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Carpanta V, Clement H, Arenas I, Corzo G. A consensus recombinant elapid long-chain α-neurotoxin and how protein folding matters for antibody recognition and neutralization of elapid venoms. Biochem Biophys Res Commun 2024; 732:150420. [PMID: 39047403 DOI: 10.1016/j.bbrc.2024.150420] [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: 05/31/2024] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Antivenoms are essential in the treatment of the neurotoxicity caused by elapid snakebites. However, there are elapid neurotoxins, e.g., long-chain α-neurotoxins (also known as long-chain three-finger toxins) that are barely neutralized by commercial elapid antivenoms; so, recombinant elapid neurotoxins could be an alternative or complements for improving antibody production against the lethal long-chain α-neurotoxins from elapid venoms. This work communicates the expression of a recombinant long-chain α-neurotoxin, named HisrLcNTx or rLcNTx, which based on the most lethal long-chain α-neurotoxins reported, was constructed de novo. The gene of rLcNTx was synthesized and introduced into the expression vector pQE30, which contains a proteolytic cleavage region for exscinding the mature protein, and His residues in tandem for affinity purification. The cloned pQE30/rLcNTx was transfected into Escherichia coli Origami cells to express rLcNTx. After expression, it was found in inclusion bodies, and folded in multiple Cys-Cys structural isoforms. To observe the capability of those isoforms to generate antibodies against native long-chain α-neurotoxins, groups of rabbits were immunized with different cocktails of Cys-Cys rLcNTx isoforms. In vitro, and in vivo analyses revealed that rabbit antibodies raised against different rLcNTx Cys-Cys isoforms were able to recognize pure native long-chain α-neurotoxins and their elapid venoms, but they were unable to neutralize bungarotoxin, a classical long-chain α-neurotoxin, and other elapid venoms. The rLcNTx Cys-Cys isoform 2 was the immunogen that produced the best neutralizing antibodies in rabbits. Yet to neutralize the elapid venoms from the black mamba Dendroaspis polylepis, and the coral shield cobra Aspidelaps lubricus, it was required to use two types of antibodies, the ones produced using rLcNTx Cys-Cys isoform 2 and antibodies produced using short-chain α-neurotoxins. Expression of recombinant elapid neurotoxins as immunogens could be an alternative to improve elapid antivenoms; nevertheless, recombinant elapid neurotoxins must be well-folded to be used as immunogens for obtaining neutralizing antibodies.
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Affiliation(s)
- Víctor Carpanta
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, UNAM, Apartado Postal 510-3, Cuernavaca, Morelos, 61500, Mexico
| | - Herlinda Clement
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, UNAM, Apartado Postal 510-3, Cuernavaca, Morelos, 61500, Mexico
| | - Iván Arenas
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, UNAM, Apartado Postal 510-3, Cuernavaca, Morelos, 61500, Mexico
| | - Gerardo Corzo
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, UNAM, Apartado Postal 510-3, Cuernavaca, Morelos, 61500, Mexico.
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2
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Bilog M, Vedad J, Capadona C, Profit AA, Desamero RZB. Key charged residues influence the amyloidogenic propensity of the helix-1 region of serum amyloid A. Biochim Biophys Acta Gen Subj 2024; 1868:130690. [PMID: 39117048 DOI: 10.1016/j.bbagen.2024.130690] [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: 04/12/2024] [Revised: 07/15/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
Increased plasma levels of serum amyloid A (SAA), an acute-phase protein that is secreted in response to inflammation, may lead to the accumulation of amyloid in various organs thereby obstructing their functions. Severe cases can lead to a systemic disorder called AA amyloidosis. Previous studies suggest that the N-terminal helix is the most amyloidogenic region of SAA. Moreover, computational studies implicated a significant role for Arg-1 and the residue-specific interactions formed during the fibrillization process. With a focus on the N-terminal region of helix-1, SAA1-13, mutational analysis was employed to interrogate the roles of the amino acid residues, Arg-1, Ser-5, Glu-9, and Asp-12. The truncated SAA1-13 fragment was systematically modified by substituting the key residues with alanine or uncharged but structurally similar amino acids. We monitored the changes in the amyloidogenic propensities, associated conformational markers, and morphology of the amyloids resulting from the mutation of SAA1-13. Mutating out Arg-1 resulted in much reduced aggregation propensity and a lack of detectable β-structures alluding to the importance of salt-bridge interactions involving Arg-1. Our data revealed that by systematically mutating the key amino acid residues, we can modulate the amyloidogenic propensity and alter the time-dependent conformational variation of the peptide. When the behaviors of each mutant peptide were analyzed, they provided evidence consistent with the aggregation pathway predicted by MD simulation studies. Here, we detail the important temporal molecular interactions formed by Arg-1 with Ser-5, Glu-9, and Asp-12 and discuss its mechanistic implications on the self-assembly of the helix-1 region of SAA.
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Affiliation(s)
- Marvin Bilog
- Department of Chemistry and the Institute of Macromolecular Assembly, York College of the City University of New York, Jamaica, New York 11451, United States; PhD Programs in Biochemistry, Graduate Center of the City University of New York, NY, New York, 10016, United States
| | - Jayson Vedad
- PhD Programs in Chemistry, Graduate Center of the City University of New York, NY, New York, 10016, United States; Chemistry and Biochemistry Department, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York, 11210, United States
| | - Charisse Capadona
- Department of Chemistry and the Institute of Macromolecular Assembly, York College of the City University of New York, Jamaica, New York 11451, United States
| | - Adam A Profit
- Department of Chemistry and the Institute of Macromolecular Assembly, York College of the City University of New York, Jamaica, New York 11451, United States; PhD Programs in Chemistry, Graduate Center of the City University of New York, NY, New York, 10016, United States; PhD Programs in Biochemistry, Graduate Center of the City University of New York, NY, New York, 10016, United States
| | - Ruel Z B Desamero
- Department of Chemistry and the Institute of Macromolecular Assembly, York College of the City University of New York, Jamaica, New York 11451, United States; PhD Programs in Chemistry, Graduate Center of the City University of New York, NY, New York, 10016, United States; PhD Programs in Biochemistry, Graduate Center of the City University of New York, NY, New York, 10016, United States.
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3
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Stepanenko OV, Sulatsky MI, Mikhailova EV, Stepanenko OV, Sulatskaya AI. Degradation of pathogenic amyloids induced by matrix metalloproteinase-9. Int J Biol Macromol 2024; 281:136362. [PMID: 39395518 DOI: 10.1016/j.ijbiomac.2024.136362] [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: 08/02/2024] [Revised: 09/27/2024] [Accepted: 10/04/2024] [Indexed: 10/14/2024]
Abstract
Over the past decade, the greatest promise for treating severe and currently incurable systemic and neurodegenerative diseases has turned to agents capable of effectively degrading pathological amyloid deposits without causing side effects. Specifically, amyloid destruction observed in immunotherapy is hypothesized to occur through activation of proteolytic enzymes. This study examines poorly understood effects of an immune enzyme, extracellular matrix metalloproteinase-9 (MMP9), on amyloids associated with Alzheimer's and Parkinson's diseases, lysozyme, insulin, and dialysis-related amyloidoses. The study establishes the universality of MMP9's effect on various amyloids, with its efficacy largely depending on the fibrillar cluster size. Irreversible amyloid degradation by MMP9 is attributed to the destruction of intramolecular interactions rather than intermolecular hydrogen bonds in the fibril backbone. This process results in the loss of ordered fiber structure without reducing aggregate size or increasing cytotoxicity. Thus, MMP9 can mitigate side effects of anti-amyloid therapy associated with the formation of low-molecular-weight degradation products that may accelerate fibrillogenesis and amyloid propagation between tissues and organs. MMP9 shows promise as a component of safe anti-amyloid drugs by enhancing the accessibility of binding sites through "loosening" amyloid clusters, which facilitates subsequent fragmentation and monomerization by other enzymes.
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Affiliation(s)
- Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia.
| | - Maksim I Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia.
| | - Ekaterina V Mikhailova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia.
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia.
| | - Anna I Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia.
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4
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Bakar KA, Lam SD, Feroz SR. Binding characteristics of the major kratom alkaloid, mitragynine, towards serum albumin: Spectroscopic, calorimetric, microscopic, and computational investigations. Chem Biol Interact 2024; 404:111264. [PMID: 39393752 DOI: 10.1016/j.cbi.2024.111264] [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: 08/14/2024] [Revised: 09/26/2024] [Accepted: 10/08/2024] [Indexed: 10/13/2024]
Abstract
Mitragynine (MTG) is a prominent indole alkaloid that is present abundantly in Mitragyna speciosa, commonly referred to as kratom. MTG has garnered significant attention due to its selective agonistic characteristics towards opioid receptors and related analgesic effects. In the circulatory system, the in vivo efficacy of MTG is dictated by its interaction with plasma proteins, primarily human serum albumin (HSA). In the present study, we utilized a broad methodology that included spectroscopic, calorimetric, microscopic, and in silico approaches to characterize the interaction between MTG and HSA. Alterations in the UV absorption spectrum of HSA by the presence of MTG demonstrated a ground-state complexation between the protein and the ligand. The Ka values obtained for the MTG-HSA interaction were in the range 103-104 M-1 based on analysis of fluorescence and ITC data, respectively, indicating an intermediate binding affinity. The binding reaction was thermodynamically favorable as revealed by ΔH, ΔS, and ΔG values of -16.42 kJ mol-1, 39.97 J mol-1 K-1, and -28.34 kJ mol-1, respectively. Furthermore, CD spectroscopy results suggested MTG binding induced minimal effects on the structural integrity of HSA, supported by computational methods. Changes in the dimensions of HSA particles due to aggregation, as observed using atomic force microscopy in the presence of MTG. Competitive drug displacement results seemingly suggested site III of HSA located at subdomain IB as the preferred binding site of MTG, but were in inconclusive. However, docking results showed the clear preference of MTG to bind to site III, facilitated by hydrophobic (alkyl and pi-alkyl) and van der Waals forces, together with carbon hydrogen bonds. Additionally, the MTG-HSA complexation was demonstrated to be stable based on molecular dynamics analysis. The outcomes of this study shed light on the therapeutic potential of MTG and can help in the design of more effective derivatives of the compound.
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Affiliation(s)
- Khairul Azreena Bakar
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Su Datt Lam
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia; Structural Biology and Protein Engineering Group, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia; Center for Global Health Research (CGHR), Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - Shevin Rizal Feroz
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia; Structural Biology and Protein Engineering Group, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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5
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Qin X, Guo Y, Li R, Bitter JH, Scott EL, Zhang C. Enhanced Delivery of Biomolecules into Caco2 Cells Based on the Cell-Penetrating Ability of Keratin Peptides. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 39383509 DOI: 10.1021/acsami.4c13236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2024]
Abstract
Keratin, as a promising bioresource, possesses significant potential for diverse biological applications due to its favorable biocompatibility, low toxicity, biodegradability, and cell adhesion ability. However, there are few studies on the cell-penetrating ability of keratin peptides (KEPs) for biomolecule delivery. Therefore, this study explored the cell-penetrating ability of KEPs with different molecular weights (Mw) on Caco2 cells using fluorescein-labeled insulin (FITC-INS) as the target intracellular biomolecule. The potential cell-penetrating mechanism was elaborated by combining cellular investigation with the physicochemical characterization of KEPs. The result shows that the KEPs <3 kDa (KEP1) exhibited the highest cell-penetrating ability at 2 mg/mL, allowing efficient delivery of FITC-INS into Caco2 cells without covalent bonding. The cellular uptake mechanism was energy-dependent, mainly involving macropinocytosis. The further fractionation of KEP1 reveals that the most effective components consisted of 8-19 amino acids, including specific hydrophobic peptides (e.g., RVVIEPSPVVV and IIIQPSPVVV), PPII amphipathic peptides (e.g., PPPVVVTFP and FIQPPPVVV), and Cys-rich peptides (e.g., LCAPTPCGPTPL and CLPCRPCGPTPL). Additionally, analysis of the secondary and tertiary structure and amino acid composition illustrated that KEP1 exhibited rich hydrophobic residues and disulfide bonds, which probably contributed to its cell-penetrating ability, as opposed to its small particle size and electrostatic interactions. This study reveals the cell-penetrating ability of KEPs, thus highlighting their potential as biomaterials for noncovalently delivering biomolecules.
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Affiliation(s)
- Xiaojie Qin
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Biobased Chemistry and Technology, Wageningen University and Research, Wageningen 6700AA, Netherlands
| | - Yujie Guo
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ruilin Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Johannes H Bitter
- Biobased Chemistry and Technology, Wageningen University and Research, Wageningen 6700AA, Netherlands
| | - Elinor L Scott
- Biobased Chemistry and Technology, Wageningen University and Research, Wageningen 6700AA, Netherlands
| | - Chunhui Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Li H, Tuttle MD, Zilm KW, Batista VS. Rapid Quantification of Protein Secondary Structure Composition from a Single Unassigned 1D 13C Nuclear Magnetic Resonance Spectrum. J Am Chem Soc 2024; 146:27542-27554. [PMID: 39322561 DOI: 10.1021/jacs.4c08300] [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: 09/27/2024]
Abstract
The function of a protein is predicated upon its three-dimensional fold. Representing its complex structure as a series of repeating secondary structural elements is one of the most useful ways by which we study, characterize, and visualize a protein. Consequently, experimental methods that quantify the secondary structure content allow us to connect a protein's structure to its function. Here, we introduce an automated gradient descent-based method we refer to as secondary-structure distribution by NMR that allows for rapid quantification of the protein secondary structure composition of a protein from a single, 1D 13C NMR spectrum without chemical shift assignments. The analysis of nearly 900 proteins with known structure and chemical shifts demonstrates the capabilities of our approach. We show that these results rival alternative techniques such as FT-IR and circular dichroism that are commonly used to estimate secondary structure compositions. The resulting method requires only the primary sequence of the protein and its referenced 13C NMR spectrum. Each residue is modeled in an ensemble of secondary structures with percentage contributions from random coil, α-helix, and β-sheet secondary structures obtained by minimizing the difference between a simulated and experimental 1D 13C NMR spectrum. The capabilities of the method are demonstrated as applied to samples at natural abundance or enriched in 13C, acquired by either solution or solid-state NMR, and even on low magnetic field benchtop NMR spectrometers. This approach allows for rapid characterization of protein secondary structure across traditionally challenging to characterize states including liquid-liquid phase-separated, membrane-bound, or aggregated states.
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Affiliation(s)
- Haote Li
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Marcus D Tuttle
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Kurt W Zilm
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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7
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Islam MS, Alatishe A, Lee-Lopez CC, Serrano F, Yukl ET. H-NOX Influences Biofilm Formation, Central Metabolism, and Quorum Sensing in Paracoccus denitrificans. J Proteome Res 2024. [PMID: 39370609 DOI: 10.1021/acs.jproteome.4c00466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
The transition from planktonic to biofilm growth in bacteria is often accompanied by greater resistance to antibiotics and other stressors, as well as distinct alterations in physical traits, genetic activity, and metabolic restructuring. In many species, the heme nitric oxide/oxygen binding proteins (H-NOX) play an important role in this process, although the signaling mechanisms and pathways in which they participate are quite diverse and largely unknown. In Paracoccus denitrificans, deletion of the hnox gene results in a severe biofilm-deficient phenotype. Quantitative proteomics was used to assemble a comprehensive data set of P. denitrificans proteins showing altered abundance of those involved in several important metabolic pathways. Further, decreased levels of pyruvate and elevated levels of C16 homoserine lactone were detected for the Δhnox strain, associating the biofilm deficiency with altered central carbon metabolism and quorum sensing, respectively. These results expand our knowledge of the important role of H-NOX signaling in biofilm formation.
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Affiliation(s)
- Md Shariful Islam
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
- Department of Mathematics and Physics, North South University, Bashundhara RA, Dhaka 1229, Bangladesh
| | - Aishat Alatishe
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
| | - Cameron C Lee-Lopez
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
| | - Fred Serrano
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
| | - Erik T Yukl
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, United States
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8
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Cho C, Fei C, Jiang B, Yang W, Yuan HS. Molecular mechanisms for DNA methylation defects induced by ICF syndrome-linked mutations in DNMT3B. Protein Sci 2024; 33:e5131. [PMID: 39290110 PMCID: PMC11408749 DOI: 10.1002/pro.5131] [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: 04/23/2024] [Revised: 06/19/2024] [Accepted: 07/14/2024] [Indexed: 09/19/2024]
Abstract
DNA methyltransferase 3B (DNMT3B) plays a crucial role in DNA methylation during mammalian development. Mutations in DNMT3B are associated with human genetic diseases, particularly immunodeficiency, centromere instability, facial anomalies (ICF) syndrome. Although ICF syndrome-related missense mutations in the DNMT3B have been identified, their precise impact on protein structure and function remains inadequately explored. Here, we delve into the impact of four ICF syndrome-linked mutations situated in the DNMT3B dimeric interface (H814R, D817G, V818M, and R823G), revealing that each of these mutations compromises DNA-binding and methyltransferase activities to varying degrees. We further show that H814R, D817G, and V818M mutations severely disrupt the proper assembly of DNMT3B homodimer, whereas R823G does not. We also determined the first crystal structure of the methyltransferase domain of DNMT3B-DNMT3L tetrameric complex hosting the R823G mutation showing that the R823G mutant displays diminished hydrogen bonding interactions around T775, K777, G823, and Q827 in the protein-DNA interface, resulting in reduced DNA-binding affinity and a shift in sequence preference of +1 to +3 flanking positions. Altogether, our study uncovers a wide array of fundamental defects triggered by DNMT3B mutations, including the disassembly of DNMT3B dimers, reduced DNA-binding capacity, and alterations in flanking sequence preferences, leading to aberrant DNA hypomethylation and ICF syndrome.
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Affiliation(s)
- Chao‐Cheng Cho
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan, ROC
| | - Cheng‐Yin Fei
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan, ROC
| | - Bo‐Chen Jiang
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan, ROC
| | - Wei‐Zen Yang
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan, ROC
| | - Hanna S. Yuan
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan, ROC
- Graduate Institute of Biochemistry and Molecular BiologyNational Taiwan UniversityTaipeiTaiwan, ROC
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Ayimbila F, Tantimongcolwat T, Ruankham W, Pingaew R, Prachayasittikul V, Worachartcheewan A, Prachayasittikul V, Prachayasittikul S, Phopin K. Insight into the binding mechanisms of fluorinated 2-aminothiazole sulfonamide and human serum albumin: Spectroscopic and in silico approaches. Int J Biol Macromol 2024; 277:134048. [PMID: 39116983 DOI: 10.1016/j.ijbiomac.2024.134048] [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: 05/14/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 08/10/2024]
Abstract
4-Fluoro-N-(thiazol-2-yl)benzenesulfonamide (3) is a novel fluorinated compound, containing various biological activities. Therefore, absorption spectroscopy, fluorescence quenching, molecular docking, and molecular simulation were employed to investigate the interaction between 3 and human serum albumin (HSA). Firstly, compound 3 meets all criteria for drug-likeness prediction. UV absorption spectra revealed the interaction of 3 with HSA altered the microenvironment of protein, as well as circular dichroism spectroscopic analysis indicated slightly conformational changes and a reduction in α-helical content. The binding parameters of the HSA-3 complex suggested that fluorescence quenching is driven by combined static and dynamic processes. Additionally, the stability of the complex is attributed to conventional hydrogen and hydrophobic bonding interactions. Furthermore, esterase-like activity indicated that the binding of 3 might disrupt HSA's bond networks, leading to structural alterations. Consequently, the strong binding constant (Ka ≈ 1.204 × 106 M-1) aligns with the predicted unbound fraction (0.28) in serum, indicating that thiazole 3 has good bioavailability in plasma and can be effectively transported to target sites, thereby exerting its pharmaceutical effects. However, careful dosage management is essential to prevent potential adverse effects. Overall, these findings highlight the potential of 3 as a therapeutic agent, emphasizing the need for further research to optimize its uses.
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Affiliation(s)
- Francis Ayimbila
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Tanawut Tantimongcolwat
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Waralee Ruankham
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Ratchanok Pingaew
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Veda Prachayasittikul
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Apilak Worachartcheewan
- Department of Community Medical Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Virapong Prachayasittikul
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Supaluk Prachayasittikul
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Kamonrat Phopin
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand; Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
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10
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Lozada SL, Gómez JA, Menéndez K, Gómez T, Montes de Oca D, Durán JL, Fernández OL, Perera Y, Rivas G, Boggiano-Ayo T, Ledon N, Carmenate T. Oxidative refolding by Copper-catalyzed air oxidation consistently increases the homogeneity and activity of a Novel Interleukin-2 mutein. J Biotechnol 2024; 393:81-90. [PMID: 39032699 DOI: 10.1016/j.jbiotec.2024.07.013] [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: 04/01/2024] [Revised: 06/19/2024] [Accepted: 07/16/2024] [Indexed: 07/23/2024]
Abstract
Interleukin-2 (IL-2) has been used in cancer treatment for over 30 years. However, due to its high toxicity, new mutant variants have been developed. These variants retain some of the biological properties of the original molecule but offer other therapeutic advantages. At the Center of Molecular Immunology, the IL-2 no-alpha mutein, an IL-2 agonist with lower toxicity than wtIL-2, has been designed, produced, and is currently being evaluated in a Phase I/II clinical trial. The mutein is produced in E. coli as an insoluble material that must be refolded in vitro to yield a fully active protein. Controlled oxidation steps are essential in the purification process of recombinant proteins produced in E. coli to ensure the proper formation of the disulfide bonds in the molecules. In this case, the new purification process includes a copper-catalyzed air oxidation step to induce disulfide bond establishment. The optimal conditions of pH, copper, protein and detergent concentration for this step were determined through screening. The produced protein demonstrated a conserved 3D structure, higher purity, and greater biological activity than the obtained by established process without the oxidation step. Four batches were produced and evaluated, demonstrating the consistency of the new process.
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Affiliation(s)
- Sum Lai Lozada
- Bioprocess R&D Direction, Center of Molecular Immunology, Havana, Cuba.
| | - Jose Alberto Gómez
- Department of Quality Control. Center of Molecular Immunology, Havana, Cuba.
| | | | - Tania Gómez
- Department of Quality Control. Center of Molecular Immunology, Havana, Cuba.
| | | | - Jose L Durán
- Bioprocess R&D Direction, Center of Molecular Immunology, Havana, Cuba.
| | | | - Yoel Perera
- Centro Nacional de Biopreparados, Mayabeque, Cuba.
| | - Gabriela Rivas
- Department of Quality Control. Center of Molecular Immunology, Havana, Cuba.
| | | | - Nuris Ledon
- Research Direction, Center of Molecular Immunology, Havana, Cuba; School of Pharmacy, University of Havana, Havana, Cuba.
| | - Tania Carmenate
- Immune-regulation Department, Immunology and Immunotherapy Direction. Center of Molecular Immunology, PO Box 16040, Havana, Cuba.
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11
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Belguesmia Y, Guay LD, Teiar R, Rahman MRT, Dussert E, Biron E, Drider D. Synthesis, antimicrobial activity, and mechanistic studies of enterocin DD14, a leaderless two-peptide bacteriocin. Int J Biol Macromol 2024; 280:135716. [PMID: 39304058 DOI: 10.1016/j.ijbiomac.2024.135716] [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: 07/31/2024] [Revised: 09/13/2024] [Accepted: 09/14/2024] [Indexed: 09/22/2024]
Abstract
Bacteriocins are promising alternatives to antibiotics in the food, veterinary and medical sectors, but their study and use is often hampered by the low yields and high costs associated with their purification from naturally occurring bacteria. Chemical synthesis has emerged as a means to overcome this limitation and design more active variants. In this study, microwave-assisted solid-phase peptide synthesis was used to produce the leaderless two-peptide bacteriocin enterocin DD14 (EntDD14), composed of EntDD14A (44 amino acids) and EntDD14B (43 amino acids). The resulting synthetic peptides, syn-EntDD14A and syn-EntDD14B, were tested against Gram-positive bacteria including Listeria, Staphylococcus and Enterococcus strains. Both peptides were found to be necessary for optimal, but not synergistic, antibacterial activity and to act through a pore-forming mechanism. Both peptides exhibited moderate cytotoxicity against eukaryotic cells.
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Affiliation(s)
| | - Louis-David Guay
- Faculté de pharmacie, Université Laval et Centre de recherche du CHU de Québec-Université Laval, Québec, Canada
| | - Radja Teiar
- UMRT BioEcoAgro 1158 INRAe Université de Lille, France
| | - Md Ramim Tanver Rahman
- Faculté de pharmacie, Université Laval et Centre de recherche du CHU de Québec-Université Laval, Québec, Canada
| | | | - Eric Biron
- Faculté de pharmacie, Université Laval et Centre de recherche du CHU de Québec-Université Laval, Québec, Canada.
| | - Djamel Drider
- UMRT BioEcoAgro 1158 INRAe Université de Lille, France.
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12
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Nazir A, Ijaz M, Rehman HM, Sajjad M. Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi. Proteins 2024. [PMID: 39291641 DOI: 10.1002/prot.26748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 08/22/2024] [Accepted: 08/30/2024] [Indexed: 09/19/2024]
Abstract
High thermostability of the enzymes is one of the distinguishing characteristics that increase their industrial utility. In the current research work, rigidifying the flexible amino acid residues of a lysophospholipase (Pa-LPL) from Pyrococcus abyssi was used as a protein engineering approach to improve its thermostability. A truncated variant of Pa-LPL (t-LPL∆12) was constructed by trimming its 12 amino acid residues (50-61) through overlap extension PCR. The truncated enzyme worked optimally at 65°C and pH 6.5 with remarkable thermostability at 65°C-85°C. In comparison to wild-type Pa-LPL, 5.8 and 1.2-fold increase in half-life (t1/2) of t-LPL∆12 was observed at 65 (optimum temperature) and 95°C, respectively. The activity of t-LPL∆12 was stimulated by 1 mM Cu2+ followed by Ca2+, Ni2+, Co2+, and Mg2+. Both substrate docking and experimental results indicated that the truncated enzyme could hydrolyze a variety of p-nitrophenyl esters. Km, Vmax, and Kcat for enzymatic hydrolysis of p-nitrophenyl butyrate were calculated to be 1 ± 0.087 mM, 1456 ± 36.474 U/mg, and 1.397 × 1011 min-1, respectively. In short, broad substrate specificity and thermostability of t-LPL∆12 are some of the distinctive features that make it an ideal candidate for degumming of vegetable oils.
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Affiliation(s)
- Arshia Nazir
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Maham Ijaz
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
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13
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Xu F, Shen Y, Pan Z, Zhou X, Gu W, Dong J, Yin S, Liu S, Xu M, Chen B. The hemostatic molecular mechanism of Sanguisorbae Radix's pharmacological active components based on HSA: Spectroscopic investigations, molecular docking and dynamics simulation. Heliyon 2024; 10:e37020. [PMID: 39296229 PMCID: PMC11407948 DOI: 10.1016/j.heliyon.2024.e37020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 07/15/2024] [Accepted: 08/26/2024] [Indexed: 09/21/2024] Open
Abstract
The interactions between human serum albumin (HSA) and the hemostatic components of the Chinese medicine Sanguisorbae Radix (SR), specifically phenolic acid compounds such as caffeic acid (CA), ferulic acid (FA) and their 1:1 mixture (1:1) were studied to investigate the molecular mechanism underlying the hemostatic effect of SR. Network pharmacology combined with the experimental and computational data revealed that HSA is one of the hemostatic targets to SR phenolic acids. SDS-PAGE and multi-spectroscopy demonstrated that the phenolic acids bind to the Sudlow site I on HSA, altering its structure and influencing its migration velocity. There is an observed synergistic effect upon the mixture of CA and FA. Quantum chemistry, molecular docking, and molecular dynamics simulations indicate that the binding of phenolic acids to HSA is stable, and variations in binding efficiency are associated with the hydrophobicity of the substituent at the C3 position of the side chain, and also, the key amino acids and functional groups for hemostasis of SR were identified, along with the active sites that contribute to the synergistic enhancement by phenolic acids.
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Affiliation(s)
- Fei Xu
- National Key Laboratory on Technologies for Chinese Medicine Pharmaceutical Process Control and Intelligent Manufacture, Nanjing University of Chinese Medicine/Jangsu Kanion Pharmaceutical Co., Ltd., Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center of TCM External Medication Development and Application, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - YuQing Shen
- The Second People's Hospital of Taizhou City, Taizhou, 225500, China
| | - ZhiQiang Pan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xuan Zhou
- School of Elderly Care Services and Management, Nanjing University of Chinese Medicine, 210023, China
| | - Wei Gu
- Jiangsu Provincial Engineering Research Center of TCM External Medication Development and Application, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Jiangsu Key Laboratory of Chinese Medicine Processing, Nanjing, 210023, China
| | - Jie Dong
- Jiangsu Provincial Engineering Research Center of TCM External Medication Development and Application, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shaoping Yin
- Jiangsu Provincial Engineering Research Center of TCM External Medication Development and Application, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - ShengJin Liu
- National Key Laboratory on Technologies for Chinese Medicine Pharmaceutical Process Control and Intelligent Manufacture, Nanjing University of Chinese Medicine/Jangsu Kanion Pharmaceutical Co., Ltd., Nanjing, 210023, China
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Ming Xu
- Jiangsu Sunan Pharmaceutical Group Co., Ltd., Zhenjiang, 212400, China
| | - Baoduan Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
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14
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Yang P, Wang W, Hu Y, Wang Y, Xu Z, Liao X. Exploring high hydrostatic pressure effects on anthocyanin binding to serum albumin and food-derived transferrins. Food Chem 2024; 452:139544. [PMID: 38723571 DOI: 10.1016/j.foodchem.2024.139544] [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: 02/18/2024] [Revised: 04/20/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024]
Abstract
This study investigated the effects of high hydrostatic pressure (HHP) on the binding interactions of cyanindin-3-O-glucoside (C3G) to bovine serum albumin, human serum albumin (HSA), bovine lactoferrin, and ovotransferrin. Fluorescence quenching revealed that HHP reduced C3G-binding affinity to HSA, while having a largely unaffected role for the other proteins. Notably, pretreating HSA at 500 MPa significantly increased its dissociation constant with C3G from 24.7 to 34.3 μM. Spectroscopic techniques suggested that HSA underwent relatively pronounced tertiary structural alterations after HHP treatments. The C3G-HSA binding mechanisms under pressure were further analyzed through molecular dynamics simulation. The localized structural changes in HSA under pressure might weaken its interaction with C3G, particularly polar interactions such as hydrogen bonds and electrostatic forces, consequently leading to a decreased binding affinity. Overall, the importance of pressure-induced structural alterations in proteins influencing their binding with anthocyanins was highlighted, contributing to optimizing HHP processing for anthocyanin-based products.
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Affiliation(s)
- Peiqing Yang
- Beijing Key Laboratory for Food Non-thermal processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Fruit & Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Wenxin Wang
- Beijing Key Laboratory for Food Non-thermal processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Fruit & Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Yichen Hu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China.
| | - Yongtao Wang
- Beijing Key Laboratory for Food Non-thermal processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Fruit & Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Zhenzhen Xu
- Beijing Key Laboratory for Food Non-thermal processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Fruit & Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xiaojun Liao
- Beijing Key Laboratory for Food Non-thermal processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Fruit & Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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15
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Mrázková L, Lubos M, Voldřich J, Kužmová E, Zrubecká D, Gwozdiaková P, Buděšínský M, Asai S, Marek A, Pícha J, Tencerová M, Ferenčáková M, Barrera GA, Kaminský J, Jiráček J, Žáková L. The final walk with preptin. PLoS One 2024; 19:e0309726. [PMID: 39264940 PMCID: PMC11392399 DOI: 10.1371/journal.pone.0309726] [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: 05/09/2024] [Accepted: 08/17/2024] [Indexed: 09/14/2024] Open
Abstract
Preptin, a 34-amino acid peptide derived from pro-IGF2, is believed to influence various physiological processes, including insulin secretion and the regulation of bone metabolism. Despite its recognized involvement, the precise physiological role of preptin remains enigmatic. To address this knowledge gap, we synthesized 16 analogs of preptin, spanning a spectrum from full-length forms to fragments, and conducted comprehensive comparative activity evaluations alongside native human, mouse and rat preptin. Our study aimed to elucidate the physiological role of preptin. Contrary to previous indications of broad biological activity, our thorough analyses across diverse cell types revealed no significant biological activity associated with preptin or its analogs. This suggests that the associations of preptin with various diseases or tissue-specific abundance fluctuations may be influenced by factors beyond preptin itself, such as higher levels of IGF2 or IGF2 proforms present in tissues. In conclusion, our findings challenge the conventional notion of preptin as an isolated biologically active molecule and underscore the complexity of its interactions within biological systems. Rather than acting independently, the observed effects of preptin may arise from experimental conditions, elevated preptin concentrations, or interactions with related molecules such as IGF2.
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Affiliation(s)
- Lucie Mrázková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Department of Cell Biology, Charles University, Prague, Czech Republic
| | - Marta Lubos
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Voldřich
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Erika Kužmová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Denisa Zrubecká
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petra Gwozdiaková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Seiya Asai
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Pícha
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michaela Tencerová
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michaela Ferenčáková
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Jiráček
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lenka Žáková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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16
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Arnittali M, Tegopoulos SN, Kyritsis A, Harmandaris V, Papagiannopoulos A, Rissanou AN. Exploring the Origins of Association of Poly(acrylic acid) Polyelectrolyte with Lysozyme in Aqueous Environment through Molecular Simulations and Experiments. Polymers (Basel) 2024; 16:2565. [PMID: 39339029 PMCID: PMC11434948 DOI: 10.3390/polym16182565] [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: 07/28/2024] [Revised: 09/05/2024] [Accepted: 09/06/2024] [Indexed: 09/30/2024] Open
Abstract
This study provides a detailed picture of how a protein (lysozyme) complexes with a poly(acrylic acid) polyelectrolyte (PAA) in water at the atomic level using a combination of all-atom molecular dynamics simulations and experiments. The effect of PAA and temperature on the protein's structure is explored. The simulations reveal that a lysozyme's structure is relatively stable except from local conformational changes induced by the presence of PAA and temperature increase. The effect of a specific thermal treatment on the complexation process is investigated, revealing both structural and energetic changes. Certain types of secondary structures (i.e., α-helix) are found to undergo a partially irreversible shift upon thermal treatment, which aligns qualitatively with experimental observations. This uncovers the origins of thermally induced aggregation of lysozyme with PAA and points to new PAA/lysozyme bonds that are formed and potentially enhance the stability in the complexes. As the temperature changes, distinct amino acids are found to exhibit the closest proximity to PAA, resulting into different PAA/lysozyme interactions; consequently, a different complexation pathway is followed. Energy calculations reveal the dominant role of electrostatic interactions. This detailed information can be useful for designing new biopolymer/protein materials and understanding protein function under immobilization of polyelectrolytes and upon mild denaturation processes.
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Affiliation(s)
- Maria Arnittali
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology Hellas, IACM/FORTH, GR-71110 Heraklion, Greece; (M.A.); (V.H.)
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Greece
- Computation-Based Science and Technology Research Center, The Cyprus Institute, Nicosia 2121, Cyprus
| | - Sokratis N. Tegopoulos
- School of Applied Mathematical and Physical Sciences, National Technical University of Athens, GR-15772 Athens, Greece; (S.N.T.); (A.K.)
| | - Apostolos Kyritsis
- School of Applied Mathematical and Physical Sciences, National Technical University of Athens, GR-15772 Athens, Greece; (S.N.T.); (A.K.)
| | - Vagelis Harmandaris
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology Hellas, IACM/FORTH, GR-71110 Heraklion, Greece; (M.A.); (V.H.)
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Greece
- Computation-Based Science and Technology Research Center, The Cyprus Institute, Nicosia 2121, Cyprus
| | - Aristeidis Papagiannopoulos
- Theoretical & Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, GR-11635 Athens, Greece
| | - Anastassia N. Rissanou
- Theoretical & Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, GR-11635 Athens, Greece
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17
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Bruque MG, Rodger A, Hoffmann SV, Jones NC, Aucamp J, Dafforn TR, Thomas ORT. Analysis of the Structure of 14 Therapeutic Antibodies Using Circular Dichroism Spectroscopy. Anal Chem 2024. [PMID: 39255385 PMCID: PMC11428090 DOI: 10.1021/acs.analchem.4c01882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Understanding the impact of the manufacturing environment on therapeutic monoclonal antibody (mAb) structures requires new process analytical technology. Here, we describe the creation of a new reference set for the circular dichroism (CD) spectra of mAbs. Data sets of the highest quality were collected by synchrotron radiation CD for 14 different mAbs in both native and acid-stressed states. Deconvolution of far-UV spectra for the mAb cohort identified two current reference sets (SP175 and SMP180) as assigning accurate secondary structures, irrespective of the analysis program employed. Scrutiny of spectra revealed significant variation in the far-UV and especially near-UV CD of the 14 mAbs. Two spectral features were found to be sensitive to changes in solution pH, i.e., the far-UV positive peak at 201-202 nm and the near-UV negative exciton couplet around 230-240 nm. The latter feature offers attractive possibilities for in-line CD-based monitoring of the mAb structure during manufacture.
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Affiliation(s)
- Maria G Bruque
- School of Chemical Engineering, University of Birmingham, Edgbaston B15 2TT, U.K
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Alison Rodger
- Research School of Chemistry, The Australian National University, Canberra 2601, Australia
| | | | - Nykola C Jones
- ISA,Department of Physics and Astronomy, Aarhus University, Aarhus 8000, Denmark
| | | | - Tim R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Owen R T Thomas
- School of Chemical Engineering, University of Birmingham, Edgbaston B15 2TT, U.K
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18
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Lill A, Herbst A, Langhans M, Paech S, Hamacher K, Biesalski M, Meckel T, Schmitz K. Investigating Cellulose Binding of Peptides Derived from Carbohydrate Binding Module 1. Biomacromolecules 2024; 25:5902-5908. [PMID: 39103164 PMCID: PMC11389687 DOI: 10.1021/acs.biomac.4c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Carbohydrate-binding modules (CBM) have emerged as useful tools for a wide range of tasks, including the use as purification tags or for cellulose fiber modification. For this purpose, the CBM needs to be attached to a target protein leading to large constructs. We investigated if short peptides from the carbohydrate binding site of CBMs can bind in a similar way as native, full-length CBMs to nanocrystalline cellulose (NCC) or cotton linter paper. We designed our cellulose-binding peptides to be less hydrophobic and shorter than those previously reported. Starting from the binding site of Cel7A-CBM1, we incorporated the essential amino acids involved in cellulose binding into our peptides. These peptides, as well as control peptides with scrambled sequences or a lack of essential amino acids, bound to cellulose with similar affinity as CBM regardless of their secondary structure, sequence, or hydrophobicity. This unspecific mode of cellulose binding displayed by the presented peptides may be exploited to functionalize cellulose-based biomaterials by means of peptide-conjugates.
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Affiliation(s)
- Annika Lill
- Biological Chemistry, Chemistry Department, Technical University of Darmstadt, Darmstadt 64278, Germany
| | - Alexandra Herbst
- Biological Chemistry, Chemistry Department, Technical University of Darmstadt, Darmstadt 64278, Germany
| | - Markus Langhans
- Macromolecular and Paper Chemistry, Chemistry Department, Technical University of Darmstadt, Darmstadt 64278, Germany
| | - Steffen Paech
- Macromolecular and Paper Chemistry, Chemistry Department, Technical University of Darmstadt, Darmstadt 64278, Germany
| | - Kay Hamacher
- Computational Biology and Simulation, Biology Department, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Markus Biesalski
- Macromolecular and Paper Chemistry, Chemistry Department, Technical University of Darmstadt, Darmstadt 64278, Germany
| | - Tobias Meckel
- Macromolecular and Paper Chemistry, Chemistry Department, Technical University of Darmstadt, Darmstadt 64278, Germany
| | - Katja Schmitz
- Biological Chemistry, Chemistry Department, Technical University of Darmstadt, Darmstadt 64278, Germany
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19
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Woodbury BM, Newcomer RL, Alexandrescu AT, Teschke CM. Templated trimerization of the phage L decoration protein on capsids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.08.611893. [PMID: 39282432 PMCID: PMC11398494 DOI: 10.1101/2024.09.08.611893] [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] [Indexed: 09/19/2024]
Abstract
The 134-residue phage L decoration protein (Dec) forms a capsid-stabilizing homotrimer that has an asymmetric tripod-like structure when bound to phage L capsids. The N-termini of the trimer subunits consist of spatially separated globular OB-fold domains that interact with the virions of phage L or the related phage P22. The C-termini of the trimer form a three-stranded intertwined spike structure that accounts for nearly all the interactions that stabilize the trimer. A Dec mutant with the spike residues 99-134 deleted (Dec 1-98 ) was used to demonstrate that the stable globular OB-fold domain folds independently of the C-terminal residues. However, Dec 1-98 was unable to bind phage P22 virions, indicating the C-terminal spike is essential for stable capsid interaction. The full-length Dec trimer is disassembled into monomers by acidification to pH <2. These monomers retain the folded globular OB-fold domain structure, but the spike is unfolded. Increasing the pH of the Dec monomer solution to pH 6 allowed for slow trimer formation in vitro over the course of days. The infectious cycle of phage L is only around an hour, however, implying Dec trimer assembly in vivo is templated by the phage capsid. The Thermodynamic Hypothesis holds that protein folding is determined by the amino acid sequence. Dec serves as an unusual example of an oligomeric folding step that is kinetically accelerated by a viral capsid template. The capsid templating mechanism could satisfy the flexibility needed for Dec to adapt to the unusual quasi-symmetric binding site on the mature phage L capsid.
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Affiliation(s)
- Brianna M. Woodbury
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd, Storrs, CT, 06269-3125, USA
| | - Rebecca L. Newcomer
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd, Storrs, CT, 06269-3125, USA
| | - Andrei T. Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd, Storrs, CT, 06269-3125, USA
| | - Carolyn M. Teschke
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd, Storrs, CT, 06269-3125, USA
- Department of Chemistry, University of Connecticut, 55 N. Eagleville Rd, Storrs, CT, 06269-3060, USA
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20
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Ito G, Tomita T, Utsunomiya-Tate N. Effects of bound nucleotides on the secondary structure, thermal stability, and phosphorylation of Rab3A. Biochem Biophys Res Commun 2024; 723:150199. [PMID: 38824807 DOI: 10.1016/j.bbrc.2024.150199] [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: 05/07/2024] [Revised: 05/08/2024] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
Rab3A is a member of the Rab GTPase family involved in synaptic vesicle trafficking. Recent evidence has demonstrated that Rab3A is phosphorylated by leucine-rich repeat kinase 2 (LRRK2) that is implicated in both familial and sporadic forms of Parkinson's disease (PD), and an abnormal increase in Rab3A phosphorylation has been proposed as a cause of PD. Despite the potential importance of Rab3A in PD pathogenesis, its structural information is limited and the effects of bound nucleotides on its biophysical and biochemical properties remain unclear. Here, we show that GDP-bound Rab3A is preferentially phosphorylated by LRRK2 compared with GTP-bound Rab3A. The secondary structure of Rab3A, measured by circular dichroism (CD) spectroscopy, revealed that Rab3A is resistant to heat-induced denaturation at pH 7.4 or 9.0 regardless of the nucleotides bound. In contrast, Rab3A underwent heat-induced denaturation at pH 5.0 at a lower temperature in its GDP-bound form than in its GTP-bound form. The unfolding temperature of Rab3A was studied by differential scanning fluorimetry, which showed a significantly higher unfolding temperature in GTP-bound Rab3A than in GDP-bound Rab3A, with the highest at pH 7.4. These results suggest that Rab3A has unusual thermal stability under physiologically relevant conditions and that bound nucleotides influence both thermal stability and phosphorylation by LRRK2.
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Affiliation(s)
- Genta Ito
- Department of Biomolecular Chemistry, Faculty of Pharmaceutical Sciences, Teikyo University, Japan.
| | - Taisuke Tomita
- Social Cooperation Program of Brain and Neurological Disorders, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Japan; Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Japan
| | - Naoko Utsunomiya-Tate
- Department of Biomolecular Chemistry, Faculty of Pharmaceutical Sciences, Teikyo University, Japan
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21
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Satalkar V, Degaga GD, Li W, Pang YT, McShan AC, Gumbart JC, Mitchell JC, Torres MP. Generative β-hairpin design using a residue-based physicochemical property landscape. Biophys J 2024; 123:2790-2806. [PMID: 38297834 PMCID: PMC11393682 DOI: 10.1016/j.bpj.2024.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/20/2023] [Accepted: 01/25/2024] [Indexed: 02/02/2024] Open
Abstract
De novo peptide design is a new frontier that has broad application potential in the biological and biomedical fields. Most existing models for de novo peptide design are largely based on sequence homology that can be restricted based on evolutionarily derived protein sequences and lack the physicochemical context essential in protein folding. Generative machine learning for de novo peptide design is a promising way to synthesize theoretical data that are based on, but unique from, the observable universe. In this study, we created and tested a custom peptide generative adversarial network intended to design peptide sequences that can fold into the β-hairpin secondary structure. This deep neural network model is designed to establish a preliminary foundation of the generative approach based on physicochemical and conformational properties of 20 canonical amino acids, for example, hydrophobicity and residue volume, using extant structure-specific sequence data from the PDB. The beta generative adversarial network model robustly distinguishes secondary structures of β hairpin from α helix and intrinsically disordered peptides with an accuracy of up to 96% and generates artificial β-hairpin peptide sequences with minimum sequence identities around 31% and 50% when compared against the current NCBI PDB and nonredundant databases, respectively. These results highlight the potential of generative models specifically anchored by physicochemical and conformational property features of amino acids to expand the sequence-to-structure landscape of proteins beyond evolutionary limits.
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Affiliation(s)
- Vardhan Satalkar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Gemechis D Degaga
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Wei Li
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Matthew P Torres
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia.
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22
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Lill A, Schweipert M, Nehls T, Wurster E, Lermyte F, Meyer-Almes FJ, Schmitz K. Design and synthesis of peptides as stabilizers of histone deacetylase 4. J Pept Sci 2024; 30:e3603. [PMID: 38623824 DOI: 10.1002/psc.3603] [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: 12/23/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024]
Abstract
Histone deacetylase 4 (HDAC4) contributes to gene repression by complex formation with HDAC3 and the corepressor silencing mediator for retinoid or thyroid hormone receptors (SMRT). We hypothesized that peptides derived from the class IIa specific binding site of SMRT would stabilize a specific conformation of its target protein and modulate its activity. Based on the SMRT-motif 1 (SM1) involved in the interaction of SMRT with HDAC4, we systematically developed cyclic peptides that exhibit Ki values that are 9 to 56 times lower than that of the linear SMRT peptide. The peptide macrocycles stabilize the wildtype of the catalytic domain of HDAC4 (cHDAC4) considerably better than its thermally more stable 'gain-of-function' (GOF) variant, cHDAC4-H976Y. Molecular docking and mutagenesis studies indicated that the cyclic peptides bind in a similar but not identical manner as the linear SMRT peptide to a discontinuous binding site. Ion mobility mass spectrometry showed no major changes in the protein fold upon peptide binding. Consistent with these results, preliminary hydrogen-deuterium exchange mass spectrometry measurements indicated only minor conformational changes. Taken together, the cyclic SMRT peptides most likely stabilize the apo form of cHDAC4.
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Affiliation(s)
- Annika Lill
- Biological Chemistry, Clemens-Schöpf-Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Markus Schweipert
- Physical Biochemistry, Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Darmstadt, Germany
| | - Thomas Nehls
- Conformation-Sensitive Mass Spectrometry Laboratory, Clemens-Schöpf-Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Eva Wurster
- Physical Biochemistry, Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Darmstadt, Germany
| | - Frederik Lermyte
- Conformation-Sensitive Mass Spectrometry Laboratory, Clemens-Schöpf-Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Franz-Josef Meyer-Almes
- Physical Biochemistry, Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Darmstadt, Germany
| | - Katja Schmitz
- Biological Chemistry, Clemens-Schöpf-Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
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23
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Kim SY, Randall JR, Gu R, Nguyen QD, Davies BW. Antibacterial action, proteolytic immunity, and in vivo activity of a Vibrio cholerae microcin. Cell Host Microbe 2024:S1931-3128(24)00319-6. [PMID: 39260372 DOI: 10.1016/j.chom.2024.08.012] [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: 03/18/2024] [Revised: 06/24/2024] [Accepted: 08/16/2024] [Indexed: 09/13/2024]
Abstract
Microcins are small antibacterial proteins that mediate interbacterial competition. Their narrow-spectrum activity provides opportunities to discover microbiome-sparing treatments. However, microcins have been found almost exclusively in Enterobacteriaceae. Their broader existence and potential implications in other pathogens remain unclear. Here, we identify and characterize a microcin active against pathogenic Vibrio cholerae: MvcC. We show that MvcC is reliant on the outer membrane porin OmpT to cross the outer membrane. MvcC then binds the periplasmic protein OppA to reach and disrupt the cytoplasmic membrane. We demonstrate that MvcC's cognate immunity protein is a protease, which precisely cleaves MvcC to neutralize its activity. Importantly, we show that MvcC is active against diverse cholera isolates and in a mouse model of V. cholerae colonization. Our results provide a detailed analysis of a microcin outside of Enterobacteriaceae and its potential to influence V. cholerae infection.
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Affiliation(s)
- Sun-Young Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Justin R Randall
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Richard Gu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Quoc D Nguyen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Bryan W Davies
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, TX, USA.
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24
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Jain S, Zhong Q. Enhancing the functionality of pea proteins by conjugation with propylene glycol alginate via transacylation reaction assisted with ultrasonication. Food Chem 2024; 449:139179. [PMID: 38574527 DOI: 10.1016/j.foodchem.2024.139179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/05/2024] [Accepted: 03/27/2024] [Indexed: 04/06/2024]
Abstract
Pea proteins lack the desirable functional characteristics for food and beverage applications. In this study, transacylation reaction assisted with ultrasonication was used to glycate pea proteins with propylene glycol alginate to enhance their functional properties. The reaction was carried out at pH 11.0 for different pea protein isolate: propylene glycol alginate mass ratios and time durations in a sonic bath at 40 °C. Glycation was confirmed in gel electrophoresis, and ultrasonication enhanced the glycation, with optimal degrees of glycation observed at 45 min reaction time and mass ratios of 2:1 (37.73%) and 1:1 (35.96%). The transacylation reaction increased random coil content of pea proteins by 28% and enhanced their solubility by 2.02 times at pH 7.0, water holding capacity by >50% at pH 7.0, foaming properties, emulsifying properties, and heat stability. This study offers a novel approach that can enhance functionality and applicability of pea proteins.
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Affiliation(s)
- Surangna Jain
- Department of Food Science, University of Tennessee, Knoxville, TN, USA.
| | - Qixin Zhong
- Department of Food Science, University of Tennessee, Knoxville, TN, USA.
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25
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Ikujuni AP, Dhar R, Cordova A, Bowman AM, Noga S, Slusky JSG. Discovery and Characterization of Two Folded Intermediates for Outer Membrane Protein TolC Biogenesis. J Mol Biol 2024; 436:168652. [PMID: 38871177 PMCID: PMC11297670 DOI: 10.1016/j.jmb.2024.168652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 05/12/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
TolC is the outer membrane protein responsible for antibiotic efflux in E. coli. Compared to other outer membrane proteins it has an unusual fold and has been shown to fold independently of commonly used periplasmic chaperones, SurA and Skp. Here we find that the assembly of TolC involves the formation of two folded intermediates using circular dichroism, gel electrophoresis, site-specific disulfide bond formation and radioactive labeling. First the TolC monomer folds, and then TolC assembles into a trimer both in detergent-free buffer and in the presence of detergent micelles. We find that a TolC trimer also forms in the periplasm and is present in the periplasm before it inserts in the outer membrane. The monomeric and trimeric folding intermediates may be used in the future to develop a new approach to antibiotic efflux pump inhibition by targeting the assembly pathway of TolC.
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Affiliation(s)
- Ayotunde Paul Ikujuni
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States
| | - Rik Dhar
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States
| | - Andres Cordova
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States
| | - Alexander M Bowman
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States
| | - Sarah Noga
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States
| | - Joanna S G Slusky
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States; Computational Biology Program, The University of Kansas, 2030 Becker Dr., Lawrence, KS 66045-7534, United States.
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26
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Sundaram R, Gandhi S, Jonak C, Vasudevan D. Characterization of the Arabidopsis thaliana chromatin remodeler DEK3 for its interaction with histones and DNA. Biochimie 2024:S0300-9084(24)00177-9. [PMID: 39097158 DOI: 10.1016/j.biochi.2024.07.018] [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: 06/03/2024] [Revised: 07/04/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Chromatin structure and dynamics regulate all DNA-templated processes, such as transcription, replication, and repair. Chromatin binding factors, chromatin architectural proteins, and nucleosome remodelers modulate chromatin structure and dynamics and, thereby, the various DNA-dependent processes. Arabidopsis thaliana DEK3, a member of the evolutionarily conserved DEK domain-containing chromatin architectural proteins, is an important factor for chromatin structure and function, involved in transcriptional programming to regulate flowering time and abiotic stress tolerance. AtDEK3 contains an uncharacterized N-terminal domain, a middle SAF domain (winged helix-like domain), and a C-terminal DEK domain, but their role in the interaction of AtDEK3 with histones and DNA remained poorly understood. Using biochemical and biophysical analyses, we provide a comprehensive in vitro characterization of the different AtDEK3 domains for their interaction with histone H3/H4 and DNA. AtDEK3 directly interacts with histone H3/H4 tetramers through its N-terminal domain and the C-terminal DEK domain in a 1:1 stoichiometry. Upon interaction with H3/H4, the unstructured N-terminal domain of AtDEK3 undergoes a conformational change and adopts an alpha-helical conformation. In addition, the in-solution envelope structures of the AtDEK3 domains and their complex with H3/H4 have been characterized. The SAF and DEK domains associate with double-stranded and four-way junction DNA. As DEK3 possesses a histone-interacting domain at the N- and the C-terminus and a DNA-binding domain in the middle and at the C-terminus, the protein might play a complex role as a chromatin remodeler.
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Affiliation(s)
- Rajivgandhi Sundaram
- Institute of Life Sciences, Bhubaneswar, 751023, India; Manipal Academy of Higher Education, Manipal, 576104, India
| | - Surajit Gandhi
- Institute of Life Sciences, Bhubaneswar, 751023, India; Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Claudia Jonak
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Bioresources Unit, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria
| | - Dileep Vasudevan
- Institute of Life Sciences, Bhubaneswar, 751023, India; Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, India.
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27
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Ramirez-Velez I, Namjoshi AA, Effiong UM, Peppas NA, Belardi B. Paracellular Delivery of Protein Drugs with Smart EnteroPatho Nanoparticles. ACS NANO 2024. [PMID: 39096293 DOI: 10.1021/acsnano.4c02116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
Abstract
A general platform for the safe and effective oral delivery of biologics would revolutionize the administration of protein-based drugs, improving access for patients and lowering the financial burden on the health-care industry. Because of their dimensions and physiochemical properties, nanomaterials stand as promising vehicles for navigating the complex and challenging environment in the gastrointestinal (GI) tract. Recent developments have led to materials that protect protein drugs from degradation and enable controlled release in the small intestine, the site of absorption for most proteins. Yet, once present in the small intestine, the protein must transit through the secreted mucus and epithelial cells of the intestinal mucosa into systemic circulation, a process that remains a bottleneck for nanomaterial-based delivery. One attractive pathway through the intestinal mucosa is the paracellular route, which avoids cell trafficking and other degradative processes in the interior of cells. Direct flux between cells is regulated by epithelial tight junctions (TJs) that seal the paracellular space and prevent protein flux. Here, we describe a smart nanoparticle system that directly and transiently disrupts TJs for improved protein delivery, an unrealized goal to-date. We take inspiration from enteropathogenic bacteria that adhere to intestinal epithelia and secrete inhibitors that block TJ interactions in the local environment. To mimic these natural mechanisms, we engineer nanoparticles (EnteroPatho NPs) that attach to the epithelial glycocalyx and release TJ modulators in response to the intestinal pH. We show that EnteroPatho NPs lead to TJ disruption and paracellular protein delivery, giving rise to a general platform for oral delivery.
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Affiliation(s)
- Isabela Ramirez-Velez
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Aditya A Namjoshi
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Unyime M Effiong
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Nicholas A Peppas
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Biomaterials, Drug Delivery and Regenerative Medicine, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Surgery and Perioperative Care, Dell Medical School, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Brian Belardi
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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28
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Ding P, Yang K, Wang H, Kuang L, Gao L, Luo J, Tuo X. Exploring the therapeutic potential of rutin through investigating its inhibitory mechanism on lactate dehydrogenase: Multi-spectral methods and computer simulation. Bioorg Chem 2024; 149:107503. [PMID: 38823312 DOI: 10.1016/j.bioorg.2024.107503] [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: 04/14/2024] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/03/2024]
Abstract
Lactate dehydrogenase (LDH), a crucial enzyme in anaerobic glycolysis, plays a pivotal role in the energy metabolism of tumor cells, positioning it as a promising target for tumor treatment. Rutin, a plant-based flavonoid, offers benefits like antioxidant, antiapoptotic, and antineoplastic effects. This study employed diverse experiments to investigate the inhibitory mechanism of rutin on LDH through a binding perspective. The outcomes revealed that rutin underwent spontaneous binding within the coenzyme binding site of LDH, leading to the formation of a stable binary complex driven by hydrophobic forces, with hydrogen bonds also contributing significantly to sustaining the stability of the LDH-rutin complex. The binding constant (Ka) for the LDH-rutin system was 2.692 ± 0.015 × 104 M-1 at 298 K. Furthermore, rutin induced the alterations in the secondary structure conformation of LDH, characterized by a decrease in α-helix and an increase in antiparallel and parallel β-sheet, and β-turn. Rutin augmented the stability of coenzyme binding to LDH, which could potentially hinder the conversion process among coenzymes. Specifically, Arg98 in the active site loop of LDH provided essential binding energy contribution in the binding process. These outcomes might explain the dose-dependent inhibition of the catalytic activity of LDH by rutin. Interestingly, both the food additives ascorbic acid and tetrahydrocurcumin could reduce the binding stability of LDH and rutin. Meanwhile, these food additives did not produce positive synergism or antagonism on the rutin binding to LDH. Overall, this research could offer a unique insight into the therapeutic potential and medicinal worth of rutin.
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Affiliation(s)
- Pei Ding
- School of Pharmacy, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Kaiyu Yang
- School of Pharmacy, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Huixiao Wang
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Lin Kuang
- School of Pharmacy, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Linna Gao
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Jiaqing Luo
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Xun Tuo
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, Jiangxi, China.
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29
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Baber H, Aghajani A, Gallimore BH, Bethel C, Hyatt JG, King EFB, Price HP, Maciej-Hulme ML, Sari S, Winter A. Galactokinase-like protein from Leishmania donovani: Biochemical and structural characterization of a recombinant protein. Biochimie 2024; 223:31-40. [PMID: 38579894 DOI: 10.1016/j.biochi.2024.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/07/2024]
Abstract
Leishmaniasis is a spectrum of conditions caused by infection with the protozoan Leishmania spp. parasites. Leishmaniasis is endemic in 98 countries around the world, and resistance to current anti-leishmanial drugs is rising. Our work has identified and characterised a previously unstudied galactokinase-like protein (GalK) in Leishmania donovani, which catalyses the MgATP-dependent phosphorylation of the C-1 hydroxyl group of d-galactose to galactose-1-phosphate. Here, we report the production of the catalytically active recombinant protein in E. coli, determination of its substrate specificity and kinetic constants, as well as analysis of its molecular envelope using in solution X-ray scattering. Our results reveal kinetic parameters in range with other galactokinases with an average apparent Km value of 76 μM for galactose, Vmax and apparent Kcat values with 4.46376 × 10-9 M/s and 0.021 s-1, respectively. Substantial substrate promiscuity was observed, with galactose being the preferred substrate, followed by mannose, fructose and GalNAc. LdGalK has a highly flexible protein structure suggestive of multiple conformational states in solution, which may be the key to its substrate promiscuity. Our data presents novel insights into the galactose salvaging pathway in Leishmania and positions this protein as a potential target for the development of pharmaceuticals seeking to interfere with parasite substrate metabolism.
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Affiliation(s)
- Hasana Baber
- School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
| | - Arega Aghajani
- School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
| | - B Harold Gallimore
- School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
| | - Cassandra Bethel
- School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
| | - James G Hyatt
- School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
| | - Elizabeth F B King
- School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
| | - Helen P Price
- School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
| | - Marissa L Maciej-Hulme
- School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
| | - Suat Sari
- Hacettepe University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 06100, Ankara, Turkey
| | - Anja Winter
- School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK.
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30
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Sari TP, Dhamane AH, Pawar K, Bajaj M, Badgujar PC, Tarafdar A, Bodana V, Pareek S. High-pressure microfluidisation positively impacts structural properties and improves functional characteristics of almond proteins obtained from almond meal. Food Chem 2024; 448:139084. [PMID: 38569403 DOI: 10.1016/j.foodchem.2024.139084] [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: 10/02/2023] [Revised: 03/07/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Almond protein isolate (API) obtained from almond meal was processed using dynamic high-pressure microfluidisation (0, 40, 80, 120, and 160 MPa pressure; single pass). Microfluidisation caused significant reductions in the particle size and increased absolute zeta potential. SDS-PAGE analysis indicated reduction in band intensity and the complete disappearance of bands beyond 80 MPa. Structural analysis (by circular dichroism, UV-Vis, and intrinsic-fluorescence spectra) of the API revealed disaggregation (up to 80 MPa) and then re-aggregation beyond 80 MPa. Significant increments in protein digestibility (1.16-fold) and the protein digestibility corrected amino acid score (PDCAAS; 1.15-fold) were observed for the API (80 MPa) than control. Furthermore, significant improvements (P < 0.05) in the functional properties were observed, viz., the antioxidant activity, protein solubility, and emulsifying properties. Overall, the results revealed that moderate microfluidisation treatment (80 MPa) is an effective and sustainable technique for enhancing physico-chemical and functional attributes of API, thus potentially enabling its functional food/nutraceuticals application.
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Affiliation(s)
- T P Sari
- Department of Food Science and Technology, National Institute of Food Technology Entrepreneurship and Management, Kundli, Sonipat 131 028, Haryana, India
| | - Amresh H Dhamane
- Department of Food Science and Technology, National Institute of Food Technology Entrepreneurship and Management, Kundli, Sonipat 131 028, Haryana, India
| | - Kamlesh Pawar
- Centre of Excellence in Epigenetics, Department of Life Sciences, Shiv Nadar Institution of Eminence, Delhi NCR 201 314, India
| | - Mudit Bajaj
- Department of Food Science and Technology, National Institute of Food Technology Entrepreneurship and Management, Kundli, Sonipat 131 028, Haryana, India
| | - Prarabdh C Badgujar
- Department of Food Science and Technology, National Institute of Food Technology Entrepreneurship and Management, Kundli, Sonipat 131 028, Haryana, India.
| | - Ayon Tarafdar
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, Uttar Pradesh, India
| | - Vikrant Bodana
- Department of Food Science and Technology, National Institute of Food Technology Entrepreneurship and Management, Kundli, Sonipat 131 028, Haryana, India
| | - Sunil Pareek
- Department of Agriculture and Environmental Sciences, National Institute of Food Technology Entrepreneurship and Management, Kundli, Sonipat 131 028, Haryana, India
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31
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Bhat AR, Patel R. Exploring the binding mechanism and esterase-like activity of human serum albumin with levofloxacin and its choline based conjugates: A biophysical approach. Int J Biol Macromol 2024; 274:133011. [PMID: 38852730 DOI: 10.1016/j.ijbiomac.2024.133011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
Human serum albumin (HSA) effectively binds to compounds having different molecular weight and thus facilitates their distribution in the living organisms. Thus, the binding interactions between a potential antibacterial drug (levofloxacin) and synthesized choline based levofloxacinate conjugates with HSA have been explored. The binding efficacy and mechanism were explored by utilizing different spectroscopic techniques; UV-Visible, steady state fluorescence, time resolved fluorescence and esterase-like activity. The interactions between the ligands and protein were electrostatic as well as hydrophobic in nature. The influence of different ligands having different alkyl chain shows quenching of the fluorescence emission of HSA. The spontaneous binding/quenching of HSA with ligands was static in nature, validated by steady state and time resolved fluorescence spectroscopy. Also, the impact of these ligands on the conformation of the native HSA structure was evaluated by using circular dichroism spectroscopy. In combination to the structural change study, the native protein functionality was observed (in terms of 'esterase-like activity') which has been found to be on lower side due to ligand binding. Further, we have performed the reverse study to check the impact of HSA on the fluorescent fluoroquinolone drug. The current study may prove helpful in elucidating the chemico-biological interactions which may prove useful in the pharmaceuticals, pharmacology, and different biochemistry fields.
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Affiliation(s)
- Ab Raouf Bhat
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Rajan Patel
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
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32
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La Manna S, Cugudda A, Mercurio FA, Leone M, Fortuna S, Di Natale C, Lagreca E, Netti PA, Panzetta V, Marasco D. PEGylated SOCS3 Mimetics Encapsulated into PLGA-NPs as Selective Inhibitors of JAK/STAT Pathway in TNBC Cells. Int J Nanomedicine 2024; 19:7237-7251. [PMID: 39050870 PMCID: PMC11268778 DOI: 10.2147/ijn.s441205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 05/28/2024] [Indexed: 07/27/2024] Open
Abstract
Introduction SOCS3 (suppressor of cytokine signaling 3) protein is a crucial regulator of cytokine-induced inflammation, and its administration has been shown to have therapeutic effects. Recently, we designed a chimeric proteomimetic of SOCS3, mimicking the interfacing regions of a ternary complex composed of SOCS3, JAK2 (Janus kinase 2) and gp130 (glycoprotein 130) proteins. The derived chimeric peptide, KIRCONG chim, demonstrated limited mimetic function owing to its poor water solubility. Methods We report investigations concerning a PEGylated variant of KIRCONG mimetic, named KIRCONG chim, bearing a PEG (Polyethylene glycol) moiety as a linker of noncontiguous SOCS3 regions. Its ability to bind to the catalytic domain of JAK2 was evaluated through MST (MicroScale Thermophoresis), as well as its stability in biological serum assays. The structural features of the cyclic compounds were investigated by CD (circular dichroism), nuclear magnetic resonance (NMR), and molecular dynamic (MD) studies. To evaluate the cellular effects, we employed a PLGA-nanoparticle as a delivery system after characterization using DLS and SEM techniques. Results KIRCONG chim PEG-revealed selective penetration into triple-negative breast cancer (TNBC) MDA-MB-231 cells with respect to the human breast epithelial cell line (MCF10A), acting as a potent inhibitor of STAT3 phosphorylation. Discussion Overall, the data indicated that miniaturization of the SOCS3 protein is a promising therapeutic approach for aberrant dysregulation of JAK/STAT during cancer progression.
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Affiliation(s)
- Sara La Manna
- Department of Pharmacy, CIRPEB: Research Center on Bioactive Peptides- University of Naples Federico II, Naples, 80131, Italy
| | - Alessia Cugudda
- Department of Pharmacy, CIRPEB: Research Center on Bioactive Peptides- University of Naples Federico II, Naples, 80131, Italy
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging (CNR), Naples, 80131, Italy
| | - Sara Fortuna
- Italian Institute of Technology (IIT), Genova, 16152, Italy
| | - Concetta Di Natale
- Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples Federico II, Naples, 80125, Italy
| | - Elena Lagreca
- Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples Federico II, Naples, 80125, Italy
| | - Paolo Antonio Netti
- Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples Federico II, Naples, 80125, Italy
| | - Valeria Panzetta
- Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples Federico II, Naples, 80125, Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB: Research Center on Bioactive Peptides- University of Naples Federico II, Naples, 80131, Italy
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Camargo L, Gering I, Mastalipour M, Kraemer-Schulien V, Bujnicki T, Willbold D, Coronado MA, Eberle RJ. A Snake Venom Peptide and Its Derivatives Prevent Aβ 42 Aggregation and Eliminate Toxic Aβ 42 Aggregates In Vitro. ACS Chem Neurosci 2024; 15:2600-2611. [PMID: 38957957 PMCID: PMC11258689 DOI: 10.1021/acschemneuro.4c00089] [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: 02/07/2024] [Revised: 05/28/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024] Open
Abstract
Over a century has passed since Alois Alzheimer first described Alzheimer's disease (AD), and since then, researchers have made significant strides in understanding its pathology. One key feature of AD is the presence of amyloid-β (Aβ) peptides, which form amyloid plaques, and therefore, it is a primary target for treatment studies. Naturally occurring peptides have garnered attention for their potential pharmacological benefits, particularly in the central nervous system. In this study, nine peptide derivatives of Crotamine, a polypeptide from Crotalus durissus terrificus Rattlesnake venom, as well as one d-enantiomer, were evaluated for their ability to modulate Aβ42 aggregation through various assays such as ThT, QIAD, SPR, and sFIDA. All tested peptides were able to decrease Aβ42 aggregation and eliminate Aβ42 aggregates. Additionally, all of the peptides showed an affinity for Aβ42. This study is the first to describe the potential of crotamine derivative peptides against Aβ42 aggregation and to identify a promising d-peptide that could be used as an effective pharmacological tool against AD in the future.
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Affiliation(s)
- Luana
Cristina Camargo
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
- Faculty
of Mathematics and Natural Sciences, Institute of Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Ian Gering
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
| | - Mohammadamin Mastalipour
- Faculty
of Mathematics and Natural Sciences, Institute of Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Victoria Kraemer-Schulien
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
| | - Tuyen Bujnicki
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
| | - Dieter Willbold
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
- Faculty
of Mathematics and Natural Sciences, Institute of Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Mônika A. Coronado
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
- Faculty
of Mathematics and Natural Sciences, Institute of Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Raphael J. Eberle
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
- Faculty
of Mathematics and Natural Sciences, Institute of Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
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34
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Rahman MM, Zamakhaeva S, Rush JS, Chaton CT, Kenner CW, Hla YM, Tsui HCT, Uversky VN, Winkler ME, Korotkov KV, Korotkova N. O-glycosylation of intrinsically disordered regions regulates homeostasis of membrane proteins in streptococci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592596. [PMID: 38746434 PMCID: PMC11092751 DOI: 10.1101/2024.05.05.592596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Proteins harboring intrinsically disordered regions (IDRs) lacking stable secondary or tertiary structures are abundant across the three domains of life. These regions have not been systematically studied in prokaryotes. Our genome-wide analysis identifies extracytoplasmic serine/threonine-rich IDRs in several biologically important membrane proteins in streptococci. We demonstrate that these IDRs are O-glycosylated with glucose by glycosyltransferases GtrB and PgtC2 in Streptococcus pyogenes and Streptococcus pneumoniae, and with N-acetylgalactosamine by a Pgf-dependent mechanism in Streptococcus mutans. Absence of glycosylation leads to a defect in biofilm formation under ethanol-stressed conditions in S. mutans. We link this phenotype to the C-terminal IDR of a post-translocation secretion chaperone PrsA. O-glycosylation of the IDR protects this region from proteolytic degradation. The IDR length attenuates the efficiency of glycosylation and, consequently, the expression level of PrsA. Taken together, our data reveal that O-glycosylation of IDRs functions as a dynamic switch of protein homeostasis in streptococci.
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Affiliation(s)
- Mohammad M. Rahman
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA
| | - Svetlana Zamakhaeva
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA
| | - Jeffrey S. Rush
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Catherine T. Chaton
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Cameron W. Kenner
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA
| | - Yin Mon Hla
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA
| | | | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Malcolm E. Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Konstantin V. Korotkov
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Natalia Korotkova
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
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35
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Heath SG, Gray SG, Hamzah EM, O'Connor KM, Bozonet SM, Botha AD, de Cordovez P, Magon NJ, Naughton JD, Goldsmith DLW, Schwartfeger AJ, Sunde M, Buell AK, Morris VK, Göbl C. Amyloid formation and depolymerization of tumor suppressor p16 INK4a are regulated by a thiol-dependent redox mechanism. Nat Commun 2024; 15:5535. [PMID: 38951545 PMCID: PMC11217399 DOI: 10.1038/s41467-024-49581-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/12/2024] [Indexed: 07/03/2024] Open
Abstract
The conversion of a soluble protein into polymeric amyloid structures is a process that is poorly understood. Here, we describe a fully redox-regulated amyloid system in which cysteine oxidation of the tumor suppressor protein p16INK4a leads to rapid amyloid formation. We identify a partially-structured disulfide-bonded dimeric intermediate species that subsequently assembles into fibrils. The stable amyloid structures disassemble when the disulfide bond is reduced. p16INK4a is frequently mutated in cancers and is considered highly vulnerable to single-point mutations. We find that multiple cancer-related mutations show increased amyloid formation propensity whereas mutations stabilizing the fold prevent transition into amyloid. The complex transition into amyloids and their structural stability is therefore strictly governed by redox reactions and a single regulatory disulfide bond.
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Affiliation(s)
- Sarah G Heath
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Shelby G Gray
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Emilie M Hamzah
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Karina M O'Connor
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Stephanie M Bozonet
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Alex D Botha
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Pierre de Cordovez
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Nicholas J Magon
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Jennifer D Naughton
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Dylan L W Goldsmith
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Margaret Sunde
- School of Medical Sciences and Sydney Nano, The University of Sydney, Sydney, Australia
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Vanessa K Morris
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
| | - Christoph Göbl
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
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Kronenberg J, Chu S, Olsen A, Britton D, Halvorsen L, Guo S, Lakshmi A, Chen J, Kulapurathazhe MJ, Baker CA, Wadsworth BC, Van Acker CJ, Lehman JG, Otto TC, Renfrew PD, Bonneau R, Montclare JK. Computational Design of Phosphotriesterase Improves V-Agent Degradation Efficiency. ChemistryOpen 2024; 13:e202300263. [PMID: 38426687 PMCID: PMC11230934 DOI: 10.1002/open.202300263] [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: 01/17/2024] [Indexed: 03/02/2024] Open
Abstract
Organophosphates (OPs) are a class of neurotoxic acetylcholinesterase inhibitors including widely used pesticides as well as nerve agents such as VX and VR. Current treatment of these toxins relies on reactivating acetylcholinesterase, which remains ineffective. Enzymatic scavengers are of interest for their ability to degrade OPs systemically before they reach their target. Here we describe a library of computationally designed variants of phosphotriesterase (PTE), an enzyme that is known to break down OPs. The mutations G208D, F104A, K77A, A80V, H254G, and I274N broadly improve catalytic efficiency of VX and VR hydrolysis without impacting the structure of the enzyme. The mutation I106 A improves catalysis of VR and L271E abolishes activity, likely due to disruptions of PTE's structure. This study elucidates the importance of these residues and contributes to the design of enzymatic OP scavengers with improved efficiency.
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Affiliation(s)
- Jacob Kronenberg
- Department of Chemical and Biomolecular EngineeringNew York University Tandon School of EngineeringBrooklynNew YorkUnited States
| | - Stanley Chu
- Department of Chemical and Biomolecular EngineeringNew York University Tandon School of EngineeringBrooklynNew YorkUnited States
| | - Andrew Olsen
- Department of Chemical and Biomolecular EngineeringNew York University Tandon School of EngineeringBrooklynNew YorkUnited States
| | - Dustin Britton
- Department of Chemical and Biomolecular EngineeringNew York University Tandon School of EngineeringBrooklynNew YorkUnited States
| | - Leif Halvorsen
- Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUnited States
- Center for Computational BiologyFlatiron InstituteNew YorkNew YorkUnited States
| | - Shengbo Guo
- Department of Chemical and Biomolecular EngineeringNew York University Tandon School of EngineeringBrooklynNew YorkUnited States
| | - Ashwitha Lakshmi
- Department of Chemical and Biomolecular EngineeringNew York University Tandon School of EngineeringBrooklynNew YorkUnited States
| | - Jason Chen
- Department of Chemical and Biomolecular EngineeringNew York University Tandon School of EngineeringBrooklynNew YorkUnited States
| | - Maria Jinu Kulapurathazhe
- Department of Chemical and Biomolecular EngineeringNew York University Tandon School of EngineeringBrooklynNew YorkUnited States
| | - Cetara A. Baker
- Medical Toxicology Research DivisionU.S. Army Medical Research Institute of Chemical DefenseAberdeen Proving GroundMarylandUnited States
| | - Benjamin C. Wadsworth
- Medical Toxicology Research DivisionU.S. Army Medical Research Institute of Chemical DefenseAberdeen Proving GroundMarylandUnited States
| | - Cynthia J. Van Acker
- Medical Toxicology Research DivisionU.S. Army Medical Research Institute of Chemical DefenseAberdeen Proving GroundMarylandUnited States
| | - John G. Lehman
- Medical Toxicology Research DivisionU.S. Army Medical Research Institute of Chemical DefenseAberdeen Proving GroundMarylandUnited States
| | - Tamara C. Otto
- Medical Toxicology Research DivisionU.S. Army Medical Research Institute of Chemical DefenseAberdeen Proving GroundMarylandUnited States
| | - P. Douglas Renfrew
- Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUnited States
- Center for Computational BiologyFlatiron InstituteNew YorkNew YorkUnited States
| | - Richard Bonneau
- Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUnited States
- Center for Computational BiologyFlatiron InstituteNew YorkNew YorkUnited States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular EngineeringNew York University Tandon School of EngineeringBrooklynNew YorkUnited States
- Department of BiomaterialsNew York University College of DentistryNew YorkNew YorkUnited States
- Department of RadiologyNew York University Grossman School of MedicineNew YorkNew YorkUnited States
- Department of Biomedical EngineeringNew York University Tandon School of EngineeringBrooklynNew YorkUnited States
- Department of ChemistryNew York UniversityNew YorkNew YorkUnited States
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37
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Mariño L, Belén Uceda A, Leal F, Adrover M. Insight into the Effect of Methylglyoxal on the Conformation, Function, and Aggregation Propensity of α-Synuclein. Chemistry 2024; 30:e202400890. [PMID: 38687053 DOI: 10.1002/chem.202400890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024]
Abstract
It is well-known that people suffering from hyperglycemia have a higher propensity to develop Parkinson's disease (PD). One of the most plausible mechanisms linking these two pathologies is the glycation of neuronal proteins and the pathological consequences of it. α-Synuclein, a key component in PD, can be glycated at its fifteen lysine. In fact, the end products of this process have been detected on aggregated α-synuclein isolated from in vivo. However, the consequences of glycation are not entirely clear, which are of crucial importance to understand the mechanism underlying the connection between diabetes and PD. To better clarify this, we have here examined how methylglyoxal (the most important carbonyl compound found in the cytoplasm) affects the conformation and aggregation propensity of α-synuclein, as well as its ability to cluster and fuse synaptic-like vesicles. The obtained data prove that methylglyoxal induces the Lys-Lys crosslinking through the formation of MOLD. However, this does not have a remarkable effect on the averaged conformational ensemble of α-synuclein, although it completely depletes its native propensity to form soluble oligomers and insoluble amyloid fibrils. Moreover, methylglyoxal has a disrupting effect on the ability of α-synuclein to bind, cluster and fusion synaptic-like vesicles.
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Affiliation(s)
- Laura Mariño
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra, Valldemossa km 7.5, E-07122, Palma de Mallorca, Spain
| | - Ana Belén Uceda
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra, Valldemossa km 7.5, E-07122, Palma de Mallorca, Spain
| | - Francisco Leal
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra, Valldemossa km 7.5, E-07122, Palma de Mallorca, Spain
| | - Miquel Adrover
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra, Valldemossa km 7.5, E-07122, Palma de Mallorca, Spain
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38
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Cunha RS, Cruz PF, Costa T, Almeida ZL, de Lima MEF, Serpa C, Chaves OA. Revisiting and Updating the Interaction between Human Serum Albumin and the Non-Steroidal Anti-Inflammatory Drugs Ketoprofen and Ketorolac. Molecules 2024; 29:3001. [PMID: 38998953 PMCID: PMC11243439 DOI: 10.3390/molecules29133001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/14/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Ketoprofen (KTF) and ketorolac (KTL) are among the most primarily used non-steroidal anti-inflammatory drugs (NSAIDs) in humans to alleviate moderate pain and to treat inflammation. Their binding affinity with albumin (the main globular protein responsible for the biodistribution of drugs in the bloodstream) was previously determined by spectroscopy without considering some conventional pitfalls. Thus, the present work updates the biophysical characterization of the interactions of HSA:KTF and HSA:KTL by 1H saturation-transfer difference nuclear magnetic resonance (1H STD-NMR), ultraviolet (UV) absorption, circular dichroism (CD), steady-state, and time-resolved fluorescence spectroscopies combined with in silico calculations. The binding of HSA:NSAIDs is spontaneous, endothermic, and entropically driven, leading to a conformational rearrangement of HSA with a slight decrease in the α-helix content (7.1% to 7.6%). The predominance of the static quenching mechanism (ground-state association) was identified. Thus, both Stern-Volmer quenching constant (KSV) and binding constant (Kb) values enabled the determination of the binding affinity. In this sense, the KSV and Kb values were found in the order of 104 M-1 at human body temperature, indicating moderate binding affinity with differences in the range of 0.7- and 3.4-fold between KTF and KTL, which agree with the previously reported experimental pharmacokinetic profile. According to 1H STD-NMR data combined with in silico calculations, the aromatic groups in relation to the aliphatic moiety of the drugs interact preferentially with HSA into subdomain IIIA (site II) and are stabilized by interactions via hydrogen bonding and hydrophobic forces. In general, the data obtained in this study have been revised and updated in comparison to those previously reported by other authors who did not account for inner filter corrections, spectral backgrounds, or the identification of the primary mathematical approach for determining the binding affinity of HSA:KTF and HSA:KTL.
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Affiliation(s)
- Rita S. Cunha
- Department of Chemistry, Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Pedro F. Cruz
- Department of Chemistry, Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Telma Costa
- Department of Chemistry, Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Zaida L. Almeida
- Department of Chemistry, Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Marco Edilson Freire de Lima
- Departament of Organic Chemistry, Institute of Chemistry, Federal Rural University of Rio de Janeiro, Seropédica 23890-000, RJ, Brazil
| | - Carlos Serpa
- Department of Chemistry, Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Otávio A. Chaves
- Department of Chemistry, Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
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Kronenberg J, Jung Y, Chen J, Kulapurathazhe MJ, Britton D, Kim S, Chen X, Tu RS, Montclare JK. Structure-Dependent Water Responsiveness of Protein Block Copolymers. ACS APPLIED BIO MATERIALS 2024; 7:3714-3720. [PMID: 38748757 PMCID: PMC11190970 DOI: 10.1021/acsabm.4c00045] [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: 01/10/2024] [Revised: 04/28/2024] [Accepted: 05/07/2024] [Indexed: 06/18/2024]
Abstract
Biological water-responsive (WR) materials are abundant in nature, and they are used as mechanical actuators for seed dispersal by many plants such as wheat awns and pinecones. WR biomaterials are of interest for applications as high-energy actuators, which can be useful in soft robotics or for capturing energy from natural water evaporation. Recent work on WR silk proteins has shown that β-sheet nanocrystalline domains with high stiffness correlate with the high WR actuation energy density, but the fundamental mechanisms to drive water responsiveness in proteins remain poorly understood. Here, we design, synthesize, and study protein block copolymers consisting of two α-helical domains derived from cartilage oligomeric matrix protein coiled-coil (C) flanking an elastin-like peptide domain (E), namely, CEC. We use these protein materials to create WR actuators with energy densities that outperform mammalian muscle. To elucidate the effect of structure on WR actuation, CEC was compared to a variant, CECL44A, in which a point mutation disrupts the α-helical structure of the C domain. Surprisingly, CECL44A outperformed CEC, showing higher energy density and less susceptibility to degradation after repeated cycling. We show that CECL44A exhibits a higher degree of intermolecular interactions and is stiffer than CEC at high relative humidity (RH), allowing for less energy dissipation during water responsiveness. These results suggest that strong intermolecular interactions and the resulting, relatively steady protein structure are important for water responsiveness.
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Affiliation(s)
- Jacob Kronenberg
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Yeojin Jung
- Advanced
Science Research Center (ASRC) at the Graduate Center, City University of New York, New York, New York 10031, United States
- Department
of Chemical Engineering, City College of
New York, New York, New York 10031, United States
| | - Jason Chen
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Maria Jinu Kulapurathazhe
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Dustin Britton
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Seungri Kim
- Advanced
Science Research Center (ASRC) at the Graduate Center, City University of New York, New York, New York 10031, United States
- Department
of Chemical Engineering, City College of
New York, New York, New York 10031, United States
| | - Xi Chen
- Advanced
Science Research Center (ASRC) at the Graduate Center, City University of New York, New York, New York 10031, United States
- Department
of Chemical Engineering, City College of
New York, New York, New York 10031, United States
- PhD
Programs in Chemistry and Physics at the Graduate Center, City University of New York, New York, New York 10016, United States
| | - Raymond S. Tu
- Department
of Chemical Engineering, City College of
New York, New York, New York 10031, United States
| | - Jin Kim Montclare
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Department
of Chemistry, New York University, New York, New York 10031, United States
- Department
of Biomaterials, New York University College
of Dentistry, New York, New York 10010, United States
- Department
of Radiology, New York University Grossman
School of Medicine, New York, New York 10016, United States
- Department
of Biomedical Engineering, New York University
Tandon School of Engineering, Brooklyn, New York 11203, United States
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Fry HC, Liu Y, Taylor SK. Design and Function of α-Helix-Rich, Heme-Binding Peptide Materials. Biomacromolecules 2024; 25:3398-3408. [PMID: 38752597 DOI: 10.1021/acs.biomac.4c00049] [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: 06/11/2024]
Abstract
Peptide materials often employ short peptides that self-assemble into unique nanoscale architectures and have been employed across many fields relevant to medicine and energy. A majority of peptide materials are high in β-sheet, secondary structure content, including heme-binding peptide materials. To broaden the structural diversity of heme-binding peptide materials, a small series of peptides were synthesized to explore the design criteria required for (1) folding into an α-helix structure, (2) assembling into a nanoscale material, (3) binding heme, and (4) demonstrating functions similar to that of heme proteins. One peptide was identified to meet all four criteria, including the heme protein function of CO binding and its microsecond-to-millisecond recombination rates, as measured by transient absorption spectroscopy. Implications of new design criteria and peptide material function through heme incorporation are discussed.
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Affiliation(s)
- H Christopher Fry
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, Illinois 60439, United States
| | - Yuzi Liu
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, Illinois 60439, United States
| | - Sunny K Taylor
- Pritzker School for Molecular Engineering, University of Chicago, 5640 S. Ellis Ave., Chicago, Illinois 60637, United States
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Lewis BR, Uddin MR, Kuo KM, Shah LMN, Harris NJ, Booth PJ, Hammerschmid D, Gumbart JC, Zgurskaya HI, Reading E. Mg 2+-dependent mechanism of environmental versatility in a multidrug efflux pump. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.597921. [PMID: 38915626 PMCID: PMC11195059 DOI: 10.1101/2024.06.10.597921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Tripartite resistance nodulation and cell division multidrug efflux pumps span the periplasm and are a major driver of multidrug resistance among Gram-negative bacteria. The periplasm provides a distinct environment between the inner and outer membranes of Gram-negative bacteria. Cations, such as Mg2+, become concentrated within the periplasm and, in contrast to the cytoplasm, its pH is sensitive to conditions outside the cell. Here, we reveal an interplay between Mg2+ and pH in modulating the dynamics of the periplasmic adaptor protein, AcrA, and its function within the prototypical AcrAB-TolC multidrug efflux pump from Escherichia coli. In the absence of Mg2+, AcrA becomes increasingly plastic within acidic conditions, but when Mg2+ is bound this is ameliorated, resulting in domain specific organisation in neutral to weakly acidic regimes. We establish a unique histidine residue directs these structural dynamics and is essential for sustaining pump efflux activity across acidic, neutral, and alkaline conditions. Overall, we propose Mg2+ conserves the structural mobility of AcrA to ensure optimal AcrAB-TolC function within rapid changing environments commonly faced by the periplasm during bacterial infection and colonization. This work highlights that Mg2+ is an important mechanistic component in this pump class and possibly across other periplasmic lipoproteins.
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Affiliation(s)
- Benjamin Russell Lewis
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
| | - Muhammad R. Uddin
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, USA
| | - Katie M. Kuo
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, USA
| | - Laila M. N. Shah
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
| | - Nicola J. Harris
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
| | - Paula J. Booth
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
| | - Dietmar Hammerschmid
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332, USA
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, USA
| | - Eamonn Reading
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
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Shi L, Lu J, Xia X, Liu X, Li H, Li X, Zhu J, Li X, Sun H, Yang X. Clinically used drug arsenic trioxide targets XIAP and overcomes apoptosis resistance in an organoid-based preclinical cancer model. Chem Sci 2024; 15:8311-8322. [PMID: 38846391 PMCID: PMC11151819 DOI: 10.1039/d4sc01294a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/29/2024] [Indexed: 06/09/2024] Open
Abstract
Drug resistance in tumor cells remains a persistent clinical challenge in the pursuit of effective anticancer therapy. XIAP, a member of the inhibitor of apoptosis protein (IAP) family, suppresses apoptosis via its Baculovirus IAP Repeat (BIR) domains and is responsible for drug resistance in various human cancers. Therefore, XIAP has attracted significant attention as a potential therapeutic target. However, no XIAP inhibitor is available for clinical use to date. In this study, we surprisingly observed that arsenic trioxide (ATO) induced a rapid depletion of XIAP in different cancer cells. Mechanistic studies revealed that arsenic attacked the cysteine residues of BIR domains and directly bound to XIAP, resulting in the release of zinc ions from this protein. Arsenic-XIAP binding suppressed the normal anti-apoptosis functions of BIR domains, and led to the ubiquitination-dependent degradation of XIAP. Importantly, we further demonstrate that arsenic sensitized a variety of apoptosis-resistant cancer cells, including patient-derived colon cancer organoids, to the chemotherapy drug using cisplatin as a showcase. These findings suggest that targeting XIAP with ATO offers an attractive strategy for combating apoptosis-resistant cancers in clinical practice.
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Affiliation(s)
- Liwa Shi
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai 519000 China
| | - Jing Lu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai 519000 China
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
| | - Xin Xia
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai 519000 China
| | - Xue Liu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai 519000 China
| | - Hongyan Li
- Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Hong Kong SAR China
| | - Xinghua Li
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
| | - Jun Zhu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai 519000 China
| | - Xiaofeng Li
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
| | - Hongzhe Sun
- Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Hong Kong SAR China
| | - Xinming Yang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai 519000 China
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43
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Sahoo BR, Subramanian V, Bardwell JCA. Backbone 1H, 13C, and 15N chemical shift assignments for human SERF2. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:51-57. [PMID: 38466543 DOI: 10.1007/s12104-024-10167-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/28/2024] [Indexed: 03/13/2024]
Abstract
Human small EDRK-rich factor protein SERF2 is a cellular driver of protein amyloid formation, a process that has been linked to neurodegenerative diseases including Alzheimer's and Parkinson's disease. SERF2 is a 59 amino acid protein, highly charged, and well conserved whose structure and physiological function is unclear. SERF family proteins including human SERF2 have shown a tendency to form fuzzy complexes with misfolded proteins such as α-Synuclein which has been linked to Parkinson's disease. SERF family proteins have been recently identified to bind nucleic acids, but the binding mechanism(s) remain enigmatic. Here, using multidimensional solution NMR, we report the 1H, 15N, and 13C chemical shift assignments (~ 86% of backbone resonance assignments) for human SERF2. TALOS-N predicted secondary structure of SERF2 showed three very short helices (3-4 residues long) in the N-terminal region of the protein and a long helix in the C-terminal region spanning residues 37-46 which is consistent with the helical content indicated by circular dichroism spectroscopy. Paramagnetic relaxation enhancement NMR analysis revealed that a short C-terminal region E53-K55 is in the proximity of the N-terminus. Having the backbone assignment of SERF2 allowed us to probe its interaction with α-Synuclein and to identify the residues in SERF2 binding interfaces that likely promote α-Synuclein aggregation.
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Affiliation(s)
- Bikash R Sahoo
- Howard Hughes Medical Institute, Chevy Chase, MD-20815, USA.
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI-48109, USA.
| | | | - James C A Bardwell
- Howard Hughes Medical Institute, Chevy Chase, MD-20815, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI-48109, USA
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Javid M, Shahverdi AR, Ghasemi A, Moosavi-Movahedi AA, Ebrahim-Habibi A, Sepehrizadeh Z. Decoding the Structure-Function Relationship of the Muramidase Domain in E. coli O157.H7 Bacteriophage Endolysin: A Potential Building Block for Chimeric Enzybiotics. Protein J 2024; 43:522-543. [PMID: 38662183 DOI: 10.1007/s10930-024-10195-z] [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] [Accepted: 03/23/2024] [Indexed: 04/26/2024]
Abstract
Bacteriophage endolysins are potential alternatives to conventional antibiotics for treating multidrug-resistant gram-negative bacterial infections. However, their structure-function relationships are poorly understood, hindering their optimization and application. In this study, we focused on the individual functionality of the C-terminal muramidase domain of Gp127, a modular endolysin from E. coli O157:H7 bacteriophage PhaxI. This domain is responsible for the enzymatic activity, whereas the N-terminal domain binds to the bacterial cell wall. Through protein modeling, docking experiments, and molecular dynamics simulations, we investigated the activity, stability, and interactions of the isolated C-terminal domain with its ligand. We also assessed its expression, solubility, toxicity, and lytic activity using the experimental data. Our results revealed that the C-terminal domain exhibits high activity and toxicity when tested individually, and its expression is regulated in different hosts to prevent self-destruction. Furthermore, we validated the muralytic activity of the purified refolded protein by zymography and standardized assays. These findings challenge the need for the N-terminal binding domain to arrange the active site and adjust the gap between crucial residues for peptidoglycan cleavage. Our study shed light on the three-dimensional structure and functionality of muramidase endolysins, thereby enriching the existing knowledge pool and laying a foundation for accurate in silico modeling and the informed design of next-generation enzybiotic treatments.
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Affiliation(s)
- Mehri Javid
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Reza Shahverdi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Atiyeh Ghasemi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Azadeh Ebrahim-Habibi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Zargham Sepehrizadeh
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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45
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Pelaez-Aguilar AE, Mata-Salgado F, Morales-Ortiz A, Millán-Pacheco C, Olvera-Carranza C, Salgado-Delgado J, Pastor N, Rivillas-Acevedo L. Cu(II) binding to the λ6aJL2-R24G antibody light chain protein associated with light chain amyloidosis disease: The role of histidines. Int J Biol Macromol 2024; 270:132393. [PMID: 38761898 DOI: 10.1016/j.ijbiomac.2024.132393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/29/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
Light chain amyloidosis is a conformational disease caused by the abnormal proliferation and deposition of antibody light chains as amyloid fibers in organs and tissues. The effect of Cu(II) binding to the model recombinant protein 6aJL2-R24G was previously characterized in our group, and we found an acceleration of the aggregation kinetics of the protein. In this study, in order to confirm the Cu(II) binding sites, histidine variants of 6aJL2-R24G were prepared and the effects of their interaction with Cu(II) were analyzed by circular dichroism, fluorescence spectroscopy, isothermal calorimetry titrations, and molecular dynamics simulations. Confirming our earlier work, we found that His8 and His99 are the highest affinity Cu(II) binding sites, and that Cu(II) binding to both sites is a cooperative event.
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Affiliation(s)
- Angel E Pelaez-Aguilar
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Fernanda Mata-Salgado
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
| | - Alan Morales-Ortiz
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
| | - César Millán-Pacheco
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
| | - Clarita Olvera-Carranza
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Jesus Salgado-Delgado
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico.
| | - Lina Rivillas-Acevedo
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico.
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46
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Yang X, Porcel E, Marichal L, Gonzalez-Vargas C, Khitous A, Salado-Leza D, Li X, Renault JP, Pin S, Remita H, Wien F, Lacombe S. Human Serum Albumin in the Presence of Small Platinum Nanoparticles. J Pharm Sci 2024; 113:1645-1652. [PMID: 38336007 DOI: 10.1016/j.xphs.2024.02.002] [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] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
Noble metal materials, especially platinum nanoparticles (Pt NPs), have immense potential in nanomedicine as therapeutic agents on account of their high electron density and their high surface area. Intravenous injection is proposed as the best mode to deliver the product to patients. However, our understanding of the reaction of nanoparticles with blood components, especially proteins, is far behind the explosive development of these agents. Using synchrotron radiation circular dichroism (SRCD), we investigated the structural and stability changes of human serum albumin (HSA) upon interaction with PEG-OH coated Pt NPs at nanomolar concentrations, conditions potentially encountered for intravenous injection. There is no strong complexation found between HSA and Pt NPs. However, for the highest molar ratio of NP:HSA of 1:1, an increase of 18 °C in the thermal unfolding of HSA was observed, which is attributed to increased thermal stability of HSA generated by preferential hydration. This work proposes a new and fast method to probe the potential toxicity of nanoparticles intended for clinical use with intravenous injection.
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Affiliation(s)
- Xiaomin Yang
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | - Erika Porcel
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | - Laurent Marichal
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Cesar Gonzalez-Vargas
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | - Amine Khitous
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France; Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Daniela Salado-Leza
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France; CONAHCYT, Institute of Physics, Autonomous University of San Luis Potosi, 78295 San Luis Potosi, Mexico
| | - Xue Li
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | | | - Serge Pin
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Hynd Remita
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Frank Wien
- Synchrotron Soleil, 91190 Saint-Aubin, France.
| | - Sandrine Lacombe
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France.
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Beech JL, Maurya AK, Rodrigues da Silva R, Akpoto E, Asundi A, Fecko JA, Yennawar NH, Sarangi R, Tassone C, Weiss TM, DuBois JL. Understanding the stability of a plastic-degrading Rieske iron oxidoreductase system. Protein Sci 2024; 33:e4997. [PMID: 38723110 PMCID: PMC11081424 DOI: 10.1002/pro.4997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/01/2024] [Accepted: 04/06/2024] [Indexed: 05/13/2024]
Abstract
Rieske oxygenases (ROs) are a diverse metalloenzyme class with growing potential in bioconversion and synthetic applications. We postulated that ROs are nonetheless underutilized because they are unstable. Terephthalate dioxygenase (TPADO PDB ID 7Q05) is a structurally characterized heterohexameric α3β3 RO that, with its cognate reductase (TPARED), catalyzes the first intracellular step of bacterial polyethylene terephthalate plastic bioconversion. Here, we showed that the heterologously expressed TPADO/TPARED system exhibits only ~300 total turnovers at its optimal pH and temperature. We investigated the thermal stability of the system and the unfolding pathway of TPADO through a combination of biochemical and biophysical approaches. The system's activity is thermally limited by a melting temperature (Tm) of 39.9°C for the monomeric TPARED, while the independent Tm of TPADO is 50.8°C. Differential scanning calorimetry revealed a two-step thermal decomposition pathway for TPADO with Tm values of 47.6 and 58.0°C (ΔH = 210 and 509 kcal mol-1, respectively) for each step. Temperature-dependent small-angle x-ray scattering and dynamic light scattering both detected heat-induced dissociation of TPADO subunits at 53.8°C, followed by higher-temperature loss of tertiary structure that coincided with protein aggregation. The computed enthalpies of dissociation for the monomer interfaces were most congruent with a decomposition pathway initiated by β-β interface dissociation, a pattern predicted to be widespread in ROs. As a strategy for enhancing TPADO stability, we propose prioritizing the re-engineering of the β subunit interfaces, with subsequent targeted improvements of the subunits.
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Affiliation(s)
- Jessica Lusty Beech
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMontanaUSA
| | - Anjani K. Maurya
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | | | - Emmanuel Akpoto
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMontanaUSA
| | - Arun Asundi
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Julia Ann Fecko
- The Huck Institutes of the Life SciencesThe Pennsylvania State University, University ParkState CollegePennsylvaniaUSA
| | - Neela H. Yennawar
- The Huck Institutes of the Life SciencesThe Pennsylvania State University, University ParkState CollegePennsylvaniaUSA
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Christopher Tassone
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Jennifer L. DuBois
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMontanaUSA
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48
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Hsieh KC, Ting Y. Atmospheric cold plasma reduces Ara h 1 antigenicity in roasted peanuts by altering the protein structure and amino acid profile. Food Chem 2024; 441:138115. [PMID: 38183716 DOI: 10.1016/j.foodchem.2023.138115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 10/23/2023] [Accepted: 11/27/2023] [Indexed: 01/08/2024]
Abstract
Ara h 1 is the major allergen in peanuts. To enhance the unique flavor, peanuts are usually roasted at high temperatures. However, roasting can increase the allergenic potential, owing to glycation of allergens. Atmospheric cold plasma (ACP) is a non-thermal processing technology that generates reactive species, enabling protein structural changes. Herein, glucose was also added to the ACP-treated peanut protein before roasting. The content and antigenicity of the advanced glycation end products were measured. The antigenicity was evaluated by ELISA and in vitro digestion assays. The amino acid profile and secondary and tertiary protein structures were also assessed. The antigenicity of Ara h 1 decreased by 91 % and 76 % after 30 min of air and nitrogen plasma treatment, respectively. The glycation degree and thermal and digestive stabilities were also reduced. These results correlated with the structural changes, denaturation, and aggregation. Therefore, cold plasma may reduce the allergic effects of peanuts.
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Affiliation(s)
- Kuan-Chen Hsieh
- Institute of Food Science and Technology, National Taiwan University, No.1, Sec. 4, Roosevelt Rd, Taipei, Taiwan
| | - Yuwen Ting
- Institute of Food Science and Technology, National Taiwan University, No.1, Sec. 4, Roosevelt Rd, Taipei, Taiwan.
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49
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Lenda R, Zhukova L, Ożyhar A, Bystranowska D. Deciphering the dual nature of nesfatin-1: a tale of zinc ion's Janus-faced influence. Cell Commun Signal 2024; 22:298. [PMID: 38812013 PMCID: PMC11134965 DOI: 10.1186/s12964-024-01675-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: 02/27/2024] [Accepted: 05/21/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND Nucleobindin-2 (Nucb2) and nesfatin-1 (N1) are widely distributed hormones that regulate numerous physiological processes, from energy homeostasis to carcinogenesis. However, the role of nesfatin-2 (N2), the second product of Nucb2 proteolytic processing, remains elusive. To elucidate the relationship between the structure and function of nesfatins, we investigated the properties of chicken and human homologs of N1, as well as a fragment of Nucb2 consisting of N1 and N2 conjoined in a head-to-tail manner (N1/2). RESULTS Our findings indicate that Zn(II) sensing, in the case of N1, is conserved between chicken and human species. However, the data presented here reveal significant differences in the molecular features of the analyzed peptides, particularly in the presence of Zn(II). We demonstrated that Zn(II) has a Janus effect on the M30 region (a crucial anorexigenic core) of N1 and N1/2. In N1 homologs, Zn(II) binding results in the concealment of the M30 region driven by a disorder-to-order transition and adoption of the amyloid fold. In contrast, in N1/2 molecules, Zn(II) binding causes the exposure of the M30 region and its destabilization, resulting in strong exposure of the region recognized by prohormone convertases within the N1/2 molecule. CONCLUSIONS In conclusion, we found that Zn(II) binding is conserved between chicken and human N1. However, despite the high homology of chicken and human N1, their interaction modes with Zn(II) appear to differ. Furthermore, Zn(II) binding might be essential for regulating the function of nesfatins by spatiotemporally hindering the N1 anorexigenic M30 core and concomitantly facilitating N1 release from Nucb2.
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Affiliation(s)
- Rafał Lenda
- Department of Biochemistry, Molecular Biology and Biotechnology, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław, 50-370, Poland
| | - Lilia Zhukova
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław, 50-370, Poland
| | - Dominika Bystranowska
- Department of Biochemistry, Molecular Biology and Biotechnology, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław, 50-370, Poland.
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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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