung disease. B-YL (41 amino acids) is a highly surface-active, sulfur-free peptide mimic of SP-B (79 amino acids) in which the four cysteine residues are replaced by tyrosine. Mammalian SP-C (35 amino acids) contains two cysteine-linked palmitoyl groups at positions 5 and 6 in the N-terminal region that override the β-sheet propensities of the native sequence. Canine SP-C (34 amino acids) is exceptional because it has only one palmitoylated cysteine residue at position 4 and a phenylalanine at position 5. We developed canine SP-C constructs in which the palmitoylated cysteine residue at position 4 is replaced by phenylalanine (SP-Cff) or serine (SP-Csf) and a glutamic acid-lysine ion-lock was placed at sequence positions 20-24 of the hydrophobic helical domain to enhance its alpha helical propensity. AI modeling, molecular dynamics, circular dichroism spectroscopy, Fourier Transform InfraRed spectroscopy, and electron spin resonance studies showed that the secondary structure of canine SP-Cff ion-lock peptide was like that of native SP-C, suggesting that substitution of phenylalanine for cysteine has no apparent effect on the secondary structure of the peptide. Captive bubble surfactometry demonstrated higher surface activity for canine SP-Cff ion-lock peptide in combination with B-YL in surfactant lipids than with canine SP-Csf ion-lock peptide. These studies demonstrate the potential of canine SP-Cff ion-lock peptide to enhance the functionality of the SP-B peptide mimic B-YL in synthetic surfactant lipids.
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Affiliation(s)
- Frans J. Walther
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Alan J. Waring
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
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14
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Pahan S, Dey S, George G, Mahapatra SP, Puneeth Kumar DRGKR, Gopi HN. Design of Chiral β-Double Helices from γ-Peptide Foldamers. Angew Chem Int Ed Engl 2024; 63:e202316309. [PMID: 38009917 DOI: 10.1002/anie.202316309] [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: 10/27/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Chirality is ubiquitous in nature, and homochirality is manifested in many biomolecules. Although β-double helices are rare in peptides and proteins, they consist of alternating L- and D-amino acids. No peptide double helices with homochiral amino acids have been observed. Here, we report chiral β-double helices constructed from γ-peptides consisting of alternating achiral (E)-α,β-unsaturated 4,4-dimethyl γ-amino acids and chiral (E)-α,β-unsaturated γ-amino acids in both single crystals and in solution. The two independent strands of the same peptide intertwine to form a β-double helix structure, and it is stabilized by inter-strand hydrogen bonds. The peptides with chiral (E)-α,β-unsaturated γ-amino acids derived from α-L-amino acids adopt a (P)-β-double helix, whereas peptides consisting of (E)-α,β-unsaturated γ-amino acids derived from α-D-amino acids adopt an (M)-β-double helix conformation. The circular dichroism (CD) signature of the (P) and (M)-β-double helices and the stability of these peptides at higher temperatures were examined. Furthermore, ion transport studies suggested that these peptides transport ions across membranes. Even though the structural analogy suggests that these new β-double helices are structurally different from those of the α-peptide β-double helices, they retain ion transport activity. The results reported here may open new avenues in the design of functional foldamers.
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Affiliation(s)
- Saikat Pahan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Sanjit Dey
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Gijo George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Souvik Panda Mahapatra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - DRGKoppalu R Puneeth Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Hosahudya N Gopi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
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15
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Aziznia S, Askari G, Emamdjomeh Z, Salami M. Effect of ultrasonic assisted grafting on the structural and functional properties of mung bean protein isolate conjugated with maltodextrin through maillard reaction. Int J Biol Macromol 2024; 254:127616. [PMID: 37918607 DOI: 10.1016/j.ijbiomac.2023.127616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/29/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023]
Abstract
Four different methods of maillard reaction including ultrasound (150 W, 10 min) assisted, classical wet heating (80 °C, 60min), moderate water bath heating (60°C, 12 to 30 h) and dry state method (60 °C, 79 % relative humidity and 48 h) were used to Mung bean protein isolate - Maltodexrtin conjugates (MPI-MD) preparation. The samples prepared under ultrasound and wet heating were chosen for further analysis according to degree of graft and UV-absorbance at 420 nm. Higher glycosylation at short time and lower browning were obtained under ultrasound treatment. Covalent attachment in conjugates confirmed by SDS-polyacrylamide gel electrophoresis. The structural analysis revealed prominent unfolding effect of ultrasound waves on the protein's molecules. The decrease of α-helix content was related to the exposure of buried amino group residues during reaction. Glycation of MPI under ultrasound caused changes in tertiary structure of protein and leads to decrease in the fluorescence intensity compared with native and wet heating treatments. FTIR spectra confirmed the conjugation of the MPI and MD and suggested that protein structure was changed and ultrasound promoted the graft reaction more than wet heating treatment. Conjugated MPI showed higher emulsification and solubility index than MPI, moreover the effect of ultrasonic waves on ameliorated functional properties was impressive than those for wet heating treatment. Overall, this study showed use of ultrasonication in maillard reaction was a suitable method for producing MPI- MD conjugates and improved the efficiency of graft reaction and functional properties of grafts.
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Affiliation(s)
- Somayeh Aziznia
- Department of Food Science and Technology, Faculty of Agriculture, University of Tehran, Iran.
| | - Gholamreza Askari
- Department of Food Science and Technology, Faculty of Agriculture, University of Tehran, Iran.
| | - Zahra Emamdjomeh
- Department of Food Science and Technology, Faculty of Agriculture, University of Tehran, Iran.
| | - Maryam Salami
- Department of Food Science and Technology, Faculty of Agriculture, University of Tehran, Iran.
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16
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Ricotti S, Garay AS, Etcheverrigaray M, Amadeo GI, De Groot AS, Martin W, Mufarrege EF. Development of IFNβ-1a versions with reduced immunogenicity and full in vitro biological activity for the treatment of multiple sclerosis. Clin Immunol 2023; 257:109831. [PMID: 37931868 DOI: 10.1016/j.clim.2023.109831] [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: 08/02/2023] [Revised: 10/18/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023]
Abstract
IFNβ (recombinant interferon Beta) has been widely used for the treatment of Multiple sclerosis for the last four decades. Despite the human origin of the IFNβ sequence, IFNβ is immunogenic, and unwanted immune responses in IFNβ-treated patients may compromise its efficacy and safety in the clinic. In this study, we applied the DeFT (De-immunization of Functional Therapeutics) approach to producing functional, de-immunized versions of IFNβ-1a. Two de-immunized versions of IFNβ-1a were produced in CHO cells and designated as IFNβ-1a(VAR1) and IFNβ-1a(VAR2). First, the secondary and tertiary protein structures were analyzed by circular dichroism spectroscopy. Then, the variants were also tested for functionality. While IFNβ-1a(VAR2) showed similar in vitro antiviral activity to the original protein, IFNβ-1a(VAR1) exhibited 40% more biological potency. Finally, in vivo assays using HLA-DR transgenic mice revealed that the de-immunized variants showed a markedly reduced immunogenicity when compared to the originator.
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Affiliation(s)
- Sonia Ricotti
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, Santa Fe S3000ZAA, Argentina
| | - Alberto Sergio Garay
- Laboratory of Molecular Modeling, FBCB (School of Biochemistry and Biological Sciences), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, Santa Fe S3000ZAA, Argentina
| | - Marina Etcheverrigaray
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, Santa Fe S3000ZAA, Argentina
| | - Gabriel Ignacio Amadeo
- Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, Santa Fe S3000ZAA, Argentina
| | - Anne S De Groot
- EpiVax, Inc., Providence, RI 02903, USA; Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | | | - Eduardo Federico Mufarrege
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, Santa Fe S3000ZAA, Argentina.
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17
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Amith W, Dutagaci B. Complex Conformational Space of the RNA Polymerase II C-Terminal Domain upon Phosphorylation. J Phys Chem B 2023; 127:9223-9235. [PMID: 37870995 PMCID: PMC10626582 DOI: 10.1021/acs.jpcb.3c02655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 10/03/2023] [Indexed: 10/25/2023]
Abstract
Intrinsically disordered proteins (IDPs) have been closely studied during the past decade due to their importance in many biological processes. The disordered nature of this group of proteins makes it difficult to observe its full span of the conformational space using either experimental or computational studies. In this article, we explored the conformational space of the C-terminal domain (CTD) of RNA polymerase II (Pol II), which is also an intrinsically disordered low complexity domain, using enhanced sampling methods. We provided a detailed conformational analysis of model systems of CTD with different lengths; first with the last 44 residues of the human CTD sequence and finally the CTD model with 2-heptapeptide repeating units. We then investigated the effects of phosphorylation on CTD conformations by performing simulations at different phosphorylated states. We obtained broad conformational spaces in nonphosphorylated CTD models, and phosphorylation has complex effects on the conformations of the CTD. These complex effects depend on the length of the CTD, spacing between the multiple phosphorylation sites, ion coordination, and interactions with the nearby residues.
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Affiliation(s)
- Weththasinghage
D. Amith
- Department of Molecular and
Cell Biology, University of California,
Merced, Merced, California 95343, United States
| | - Bercem Dutagaci
- Department of Molecular and
Cell Biology, University of California,
Merced, Merced, California 95343, United States
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18
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Li Q, Min J, Zhang J, Reches M, Shen Y, Su R, Wang Y, Qi W. Enzyme-Driven, Switchable Catalysis Based on Dynamic Self-Assembly of Peptides. Angew Chem Int Ed Engl 2023; 62:e202309830. [PMID: 37602955 DOI: 10.1002/anie.202309830] [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: 07/11/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 08/22/2023]
Abstract
Covalent regulatory systems of enzymes are widely used to modulate biological enzyme activities. Inspired by the regulation of reactive-site phosphorylation in organisms, we developed peptide-based catecholase mimetics with switchable catalytic activity and high selectivity through the co-assembly of nanofibers comprising peptides and copper ions (Cu2+ ). Through careful design and modification of the peptide backbone structure based on the change in the free energy of the system, we identified the peptide with the most effective reversible catalytic activity. Kinase/phosphatase switches were used to control the reversible transition of nanofiber formation and depolymerization, as well as to modulate the active-site microenvironment. Notably, the self-assembly and disassembly processes of nanofibers were simulated using coarse-grained molecular dynamics. Furthermore, theoretical calculations confirmed the coordination of the peptide and Cu2+ , forming a zipper-like four-ligand structure at the catalytically active center of the nanofibers. Additionally, we conducted a comprehensive analysis of the catalytic mechanism. This study opens novel avenues for designing biomimetic enzymes with ordered structures and dynamic catalytic activities.
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Affiliation(s)
- Qing Li
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Jiwei Min
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Jiaxing Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Meital Reches
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yuhe Shen
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
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19
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Anand PK, Kaur G, Saini V, Kaur J, Kaur J. N-terminal PPE domain plays an integral role in extracellular transportation and stability of the immunomodulatory Rv3539 protein of the Mycobacterium tuberculosis. Biochimie 2023; 213:30-40. [PMID: 37156406 DOI: 10.1016/j.biochi.2023.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/31/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023]
Abstract
Multigene PE/PPE family is exclusively present in mycobacterium species. Only few selected genes of this family have been characterized till date. Rv3539 was annotated as PPE63 with conserved PPE domain at N-terminal and PE-PPE at C-terminal. An α/β hydrolase structural fold, characteristic of lipase/esterase, was present in the PE-PPE domain. To assign the biochemical function to Rv3539, the corresponding gene was cloned in pET-32a (+) as full-length, PPE, and PE-PPE domains individually, followed by expression in E. Coli C41 (DE3). All three proteins demonstrated esterase activity. However, the enzyme activity in the N-terminal PPE domain was very low. The enzyme activity of Rv3539 and PE-PPE proteins was approximately same with the pNP-C4 as optimum substrate at 40 °C and pH 8.0. The loss of enzyme activity after mutating the predicted catalytic triad (Ser296Ala, Asp369Ala, and His395Ala) found only in the PE-PPE domain, confirmed the candidature of the bioinformatically predicted active site residue. The optimal activity and thermostability of the Rv3539 protein was altered by removing the PPE domain. CD-spectroscopy analysis confirmed the role of PPE domain to the thermostability of Rv3539 by maintaining the structural integrity at higher temperatures. The presence of the N-terminal PPE domain directed the Rv3539 protein to the cell membrane/wall and the extracellular compartment. The Rv3539 protein could generate humoral response in TB patients. Therefore, results demonstrated that Rv3539 demonstrated esterase activity. PE-PPE domain of Rv3539 is functionally automated, however, N-terminus domain played a role in protein stabilization and its transportation. Both domains participated in immunomodulation.
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Affiliation(s)
- Pradeep Kumar Anand
- Department of Biotechnology, BMS Block-1, South Campus, Panjab University, Chandigarh, 160014, India.
| | - Gagandeep Kaur
- Department of Biotechnology, BMS Block-1, South Campus, Panjab University, Chandigarh, 160014, India.
| | - Varinder Saini
- Department of Pulmonary Medicine, Government Medical College and Hospital, Chandigarh, India.
| | - Jasbinder Kaur
- Department of Biochemistry, Government Medical College and Hospital, Chandigarh, India.
| | - Jagdeep Kaur
- Department of Biotechnology, BMS Block-1, South Campus, Panjab University, Chandigarh, 160014, India.
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20
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Conlon JM, Guilhaudis L, Attoub S, Coquet L, Leprince J, Jouenne T, Mechkarska M. Purification, conformational analysis and cytotoxic activities of host-defense peptides from the Tungara frog Engystomops pustulosus (Leptodactylidae; Leiuperinae). Amino Acids 2023; 55:1349-1359. [PMID: 37548712 PMCID: PMC10689532 DOI: 10.1007/s00726-023-03312-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 08/01/2023] [Indexed: 08/08/2023]
Abstract
The amphibian family Leptodactylidae is divided into three sub-families: Leiuperinae, Leptodactylinae, and Paratelmatobiinae. Host-defense peptides (HDPs) present in the skins of frogs belonging to the Leptodactylinae have been studied extensively, but information is limited regarding peptides from Leiuperinae species. Peptidomic analysis of norepinephrine-stimulated skin secretions from the Tungara frog Engystomops pustulosus (Leiuperinae) collected in Trinidad led to the isolation and structural characterization of previously undescribed pustulosin-1 (FWKADVKEIG KKLAAKLAEELAKKLGEQ), [Q28E] pustulosin-1 (pustulosin-2), and pustulosin-3 (DWKETAKELLKKIGAKVAQVISDKLNPAPQ). The primary structures of these peptides do not resemble those of previously described frog skin HDPs. In addition, the secretions contained tigerinin-1EP (GCKTYLIEPPVCT) with structural similarity to the tigerinins previously identified in skin secretions from frogs from the family Dicroglossidae. Pustulosin-1 and -3 adopted extended α-helical conformations in 25% trifluoroethanol-water and in the presence of cell membrane models (sodium dodecylsulfate and dodecylphosphocholine micelles). Pustulosin-1 and -3 displayed cytotoxic activity against a range of human tumor-derived cell lines (A549, MDA-MB-231, and HT29), but their therapeutic potential for development into anti-cancer agents is limited by their comparable cytotoxic activity against non-neoplastic human umbilical vein endothelial cells. The peptides also displayed weak antimicrobial activity against Escherichia coli (MIC = 125 µM) but were inactive against Staphylococcus aureus. Tigerinin-1EP was inactive against both the tumor-derived cells and bacteria.
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Affiliation(s)
- J Michael Conlon
- Diabetes Research Centre, School of Biomedical Sciences, Ulster University, Coleraine, BT52 1SA, Northern Ireland, UK.
| | - Laure Guilhaudis
- Laboratoire COBRA (UMR 6014 & FR 3038), INSA de Rouen, CNRS, Université Rouen Normandie, 76000, Rouen, France
| | - Samir Attoub
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, United Arab Emirates University, 17666, Al Ain, United Arab Emirates
| | - Laurent Coquet
- CNRS UAR2026, HeRacLeS-PISSARO PBS UMR 6270, Université Rouen Normandie, 76000, Rouen, France
| | - Jérôme Leprince
- CNRS UAR2026, HeRacLeS-PISSARO PBS UMR 6270, Université Rouen Normandie, 76000, Rouen, France
- INSERM, Normandie Université, NorDiC UMR 1239, HeRacLeS, US 51, PRIMACEN, Université Rouen Normandie, 76000, Rouen, France
| | - Thierry Jouenne
- CNRS UAR2026, HeRacLeS-PISSARO PBS UMR 6270, Université Rouen Normandie, 76000, Rouen, France
| | - Milena Mechkarska
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine Campus, St. Augustine, Trinidad and Tobago
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21
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Jia Y, Schroeder B, Pfeifer Y, Fröhlich C, Deng L, Arkona C, Kuropka B, Sticht J, Ataka K, Bergemann S, Wolber G, Nitsche C, Mielke M, Leiros HKS, Werner G, Rademann J. Kinetics, Thermodynamics, and Structural Effects of Quinoline-2-Carboxylates, Zinc-Binding Inhibitors of New Delhi Metallo-β-lactamase-1 Re-sensitizing Multidrug-Resistant Bacteria for Carbapenems. J Med Chem 2023; 66:11761-11791. [PMID: 37585683 DOI: 10.1021/acs.jmedchem.3c00171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Carbapenem resistance mediated by metallo-β-lactamases (MBL) such as New Delhi metallo-β-lactamase-1 (NDM-1) has become a major factor threatening the efficacy of essential β-lactam antibiotics. Starting from hit fragment dipicolinic acid (DPA), 8-hydroxy- and 8-sulfonamido-quinoline-2-carboxylic acids were developed as inhibitors of NDM-1 with highly improved inhibitory activity and binding affinity. The most active compounds formed reversibly inactive ternary protein-inhibitor complexes with two zinc ions as proven by native protein mass spectrometry and bio-layer interferometry. Modification of the NDM-1 structure with remarkable entropic gain was shown by isothermal titration calorimetry and NMR spectroscopy of isotopically labeled protein. The best compounds were potent inhibitors of NDM-1 and other representative MBL with no or little inhibition of human zinc-binding enzymes. These inhibitors significantly reduced the minimum inhibitory concentrations (MIC) of meropenem for multidrug-resistant bacteria recombinantly expressing blaNDM-1 as well as for several multidrug-resistant clinical strains at concentrations non-toxic to human cells.
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Affiliation(s)
- Yuwen Jia
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Barbara Schroeder
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Yvonne Pfeifer
- FG13 Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Burgstraße 37, Wernigerode 38855, Germany
| | - Christopher Fröhlich
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - Lihua Deng
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Christoph Arkona
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Benno Kuropka
- Core Facility BioSupraMol, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Jana Sticht
- Core Facility BioSupraMol, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Kenichi Ataka
- Department of Physics, Freie Universität Berlin, Arnimallee 14, Berlin 14195, Germany
| | - Silke Bergemann
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Martin Mielke
- Department of Infectious Diseases, Robert Koch Institute, Nordufer 20, Berlin 13353, Germany
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - Guido Werner
- FG13 Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Burgstraße 37, Wernigerode 38855, Germany
| | - Jörg Rademann
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
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22
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Anand PK, Saini V, Kaur J, Kumar A, Kaur J. Cell wall and immune modulation by Rv1800 (PPE28) helps M. smegmatis to evade intracellular killing. Int J Biol Macromol 2023; 247:125837. [PMID: 37455004 DOI: 10.1016/j.ijbiomac.2023.125837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/27/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Rv1800 is predicted as PPE family protein found in pathogenic mycobacteria only. Under acidic stress, the rv1800 gene was expressed in M. tuberculosis H37Ra. In-silico study showed lipase/esterase activity in C-terminus PE-PPE domain having pentapeptide motif with catalytic Ser-Asp-His residue. Full-length Rv1800 and C-terminus PE-PPE domain proteins showed esterase activity with pNP-C4 at the optimum temperature of 40 °C and pH 8.0. However, the N-terminus PPE domain showed no esterase activity, but involved in thermostability of Rv1800 full-length protein. M. smegmatis expressing rv1800 (MS_Rv1800) showed altered colony morphology and a significant resistance to numerous environmental stresses, antibiotics and higher lipid content. In extracellular and membrane fraction, Rv1800 protein was detected, while C terminus PE-PPE was present in cytoplasm, suggesting the role of N-terminus PPE domain in transportation of protein. MS_Rv1800 infected macrophage showed higher intracellular survival and low production of ROS, NO and expression levels of iNOS and pro-inflammatory cytokines, while induced expression of the anti-inflammatory cytokines. The Rv1800, PPE and PE-PPE showed antibody-mediated immunity in MDR-TB and PTB patients. Overall, these results confirmed the esterase activity in the C-terminus and function of N-terminus in thermostabilization and transportation; predicting the role of Rv1800 in immune/lipid modulation to support intracellular mycobacterium survival.
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Affiliation(s)
- Pradeep Kumar Anand
- Department of Biotechnology, BMS Block-1, South Campus, Panjab University, Chandigarh, 160014, India
| | - Varinder Saini
- Department of Pulmonary Medicine, Government Medical College and Hospital, Chandigarh, India
| | - Jasbinder Kaur
- Department of Biochemistry, Government Medical College and Hospital, Chandigarh, India
| | - Arbind Kumar
- Department of Biotechnology, BMS Block-1, South Campus, Panjab University, Chandigarh, 160014, India
| | - Jagdeep Kaur
- Department of Biotechnology, BMS Block-1, South Campus, Panjab University, Chandigarh, 160014, India.
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23
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To J, Zhang X, Tam JP. Design of Potent and Salt-Insensitive Antimicrobial Branched Peptides. Polymers (Basel) 2023; 15:3594. [PMID: 37688220 PMCID: PMC10489980 DOI: 10.3390/polym15173594] [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: 07/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023] Open
Abstract
Dendrimeric and branched peptides are polypeptides formed by diverse types of scaffolds to give them different forms. Previously, we reported a cascade-type, Lys-scaffolded antimicrobial peptide dendrimer D4R tethered with four RLYR tetrapeptides. Antimicrobial D4R is broad-spectrum, salt insensitive, and as potent as the natural-occurring tachyplesins, displaying minimum inhibitory concentrations (MIC) < 1 μM. However, the relationships between scaffolds and antimicrobial potency remain undefined. Here, we report the design of four novel types of peptide antimicrobials whose scaffolded backbones are lysine (Lys), iso-Lys, ornithine (Orn), or iso-Orn tethered with RLYR on their α- or sidechain-amines to give ε-, δ-, and their α-branched peptides. When assayed against ten microorganisms, the Lys-scaffolded α- and ε-branched peptides are broadly active, salt insensitive, and as potent as D4R and tachyplesins, whereas the corresponding Orn-scaffolded α- and δ-branched peptides are salt sensitive and much less potent, displaying MICs ranging from 1 to >500 μM. Structure-activity relationship studies suggested that Lys-scaffolds, but not Orn-scaffolds, can support a reverse turn to organize RLYR tetrapeptides as parallel β-strands to form an amphipathic structure with Leu-Tyr as a hydrophobic core. Together, these results provide a structural approach for designing potent and salt-insensitive dendrimeric or branched peptide antimicrobials.
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Affiliation(s)
| | | | - James P. Tam
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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24
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Barreiro DS, Oliveira RNS, Pauleta SR. Biochemical Characterization of the Copper Nitrite Reductase from Neisseria gonorrhoeae. Biomolecules 2023; 13:1215. [PMID: 37627281 PMCID: PMC10452240 DOI: 10.3390/biom13081215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/16/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
The copper-containing nitrite reductase from Neisseria gonorrhoeae has been shown to play a critical role in the infection mechanism of this microorganism by producing NO and abolishing epithelial exfoliation. This enzyme is a trimer with a type 1 copper center per subunit and a type 2 copper center in the subunits interface, with the latter being the catalytic site. The two centers were characterized for the first time by EPR and CD spectroscopy, showing that the type 1 copper center has a high rhombicity due to its lower symmetry and more tetragonal structure, while the type 2 copper center has the usual properties, but with a smaller hyperfine coupling constant (A// = 10.5 mT). The thermostability of the enzyme was analyzed by differential scanning calorimetry, which shows a single endothermic transition in the thermogram, with a maximum at 94 °C, while the CD spectra in the visible region indicate the presence of the type 1 copper center up to 80 °C. The reoxidation of the N. gonorrhoeae copper-containing nitrite reductase in the presence of nitrite were analyzed by visible spectroscopy and showed a pH dependence, being higher at pH 5.5-6.0. The high thermostability of this enzyme may be important to maintaining a high activity in the extracellular space and to making it less susceptible to denaturation and proteolysis, contributing to the proliferation of N. gonorrhoeae.
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Affiliation(s)
- Daniela S. Barreiro
- Microbial Stress Lab, UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ricardo N. S. Oliveira
- Microbial Stress Lab, UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Sofia R. Pauleta
- Microbial Stress Lab, UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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25
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Conlon JM, Guilhaudis L, Attoub S, Coquet L, Leprince J, Jouenne T, Mechkarska M. Purification, Conformational Analysis and Cytotoxic Activities of Host-Defense Peptides from the Giant Gladiator Treefrog Boana boans (Hylidae: Hylinae). Antibiotics (Basel) 2023; 12:1102. [PMID: 37508198 PMCID: PMC10376367 DOI: 10.3390/antibiotics12071102] [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: 05/29/2023] [Revised: 06/16/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Frogs from the extensive amphibian family Hylidae are a rich source of peptides with therapeutic potential. Peptidomic analysis of norepinephrine-stimulated skin secretions from the Giant Gladiator Treefrog Boana boans (Hylidae: Hylinae) collected in Trinidad led to the isolation and structural characterization of five host-defense peptides with limited structural similarity to figainin 2 and picturin peptides from other frog species belonging to the genus Boana. In addition, the skin secretions contained high concentrations of tryptophyllin-BN (WRPFPFL) in both C-terminally α-amidated and non-amidated forms. Figainin 2BN (FLGVALKLGKVLG KALLPLASSLLHSQ) and picturin 1BN (GIFKDTLKKVVAAVLTTVADNIHPK) adopt α-helical conformations in trifluroethanol-water mixtures and in the presence of cell membrane models (sodium dodecylsulfate and dodecylphosphocholine micelles). The CD data also indicate contributions from turn structures. Both peptides and picturin 2BN (GLMDMLKKVGKVALT VAKSALLP) inhibited the growth of clinically relevant Gram-negative and Gram-positive bacteria with MIC values in the range 7.8-62.5 µM. Figainin 2BN was potently cytotoxic to A549, MDA-MB-231 and HT-29 human tumor-derived cells (LC50 = 7-14 µM) but displayed comparable potency against non-neoplastic HUVEC cells (LC50 = 15 µM) indicative of lack of selectivity for cancer cells.
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Affiliation(s)
- J Michael Conlon
- Diabetes Research Centre, School of Biomedical Sciences, University of Ulster, Coleraine BT52 1SA, UK
| | - Laure Guilhaudis
- Laboratoire COBRA (UMR 6014 & FR 3038), UNIROUEN, INSA de Rouen, CNRS, Université Rouen Normandie, 76000 Rouen, France
| | - Samir Attoub
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 17666, United Arab Emirates
| | - Laurent Coquet
- CNRS UAR2026 HeRacLeS-PISSARO, CNRS UMR 6270 PBS, Université Rouen Normandie, 76821 Mont-Saint-Aignan, France
| | - Jérôme Leprince
- Inserm U1239, PRIMACEN, Institute for Research and Innovation in Biomedicine (IRIB), Université Rouen Normandie, 76000 Rouen, France
| | - Thierry Jouenne
- CNRS UAR2026 HeRacLeS-PISSARO, CNRS UMR 6270 PBS, Université Rouen Normandie, 76821 Mont-Saint-Aignan, France
| | - Milena Mechkarska
- Department of Life Sciences, Faculty of Science and Technology, St. Augustine Campus, The University of The West Indies, St. Augustine, Trinidad and Tobago
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26
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Nishikubo K, Hasegawa M, Izumi Y, Fujii K, Matsuo K, Matsumoto Y, Yokoya A. Structural study of wild-type and phospho-mimic XRCC4 dimer and multimer proteins using circular dichroism spectroscopy. Int J Radiat Biol 2023; 99:1684-1691. [PMID: 37171809 DOI: 10.1080/09553002.2023.2214210] [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: 06/02/2022] [Accepted: 05/05/2023] [Indexed: 05/13/2023]
Abstract
PURPOSE To investigate the structural features of wild-type and phospho-mimicking mutated XRCC4 protein, a protein involved in DNA double-strand break repair. MATERIALS AND METHODS XRCC4 with a HisTag were expressed by E. coli harboring plasmid DNA and purified. Phospho-mimicking mutants in which one phosphorylation site was replaced with aspartic acid were also prepared in order to reproduce the negative charge resulting from phosphorylation. The proteins were separated into dimers and multimers by gel filtration chromatography. Circular dichroism (CD) spectroscopy was performed in the region from ultraviolet to vacuum-ultraviolet. The CD spectra were analyzed with two analysis programs to evaluate the secondary structures of the wild-type and phospho-mimicked dimers and multimers. RESULT AND DISCUSSION The proportion of β-strand in the wild-type dimers was very low, particularly in their C-terminal region, including the five phosphorylation sites. The secondary structure of the phospho-mimic hardly changed in the dimeric form. In contrast, the β-strand content increased and the α-helix content decreased upon multimerization of the wild-type protein. The structural change of multimers slightly depended on the phospho-mimic site. These results suggest that the β-strand structure stabilizes the multimerization of XRCC4 and it is regulated by phosphorylation at the C-terminal site in living cells. CONCLUSION An increase in the β-strand content in XRCC4 is essential for stabilization of the multimeric form through C-terminal phosphorylation, allowing the formation of the large double-strand break repair machinery.
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Affiliation(s)
- Kai Nishikubo
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki, Japan
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum Sciences and Technology (QST), Tokai, Ibaraki, Japan
| | - Maho Hasegawa
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki, Japan
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum Sciences and Technology (QST), Tokai, Ibaraki, Japan
| | - Yudai Izumi
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum Sciences and Technology (QST), Tokai, Ibaraki, Japan
| | - Kentaro Fujii
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum Sciences and Technology (QST), Tokai, Ibaraki, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Yoshihisa Matsumoto
- Laboratory for Zero-Carbon Energy, Institute of Innovative Research, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Akinari Yokoya
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki, Japan
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum Sciences and Technology (QST), Tokai, Ibaraki, Japan
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27
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Foley MH, Walker ME, Stewart AK, O'Flaherty S, Gentry EC, Patel S, Beaty VV, Allen G, Pan M, Simpson JB, Perkins C, Vanhoy ME, Dougherty MK, McGill SK, Gulati AS, Dorrestein PC, Baker ES, Redinbo MR, Barrangou R, Theriot CM. Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut. Nat Microbiol 2023; 8:611-628. [PMID: 36914755 PMCID: PMC10066039 DOI: 10.1038/s41564-023-01337-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/08/2023] [Indexed: 03/16/2023]
Abstract
Bile acids (BAs) mediate the crosstalk between human and microbial cells and influence diseases including Clostridioides difficile infection (CDI). While bile salt hydrolases (BSHs) shape the BA pool by deconjugating conjugated BAs, the basis for their substrate selectivity and impact on C. difficile remain elusive. Here we survey the diversity of BSHs in the gut commensals Lactobacillaceae, which are commonly used as probiotics, and other members of the human gut microbiome. We structurally pinpoint a loop that predicts BSH preferences for either glycine or taurine substrates. BSHs with varying specificities were shown to restrict C. difficile spore germination and growth in vitro and colonization in pre-clinical in vivo models of CDI. Furthermore, BSHs reshape the pool of microbial conjugated bile acids (MCBAs) in the murine gut, and these MCBAs can further restrict C. difficile virulence in vitro. The recognition of conjugated BAs by BSHs defines the resulting BA pool, including the expansive MCBAs. This work provides insights into the structural basis of BSH mechanisms that shape the BA landscape and promote colonization resistance against C. difficile.
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Affiliation(s)
- Matthew H Foley
- Department of Pathobiology and Population Health, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Morgan E Walker
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Allison K Stewart
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Sarah O'Flaherty
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Shakshi Patel
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Violet V Beaty
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Garrison Allen
- Department of Pathobiology and Population Health, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Meichen Pan
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Joshua B Simpson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caroline Perkins
- Department of Pathobiology and Population Health, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Molly E Vanhoy
- Department of Pathobiology and Population Health, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Michael K Dougherty
- Department of Pediatrics, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah K McGill
- Department of Pediatrics, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ajay S Gulati
- Department of Pediatrics, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Erin S Baker
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Departments of Biochemistry and Biophysics, and Microbiology and Immunology, and the Integrated Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA.
| | - Casey M Theriot
- Department of Pathobiology and Population Health, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.
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Rajan R, Matsumura K. Design of self-assembled glycopolymeric zwitterionic micelles as removable protein stabilizing agents. NANOSCALE ADVANCES 2023; 5:1767-1775. [PMID: 36926568 PMCID: PMC10012880 DOI: 10.1039/d3na00002h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/20/2023] [Indexed: 06/15/2023]
Abstract
Developing stabilizers that protect proteins from denaturation under stress, and are easy to remove from solutions, is a challenge in protein therapeutics. In this study, micelles made of trehalose, a zwitterionic polymer (poly-sulfobetaine; poly-SPB), and polycaprolactone (PCL) were synthesized by a one-pot reversible addition-fragmentation chain-transfer (RAFT) polymerization reaction. The micelles protect lactate dehydrogenase (LDH) and human insulin from denaturation due to stresses like thermal incubation and freezing, and help them retain higher-order structures. Importantly, the protected proteins are readily isolated from the micelles by ultracentrifugation, with over 90% recovery, and almost all enzymatic activity is retained. This suggests the great potential of poly-SPB-based micelles for use in applications requiring protection and removal as required. The micelles may also be used to effectively stabilize protein-based vaccines and drugs.
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Affiliation(s)
- Robin Rajan
- School of Materials Science, Japan Advanced Institute of Science and Technology 1-1 Asahidai Nomi Ishikawa 923-1292 Japan
| | - Kazuaki Matsumura
- School of Materials Science, Japan Advanced Institute of Science and Technology 1-1 Asahidai Nomi Ishikawa 923-1292 Japan
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29
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Izumi Y, Matsuo K, Yokoya A. Secondary structural analyses of histone H2A-H2B proteins extracted from heated cells. Chirality 2023; 35:165-171. [PMID: 36578136 DOI: 10.1002/chir.23529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/18/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022]
Abstract
Histone proteins, building blocks of chromatins, participate in enzymatic reactions in cells heated at around 45°C though in vitro the denaturation of histones significantly proceeds at a similar temperature. It implies that unidentified mechanisms prevent thermal denaturation of histones in vivo. However, studies on the histone structures in the heated cells have been scarce. Here, we analyzed the secondary structures of histone H2A-H2B proteins originating from the heated cells using circular dichroism spectroscopy. The secondary structure contents of the H2A-H2B extracted from the heated cells differed from those of H2A-H2B both native and denatured in vitro but reverted to the native structures by incubating the heated cells at 37°C within 2 h. Such structural flexibility may play a role in protecting genomic functions governed by chromatin structures from heat stresses.
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Affiliation(s)
- Yudai Izumi
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology (QST), Ibaraki, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Research Center (HiSOR), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Akinari Yokoya
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology (QST), Ibaraki, Japan
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30
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Kato F, Yamaguchi Y, Inouye K, Matsuo K, Ishida Y, Inouye M. A novel gyrase inhibitor from toxin-antitoxin system expressed by Staphylococcus aureus. FEBS J 2023; 290:1502-1518. [PMID: 36148483 DOI: 10.1111/febs.16634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 11/30/2022]
Abstract
Toxin-antitoxin (TA) systems consist of a toxin inhibiting essential cellular functions (such as DNA, RNA and protein synthesis), and its cognate antitoxin neutralizing the toxicity. Recently, we identified a TA system termed TsbA/TsbT in the Staphylococcus aureus genome. The induction of the tsbT gene in Escherichia coli halted both DNA and RNA synthesis, reduced supercoiled plasmid and resulted in increasingly relaxed DNA. These results suggested that DNA gyrase was the target of TsbT. In addition, TsbT inhibited both E. coli and S. aureus DNA gyrase activity and induced linearization of plasmid DNA in vitro. Taken together, these results demonstrate that the TsbT toxin targets DNA gyrase in vivo. Site-directed mutagenesis experiments showed that the E27 and D37 residues in TsbT are critical for toxicity. Secondary structure prediction combining the analysis of vacuum-ultraviolet circular-dichroism spectroscopy and neural network method demonstrated that the 22nd-32nd residues of TsbT form an α-helix structure, and that the E27 residue is located around the centre of the α-helix segment. These findings give new insights not only into S. aureus TA systems, but also into bacterial toxins targeting DNA topoisomerases.
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Affiliation(s)
- Fuminori Kato
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
| | - Yoshihiro Yamaguchi
- Department of Biology and Geosciences, Graduate School of Sciences, Osaka City University, Japan
| | - Keiko Inouye
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yojiro Ishida
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Masayori Inouye
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, USA
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31
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Guo H, Feng Y, Deng Y, Yan T, Liang Z, Zhou Y, Zhang W, Xu E, Liu D, Wang W. Continuous flow modulates zein nanoprecipitation solvent environment to obtain colloidal particles with high curcumin loading. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2022.108089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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Keating PM, Pennington HN, Collins SD, Lee J. Purification and characterization of the Lassa virus transmembrane domain. Biochem Biophys Rep 2022; 33:101409. [PMID: 36583076 PMCID: PMC9792740 DOI: 10.1016/j.bbrep.2022.101409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Lassa virus (LASV) is the most prevalent arenavirus afflicting humans and has high potential to become a threat to global public health. The transmembrane domain (TM) of the LASV glycoprotein complex forms critical interactions with the LASV stable signal peptide that are important for the maturation and fusion activity of the virus. A further study of the structure-based molecular mechanisms is required to understand the role of the TM in the lifecycle of LASV in greater detail. However, it is challenging to obtain the TM in high quantity and purity due to its hydrophobic nature which results in solubility issues that makes it prone to aggregation in typical buffer systems. Here, we designed a purification and detergent screen protocol for the highly insoluble TM to enhance the yield and purity for structural studies. Based on the detergents tested, the TM had the highest incorporation in LMPG. Circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy were utilized to confirm the best detergent system for structural studies. Through CD spectroscopy, we were able to characterize the secondary structure of the TM as largely alpha-helical, while NMR spectroscopy showed a well-structured and stable TM in LMPG. From these results, LMPG was determined to be the optimal detergent for further structural studies.
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Recombinant Globular Domain of TcpA Pilin from Vibrio cholerae El Tor: Recovery from Inclusion Bodies and Structural Characterization. Life (Basel) 2022; 12:life12111802. [DOI: 10.3390/life12111802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
The production of recombinant proteins in Escherichia coli cells is often hampered by aggregation of newly synthesized proteins and formation of inclusion bodies. Here we propose the use of transverse urea gradient electrophoresis (TUGE) in testing the capability of folding of a recombinant protein from inclusion bodies dissolved in urea. A plasmid encoding the amino acid sequence 55–224 of TcpA pilin (C-terminal globular domain: TcpA-C) from Vibrio cholerae El Tor enlarged by a His-tag on its N-terminus was expressed in E. coli cells. The major fraction (about 90%) of the target polypeptide was detected in cell debris. The polypeptide was isolated from the soluble fraction and recovered from inclusion bodies after their urea treatment. Some structural properties of the polypeptide from each sample proved identical. The refolding protocol was developed on the basis of TUGE data and successfully used for the protein large-scale recovery from inclusion bodies. Spectral, hydrodynamic, and thermodynamic characteristics of the recombinant TcpA recovered from inclusion bodies indicate the presence of a globular conformation with a pronounced secondary structure and a rigid tertiary structure, which is promising for the design of immunodiagnostics preparations aimed to assess the pilin level in different strains of V. cholerae and to develop cholera vaccines.
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34
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Engineered multivalent self-assembled binder protein against SARS-CoV-2 RBD. Biochem Eng J 2022; 187:108596. [PMID: 36034180 PMCID: PMC9396458 DOI: 10.1016/j.bej.2022.108596] [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: 06/13/2022] [Revised: 08/02/2022] [Accepted: 08/17/2022] [Indexed: 02/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic since December 2019, and with it, a push for innovations in rapid testing and neutralizing antibody treatments in an effort to solve the spread and fatality of the disease. One such solution to both of these prevailing issues is targeting the interaction of SARS-CoV-2 spike receptor binding domain (RBD) with the human angiotensin-converting enzyme 2 (ACE2) receptor protein. Structural studies have shown that the N-terminal alpha-helix comprised of the first 23 residues of ACE2 plays an important role in this interaction. Where it is typical to design a binding domain to fit a target, we have engineered a protein that relies on multivalency rather than the sensitivity of a monomeric ligand to provide avidity to its target by fusing the N-terminal helix of ACE2 to the coiled-coil domain of the cartilage oligomeric matrix protein. The resulting ACE-MAP is able to bind to the SARS-CoV-2 RBD with improved binding affinity, is expressible in E. coli, and is thermally stable and relatively small (62 kDa). These properties suggest ACE-MAP and the MAP scaffold to be a promising route towards developing future diagnostics and therapeutics to SARS-CoV-2.
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35
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Kanagasingam S, von Ruhland C, Welbury R, Singhrao SK. Antimicrobial, Polarizing Light, and Paired Helical Filament Properties of Fragmented Tau Peptides of Selected Putative Gingipains. J Alzheimers Dis 2022; 89:1279-1291. [PMID: 36031895 DOI: 10.3233/jad-220486] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Tau is an established substrate for gingipains secreted by Porphyromonas gingivalis. Hyperphosphorylation of tau and neurofibrillary tangle (NFT) formation is a defining lesion of Alzheimer's disease (AD) where NFT distribution is related to Braak stage and disease severity. OBJECTIVE To assess gingipains'-fragmented tau peptides for their antimicrobial properties and for the likelihood of paired helical/straight filament (PHF/SF) formation with implications for the NFT lesion. METHODS Seven non-phosphorylated (A-G) and three phosphorylated (A-C) tau peptides, were tested for antimicrobial properties against P. gingivalis. Polarizing light properties were determined using Congo Red staining. Secondary and tertiary structures of peptides B-F were determined using transmission electron microscopy (TEM) and circular dichroism (CD) was undertaken for the soluble peptides A in phosphorylated and non-phosphorylated states. RESULTS Phosphorylated tau peptide A displayed a significant effect against planktonic P. gingivalis. The CD results demonstrated that both peptides A, in phosphorylated and non-phosphorylated states, in aqueous solution, adopted mainly β-type structures. Non-phosphorylated peptides B-F and phosphorylated peptides B-C were insoluble and fibrillar under the TEM. The secondary and tertiary structures of the non-phosphorylated peptide B demonstrated fewer helical twists, whereas peptide C displayed significantly more helical twists along the whole fiber(s) length following its phosphorylation. CONCLUSION Phosphorylated peptide A reduced P. gingivalis viability. CD spectroscopy demonstrated the phosphorylated and the non-phosphorylated peptide A predominantly formed from β-sheet structures in aqueous solution with potential antimicrobial activity. Phosphorylation of tau peptides physically changed their tertiary structure into PHFs with potential for self-aggregation and binding to the NFT lesion.
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Affiliation(s)
- Shalini Kanagasingam
- Brain and Behavior Centre, Faculty of Clinical and Biomedical Sciences, School of Dentistry, University of Central Lancashire, Preston, UK
| | - Christopher von Ruhland
- Electron and Light Microscopy Facility, College of Biomedical and Life Sciences, Cardiff University, Wales, UK
| | - Richard Welbury
- Brain and Behavior Centre, Faculty of Clinical and Biomedical Sciences, School of Dentistry, University of Central Lancashire, Preston, UK
| | - Sim K Singhrao
- Brain and Behavior Centre, Faculty of Clinical and Biomedical Sciences, School of Dentistry, University of Central Lancashire, Preston, UK
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Hill LK, Britton D, Jihad T, Punia K, Xie X, Delgado-Fukushima E, Liu CF, Mishkit O, Liu C, Hu C, Meleties M, Renfrew PD, Bonneau R, Wadghiri YZ, Montclare JK. Engineered Protein-Iron Oxide Hybrid Biomaterial for MRI-traceable Drug Encapsulation. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2022; 7:915-932. [PMID: 37274761 PMCID: PMC10237276 DOI: 10.1039/d2me00002d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Labeled protein-based biomaterials have become a popular for various biomedical applications such as tissue-engineered, therapeutic, or diagnostic scaffolds. Labeling of protein biomaterials, including with ultrasmall super-paramagnetic iron oxide (USPIO) nanoparticles, has enabled a wide variety of imaging techniques. These USPIO-based biomaterials are widely studied in magnetic resonance imaging (MRI), thermotherapy, and magnetically-driven drug delivery which provide a method for direct and non-invasive monitoring of implants or drug delivery agents. Where most developments have been made using polymers or collagen hydrogels, shown here is the use of a rationally designed protein as the building block for a meso-scale fiber. While USPIOs have been chemically conjugated to antibodies, glycoproteins, and tissue-engineered scaffolds for targeting or improved biocompatibility and stability, these constructs have predominantly served as diagnostic agents and often involve harsh conditions for USPIO synthesis. Here, we present an engineered protein-iron oxide hybrid material comprised of an azide-functionalized coiled-coil protein with small molecule binding capacity conjugated via bioorthogonal azide-alkyne cycloaddition to an alkyne-bearing iron oxide templating peptide, CMms6, for USPIO biomineralization under mild conditions. The coiled-coil protein, dubbed Q, has been previously shown to form nanofibers and, upon small molecule binding, further assembles into mesofibers via encapsulation and aggregation. The resulting hybrid material is capable of doxorubicin encapsulation as well as sensitive T2*-weighted MRI darkening for strong imaging capability that is uniquely derived from a coiled-coil protein.
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Affiliation(s)
- Lindsay K. Hill
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
- Department of Biomedical Engineering, SUNY Downstate Medical Center, Brooklyn, New York, 11203, USA
- Center for Advanced Imaging Innovation and Research (CAIR), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - Teeba Jihad
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - Kamia Punia
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - Xuan Xie
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - Erika Delgado-Fukushima
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - Che Fu Liu
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - Orin Mishkit
- Center for Advanced Imaging Innovation and Research (CAIR), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Chengliang Liu
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - Chunhua Hu
- Department of Chemistry, New York University, New York, New York, 10012, USA
| | - Michael Meleties
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
| | - P. Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, 10010, USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, 10010, USA
- Center for Genomics and Systems Biology, New York University, New York, New York, 10003, USA
- Courant Institute of Mathematical Sciences, Computer Science Department, New York University, New York, New York, 10009, USA
| | - Youssef Z. Wadghiri
- Center for Advanced Imaging Innovation and Research (CAIR), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
- Department of Chemistry, New York University, New York, New York, 10012, USA
- Department of Biomaterials, New York University College of Dentistry, New York, New York, 10010, USA
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Alghamri MS, Banerjee K, Mujeeb AA, Mauser A, Taher A, Thalla R, McClellan BL, Varela ML, Stamatovic SM, Martinez-Revollar G, Andjelkovic AV, Gregory JV, Kadiyala P, Calinescu A, Jiménez JA, Apfelbaum AA, Lawlor ER, Carney S, Comba A, Faisal SM, Barissi M, Edwards MB, Appelman H, Sun Y, Gan J, Ackermann R, Schwendeman A, Candolfi M, Olin MR, Lahann J, Lowenstein PR, Castro MG. Systemic Delivery of an Adjuvant CXCR4-CXCL12 Signaling Inhibitor Encapsulated in Synthetic Protein Nanoparticles for Glioma Immunotherapy. ACS NANO 2022; 16:8729-8750. [PMID: 35616289 PMCID: PMC9649873 DOI: 10.1021/acsnano.1c07492] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Glioblastoma (GBM) is an aggressive primary brain cancer, with a 5 year survival of ∼5%. Challenges that hamper GBM therapeutic efficacy include (i) tumor heterogeneity, (ii) treatment resistance, (iii) immunosuppressive tumor microenvironment (TME), and (iv) the blood-brain barrier (BBB). The C-X-C motif chemokine ligand-12/C-X-C motif chemokine receptor-4 (CXCL12/CXCR4) signaling pathway is activated in GBM and is associated with tumor progression. Although the CXCR4 antagonist (AMD3100) has been proposed as an attractive anti-GBM therapeutic target, it has poor pharmacokinetic properties, and unfavorable bioavailability has hampered its clinical implementation. Thus, we developed synthetic protein nanoparticles (SPNPs) coated with the transcytotic peptide iRGD (AMD3100-SPNPs) to target the CXCL2/CXCR4 pathway in GBM via systemic delivery. We showed that AMD3100-SPNPs block CXCL12/CXCR4 signaling in three mouse and human GBM cell cultures in vitro and in a GBM mouse model in vivo. This results in (i) inhibition of GBM proliferation, (ii) reduced infiltration of CXCR4+ monocytic myeloid-derived suppressor cells (M-MDSCs) into the TME, (iii) restoration of BBB integrity, and (iv) induction of immunogenic cell death (ICD), sensitizing the tumor to radiotherapy and leading to anti-GBM immunity. Additionally, we showed that combining AMD3100-SPNPs with radiation led to long-term survival, with ∼60% of GBM tumor-bearing mice remaining tumor free after rechallenging with a second GBM in the contralateral hemisphere. This was due to a sustained anti-GBM immunological memory response that prevented tumor recurrence without additional treatment. In view of the potent ICD induction and reprogrammed tumor microenvironment, this SPNP-mediated strategy has a significant clinical translation applicability.
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Affiliation(s)
- Mahmoud S Alghamri
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kaushik Banerjee
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Anzar A Mujeeb
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ava Mauser
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ayman Taher
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Rohit Thalla
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Brandon L McClellan
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria L Varela
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Svetlana M Stamatovic
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | | | - Anuska V Andjelkovic
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jason V Gregory
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Padma Kadiyala
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alexandra Calinescu
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jennifer A Jiménez
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - April A Apfelbaum
- Seattle Children’s Research Institute, University of Washington Seattle, WA, 98101
- Cancer Biology Ph.D. Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elizabeth R Lawlor
- Seattle Children’s Research Institute, University of Washington Seattle, WA, 98101
| | - Stephen Carney
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Andrea Comba
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Syed Mohd Faisal
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Marcus Barissi
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Marta B. Edwards
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Henry Appelman
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Yilun Sun
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106
| | - Jingyao Gan
- Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
| | - Rose Ackermann
- Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
| | - Anna Schwendeman
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
| | - Marianela Candolfi
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Michael R. Olin
- Department of Pediatrics, University of Minnesota, Minneapolis MN 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis MN 55455
| | - Joerg Lahann
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Corresponding Authors:, ,
| | - Pedro R. Lowenstein
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Biosciences Initiative in Brain Cancer, University of Michigan, Ann Arbor, MI 48109, USA
- Corresponding Authors:, ,
| | - Maria G. Castro
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Biosciences Initiative in Brain Cancer, University of Michigan, Ann Arbor, MI 48109, USA
- Corresponding Authors:, ,
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Micsonai A, Moussong É, Wien F, Boros E, Vadászi H, Murvai N, Lee YH, Molnár T, Réfrégiers M, Goto Y, Tantos Á, Kardos J. BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy. Nucleic Acids Res 2022; 50:W90-W98. [PMID: 35544232 PMCID: PMC9252784 DOI: 10.1093/nar/gkac345] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/18/2022] [Accepted: 05/09/2022] [Indexed: 12/15/2022] Open
Abstract
Circular dichroism (CD) spectroscopy is widely used to characterize the secondary structure composition of proteins. To derive accurate and detailed structural information from the CD spectra, we have developed the Beta Structure Selection (BeStSel) method (PNAS, 112, E3095), which can handle the spectral diversity of β-structured proteins. The BeStSel webserver provides this method with useful accessories to the community with the main goal to analyze single or multiple protein CD spectra. Uniquely, BeStSel provides information on eight secondary structure components including parallel β-structure and antiparallel β-sheets with three different groups of twist. It overperforms any available method in accuracy and information content, moreover, it is capable of predicting the protein fold down to the topology/homology level of the CATH classification. A new module of the webserver helps to distinguish intrinsically disordered proteins by their CD spectrum. Secondary structure calculation for uploaded PDB files will help the experimental verification of protein MD and in silico modelling using CD spectroscopy. The server also calculates extinction coefficients from the primary sequence for CD users to determine the accurate protein concentrations which is a prerequisite for reliable secondary structure determination. The BeStSel server can be freely accessed at https://bestsel.elte.hu.
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Affiliation(s)
- András Micsonai
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Éva Moussong
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Frank Wien
- Synchrotron SOLEIL, Gif-sur-Yvette 91192, France
| | - Eszter Boros
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Henrietta Vadászi
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Nikoletta Murvai
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest H-1117, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Budapest H-1117, Hungary
| | - Young-Ho Lee
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Republic of Korea.,Bio-Analytical Science, University of Science and Technology (UST), Daejeon 34113, Republic of Korea.,Graduate School of Analytical Science and Technology (GRAST), Chungnam National University (CNU), Daejeon 34134, Republic of Korea
| | - Tamás Molnár
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Matthieu Réfrégiers
- Synchrotron SOLEIL, Gif-sur-Yvette 91192, France.,Centre de Biophysique Moléculaire, CNRS UPR4301, Orléans, France
| | - Yuji Goto
- Global Center for Medical Engineering and Informatics, Osaka University, Osaka 565-0871, Japan
| | - Ágnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest H-1117, Hungary
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
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Investigations into the membrane activity of arenicin antimicrobial peptide AA139. Biochim Biophys Acta Gen Subj 2022; 1866:130156. [PMID: 35523364 DOI: 10.1016/j.bbagen.2022.130156] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 11/21/2022]
Abstract
Arenicin-3 is an amphipathic β-hairpin antimicrobial peptide that is produced by the lugworm Arenicola marina. In this study, we have investigated the mechanism of action of arenicin-3 and an optimized synthetic analogue, AA139, by studying their effects on lipid bilayer model membranes and Escherichia coli bacterial cells. The results show that simple amino acid changes can lead to subtle variations in their interaction with membranes and therefore alter their pre-clinical potency, selectivity and toxicity. While the mechanism of action of arenicin-3 is primarily dependent on universal membrane permeabilization, our data suggest that the analogue AA139 relies on more specific binding and insertion properties to elicit its improved antibacterial activity and lower toxicity, as exemplified by greater selectivity between lipid composition when inserting into model membranes i.e. the N-terminus of AA139 seems to insert deeper into lipid bilayers than arenicin-3 does, with a clear distinction between zwitterionic and negatively charged lipid bilayer vesicles, and AA139 demonstrates a cytoplasmic permeabilization dose response profile that is consistent with its greater antibacterial potency against E. coli cells compared to arenicin-3.
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40
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Schuelke-Sanchez AE, Cornetta AR, Kocian TA, Conger MA, Liptak MD. Ruffling is essential for Staphylococcus aureus IsdG-catalyzed degradation of heme to staphylobilin. J Inorg Biochem 2022; 230:111775. [PMID: 35247855 PMCID: PMC8930504 DOI: 10.1016/j.jinorgbio.2022.111775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/31/2022] [Accepted: 02/21/2022] [Indexed: 10/19/2022]
Abstract
Non-canonical heme oxygenases are enzymes that degrade heme to non-biliverdin products within bacterial heme iron acquisition pathways. These enzymes all contain a conserved second-sphere Trp residue that is essential for enzymatic turnover. Here, UV/Vis absorption (Abs) and circular dichroism (CD) spectroscopies were employed to show that the W67F variant of IsdG perturbs the heme substrate conformation. In general, a dynamic equilibrium between "planar" and "ruffled" substrate conformations exists within non-canonical heme oxygenases, and that the second-sphere Trp favors population of the "ruffled" substrate conformation. 1H nuclear magnetic resonance and magnetic CD spectroscopies were used to characterize the electronic structures of IsdG and IsdI variants with different substrate conformational distributions. These data revealed that the "ruffled" substrate conformation promotes partial porphyrin-to‑iron electron transfer, which makes the meso carbons of the porphyrin ring susceptible to radical attack. Finally, UV/Vis Abs spectroscopy was utilized to quantify the enzymatic rates, and electrospray ionization mass spectrometry was used to identify the product distributions, for variants of IsdG with altered substrate conformational distributions. In general, the rate of heme oxygenation by non-canonical heme oxygenases depends upon the population of the "ruffled" substrate conformation. Also, the production of staphylobilin or mycobilin by these enzymes is correlated with the population of the "ruffled" substrate conformation, since variants that favor population of the "planar" substrate conformation yield significant amounts of biliverdin. These data can be understood within the framework of a concerted rearrangement mechanism for the monooxygenation of heme to meso-hydroxyheme by non-canonical heme oxygenases.
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41
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Kumashiro M, Tsuji R, Suenaga S, Matsuo K. Formation of β-Strand Oligomers of Antimicrobial Peptide Magainin 2 Contributes to Disruption of Phospholipid Membrane. MEMBRANES 2022; 12:131. [PMID: 35207051 PMCID: PMC8877076 DOI: 10.3390/membranes12020131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 12/15/2022]
Abstract
The antimicrobial peptide magainin 2 (M2) interacts with and induces structural damage in bacterial cell membranes. Although extensive biophysical studies have revealed the interaction mechanism between M2 and membranes, the mechanism of membrane-mediated oligomerization of M2 is controversial. Here, we measured the synchrotron-radiation circular dichroism and linear dichroism (LD) spectra of M2 in dipalmitoyl-phosphatidylglycerol lipid membranes in lipid-to-peptide (L/P) molar ratios from 0-26 to characterize the conformation and orientation of M2 on the membrane. The results showed that M2 changed from random coil to α-helix structures via an intermediate state with increasing L/P ratio. Singular value decomposition analysis supported the presence of the intermediate state, and global fitting analysis revealed that M2 monomers with an α-helix structure assembled and transformed into M2 oligomers with a β-strand-rich structure in the intermediate state. In addition, LD spectra showed the presence of β-strand structures in the intermediate state, disclosing their orientations on the membrane surface. Furthermore, fluorescence spectroscopy showed that the formation of β-strand oligomers destabilized the membrane structure and induced the leakage of calcein molecules entrapped in the membrane. These results suggest that the formation of β-strand oligomers of M2 plays a crucial role in the disruption of the cell membrane.
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Affiliation(s)
- Munehiro Kumashiro
- Department of Physical Science, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan; (M.K.); (S.S.)
| | - Ryoga Tsuji
- Physics Program, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan;
| | - Shoma Suenaga
- Department of Physical Science, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan; (M.K.); (S.S.)
| | - Koichi Matsuo
- Department of Physical Science, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan; (M.K.); (S.S.)
- Physics Program, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan;
- Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
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42
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Varming AK, Rasmussen KK, Zong Z, Thulstrup PW, Kilstrup M, Lo Leggio L. Flexible linker modulates the binding affinity of the TP901-1 CI phage repressor to DNA. FEBS J 2021; 289:1135-1148. [PMID: 34665941 DOI: 10.1111/febs.16238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/16/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022]
Abstract
Temperate bacteriophages can switch between two life cycles following infection of a host bacterium: the lytic or lysogenic life cycle. The choice between these is controlled by a bistable genetic switch. We investigated the genetic switch of the lactococcal temperate bacteriophage, TP901-1, which is controlled by two regulatory proteins, the Clear 1 (CI) repressor and modulator of repression (MOR) antirepressor. CI consists of a DNA-binding N-terminal domain and a C-terminal domain responsible for oligomerization, connected by a flexible interdomain linker. Full-length CI is hexameric, whereas the truncated version CI with 58 C-terminal residues truncated (CIΔ58), missing the second C-terminal subdomain, is dimeric, but binds with the same affinity as full-length CI to the OL operator site, responsible for lytic genes transcription repression. Three variants of CIΔ58 with shorter, longer, and PP substituted linkers were produced and confirmed by circular dichroism spectroscopy and nanodifferential scanning fluorimetry to be well folded. With small-angle X-ray scattering, we delineated the conformational space sampled by the variants and wild-type in solution and found that shortening and lengthening the linker decrease and increase this, respectively, as also substantiated by molecular dynamics and as intended. Isoelectric focusing electrophoresis confirmed that all variants are able to bind to the MOR antirepressor. However, using electrophoretic mobility shift assays, we showed that shortening and lengthening the linker lead to a 94 and 17 times decrease in affinity to OL , respectively. Thus, an appropriate linker length appears to be crucial for appropriate DNA-binding and subsequent TP901-1 genetic switch function.
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Affiliation(s)
| | | | - Zhiyou Zong
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | | | - Mogens Kilstrup
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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Macha A, Liebsch F, Fricke S, Hetsch F, Neuser F, Johannes L, Kress V, Djémié T, Santamaria-Araujo JA, Vilain C, Aeby A, Van Bogaert P, Dejanovic B, Weckhuysen S, Meier JC, Schwarz G. Bi-allelic gephyrin variants impair GABAergic inhibition in a patient with epileptic encephalopathy. Hum Mol Genet 2021; 31:901-913. [PMID: 34617111 DOI: 10.1093/hmg/ddab298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/10/2021] [Accepted: 09/22/2021] [Indexed: 11/12/2022] Open
Abstract
Synaptic inhibition is essential for shaping the dynamics of neuronal networks, and aberrant inhibition is linked to epilepsy. Gephyrin (Geph) is the principal scaffolding protein at inhibitory synapses and is essential for postsynaptic clustering of glycine (GlyRs) and GABA type A receptors (GABAARs). Consequently, gephyrin is crucial for maintaining the relationship between excitation and inhibition in normal brain function and mutations in the gephyrin gene (GPHN) are associated with neurodevelopmental disorders and epilepsy. We identified bi-allelic variants in the GPHN gene, namely the missense mutation c.1264G > A and splice acceptor variant c.1315-2A > G, in a patient with developmental and epileptic encephalopathy (DEE). We demonstrate that the splice acceptor variant leads to nonsense-mediated mRNA decay (NMD). Furthermore, the missense variant (D422N) alters gephyrin structure, as examined by analytical size exclusion chromatography and CD-spectroscopy, thus leading to reduced receptor clustering and sensitivity towards calpain-mediated cleavage. Additionally, both alterations contribute to an observed reduction of inhibitory signal transmission in neurons, which likely contributes to the pathological encephalopathy.
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Affiliation(s)
- Arthur Macha
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | - Filip Liebsch
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | - Steffen Fricke
- Division Cell Physiology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.,Institute for Pathophysiology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Florian Hetsch
- Division Cell Physiology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Franziska Neuser
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | - Lena Johannes
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | - Vanessa Kress
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | - Tania Djémié
- Applied & Translational Neurogenomics Group, VIB-Center for Molecular Genetics, VIB, Antwerp, Belgium
| | - Jose A Santamaria-Araujo
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | - Catheline Vilain
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
| | - Alec Aeby
- Pediatric Neurology, Queen Fabiola Children Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Patrick Van Bogaert
- Departement of Pediatric Neurology, CHU d'Angers, and Laboratoire Angevin de Recherche en Ingénierie des Systèmes (LARIS), Université d'Angers, France
| | - Borislav Dejanovic
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | - Sarah Weckhuysen
- Applied & Translational Neurogenomics Group, VIB-Center for Molecular Genetics, VIB, Antwerp, Belgium.,Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium.,Neurology Department, University Hospital Antwerp, Antwerp, Belgium
| | - Jochen C Meier
- Division Cell Physiology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Guenter Schwarz
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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44
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Yang Y, Wang Q, Tang Y, Lei L, Zhao J, Zhang Y, Li L, Wang Q, Ming J. Effects of ionic strength and (−)-epigallocatechin gallate on physicochemical characteristics of soybean 11S and 7S proteins. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.106836] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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45
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Effects of Aβ-derived peptide fragments on fibrillogenesis of Aβ. Sci Rep 2021; 11:19262. [PMID: 34584131 PMCID: PMC8479085 DOI: 10.1038/s41598-021-98644-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/13/2021] [Indexed: 11/08/2022] Open
Abstract
Amyloid β (Aβ) peptide aggregation plays a central role in Alzheimer's disease (AD) etiology. AD drug candidates have included small molecules or peptides directed towards inhibition of Aβ fibrillogenesis. Although some Aβ-derived peptide fragments suppress Aβ fibril growth, comprehensive analysis of inhibitory potencies of peptide fragments along the whole Aβ sequence has not been reported. The aim of this work is (a) to identify the region(s) of Aβ with highest propensities for aggregation and (b) to use those fragments to inhibit Aβ fibrillogenesis. Structural and aggregation properties of the parent Aβ1-42 peptide and seven overlapping peptide fragments have been studied, i.e. Aβ1-10 (P1), Aβ6-15 (P2), Aβ11-20 (P3), Aβ16-25 (P4), Aβ21-30 (P5), Aβ26-36 (P6), and Aβ31-42 (P7). Structural transitions of the peptides in aqueous buffer have been monitored by circular dichroism and Fourier transform infrared spectroscopy. Aggregation and fibrillogenesis were analyzed by light scattering and thioflavin-T fluorescence. The mode of peptide-peptide interactions was characterized by fluorescence resonance energy transfer. Three peptide fragments, P3, P6, and P7, exhibited exceptionally high propensity for β-sheet formation and aggregation. Remarkably, only P3 and P6 exerted strong inhibitory effect on the aggregation of Aβ1-42, whereas P7 and P2 displayed moderate inhibitory potency. It is proposed that P3 and P6 intercalate between Aβ1-42 molecules and thereby inhibit Aβ1-42 aggregation. These findings may facilitate therapeutic strategies of inhibition of Aβ fibrillogenesis by Aβ-derived peptides.
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46
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A Novel Cooperative Metallo-β-Lactamase Fold Metallohydrolase from Pathogen Vibrio vulnificus Exhibits β-Lactam Antibiotic-Degrading Activities. Antimicrob Agents Chemother 2021; 65:e0032621. [PMID: 34228542 DOI: 10.1128/aac.00326-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio vulnificus is a pathogen that accounts for one of the highest mortality rates and is responsible for most reported seafood-related illnesses and deaths worldwide. Owing to the threats of pathogens with β-lactamase activity, it is important to identify and characterize β-lactamases with clinical significance. In this study, the protein sequence of the metallo-β-lactamase (MBL) fold metallohydrolase from V. vulnificus (designated Vmh) was analyzed, and its oligomeric state, β-lactamase activity, and metal binding ability were determined. BLASTp analysis indicated that the V. vulnificus Vmh protein showed no significant sequence identity with any experimentally identified Ambler class B MBLs or enzymes containing the MBL protein fold; it was also predicted to have a signal peptide of 19 amino acids at its N terminus and an MBL protein fold from amino acid residues 23 to 216. Recombinant V. vulnificus Vmh protein was overexpressed and purified. Analytical ultracentrifugation and electrospray ionization-mass spectrometry (MS) data demonstrated its monomeric state in an aqueous solution. Recombinant V. vulnificus Vmh protein showed broad degrading activities against β-lactam antibiotics, such as penicillins, cephalosporins, and imipenems, with kcat/Km values ranging from 6.23 × 102 to 1.02 × 104 M-1 s-1. The kinetic reactions of this enzyme exhibited sigmoidal behavior, suggesting the possibility of cooperativity. Zinc ions were required for the enzyme activity, which was abolished by adding the metal chelator EDTA. Inductively coupled plasma-MS indicated that this enzyme might bind two zinc ions per molecule as a cofactor.
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47
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Miles AJ, Janes RW, Wallace BA. Tools and methods for circular dichroism spectroscopy of proteins: a tutorial review. Chem Soc Rev 2021; 50:8400-8413. [PMID: 34132259 PMCID: PMC8328188 DOI: 10.1039/d0cs00558d] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Indexed: 12/31/2022]
Abstract
Circular dichroism (CD) spectroscopy is a widely-used method in biochemistry, structural biology and pharmaceutical chemistry. More than 24 000 papers published in the past decade have included CD characterisations of proteins; many of those studies have also included other complementary chemical, biophysical, and computational chemistry methods. This tutorial review describes the background to the technique of CD spectroscopy and good practice methods for high quality data collection. It specifically focuses on both established and new methods and tools available for experimental design and interpretation, data processing, visualisation, analysis, validation, archiving, and accession, including tools developed to enhance the complementarity of this method with other structural and chemical biology studies.
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Affiliation(s)
- A. J. Miles
- Institute of Structural and Molecular Biology, Birkbeck University of LondonLondon WC1E 7HXUK
| | - Robert W. Janes
- School of Biological and Chemical Sciences, Queen Mary University of LondonLondon E1 4NSUK
| | - B. A. Wallace
- Institute of Structural and Molecular Biology, Birkbeck University of LondonLondon WC1E 7HXUK
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48
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Chen Z, Chi Z, Sun Y, Lv Z. Chirality in peptide-based materials: From chirality effects to potential applications. Chirality 2021; 33:618-642. [PMID: 34342057 DOI: 10.1002/chir.23344] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/24/2021] [Accepted: 07/13/2021] [Indexed: 12/23/2022]
Abstract
Chirality is ubiquitous in nature with primary cellular functions that include construction of right-/left-handed helix and selective communications among diverse biomolecules. Of particularly intriguing are the chiral peptide-based materials that can be deliberately designed to change physicochemistry properties via tuning peptide sequences. Critically, understanding their chiral effects are fundamental for the development of novel materials in chemistry and biomedicine fields. Here, we review recent researches on chirality in peptide-based materials, summarizing relevant typical chiral effects towards recognition, amplification, and induction. Driven forces for the chiral discrimination in affinity interaction as well as the handedness preferences in supramolecular structure formation at both the macroscale and microscale are illustrated. The implementation of such chirality effects of artificial copolymers, assembled aggregates and their composites in the fields of bioseparation and bioenrichment, cell incubation, protein aggregation inhibitors, chiral smart gels, and bionic electro devices are also presented. At last, the challenges in these areas and possible directions are pointed out. The diversity of chiral roles in the origin of life and chirality design in different organic or composite systems as well as their applications in drug development and chirality detection in environmental protection are discussed.
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Affiliation(s)
- Zhonghui Chen
- Guangdong Engineering Technology Research Center for High performance Organic and Polymer Photoelectric Functional Films, State Key Laboratory of OEMT, School of Chemistry, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou, China
| | - Zhenguo Chi
- Guangdong Engineering Technology Research Center for High performance Organic and Polymer Photoelectric Functional Films, State Key Laboratory of OEMT, School of Chemistry, Sun Yat-sen University, Guangzhou, China
| | - Yifeng Sun
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou, China
| | - Ziyu Lv
- Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, China
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49
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Mortensen HG, Otzen DE, Pedersen JS. Ubiquitin forms conventional decorated micelle structures with sodium dodecyl sulfate at saturation. J Colloid Interface Sci 2021; 596:233-244. [DOI: 10.1016/j.jcis.2021.03.110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/10/2021] [Accepted: 03/19/2021] [Indexed: 12/20/2022]
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50
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Hu Q, Hu H, Zhang X, Fan K, Hong Y, Raston CL, Tang Y. In Situ Monitored Vortex Fluidic-Mediated Protein Refolding/Unfolding Using an Aggregation-Induced Emission Bioprobe. Molecules 2021; 26:4273. [PMID: 34299548 PMCID: PMC8306882 DOI: 10.3390/molecules26144273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022] Open
Abstract
Protein folding is important for protein homeostasis/proteostasis in the human body. We have established the ability to manipulate protein unfolding/refolding for β-lactoglobulin using the induced mechanical energy in the thin film microfluidic vortex fluidic device (VFD) with monitoring as such using an aggregation-induced emission luminogen (AIEgen), TPE-MI. When denaturant (guanidine hydrochloride) is present with β-lactoglobulin, the VFD accelerates the denaturation reaction in a controlled way. Conversely, rapid renaturation of the unfolded protein occurs in the VFD in the absence of the denaturant. The novel TPE-MI reacts with exposed cysteine thiol when the protein unfolds, as established with an increase in fluorescence intensity. TPE-MI provides an easy and accurate way to monitor the protein folding, with comparable results established using conventional circular dichroism. The controlled VFD-mediated protein folding coupled with in situ bioprobe AIEgen monitoring is a viable methodology for studying the denaturing of proteins.
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Affiliation(s)
- Qi Hu
- Medical Device Research Institute, College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia; (Q.H.); (H.H.); (X.Z.)
| | - Haozhen Hu
- Medical Device Research Institute, College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia; (Q.H.); (H.H.); (X.Z.)
| | - Xinyi Zhang
- Medical Device Research Institute, College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia; (Q.H.); (H.H.); (X.Z.)
| | - Kyle Fan
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia; (K.F.); (C.L.R.)
| | - Yuning Hong
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia;
| | - Colin L. Raston
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia; (K.F.); (C.L.R.)
| | - Youhong Tang
- Medical Device Research Institute, College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia; (Q.H.); (H.H.); (X.Z.)
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia; (K.F.); (C.L.R.)
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