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Bello-Madruga R, Torrent Burgas M. The limits of prediction: Why intrinsically disordered regions challenge our understanding of antimicrobial peptides. Comput Struct Biotechnol J 2024; 23:972-981. [PMID: 38404711 PMCID: PMC10884422 DOI: 10.1016/j.csbj.2024.02.008] [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: 11/28/2023] [Revised: 02/10/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
Antimicrobial peptides (AMPs) are molecules found in most organisms, playing a vital role in innate immune defense against pathogens. Their mechanism of action involves the disruption of bacterial cell membranes, causing leakage of cellular contents and ultimately leading to cell death. While AMPs typically lack a defined structure in solution, they often assume a defined conformation when interacting with bacterial membranes. Given this structural flexibility, we investigated whether intrinsically disordered regions (IDRs) with AMP-like properties could exhibit antimicrobial activity. We tested 14 peptides from different IDRs predicted to have antimicrobial activity and found that nearly all of them did not display the anticipated effects. These peptides failed to adopt a defined secondary structure and had compromised membrane interactions, resulting in a lack of antimicrobial activity. We hypothesize that evolutionary constraints may prevent IDRs from folding, even in membrane-like environments, limiting their antimicrobial potential. Moreover, our research reveals that current antimicrobial predictors fail to accurately capture the structural features of peptides when dealing with intrinsically unstructured sequences. Hence, the results presented here may have far-reaching implications for designing and improving antimicrobial strategies and therapies against infectious diseases.
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Affiliation(s)
- Roberto Bello-Madruga
- The Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Marc Torrent Burgas
- The Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
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2
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Riegerová P, Horváth M, Šebesta F, Sýkora J, Šulc M, Vlček A. Single-step purification and characterization of Pseudomonas aeruginosa azurin. Protein Expr Purif 2024; 224:106566. [PMID: 39128594 DOI: 10.1016/j.pep.2024.106566] [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: 06/13/2024] [Revised: 07/30/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
Azurin is a small periplasmic blue copper protein found in bacterial strains such as Pseudomonas and Alcaligenes where it facilitates denitrification. Azurin is extensively studied for its ability to mediate electron-transfer processes, but it has also sparked interest of the pharmaceutical community as a potential antimicrobial or anticancer agent. Here we offer a novel approach for expression and single-step purification of azurin in Escherichia coli with high yields and optimal metalation. A fusion tag strategy using an N-terminal GST tag was employed to obtain pure protein without requiring any additional purification steps. After the on-column cleavage by HRV 3C Protease, azurin is collected and additionally incubated with copper sulphate to ensure sufficient metalation. UV-VIS absorption, mass spectroscopy, and circular dichroism analysis all validated the effective production of azurin, appropriate protein folding and the development of an active site with an associated cofactor. MD simulations verified that incorporation of the N-terminal GPLGS segment does not affect azurin structure. In addition, the biological activity of azurin was tested in HeLa cells.
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Affiliation(s)
- Petra Riegerová
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23, Prague, Czech Republic.
| | - Matej Horváth
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23, Prague, Czech Republic; Department of Cell Biology, Charles University, BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Filip Šebesta
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23, Prague, Czech Republic; Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic
| | - Jan Sýkora
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23, Prague, Czech Republic
| | - Miroslav Šulc
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 128 43, Prague 2, Czech Republic
| | - Antonín Vlček
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23, Prague, Czech Republic; Queen Mary University of London, Department of Chemistry, Mile End Road, London, E1 4NS, United Kingdom.
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3
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Hjalte J, Diehl C, Leung AE, Poon JF, Porcar L, Dalgliesh R, Sjögren H, Wahlgren M, Sanchez-Fernandez A. Modulating protein unfolding and refolding via the synergistic association of an anionic and a nonionic surfactant. J Colloid Interface Sci 2024; 672:244-255. [PMID: 38838632 DOI: 10.1016/j.jcis.2024.05.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/03/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024]
Abstract
HYPOTHESIS Nonionic surfactants can counter the deleterious effect that anionic surfactants have on proteins, where the folded states are retrieved from a previously unfolded state. However, further studies are required to refine our understanding of the underlying mechanism of the refolding process. While interactions between nonionic surfactants and tightly folded proteins are not anticipated, we hypothesized that intermediate stages of surfactant-induced unfolding could define new interaction mechanisms by which nonionic surfactants can further alter protein conformation. EXPERIMENTS In this work, the behavior of three model proteins (human growth hormone, bovine serum albumin, and β-lactoglobulin) was investigated in the presence of the anionic surfactant sodium dodecylsulfate, the nonionic surfactant β-dodecylmaltoside, and mixtures of both surfactants. The transitions occurring to the proteins were determined using intrinsic fluorescence spectroscopy and far-UV circular dichroism. Based on these results, we developed a detailed interaction model for human growth hormone. Using nuclear magnetic resonance and contrast-variation small-angle neutron scattering, we studied the amino acid environment and the conformational state of the protein. FINDINGS The results demonstrate the key role of surfactant cooperation in defining the conformational state of the proteins, which can shift away or toward the folded state depending on the nonionic-to-ionic surfactant ratio. Dodecylmaltoside, initially a non-interacting surfactant, can unexpectedly associate with sodium dodecylsulfate-unfolded proteins to further impact their conformation at low nonionic-to-ionic surfactant ratio. When this ratio increases, the protein begins to retrieve the folded state. However, the native conformation cannot be fully recovered due to remnant surfactant molecules still adsorbed to the protein. This study demonstrates that the conformational landscape of the protein depends on a delicate interplay between the surfactants, ultimately controlled by the ratio between them, resulting in unpredictable changes in the protein conformation.
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Affiliation(s)
- Johanna Hjalte
- Food Technology, Engineering and Nutrition, Lund University, Box 124, 221 00 Lund, Sweden
| | - Carl Diehl
- SARomics Biostructures AB, Medicon Village, Scheelevägen 2, 223 81 Lund, Sweden
| | - Anna E Leung
- European Spallation Source, Box 176, 221 00 Lund, Sweden
| | - Jia-Fei Poon
- Food Technology, Engineering and Nutrition, Lund University, Box 124, 221 00 Lund, Sweden; European Spallation Source, Box 176, 221 00 Lund, Sweden
| | - Lionel Porcar
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Rob Dalgliesh
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK
| | - Helen Sjögren
- Ferring Pharmaceuticals A/S, Amager Strandvej 405, 2770 Kastrup, Denmark
| | - Marie Wahlgren
- Food Technology, Engineering and Nutrition, Lund University, Box 124, 221 00 Lund, Sweden
| | - Adrian Sanchez-Fernandez
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), Department of Chemical Engineering, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain.
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4
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Tang R, Zhang Z, Liu X, Zhu L, Xu Y, Chai R, Zhan W, Shen S, Liang G. Fibroblast Growth Factor Receptor 1-Specific Dehydrogelation to Release Its Inhibitor for Enhanced Lung Tumor Therapy. ACS NANO 2024. [PMID: 39392940 DOI: 10.1021/acsnano.4c11548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2024]
Abstract
Fibroblast growth factor receptor 1 (FGFR1) is emerging as a promising molecular target of lung cancer, and various FGFR1 inhibitors have exhibited significant therapeutic effects on lung cancer in preclinical research. Due to their low targeting ability or bioavailability, direct administration of these inhibitors may cause side effects. Herein, a hydrogelator, Nap-Phe-Phe-Phe-Glu-Thr-Glu-Leu-Tyr-OH (Nap-Y), was rationally designed to coassemble with an FGFR1 inhibitor nintedanib (Nin) to form a peptide hydrogel Gel Y/Nin for localized administration and FGFR1-triggered release of Nin. Upon specific phosphorylation by FGFR1 overexpressed on lung cancer cells, Nap-Y in Gel Y/Nin is converted to the hydrophilic product Nap-Phe-Phe-Phe-Glu-Thr-Glu-Leu-Tyr(H2PO3)-OH (Nap-Yp), leading to dehydrogelation of the gel and subsequent Nin release. In vitro experiments demonstrate that the release of Nin in a sustained manner from Gel Y/Nin significantly suppresses the survival, migration, and invasion of A549 cells by inhibiting FGFR1 expression and its phosphorylation function on downstream signaling molecules. Nude mouse studies show that Gel Y/Nin exhibits enhanced therapeutic efficacy on lung tumor than free Nin. We anticipate that Gel Y/Nin will be utilized for lung cancer treatment in clinical settings in the near future.
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Affiliation(s)
- Runqun Tang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 211189, China
| | - Ziyi Zhang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 211189, China
| | - Xiaoyang Liu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 211189, China
| | - Liangxi Zhu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 211189, China
| | - Yuting Xu
- Breast Surgery, Wenzhou Central Hospital, Wenzhou 325000, China
| | - Renjie Chai
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, Advanced Institute for Life and Health, Southeast University, Nanjing 210096, China
| | - Wenjun Zhan
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 211189, China
| | - Shurong Shen
- Breast Surgery, Wenzhou Central Hospital, Wenzhou 325000, China
| | - Gaolin Liang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 211189, China
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5
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Song Y, Lv H, Xu L, Liu Z, Wang J, Fang T, Deng X, Zhou Y, Li D. In vitro and in vivo activities of scutellarein, a novel polyphosphate kinase 1 inhibitor against Acinetobacter baumannii infection. Microb Cell Fact 2024; 23:269. [PMID: 39379932 PMCID: PMC11462863 DOI: 10.1186/s12934-024-02540-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 09/25/2024] [Indexed: 10/10/2024] Open
Abstract
BACKGROUND Inorganic polyphosphate (polyP)-targeted polyphosphate kinase 1 (PPK1) has attracted much attention by virtue of its importance in bacterial pathogenicity and persistence, as well as its exclusive presence in microorganisms. However, only very few drugs have been found to be efficacious in inhibiting the Acinetobacter baumannii (A. baumannii) PPK1 protein. RESULTS In this study, we identified Scutellarein (Scu), a potent PPK1 inhibitor that could significantly influence PPK1-regulated motility, biofilm formation, and bacterial persistence, which was further validated by the results of transcriptome analysis. Mechanistic explorations revealed that Scu achieved its enzyme inhibitory activity predominantly through direct engagement with the active center of PPK1. Moreover, the survival rate of Galleria mellonella larvae was increased by about 35% with 20 mg/kg of Scu treatment. The remarkable therapeutic benefits of Scu were also observed in the mouse pneumonia model, shown mainly by reduced bacterial colonization, pathological lesions, and inflammatory factors. CONCLUSION Our results revealed that Scu could attenuate the pathogenicity and persistence of A. baumannii by interfering with its important kinase PPK1.
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Affiliation(s)
- Yuping Song
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Hongfa Lv
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Lei Xu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhiying Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jianfeng Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Tianqi Fang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
- Jilin Mushuo Breeding Co., Ltd, Changchun, Jilin, 130052, China
| | - Xuming Deng
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yonglin Zhou
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western China, School of Life Sciences, Ningxia University, Yinchuan, China
| | - Dan Li
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, 130021, China.
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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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7
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Sanislav O, Tetaj R, Metali, Ratcliffe J, Phillips W, Klein AR, Sethi A, Zhou J, Mezzenga R, Saxer SS, Charnley M, Annesley SJ, Reynolds NP. Cell invasive amyloid assemblies from SARS-CoV-2 peptides can form multiple polymorphs with varying neurotoxicity. NANOSCALE 2024. [PMID: 39363846 DOI: 10.1039/d4nr03030c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
Abstract
The neurological symptoms of COVID-19, often referred to as neuro-COVID include neurological pain, memory loss, cognitive and sensory disruption. These neurological symptoms can persist for months and are known as Post-Acute Sequalae of COVID-19 (PASC). The molecular origins of neuro-COVID, and how it contributes to PASC are unknown, however a growing body of research highlights that the self-assembly of protein fragments from SARS-CoV-2 into amyloid nanofibrils may play a causative role. Previously, we identified two fragments from the SARS-CoV-2 proteins, Open Reading Frame (ORF) 6 and ORF10, that self-assemble into neurotoxic amyloid assemblies. Here we further our understanding of the self-assembly mechanisms and nano-architectures formed by these fragments and their biological responses. By solubilising the peptides in a fluorinated solvent, we eliminate insoluble aggregates in the starting materials (seeds) that change the polymorphic landscape of the assemblies. The resultant assemblies are dominated by structures with higher free energies (e.g. ribbons and amorphous aggregates) that are less toxic to cultured neurons but do affect their mitochondrial respiration. We also show the first direct evidence of cellular uptake of viral amyloids. This work highlights the importance of understanding the polymorphic behaviour of amyloids and the correlation to neurotoxicity, particularly in the context of neuro-COVID and PASC.
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Affiliation(s)
- Oana Sanislav
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Rina Tetaj
- Institute for Chemistry and Bioanalytics, School of Life Sciences, FHNW, Muttenz, 4132, Switzerland
- Department of Biochemistry and Chemistry, La Trobe University, Melbourne, Victoria 3086, Australia.
| | - Metali
- Department of Biochemistry and Chemistry, La Trobe University, Melbourne, Victoria 3086, Australia.
| | - Julian Ratcliffe
- Bio Imaging Platform, La Trobe University, Melbourne, Victoria 3086, Australia
| | - William Phillips
- Department of Biochemistry and Chemistry, La Trobe University, Melbourne, Victoria 3086, Australia.
| | - Annaleise R Klein
- Australian Nuclear Science and Technology Organisation (ANSTO), Australian Synchrotron, Clayton, Victoria 3168, Australia
| | - Ashish Sethi
- Australian Nuclear Science and Technology Organisation (ANSTO), Australian Synchrotron, Clayton, Victoria 3168, Australia
| | - Jiangtao Zhou
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, LFO, E23, 8092, Zurich, Switzerland
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, LFO, E23, 8092, Zurich, Switzerland
- Department of Materials, ETH Zurich, Zurich, 8093, Switzerland
| | - Sina S Saxer
- Institute for Chemistry and Bioanalytics, School of Life Sciences, FHNW, Muttenz, 4132, Switzerland
| | - Mirren Charnley
- Optical Sciences Centre, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
- Immune Signalling Laboratory, Peter MacCallum Cancer Centre, Parkville, Victoria 3000, Australia
| | - Sarah J Annesley
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Nicholas P Reynolds
- Department of Biochemistry and Chemistry, La Trobe University, Melbourne, Victoria 3086, Australia.
- The Biomedical and Environmental Sensor Technology (BEST) Research Centre, Biosensors Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria 3086, Australia
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8
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Saha D, Pramanik A, Freville A, Siddiqui AA, Pal U, Banerjee C, Nag S, Debsharma S, Pramanik S, Mazumder S, Maiti NC, Datta S, van Ooij C, Bandyopadhyay U. Structure-function analysis of nucleotide housekeeping protein HAM1 from human malaria parasite Plasmodium falciparum. FEBS J 2024; 291:4349-4371. [PMID: 39003571 DOI: 10.1111/febs.17216] [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: 01/20/2024] [Revised: 03/29/2024] [Accepted: 06/20/2024] [Indexed: 07/15/2024]
Abstract
Non-canonical nucleotides, generated as oxidative metabolic by-products, significantly threaten the genome integrity of Plasmodium falciparum and thereby, their survival, owing to their mutagenic effects. PfHAM1, an evolutionarily conserved inosine/xanthosine triphosphate pyrophosphohydrolase, maintains nucleotide homeostasis in the malaria parasite by removing non-canonical nucleotides, although structure-function intricacies are hitherto poorly reported. Here, we report the X-ray crystal structure of PfHAM1, which revealed a homodimeric structure, additionally validated by size-exclusion chromatography-multi-angle light scattering analysis. The two monomeric units in the dimer were aligned in a parallel fashion, and critical residues associated with substrate and metal binding were identified, wherein a notable structural difference was observed in the β-sheet main frame compared to human inosine triphosphate pyrophosphatase. PfHAM1 exhibited Mg++-dependent pyrophosphohydrolase activity and the highest binding affinity to dITP compared to other non-canonical nucleotides as measured by isothermal titration calorimetry. Modifying the pfham1 genomic locus followed by live-cell imaging of expressed mNeonGreen-tagged PfHAM1 demonstrated its ubiquitous presence in the cytoplasm across erythrocytic stages with greater expression in trophozoites and schizonts. Interestingly, CRISPR-Cas9/DiCre recombinase-guided pfham1-null P. falciparum survived in culture under standard growth conditions, indicating its assistive role in non-canonical nucleotide clearance during intra-erythrocytic stages. This is the first comprehensive structural and functional report of PfHAM1, an atypical nucleotide-cleansing enzyme in P. falciparum.
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Affiliation(s)
- Debanjan Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Atanu Pramanik
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Aline Freville
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, UK
| | - Asim Azhar Siddiqui
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Uttam Pal
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Chinmoy Banerjee
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Shiladitya Nag
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Subhashis Debsharma
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Saikat Pramanik
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Somnath Mazumder
- Department of Zoology, Raja Peary Mohan College, Uttarpara, India
| | - Nakul C Maiti
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Saumen Datta
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Christiaan van Ooij
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, UK
| | - Uday Bandyopadhyay
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Department of Biological Sciences, Bose Institute, Kolkata, India
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9
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Alemie MN, Bright R, Nguyen NH, Truong VK, Palms D, Hayball JD, Vasilev K. Surface Chemistry Induced IgG Unfolding and Modulation of Immune Responses. ACS APPLIED MATERIALS & INTERFACES 2024; 16:50507-50523. [PMID: 39263871 DOI: 10.1021/acsami.4c12883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Immunoglobulin G (IgG) comprises a significant portion of the protein corona that forms on biomaterial surfaces and holds a pivotal role in modulating host immune responses. To shed light on the important relationship between biomaterial surface functionality, IgG adsorption, and innate immune responses, we prepared, using plasma deposition, four surface coatings with specific chemistries, wettability, and charge. We found that nitrogen-containing coatings such as these deposited from allylamine (AM) and 2-methyl-2-oxazoline (POX) cause the greatest IgG unfolding, while hydrophilic acrylic acid (AC) surfaces allowed for the retention of the protein structure. Structural changes in IgG significantly modulated macrophage attachment, migration, polarization, and the expression of pro- and anti-inflammatory cytokines. Unfolded IgG on the POX and AM surfaces enhanced macrophage attachment, migration, extracellular trap release, and pro-inflammatory factors production such as IL-6 and TNF-α. Retention of IgG structure on the AC surface downregulated inflammatory responses. The findings of this study demonstrate that the retention of protein structure is an essential factor that must be taken into consideration when designing biomaterial surfaces. Our study indicates that using hydrophilic surface coatings could be a promising strategy for designing immune-modulatory biomaterials for clinical applications.
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Affiliation(s)
- Markos Negash Alemie
- Experimental Therapeutics Laboratory, UniSA Clinical and Health Sciences. University of South Australia, City East Campus, Adelaide 5000, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Richard Bright
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Ngoc Huu Nguyen
- School of Biomedical Engineering, University of Sydney, Darlington, New South Wales 2006, Australia
| | - Vi Khanh Truong
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Dennis Palms
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
| | - John D Hayball
- Experimental Therapeutics Laboratory, UniSA Clinical and Health Sciences. University of South Australia, City East Campus, Adelaide 5000, Australia
| | - Krasimir Vasilev
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
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10
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Zhou X, Khan MF, Xin Y, Chan KL, Roujeinikova A. Biochemical characterization of paralyzed flagellum proteins A (PflA) and B (PflB) from Helicobacter pylori flagellar motor. Biosci Rep 2024; 44:BSR20240692. [PMID: 39105472 PMCID: PMC11392913 DOI: 10.1042/bsr20240692] [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: 05/30/2024] [Revised: 07/29/2024] [Accepted: 08/06/2024] [Indexed: 08/07/2024] Open
Abstract
Motility by means of flagella plays an important role in the persistent colonization of Helicobacter pylori in the human stomach. The H. pylori flagellar motor has a complex structure that includes a periplasmic scaffold, the components of which are still being identified. Here, we report the isolation and characterization of the soluble forms of two putative essential H. pylori motor scaffold components, proteins PflA and PflB. We developed an on-column refolding procedure, overcoming the challenge of inclusion body formation in Escherichia coli. We employed mild detergent sarkosyl to enhance protein recovery and n-dodecyl-N,N-dimethylamine-N-oxide (LDAO)-containing buffers to achieve optimal solubility and monodispersity. In addition, we showed that PflA lacking the β-rich N-terminal domain is expressed in a soluble form, and behaves as a monodisperse monomer in solution. The methods for producing the soluble, folded forms of H. pylori PflA and PflB established in this work will facilitate future biophysical and structural studies aimed at deciphering their location and their function within the flagellar motor.
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Affiliation(s)
- Xiaotian Zhou
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria 3800, Australia
| | - Muhammad F Khan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria 3800, Australia
| | - Yue Xin
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria 3800, Australia
| | - Kar L Chan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria 3800, Australia
| | - Anna Roujeinikova
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
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11
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Kumar Y, Agrawal K, Ojha M, Pushpavanam K. Light-Activated Molecular Purification (LAMP) of Recombinant Proteins. Bioconjug Chem 2024; 35:1343-1351. [PMID: 39223465 DOI: 10.1021/acs.bioconjchem.4c00284] [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: 09/04/2024]
Abstract
The production of recombinant proteins has become a focal point in biotechnology, with potential applications in catalysis, therapeutics, and diagnostics. Before their application, these proteins undergo cumbersome downstream processing, including multiple resin-based chromatography steps (ion exchange or affinity-based) to isolate the protein of interest from host cell proteins, which are more abundant. These methods often involve (1) nonspecific binding of host cell proteins onto the resin, (2) a trial and error approach in determining elution conditions for the protein of interest, and (3) complex functionalization of the resin. These processes are also further supplemented with additional processing steps including buffer exchange through dialysis or desalting. Despite the prevalence and need for proteins, challenges persist in optimizing elution conditions and minimizing downstream processing steps, which contribute to the overall cost, impeding their translation into the market. To address these challenges, there has been a growing interest in stimuli-responsive purification systems, which allow for precise control and modulation of the purification process for protein recovery by altering their properties or behavior in response to specific external conditions, such as heat, light, or chemicals. We have developed a light-activated molecular purification (LAMP) system, a stimuli-responsive chromatography technique where the purification of recombinant proteins is triggered by light. We employed a photocleavable protein (PhoCl1) that binds specifically to Ni-NTA resin through a hexa-histidine tag at its N-terminus. We harnessed the ability of PhoCl1 to undergo photocleavage into two fragments for the development of LAMP. To demonstrate LAMP, the protein of interest (POI) is genetically fused to the C-terminus of PhoCl1. The exposure to 405 nm light (1.5 mW cm-2 for 12 h) results in the release of POI into the supernatant. We showcased the potential of LAMP by purifying highly charged green fluorescent proteins and an enzyme, riboflavin kinase. Our custom-built violet light LED setup achieved more than 50% light-induced photocleavage of the fusion constructs, resulting in the release of more than 30% of the POI into the supernatant, with the remainder retained within the resin. All the proteins purified using LAMP were more than 90% pure. Moreover, the comparison of the riboflavin kinase purified through LAMP and the traditional chromatography (Ni-NTA affinity method) revealed no significant changes in the activity levels. These highlight the broad potential of LAMP in providing a facile, yet robust stimuli-responsive protein purification technique, which leverages the potential of light to purify the proteins and overcome the limitations of current conventional chromatography systems.
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Affiliation(s)
- Yashwant Kumar
- Chemical Engineering, IIT Gandhinagar, Gujarat 382355, India
| | - Krishna Agrawal
- Biological Sciences and Engineering, IIT Gandhinagar, Gandhinagar 382355, India
| | - Manisha Ojha
- Chemical Engineering, IIT Gandhinagar, Gujarat 382355, India
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12
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Guo W, Makarov AA, Buevich AV, Jiang Y. Strategy for improving circular dichroism spectra deconvolution accuracy for macrocyclic peptides in drug discovery. J Pharm Biomed Anal 2024; 252:116476. [PMID: 39298840 DOI: 10.1016/j.jpba.2024.116476] [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: 07/25/2024] [Revised: 09/04/2024] [Accepted: 09/15/2024] [Indexed: 09/22/2024]
Abstract
Peptide therapeutics have emerged as an appealing modality in the pharmaceutical industry. Understanding peptide conformation in solution remains one of the most critical areas for peptide drug development. Circular dichroism (CD) spectroscopy is a useful technique to study the secondary structure of proteins and peptides, but the current approaches are limited to protein-focused models to predict high-order structures of peptides, and the models were built based on X-ray crystallography instead of solution-based technique, as a result, such models may have poor predictions for peptides. In this study, we present a novel CD deconvolution model to determine peptide conformation in solution. To quantitatively obtain secondary structure information using CD, a calibration model is needed beforehand to establish the relationship between each secondary structure feature and the corresponding CD response. A reference set containing the majority of cyclic peptides with known structures from solution-state NMR spectroscopy was used to build the calibration model for CD deconvolution. Improved prediction accuracy on the secondary structure determination for cyclic peptides was achieved by this model compared to the commercial standard model using commercially available platforms. This new CD deconvolution method is crucial for peptide conformational analysis in solution, and has the potential to greatly accelerate peptide drug candidate optimization in the pharmaceutical drug discovery field.
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Affiliation(s)
- Wen Guo
- Analytical Research & Development, Merck & Co., Inc., Boston, MA 02115, USA
| | - Alexey A Makarov
- Analytical Research & Development, Merck & Co., Inc., Boston, MA 02115, USA.
| | - Alexei V Buevich
- Analytical Research & Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Yuan Jiang
- Analytical Research & Development, Merck & Co., Inc., Boston, MA 02115, USA.
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13
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Murphy RD, Cosgrave M, Judge N, Tinajero-Diaz E, Portale G, Wu B, Heise A. Digital Light Processing of Thermoresponsive Hydrogels from Polyproline-Based Star Polypeptides. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2405578. [PMID: 39268774 DOI: 10.1002/smll.202405578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 08/26/2024] [Indexed: 09/15/2024]
Abstract
The first report of star poly(L-proline) crosslinkers is disclosed for digital light processing 3D printing of thermoresponsive hydrogels. Through chain end functionalization of star poly(L-proline)s with methacryloyl groups, access to high-resolution defined 3D hydrogel structures via digital light processing is achieved through photoinitiated free radical polymerization. Changing the poly(L-proline) molecular weight has a direct influence on both thermoresponsiveness and printability, while shape-morphing behavior can be induced thermally.
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Affiliation(s)
- Robert D Murphy
- Department of Chemistry, RCSI University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Muireann Cosgrave
- Department of Chemistry, RCSI University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Nicola Judge
- Department of Chemistry, RCSI University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Ernesto Tinajero-Diaz
- Department of Chemistry, RCSI University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Giuseppe Portale
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
| | - Bing Wu
- Magnetic Resonance Research Center, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Andreas Heise
- Department of Chemistry, RCSI University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin, D02 YN77, Ireland
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CURAM), Dublin, D02 YN77, Ireland
- AMBER, The SFI Advanced Materials and Bioengineering Research Centre, Dublin, D02 YN77, Ireland
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14
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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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15
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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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16
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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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17
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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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18
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Sermkaew N, Atipairin A, Krobthong S, Aonbangkhen C, Yingchutrakul Y, Uchiyama J, Songnaka N. Unveiling a New Antimicrobial Peptide with Efficacy against P. aeruginosa and K. pneumoniae from Mangrove-Derived Paenibacillus thiaminolyticus NNS5-6 and Genomic Analysis. Antibiotics (Basel) 2024; 13:846. [PMID: 39335020 PMCID: PMC11428215 DOI: 10.3390/antibiotics13090846] [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: 08/07/2024] [Revised: 08/26/2024] [Accepted: 09/03/2024] [Indexed: 09/30/2024] Open
Abstract
This study focused on the discovery of the antimicrobial peptide (AMP) derived from mangrove bacteria. The most promising isolate, NNS5-6, showed the closest taxonomic relation to Paenibacillus thiaminolyticus, with the highest similarity of 74.9%. The AMP produced by Paenibacillus thiaminolyticus NNS5-6 exhibited antibacterial activity against various Gram-negative pathogens, especially Pseudomonas aeruginosa and Klebsiella pneumoniae. The peptide sequence consisted of 13 amino acids and was elucidated as Val-Lys-Gly-Asp-Gly-Gly-Pro-Gly-Thr-Val-Tyr-Thr-Met. The AMP mainly exhibited random coil and antiparallel beta-sheet structures. The stability study indicated that this AMP was tolerant of various conditions, including proteolytic enzymes, pH (1.2-14), surfactants, and temperatures up to 40 °C for 12 h. The AMP demonstrated 4 µg/mL of MIC and 4-8 µg/mL of MBC against both pathogens. Time-kill kinetics showed that the AMP acted in a time- and concentration-dependent manner. A cell permeability assay and scanning electron microscopy revealed that the AMP exerted the mode of action by disrupting bacterial membranes. Additionally, nineteen biosynthetic gene clusters of secondary metabolites were identified in the genome. NNS5-6 was susceptible to various commonly used antibiotics supporting the primary safety requirement. The findings of this research could pave the way for new therapeutic approaches in combating antibiotic-resistant pathogens.
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Affiliation(s)
- Namfa Sermkaew
- School of Pharmacy, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand; (N.S.); (A.A.)
- Drug and Cosmetics Excellence Center, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Apichart Atipairin
- School of Pharmacy, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand; (N.S.); (A.A.)
- Drug and Cosmetics Excellence Center, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Sucheewin Krobthong
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (C.A.)
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (C.A.)
- Center of Excellence on Petrochemical and Materials Technology, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yodying Yingchutrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
| | - Jumpei Uchiyama
- Department of Bacteriology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan;
| | - Nuttapon Songnaka
- School of Pharmacy, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand; (N.S.); (A.A.)
- Drug and Cosmetics Excellence Center, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand
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19
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Li Y, Pu X, Ding Y, Yi L, Yang Y, Gu Y, Wang S. An antifouling electrochemical sensor based on a U-shaped four-in-one peptide and poly(3,4-ethylenedioxythiophene) for vancomycin detection in fresh goat milk. Food Chem 2024; 463:141056. [PMID: 39241413 DOI: 10.1016/j.foodchem.2024.141056] [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: 06/17/2024] [Revised: 08/26/2024] [Accepted: 08/28/2024] [Indexed: 09/09/2024]
Abstract
Nonspecific adsorption of biomolecules (notably, proteins) and bacteria from unsterilized food may occur on sensor surfaces, which is still a challenge for food safety sensing. To achieve sensitive detection of unsterilized raw-food materials, in this study, a U-shaped four-in-one peptide with the sequence Ac-FLKLLKKLL-DOPA3-PPPPEEKDQDKEKaa that exhibited anchoring, antifouling, antibacterial, and recognition properties was designed. The peptide-modified sensor surface effectively prevented bacterial adhesion and proliferation while resisting biomolecule adsorption (signal inhibition rate as low as 0.51 % in single-protein solutions). A highly conductive polymer layer of poly(3,4-ethylenedioxythiophene) was introduced to improve the electrochemical performance before U-shaped four-in-one peptide anchoring. The proposed sensor could accurately detect vancomycin, with a wide linear range and limit of detection of 0.05-10 μg mL-1 and 2.06 ng mL-1 (S/N = 3), respectively. Satisfactory recovery rates (101.3-105.3 %) were achieved using diluted fresh goat milk.
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Affiliation(s)
- Yonghui Li
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xujun Pu
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yangyue Ding
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China
| | - Lunzhao Yi
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Yukun Yang
- School of Life Science, Xinghuacun College (Shanxi Institute of Brewing Technology and Industry), Shanxi University, Taiyuan 030006, China.
| | - Ying Gu
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Shuo Wang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China; Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, 300071, China.
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20
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Bachelart T, Kumar S, Jouin A, Yousef M, Kieffer B, Torbeev V. Design, Synthesis and Catalytic Activity of Protein Containing Thiotyrosine as an Active Site Residue. Chembiochem 2024; 25:e202400148. [PMID: 38629812 DOI: 10.1002/cbic.202400148] [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: 02/18/2024] [Revised: 04/16/2024] [Indexed: 06/05/2024]
Abstract
Native chemical ligation is a key reaction in the toolbox of chemical methods for the synthesis of native and modified proteins. The catalysis of ligation is commonly performed by using small aryl-thiol molecules added at high concentrations. In this work, we incorporated thiotyrosine, a non-canonical amino acid containing an aryl-thiol moiety, into a designed cyclic protein « sans queue ni tête ». Importantly, the protein environment reduced the pKa of the thiol group to 5.8-5.9, which is significantly lower than the previously reported value for thiotyrosine in a short peptide (pKa 6.4). Furthermore, we demonstrated the catalytic activity of this protein both as hydrolase and in native chemical ligation of peptides. These results will be useful for the development of efficient protein catalysts (enzymes) for protein synthesis and modification.
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Affiliation(s)
- Thomas Bachelart
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400, Illkirch, France
| | - Shailesh Kumar
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400, Illkirch, France
| | - Alexis Jouin
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400, Illkirch, France
| | - Mo'ath Yousef
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400, Illkirch, France
| | - Bruno Kieffer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 1258, University of Strasbourg, 67400, Illkirch, France
| | - Vladimir Torbeev
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400, Illkirch, France
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21
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Bhopatkar AA, Bhatt N, Haque MA, Xavier R, Fung L, Jerez C, Kayed R. MAPT mutations associated with familial tauopathies lead to formation of conformationally distinct oligomers that have cross-seeding ability. Protein Sci 2024; 33:e5099. [PMID: 39145409 PMCID: PMC11325167 DOI: 10.1002/pro.5099] [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: 04/21/2024] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 08/16/2024]
Abstract
The microtubule associated protein, tau, is implicated in a multitude of neurodegenerative disorders that are collectively termed as tauopathies. These disorders are characterized by the presence of tau aggregates within the brain of afflicted individuals. Mutations within the MAPT gene that encodes the tau protein form the genetic backdrop for familial forms of tauopathies, such as frontotemporal dementia (FTD), but the molecular consequences of such alterations and their pathological effects are unclear. We sought to investigate the conformational properties of the aggregates of three tau mutants: A152T, P301L, and R406W, all implicated within FTD, and compare them to those of the native form (WT-Tau 2N4R). Our immunochemical analysis reveals that mutants and WT tau oligomers exhibit similar affinity for conformation-specific antibodies but have distinct morphology and secondary structure. Additionally, these oligomers possess different dye-binding properties and varying sensitivity to proteolytic processing. These results point to conformational variety among them. We then tested the ability of the mutant oligomers to cross-seed the aggregation of WT tau monomer. Using similar array of experiments, we found that cross-seeding with mutant aggregates leads to the formation of conformationally unique WT oligomers. The results discussed in this paper provide a novel perspective on the structural properties of oligomeric forms of WT tau 2N4R and its mutant, along with shedding some light on their cross-seeding behavior.
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Affiliation(s)
- Anukool A. Bhopatkar
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
- Present address:
Department of Pharmacology and ToxicologyUniversity of Mississippi Medical CenterJacksonMississippiUSA
| | - Nemil Bhatt
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Md Anzarul Haque
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Rhea Xavier
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Leiana Fung
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
- Present address:
Neuroscience Graduate Program, UT Southwestern Medical CenterDallasTexasUSA
| | - Cynthia Jerez
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Rakez Kayed
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
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22
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Lin S, Li J, Hu X, Chen S, Huang H, Wu Y, Li Z. Zn 2+ chelating peptide GFLGSP: Characterization of structure/Zn 2+ chelating mode and the potential mechanisms for promoting Zn 2+ transport in Caco-2 cells. Food Res Int 2024; 192:114829. [PMID: 39147518 DOI: 10.1016/j.foodres.2024.114829] [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: 05/20/2024] [Revised: 07/20/2024] [Accepted: 07/21/2024] [Indexed: 08/17/2024]
Abstract
This study focused on exploring the Zn2+ chelating peptide GFLGSP: the characterization of structure/Zn2+ chelating mode and the potential mechanisms for promoting Zn2+ transport in Caco-2 cells. The findings revealed the bidentate chelating between Zn2+ and carboxyl oxygen atom in Pro6 residue. Thereafter, the secondary structure of GFLGSP remained unchanged, but there was an increase in zeta potential and particle size. Notably, the GFLGSP-Zn2+ complex enhanced the Zn2+ transport rate and modulated ZIP4 and ZNT1 expression in a Caco-2 cells monolayer model. As revealed by molecular docking analysis, GFLGSP interacted with ZIP4 through intermolecular hydrogen bonds as well as Van der Waals forces. The Zn2+ transport mechanisms of the GFLGSP-Zn2+ complex encompassed ZIP4 (vital channel), endocytosis (primary pathway) and paracellular transport (supplementary pathway). Based on these results, the tilapia skin collagen-derived GFLGSP hold promise as the potential dietary Zn2+ supplement.
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Affiliation(s)
- Shanting Lin
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Guangzhou 510225, China; Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
| | - Jun Li
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Guangzhou 510225, China.
| | - Xiao Hu
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China; Sanya Tropical Fisheries Research Institute, Sanya 572000, China.
| | - Shengjun Chen
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Hui Huang
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yanyan Wu
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Zhenxing Li
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
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23
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Nagy G, Hoffmann SV, Jones NC, Grubmüller H. Reference Data Set for Circular Dichroism Spectroscopy Comprised of Validated Intrinsically Disordered Protein Models. APPLIED SPECTROSCOPY 2024; 78:897-911. [PMID: 38646777 PMCID: PMC11453034 DOI: 10.1177/00037028241239977] [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: 11/15/2023] [Accepted: 02/15/2024] [Indexed: 04/23/2024]
Abstract
Circular dichroism (CD) spectroscopy is an analytical technique that measures the wavelength-dependent differential absorbance of circularly polarized light and is applicable to most biologically important macromolecules, such as proteins, nucleic acids, and carbohydrates. It serves to characterize the secondary structure composition of proteins, including intrinsically disordered proteins, by analyzing their recorded spectra. Several computational tools have been developed to interpret protein CD spectra. These methods have been calibrated and tested mostly on globular proteins with well-defined structures, mainly due to the lack of reliable reference structures for disordered proteins. It is therefore still largely unclear how accurately these computational methods can determine the secondary structure composition of disordered proteins. Here, we provide such a required reference data set consisting of model structural ensembles and matching CD spectra for eight intrinsically disordered proteins. Using this set of data, we have assessed the accuracy of several published CD prediction and secondary structure estimation tools, including our own CD analysis package, SESCA. Our results show that for most of the tested methods, their accuracy for disordered proteins is generally lower than for globular proteins. In contrast, SESCA, which was developed using globular reference proteins, but was designed to be applicable to disordered proteins as well, performs similarly well for both classes of proteins. The new reference data set for disordered proteins should allow for further improvement of all published methods.
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Affiliation(s)
- Gabor Nagy
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | | | - Nykola C. Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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24
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Saade C, Pozza A, Bonneté F, Finet S, Lutz-Bueno V, Tully MD, Varela PF, Lacapère JJ, Combet S. Enhanced structure/function of mTSPO translocator in lipid:surfactant mixed micelles. Biochimie 2024; 224:3-15. [PMID: 38663457 DOI: 10.1016/j.biochi.2024.04.008] [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: 02/05/2024] [Revised: 04/06/2024] [Accepted: 04/19/2024] [Indexed: 05/06/2024]
Abstract
TSPO is a ubiquitous transmembrane protein used as a pharmacological marker in neuroimaging. The only known atomic structure of mammalian TSPOs comes from the solution NMR of mouse TSPO (mTSPO) bound to the PK11195 ligand and in a DPC surfactant environment. No structure is available in a biomimetic environment and without PK11195 which strongly stiffens the protein. We measured the effect of different amphiphilic environments on ligand-free mTSPO to study its structure/function and find optimal solubilization conditions. By replacing the SDS surfactant, where the recombinant protein is purified, with mixed lipid:surfactant (DMPC:DPC) micelles at different ratios (0:1, 1:2, and 2:1, w:w), the α-helix content and interactions and the intrinsic tryptophan (Trp) fluorescence of mTSPO are gradually increased. Small-angle X-ray scattering (SAXS) shows a more extended mTSPO/belt complex with the addition of lipids: Dmax ∼95 Å in DPC alone versus ∼142 Å in DMPC:DPC (1:2). SEC-MALLS shows that the molecular composition of the mTSPO belt is ∼98 molecules for DPC alone and ∼58 DMPC and ∼175 DPC for DMPC:DPC (1:2). Additionally, DMPC:DPC micelles stabilize mTSPO compared to DPC alone, where the protein has a greater propensity to aggregate. These structural changes are consistent with the increased affinity of mTSPO for the PK11195 ligand in presence of lipids (Kd ∼70 μM in DPC alone versus ∼0.91 μM in DMPC:DPC, 1:2), as measured by microscale thermophoresis (MST). In conclusion, mixed lipid:surfactant micelles open new possibilities for the stabilization of membrane proteins and for their study in solution in a more biomimetic amphiphilic environment.
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Affiliation(s)
- Christelle Saade
- Laboratoire Léon-Brillouin (LLB), UMR12 CEA-CNRS, Université Paris-Saclay, F-91191, Gif-sur-Yvette CEDEX, France
| | - Alexandre Pozza
- Université Paris Cité, CNRS UMR7099, Biochimie des Protéines Membranaires, F-75005, Paris, France
| | - Françoise Bonneté
- Université Paris Cité, CNRS UMR7099, Biochimie des Protéines Membranaires, F-75005, Paris, France
| | - Stéphanie Finet
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), UMR 7590 CNRS-Sorbonne Université Université, MNHN, IRD, F-75005, Paris, France
| | - Viviane Lutz-Bueno
- Laboratoire Léon-Brillouin (LLB), UMR12 CEA-CNRS, Université Paris-Saclay, F-91191, Gif-sur-Yvette CEDEX, France; Paul Scherrer Institut (PSI), Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Mark D Tully
- The European Synchrotron (ESRF), 71 Avenue des Martyrs, F-38043, Grenoble, France
| | - Paloma F Varela
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91191, Gif-sur-Yvette CEDEX, France
| | - Jean-Jacques Lacapère
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS UMR 7203, Laboratoire des BioMolécules (LBM), 4 Place Jussieu, F-75005, Paris, France
| | - Sophie Combet
- Laboratoire Léon-Brillouin (LLB), UMR12 CEA-CNRS, Université Paris-Saclay, F-91191, Gif-sur-Yvette CEDEX, France.
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25
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Florio D, Annunziata A, Panzetta V, Netti PA, Ruffo F, Marasco D. η 6-Arene Ru(II) Complexes as Modulators of Amyloid Aggregation. Inorg Chem 2024; 63:16001-16010. [PMID: 39129368 DOI: 10.1021/acs.inorgchem.4c02456] [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: 08/13/2024]
Abstract
Inorganic medicinal compounds represent a unique and versatile source of potential therapeutics in many diseases and, more recently, in neurodegeneration. Herein we investigated the effects of two η6-arene Ru(II) complexes on the self-aggregation processes of several amyloidogenic peptides endowed with different kinetics and primary sequences. The Ru(II) complexes exhibit, around the metal ion, two chlorides, one NHC = N-heterocyclic carbene, with a glucosyl and a methyl substituent and separately a hexamethylbenzene, which is named Ru1, and one benzene, named Ru2. Both complexes were demonstrated to bind monomeric amyloids suppressing aggregation as evidenced in thioflavin T (ThT) binding assays and autofluorescence experiments. Electrospray ionization mass spectrometry (ESI-MS) indicated the formation of direct adducts between amyloid and metal complexes, which determined the marked conformational variation of peptides and a rescue of cellular viability in SH-SY5Y cells. The complex Ru2 was demonstrated to be a more potent inhibitor of amyloid aggregation compared to Ru1 likely because of the less hindrance of the arene moiety. The presented data strongly support the in vitro ability of η6-arene Ru(II) complexes to suppress amyloid aggregation, providing insights into their potential application as novel therapeutics in neurodegenerative diseases.
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Affiliation(s)
- Daniele Florio
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Alfonso Annunziata
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
- Department of Chemical, Materials, and Industrial Production Engineering (DICMaPI), University of Naples Federico II, 80125 Naples, Italy
| | - Valeria Panzetta
- Department of Chemical, Materials, and Industrial Production Engineering (DICMaPI), University of Naples Federico II, 80125 Naples, Italy
- Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples Federico II, Istituto Italiano di Tecnologia, 80125 Naples, Italy
| | - Paolo A Netti
- Department of Chemical, Materials, and Industrial Production Engineering (DICMaPI), University of Naples Federico II, 80125 Naples, Italy
- Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples Federico II, Istituto Italiano di Tecnologia, 80125 Naples, Italy
| | - Francesco Ruffo
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
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26
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Pavela O, Juhász T, Tóth L, Czajlik A, Batta G, Galgóczy L, Beke-Somfai T. Mapping of the Lipid-Binding Regions of the Antifungal Protein NFAP2 by Exploiting Model Membranes. J Chem Inf Model 2024; 64:6557-6569. [PMID: 39150323 PMCID: PMC11351017 DOI: 10.1021/acs.jcim.4c00229] [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: 02/14/2024] [Revised: 08/09/2024] [Accepted: 08/09/2024] [Indexed: 08/17/2024]
Abstract
Fungal infections with high mortality rates represent an increasing health risk. The Neosartorya (Aspergillus) fischeri antifungal protein 2 (NFAP2) is a small, cysteine-rich, cationic protein exhibiting potent anti-Candida activity. As the underlying mechanism, pore formation has been demonstrated; however, molecular level details on its membrane disruption action are lacking. Herein, we addressed the lipid binding of NFAP2 using a combined computational and experimental approach to simple lipid compositions with various surface charge properties. Simulation results revealed binding preferences for negatively charged model membranes, where selectivity is mediated by anionic lipid components enriched at the protein binding site but also assisted by zwitterionic lipid species. Several potential binding routes initiated by various anchoring contacts were observed, which resulted in one main binding mode and a few variants, with NFAP2 residing on the membrane surface. Region 10NCPNNCKHKKG20 of the flexible N-terminal part of the protein showed potency to insert into the lipid bilayer, where the disulfide bond-stabilized short motif 11CPNNC15 could play a key role. In addition, several areas, including the beginning of the N-terminal (residues 1-8), played roles in facilitating initial membrane contacts. Besides, individual roles of residues such as Lys24, Lys32, Lys34, and Trp42 were also revealed by the simulations. Combined data demonstrated that the solution conformation was not perturbed markedly upon membrane interaction, and the folded part of the protein also contributed to stabilizing the bound state. Data also highlighted that the binding of NFAP2 to lipid vesicles is sensitively affected by environmental factors such as ionic strength. Electrostatic interactions driven by anionic lipids were found pivotal, explaining the reduced membrane activity observed under high salt conditions. Experimental data supported the lipid-selective binding mechanisms and pointed to salt-dependent effects, particularly to protein-assisted vesicle aggregation at low ionic strength. Our findings can contribute to the development of NFAP2-based anti-Candida agents and studies aiming at future medical use of peptide-based natural antifungal compounds.
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Affiliation(s)
- Olivér Pavela
- Institute
of Materials and Environmental Chemistry, HUN-REN Research Centre
for Natural Sciences, Magyar tudósok körútja 2, Budapest, H-1117, Hungary
- Hevesy
György PhD School of Chemistry, Eötvös Loránd
University, Budapest,
Pázmány Péter sétány 1/A, Budapest H-1117, Hungary
| | - Tünde Juhász
- Institute
of Materials and Environmental Chemistry, HUN-REN Research Centre
for Natural Sciences, Magyar tudósok körútja 2, Budapest, H-1117, Hungary
| | - Liliána Tóth
- Department
of Biotechnology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged H-6726, Hungary
| | - András Czajlik
- Department
of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1 Debrecen H-4032, Hungary
- Department
of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Tűzoltó u. 37-47, Budapest H-1094, Hungary
| | - Gyula Batta
- Department
of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1 Debrecen H-4032, Hungary
| | - László Galgóczy
- Department
of Biotechnology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged H-6726, Hungary
- Institute
of Biochemistry, HUN-REN Biological Research Centre, Temesvári krt. 62, Szeged H-6726, Hungary
| | - Tamás Beke-Somfai
- Institute
of Materials and Environmental Chemistry, HUN-REN Research Centre
for Natural Sciences, Magyar tudósok körútja 2, Budapest, H-1117, Hungary
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27
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Zhang B, Boyd SD, Zhabilov D, Ullrich M, Blackburn NJ, Winkler DD. Pathogenic R 163W Variant of the Copper Chaperone for Sod1 (Ccs) Functions as an Anti-chaperone. Biochemistry 2024; 63:2051-2062. [PMID: 39099176 DOI: 10.1021/acs.biochem.4c00223] [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: 08/06/2024]
Abstract
The copper chaperone for Sod1 (Ccs) is a metallochaperone that plays a multifaceted role in the maturation of Cu,Zn superoxide dismutase (Sod1). The Ccs mutation R163W was identified in an infant with fatal neurological abnormalities. Based on a comprehensive structural and functional analysis, we developed the first data-driven model for R163W-related pathogenic phenotypes. The work here confirms previous findings that the substitution of arginine with tryptophan at this site, which is located adjacent to a conserved Zn binding site, creates an unstable Zn-deficient protein that loses its ability to efficiently activate Sod1. Intriguingly, R163W Ccs can reduce copper (i.e., Cu(II) → Cu(I)) bound in its Sod1-like domain (D2), and this novel redox event is accompanied by disulfide bond formation. The loss of Zn binding, along with the unusual ability to bind copper in D2, diverts R163W Ccs toward aggregation. The remarkably high affinity of D2 Cu(I) binding converts R163W from a Cu chaperone to a Cu scavenger that accelerates Sod1 deactivation (i.e., an Anti-chaperone). Overall, these findings present a first-of-its-kind molecular mechanism for Ccs dysfunction that leads to pathogenesis in humans.
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Affiliation(s)
- Bei Zhang
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas 75083, United States
| | - Stefanie D Boyd
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas 75083, United States
| | - Dannie Zhabilov
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas 75083, United States
| | - Morgan Ullrich
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas 75083, United States
| | - Ninian J Blackburn
- Department of Chemical Physiology and Biochemistry, Oregon Health and Sciences University, Portland, Oregon 97239, United States
| | - Duane D Winkler
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas 75083, United States
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28
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da Silva MM, de Oliveira CFR, Almeida CV, Sobrinho IAS, Macedo MLR. A Novel Kunitz Trypsin Inhibitor from Enterolobium gummiferum Seeds Exhibits Antibiofilm Properties against Pathogenic Yeasts. Molecules 2024; 29:3777. [PMID: 39202855 PMCID: PMC11357210 DOI: 10.3390/molecules29163777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 09/03/2024] Open
Abstract
Plant peptidase inhibitors play crucial roles in plant defence mechanisms and physiological processes. In this study, we isolated and characterised a Kunitz trypsin inhibitor from Enterolobium gummiferum seeds named EgPI (E. gummiferum peptidase inhibitor). The purification process involved two chromatography steps using size exclusion and hydrophobic resins, resulting in high purity and yield. EgPI appeared as a single band of ~20 kDa in SDS-PAGE. Under reducing conditions, the inhibitor exhibited two polypeptide chains, with 15 and 5 kDa. Functional characterisation revealed that EgPI displayed an inhibition stoichiometry of 1:1 against trypsin, with a dissociation constant of 8.4 × 10-9 mol·L-1. The amino-terminal sequencing of EgPI revealed the homology with Kunitz inhibitors. Circular dichroism analysis provided insights into the secondary structure of EgPI, which displayed the signature typical of Kunitz inhibitors. Stability studies demonstrated that EgPI maintained the secondary structure necessary to exhibit its inhibitory activity up to 70 °C and over a pH range from 2 to 8. Microbiological screening revealed that EgPI has antibiofilm properties against pathogenic yeasts at 1.125 μmol·L-1, and EgPI reduced C. albicans biofilm formation by 82.7%. The high affinity of EgPI for trypsin suggests potential applications in various fields. Furthermore, its antibiofilm properties recommended its usefulness in agriculture and antimicrobial therapy research, highlighting the practical implications of our research.
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Affiliation(s)
- Matheus M. da Silva
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil; (M.M.d.S.); (C.V.A.); (I.A.S.S.)
| | - Caio F. R. de Oliveira
- Instituto Federal de Mato Grosso, Campus Guarantã do Norte, Guarantã do Norte 78520-000, MT, Brazil;
| | - Claudiane V. Almeida
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil; (M.M.d.S.); (C.V.A.); (I.A.S.S.)
| | - Ismaell A. S. Sobrinho
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil; (M.M.d.S.); (C.V.A.); (I.A.S.S.)
| | - Maria L. R. Macedo
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil; (M.M.d.S.); (C.V.A.); (I.A.S.S.)
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29
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Skog A, Paracini N, Gerelli Y, Skepö M. Translocation of Antimicrobial Peptides across Model Membranes: The Role of Peptide Chain Length. Mol Pharm 2024; 21:4082-4097. [PMID: 38993084 PMCID: PMC11304388 DOI: 10.1021/acs.molpharmaceut.4c00450] [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: 04/25/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024]
Abstract
Cushioned lipid bilayers are structures consisting of a lipid bilayer supported on a solid substrate with an intervening layer of soft material. They offer possibilities for studying the behavior and interactions of biological membranes more accurately under physiological conditions. In this work, we continue our studies of cushion formation induced by histatin 5 (24Hst5), focusing on the effect of the length of the peptide chain. 24Hst5 is a short, positively charged, intrinsically disordered saliva peptide, and here, both a shorter (14Hst5) and a longer (48Hst5) peptide variant were evaluated. Experimental surface active techniques were combined with coarse-grained Monte Carlo simulations to obtain information about these peptides. Results show that at 10 mM NaCl, both the shorter and the longer peptide variants behave like 24Hst5 and a cushion below the bilayer is formed. At 150 mM NaCl, however, no interaction is observed for 24Hst5. On the contrary, a cushion is formed both in the case of 14Hst5 and 48Hst5, and in the latter, an additional thick, diffuse, and highly hydrated layer of peptide and lipid molecules is formed, on top of the bilayer. Similar trends were observed from the simulations, which allowed us to hypothesize that positively charged patches of the amino acids lysine and arginine in all three peptides are essential for them to interact with and translocate over the bilayer. We therefore hypothesize that electrostatic interactions are important for the interaction between the solid-supported lipid bilayers and the peptide depending on the linear charge density through the primary sequence and the positively charged patches in the sequence. The understanding of how, why, and when the cushion is formed opens up the possibility for this system to be used in the research and development of new drugs and pharmaceuticals.
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Affiliation(s)
- Amanda
E. Skog
- Division
of Computational Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
| | - Nicolò Paracini
- Institut
Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Yuri Gerelli
- Institute
for Complex Systems - National Research Council (ISC−CNR), Piazzale Aldo Moro 2, 00185 Roma, Italy
- Department
of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Roma, Italy
| | - Marie Skepö
- Division
of Computational Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
- NanoLund, Lund
University, Box
118, 22100 Lund, Sweden
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30
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Morrell AH, Warren NJ, Thornton PD. The Production of Polysarcosine-Containing Nanoparticles by Ring-Opening Polymerization-Induced Self-Assembly. Macromol Rapid Commun 2024; 45:e2400103. [PMID: 38597209 DOI: 10.1002/marc.202400103] [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: 02/26/2024] [Revised: 04/02/2024] [Indexed: 04/11/2024]
Abstract
N-carboxyanhydride ring-opening polymerization-induced self-assembly (NCA ROPISA) offers a convenient route for generating poly(amino acid)-based nanoparticles in a single step, crucially avoiding the need for post-polymerization self-assembly. Most examples of NCA ROPISA make use of a poly(ethylene glycol) (PEG) hydrophilic stabilizing block, however this non-biodegradable, oil-derived polymer may cause an immunological response in some individuals. Alternative water-soluble polymers are therefore highly sought. This work reports the synthesis of wholly poly(amino acid)-based nanoparticles, through the chain-extension of a polysarcosine macroinitiator with L-Phenylalanine-NCA (L-Phe-NCA) and Alanine-NCA (Ala-NCA), via aqueous NCA ROPISA. The resulting polymeric structures comprise of predominantly anisotropic, rod-like nanoparticles, with morphologies primarily influenced by the secondary structure of the hydrophobic poly(amino acid) that enables their formation.
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Affiliation(s)
- Anna H Morrell
- School of Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Nicholas J Warren
- School of Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Paul D Thornton
- Leeds Institute of Textiles and Colour (LITAC), School of Design, University of Leeds, Leeds, LS2 9JT, UK
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31
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Ural MS, Joseph JM, Wien F, Li X, Tran MA, Taverna M, Smadja C, Gref R. A comprehensive investigation of the interactions of human serum albumin with polymeric and hybrid nanoparticles. Drug Deliv Transl Res 2024; 14:2188-2202. [PMID: 38578378 DOI: 10.1007/s13346-024-01578-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] [Accepted: 03/07/2024] [Indexed: 04/06/2024]
Abstract
Nanoparticles (NPs) engineered as drug delivery systems continue to make breakthroughs as they offer numerous advantages over free therapeutics. However, the poor understanding of the interplay between the NPs and biomolecules, especially blood proteins, obstructs NP translation to clinics. Nano-bio interactions determine the NPs' in vivo fate, efficacy and immunotoxicity, potentially altering protein function. To fulfill the growing need to investigate nano-bio interactions, this study provides a systematic understanding of two key aspects: (i) protein corona (PC) formation and (ii) NP-induced modifications on protein's structure and stability. A methodology was developed by combining orthogonal techniques to analyze both quantitative and qualitative aspects of nano-bio interactions, using human serum albumin (HSA) as a model protein. Protein quantification via liquid chromatography-mass spectrometry, and capillary zone electrophoresis (CZE) clarified adsorbed protein quantity and stability. CZE further unveiled qualitative insights into HSA forms (native, glycated HSA and cysteinylated), while synchrotron radiation circular dichroism enabled analyzing HSA's secondary structure and thermal stability. Comparative investigations of NP cores (organic vs. hybrid), and shells (with or without polyethylene glycol (PEG)) revealed pivotal factors influencing nano-bio interactions. Polymeric NPs based on poly(lactic-co-glycolic acid) (PLGA) and hybrid NPs based on metal-organic frameworks (nanoMOFs) presented distinct HSA adsorption profiles. PLGA NPs had protein-repelling properties while inducing structural modifications on HSA. In contrast, HSA exhibited a high affinity for nanoMOFs forming a PC altering thereby the protein structure. A shielding effect was gained through PEGylation for both types of NPs, avoiding the PC formation as well as the alteration of unbound HSA structure.
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Affiliation(s)
- Merve Seray Ural
- Université Paris-Saclay, Institute of Molecular Sciences of Orsay, French National Center for Scientific Research, 91405, Orsay, France
- Université Paris-Saclay, Institut Galien Paris-Saclay, French National Center for Scientific Research, 91400, Orsay, France
| | - Joice Maria Joseph
- Université Paris-Saclay, Institute of Molecular Sciences of Orsay, French National Center for Scientific Research, 91405, Orsay, France
- Université Paris-Saclay, Institut Galien Paris-Saclay, French National Center for Scientific Research, 91400, Orsay, France
| | - Frank Wien
- , Synchrotron Soleil, 91190, Saint-Aubin, France
| | - Xue Li
- Université Paris-Saclay, Institute of Molecular Sciences of Orsay, French National Center for Scientific Research, 91405, Orsay, France
| | - My-An Tran
- Université Paris-Saclay, Institute of Molecular Sciences of Orsay, French National Center for Scientific Research, 91405, Orsay, France
| | - Myriam Taverna
- Université Paris-Saclay, Institut Galien Paris-Saclay, French National Center for Scientific Research, 91400, Orsay, France
| | - Claire Smadja
- Université Paris-Saclay, Institut Galien Paris-Saclay, French National Center for Scientific Research, 91400, Orsay, France.
| | - Ruxandra Gref
- Université Paris-Saclay, Institute of Molecular Sciences of Orsay, French National Center for Scientific Research, 91405, Orsay, France.
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32
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Luo PK, Ho HM, Chiang MC, Chu LA, Chuang YH, Lyu PC, Hu IC, Chang WA, Peng SY, Jayakumar J, Chen HL, Huang MH, Sung HW. pH-Responsive β-Glucans-Complexed mRNA in LNPs as an Oral Vaccine for Enhancing Cancer Immunotherapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2404830. [PMID: 38895941 DOI: 10.1002/adma.202404830] [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: 04/03/2024] [Revised: 06/07/2024] [Indexed: 06/21/2024]
Abstract
mRNA vaccines for cancer immunotherapy are commonly delivered using lipid nanoparticles (LNPs), which, when administered intravenously, may accumulate in the liver, potentially limiting their therapeutic efficacy. To overcome this challenge, the study introduces an oral mRNA vaccine formulation tailored for efficient uptake by immune cells in the gastrointestinal (GI) tract, known for its high concentration of immune cells, including dendritic cells (DCs). This formulation comprises mRNA complexed with β-glucans (βGlus), a potential adjuvant for vaccines, encapsulated within LNPs (βGlus/mRNA@LNPs). The βGlus/mRNA complexes within the small compartments of LNPs demonstrate a distinctive ability to partially dissociate and reassociate, responding to pH changes, effectively shielding mRNA from degradation in the harsh GI environment. Upon oral administration to tumor-bearing mice, βGlus/mRNA@LNPs are effectively taken up by intestinal DCs and local nonimmune cells, bypassing potential liver accumulation. This initiates antigen-specific immune responses through successful mRNA translation, followed by drainage into the mesenteric lymph nodes to stimulate T cells and trigger specific adaptive immune responses, ultimately enhancing antitumor effects. Importantly, the vaccine demonstrates safety, with no significant inflammatory reactions observed. In conclusion, the potential of oral βGlus/mRNA@LNPs delivery presents a promising avenue in cancer immunotherapy, offering needle-free and user-friendly administration for widespread adoption and self-administration.
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Affiliation(s)
- Po-Kai Luo
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300044, Taiwan ROC
| | - Hui-Min Ho
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, 350401, Taiwan ROC
| | - Min-Chun Chiang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300044, Taiwan ROC
| | - Li-An Chu
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, 300044, Taiwan ROC
- Brain Research Center, National Tsing Hua University, Hsinchu, 300044, Taiwan ROC
| | - Ya-Han Chuang
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, 300044, Taiwan ROC
- Brain Research Center, National Tsing Hua University, Hsinchu, 300044, Taiwan ROC
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan ROC
| | - I-Chen Hu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan ROC
| | - Wan-An Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300044, Taiwan ROC
| | - Sheng-Yao Peng
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300044, Taiwan ROC
| | - Jayachandran Jayakumar
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300044, Taiwan ROC
| | - Hsin-Lung Chen
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300044, Taiwan ROC
| | - Ming-Hsi Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, 350401, Taiwan ROC
| | - Hsing-Wen Sung
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300044, Taiwan ROC
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33
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Vignesh V, Kavalappa YP, Ponesakki G, Madhan B, Shanmugam G. Lutein, a carotenoid found in numerous plants and the human eye, demonstrates the capacity to bundle collagen fibrils. Int J Biol Macromol 2024; 274:133389. [PMID: 38925203 DOI: 10.1016/j.ijbiomac.2024.133389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 05/29/2024] [Accepted: 06/21/2024] [Indexed: 06/28/2024]
Abstract
Collagen fibrils serve as the building blocks of the extracellular matrix, providing a resilient and structural framework for tissues. However, the bundling of collagen fibrils is of paramount importance in maintaining the structural integrity and functionality of various tissues in the human body. In this scenario, there is limited exploration of molecules that promote the bundling of collagen fibrils. Investigating the interactions of well-known carotenoids, commonly associated with ocular health, particularly in the retina, with collagen presents a novel and significant area of study. Here, we studied the influence of lutein, a well-known carotenoid present in many plant tissues and has several biological properties, on the structure, thermal stability, self-assembly, and fibrillation of collagen. Fibrillation kinetics and electron microscopic analyses indicated that lutein did not interfere with fibrillation process of collagen, whereas it enhances the lateral fusion of collagen fibrils leading to the formation of compact bundles of thick fibrils under physiological conditions. The hydrophobic and hydrogen bonding interactions between lutein and collagen fibrils are most likely the cause of the bundling of the fibrils. This study establishes the first investigation of collagen-carotenoid interactions, showcasing the unique property of lutein in bundling collagen fibrils, which may find potential application in tissue engineering.
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Affiliation(s)
- Venkatesan Vignesh
- Organic & Bioorganic Chemistry Laboratory, Council of Scientific and Industrial Research - Central Leather Research Institute (CSIR-CLRI), Sardar Patel Road, Adyar, Chennai 600020, India
| | - Yogendra Prasad Kavalappa
- Biochemistry and Biotechnology Laboratory, CSIR-CLRI, Sardar Patel Road, Adyar, Chennai 600 020, India
| | - Ganesan Ponesakki
- Biochemistry and Biotechnology Laboratory, CSIR-CLRI, Sardar Patel Road, Adyar, Chennai 600 020, India
| | - Balaraman Madhan
- Biochemistry and Biotechnology Laboratory, CSIR-CLRI, Sardar Patel Road, Adyar, Chennai 600 020, India
| | - Ganesh Shanmugam
- Organic & Bioorganic Chemistry Laboratory, Council of Scientific and Industrial Research - Central Leather Research Institute (CSIR-CLRI), Sardar Patel Road, Adyar, Chennai 600020, India.
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34
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Lagreca E, Caiazzo E, Di Natale C, Mollo V, Vecchione R, Ialenti A, Netti PA. Biomimetic Oil-in-Water Nanoemulsions as a Suitable Drug Delivery System to Target Inflamed Endothelial Cells. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:1286. [PMID: 39120393 PMCID: PMC11314564 DOI: 10.3390/nano14151286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 08/10/2024]
Abstract
Currently, the biomimetic approach of drawing inspiration from nature has frequently been employed in designing drug nanocarriers (NCs) of actively target various diseases, ranging from cancer to neuronal and inflammation pathologies. The cell-membrane coating can confer upon the inner nanomaterials a biological identity and the functions exhibited by the cells from which the membrane is derived. Monocyte- and macrophage-membrane-coated nanomaterials have emerged as an ideal delivery system to target inflamed vasculature. Herein, we developed two biomimetic NCs using a human-derived leukaemia monocytic cell line (THP-1), either undifferentiated or differentiated by phorbol 12-myristate 13-acetate (PMA) into adherent macrophage-like cells as membrane sources for NC coating. We employed a secondary oil-in-water nano-emulsion (SNE) as the inner core, which served as an optimal NC for high payloads of lipophilic compounds. Two different biomimetic systems were produced, combining the biomimetic features of biological membranes with the physicochemical and nano-sized characteristics of SNEs. These systems were named Monocyte NEsoSome (M-NEsoSome) and Macrophage NEsoSome (M0-NEsoSome). Their uptake ability was investigated in tumour necrosis factor alfa (TNFα)-treated human umbilical vein endothelial cells (HUVECs), selected as a model of inflamed endothelial cells. The M0 membrane coating demonstrated accelerated internalisation compared with the monocyte coating and notably surpassed the uptake rate of bare NCs. In conclusion, M0-NEsoSome NCs could be a therapeutic system for targeting inflamed endothelial cells and potentially delivering anti-inflammatory drugs in vascular inflammation.
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Affiliation(s)
- Elena Lagreca
- Center for Advanced Biomaterials for Health Care (CABHC), Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125 Naples, Italy; (E.L.); (V.M.); (P.A.N.)
- Dipartimento di Chimica dei Materiali e Produzioni Industriali (DICMaPI), University of Naples Federico II, P. le Tecchio 80, 80125 Naples, Italy
| | - Elisabetta Caiazzo
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy; (E.C.); (A.I.)
- School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Concetta Di Natale
- Dipartimento di Chimica dei Materiali e Produzioni Industriali (DICMaPI), University of Naples Federico II, P. le Tecchio 80, 80125 Naples, Italy
| | - Valentina Mollo
- Center for Advanced Biomaterials for Health Care (CABHC), Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125 Naples, Italy; (E.L.); (V.M.); (P.A.N.)
| | - Raffaele Vecchione
- Center for Advanced Biomaterials for Health Care (CABHC), Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125 Naples, Italy; (E.L.); (V.M.); (P.A.N.)
| | - Armando Ialenti
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy; (E.C.); (A.I.)
| | - Paolo Antonio Netti
- Center for Advanced Biomaterials for Health Care (CABHC), Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125 Naples, Italy; (E.L.); (V.M.); (P.A.N.)
- Dipartimento di Chimica dei Materiali e Produzioni Industriali (DICMaPI), University of Naples Federico II, P. le Tecchio 80, 80125 Naples, Italy
- Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples Federico II, P. le Tecchio 80, 80125 Naples, Italy
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35
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Singh A, Chakraborty J, Pal S, Das D. Site-selective peptide bond hydrolysis and ligation in water by short peptide-based assemblies. Proc Natl Acad Sci U S A 2024; 121:e2321396121. [PMID: 39042686 PMCID: PMC11295027 DOI: 10.1073/pnas.2321396121] [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: 12/05/2023] [Accepted: 06/20/2024] [Indexed: 07/25/2024] Open
Abstract
The evolution of complex chemical inventory from Darwin's nutrient-rich warm pond necessitated rudimentary yet efficient catalytic folds. Short peptides and their self-organized microstructures, ranging from spherical colloids to amyloidogenic aggregates might have played a crucial role in the emergence of contemporary catalytic entities. However, the question of how short peptide fragments had functions akin to contemporary complex enzymes to catalyze cleavage and formation of highly stable peptide bonds that constitute the backbone of all proteins remains an unresolved yet fundamentally important question in terms of the origins of enzymes. We report short-peptide-based spherical assemblies that demonstrated residue-specific cleavage and formation of peptide bonds of diverse peptide-based substrates under aqueous environment. Despite the short sequence length, the assemblies utilized the synergistic collaboration of four residues which included the catalytic triad of extant serine proteases with a nonproteinogenic amino acid (quinone moiety), to facilitate proteolysis, ligation, and a three-step (hydrolysis-ligation-hydrolysis) cascade. Such short-peptide-based catalytic assemblies argue for their candidacy as the earliest protein folds and open up avenues for biotechnological applications.
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Affiliation(s)
- Abhishek Singh
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
| | - Janardan Chakraborty
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
| | - Sumit Pal
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
| | - Dibyendu Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
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36
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Sermkaew N, Atipairin A, Wanganuttara T, Krobthong S, Aonbangkhen C, Yingchutrakul Y, Uchiyama J, Songnaka N. A Novel Bacitracin-like Peptide from Mangrove-Isolated Bacillus paralicheniformis NNS4-3 against MRSA and Its Genomic Insights. Antibiotics (Basel) 2024; 13:716. [PMID: 39200016 PMCID: PMC11350868 DOI: 10.3390/antibiotics13080716] [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: 06/21/2024] [Revised: 07/26/2024] [Accepted: 07/28/2024] [Indexed: 09/01/2024] Open
Abstract
The global rise of antimicrobial resistance (AMR) presents a critical challenge necessitating the discovery of novel antimicrobial agents. Mangrove microbes are valuable sources of new antimicrobial compounds. This study reports the discovery of a potent antimicrobial peptide (AMP) from Bacillus paralicheniformis NNS4-3, isolated from mangrove sediment, exhibiting significant activity against methicillin-resistant Staphylococcus aureus (MRSA). The AMP demonstrated a minimum inhibitory concentration ranging from 1 to 16 µg/mL in the tested bacteria and exhibited bactericidal effects at higher concentrations. Structural analysis revealed a bacitracin-like configuration and the peptide acted by disrupting bacterial membranes in a time- and concentration-dependent manner. The AMP maintained stability under heat, proteolytic enzymes, surfactants, and varying pH treatments. The ten biosynthetic gene clusters (BGCs) of secondary metabolites were found in the genome. Detailed sequence comparison of the predicted bacitracin BGC indicated distinct DNA sequences compared to previously reported strains. Although the antibiotic resistance genes were found, this strain was susceptible to antibiotics. Our findings demonstrated the potential of Bacillus paralicheniformis NNS4-3 and its AMP as a promising agent in combating AMR. The genetic information could be pivotal for future applications in the healthcare industry, emphasizing the need for continued exploration of marine microbial diversity in drug discovery.
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Affiliation(s)
- Namfa Sermkaew
- School of Pharmacy, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand; (N.S.); (A.A.); (T.W.)
- Drug and Cosmetics Excellence Center, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Apichart Atipairin
- School of Pharmacy, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand; (N.S.); (A.A.); (T.W.)
- Drug and Cosmetics Excellence Center, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Thamonwan Wanganuttara
- School of Pharmacy, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand; (N.S.); (A.A.); (T.W.)
- Drug and Cosmetics Excellence Center, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Sucheewin Krobthong
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (C.A.)
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (C.A.)
- Center of Excellence on Petrochemical and Materials Technology, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Yodying Yingchutrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
| | - Jumpei Uchiyama
- Department of Bacteriology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan;
| | - Nuttapon Songnaka
- School of Pharmacy, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand; (N.S.); (A.A.); (T.W.)
- Drug and Cosmetics Excellence Center, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand
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37
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Müller M, Wöltje M, Hofmaier M, Tarpara B, Urban B, Aibibu D, Cherif C. In Situ ATR-FTIR Studies on the β-Sheet Formation of Native and Regenerated Bombyx mori Silk Material in Solution and Its Potential for Drug Releasing Coatings. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 39073396 DOI: 10.1021/acs.langmuir.4c00920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Dynamic attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy at both solutions and coatings of a semicrystalline silk material derived from Bombyx mori was applied to monitor the β-sheet conformation, which is known to correlate with silk protein crystallinity. The secondary structure-sensitive Amide I band was analyzed. Two silk protein samples were studied: native-based silk buffer fibroin (NSF) was extracted from silk glands and regenerated silk fibroin (RSF) was extracted from degummed cocoons. Solutions of both NSF and RSF at 2 mg/mL featured low initial β-sheet contents of 5-12%, which further increased to 47-53% after 24 h. RSF and NSF solutions at 23 mg/mL also featured low initial β-sheet contents of 9-10%, which yet only slightly increased to 16-17% after 24 h. Coatings deposited from RSF solutions showed high surface integrity (Q > 99%) after rinsing in mineralized water, enabling interfacial drug delivery applications. RSF coatings were post-treated with either formic acid (FA) or pure methanol (MeOH) vapor to showcase inducibility of crystalline domains in RSF coatings. Such coatings were loaded with the model antibiotic drugs tetracycline (TCL) and streptomycin (STRP), and the sustained release of TCL was followed in contact with (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) (HEPES) buffer. RSF/TCL coatings post-treated with formic acid (FA) vapor followed by methanol (MeOH) vapor showed a significantly lower (52%) initial burst of rather hydrophobic TCL compared to untreated RSF/TCL coatings (72%), while no such significant release difference was observed for hydrophilic STRP. This was rationalized by a specific interaction between nonpolar TCL and hydrophobic crystalline RSF domains.
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Affiliation(s)
- M Müller
- Department Functional Colloidal Materials, Leibniz Institute of Polymer Research Dresden, Hohe Straße 6, 01069 Dresden, Germany
- Department Chemistry and Food Chemistry, TUD Dresden University of Technology, 01062 Dresden, Germany
| | - M Wöltje
- TUD Dresden University of Technology, Institute of Textile Machinery and High-Performance Material Technology, 01062 Dresden, Germany
| | - M Hofmaier
- Department Functional Colloidal Materials, Leibniz Institute of Polymer Research Dresden, Hohe Straße 6, 01069 Dresden, Germany
- Department Chemistry and Food Chemistry, TUD Dresden University of Technology, 01062 Dresden, Germany
| | - B Tarpara
- Department Functional Colloidal Materials, Leibniz Institute of Polymer Research Dresden, Hohe Straße 6, 01069 Dresden, Germany
- Department Processing Technology, Leibniz Institute of Polymer Research Dresden, Hohe Straße 6, 01069 Dresden, Germany
| | - B Urban
- Department Functional Colloidal Materials, Leibniz Institute of Polymer Research Dresden, Hohe Straße 6, 01069 Dresden, Germany
| | - D Aibibu
- TUD Dresden University of Technology, Institute of Textile Machinery and High-Performance Material Technology, 01062 Dresden, Germany
| | - C Cherif
- TUD Dresden University of Technology, Institute of Textile Machinery and High-Performance Material Technology, 01062 Dresden, Germany
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38
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Learte-Aymamí S, Martínez-Castro L, González-González C, Condeminas M, Martin-Malpartida P, Tomás-Gamasa M, Baúlde S, Couceiro JR, Maréchal JD, Macias MJ, Mascareñas JL, Vázquez ME. De Novo Engineering of Pd-Metalloproteins and Their Use as Intracellular Catalysts. JACS AU 2024; 4:2630-2639. [PMID: 39055146 PMCID: PMC11267534 DOI: 10.1021/jacsau.4c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 07/27/2024]
Abstract
The development of transition metal-based catalytic platforms that promote bioorthogonal reactions inside living cells remains a major challenge in chemical biology. This is particularly true for palladium-based catalysts, which are very powerful in organic synthesis but perform poorly in the cellular environment, mainly due to their rapid deactivation. We now demonstrate that grafting Pd(II) complexes into engineered β-sheets of a model WW domain results in cell-compatible palladominiproteins that effectively catalyze depropargylation reactions inside HeLa cells. The concave shape of the WW domain β-sheet proved particularly suitable for accommodating the metal center and protecting it from rapid deactivation in the cellular environment. A thorough NMR and computational study confirmed the formation of the metal-stapled peptides and allowed us to propose a three-dimensional structure for this novel metalloprotein motif.
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Affiliation(s)
- Soraya Learte-Aymamí
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain
| | - Laura Martínez-Castro
- Insilichem,
Departament de Química, Universitat
Autónoma de Barcelona, Cerdanyola 08193, Spain
| | - Carmen González-González
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain
| | - Miriam Condeminas
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, Barcelona 08028, Spain
- Academic
institutional affiliation:Department of Medicine and Life Sciences, Universitat Pompeu Fabra (MELIS-UPF), Carrer del Doctor Aiguader 88, Barcelona 08003, Spain
| | - Pau Martin-Malpartida
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, Barcelona 08028, Spain
| | - María Tomás-Gamasa
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain
| | - Sandra Baúlde
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain
| | - José R. Couceiro
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain
| | - Jean-Didier Maréchal
- Insilichem,
Departament de Química, Universitat
Autónoma de Barcelona, Cerdanyola 08193, Spain
| | - Maria J. Macias
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, Barcelona 08028, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain
| | - José L. Mascareñas
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain
| | - M. Eugenio Vázquez
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain
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39
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Zhao G, Richaud AD, Williamson RT, Feig M, Roche SP. De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics. ACS Chem Biol 2024; 19:1583-1592. [PMID: 38916527 PMCID: PMC11299430 DOI: 10.1021/acschembio.4c00236] [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] [Indexed: 06/26/2024]
Abstract
The binding affinity of antibodies to specific antigens stems from a remarkably broad repertoire of hypervariable loops known as complementarity-determining regions (CDRs). While recognizing the pivotal role of the heavy-chain 3 CDRs (CDR-H3s) in maximizing antibody-antigen affinity and specificity, the key structural determinants responsible for their adaptability to diverse loop sequences, lengths, and noncanonical structures are hitherto unknown. To address this question, we achieved a de novo synthesis of bulged CDR-H3 mimics excised from their full antibody context. CD and NMR data revealed that these stable standalone β-hairpin scaffolds are well-folded and retain many of the native bulge CDR-H3 features in water. In particular, the tryptophan residue, highly conserved across CDR-H3 sequences, was found to extend the kinked base of these β-bulges through a combination of stabilizing intramolecular hydrogen bond and CH/π interaction. The structural ensemble consistent with our NMR observations exposed the dynamic nature of residues at the base of the loop, suggesting that β-bulges act as molecular hinges connecting the rigid stem to the more flexible loops of CDR-H3s. We anticipate that this deeper structural understanding of CDR-H3s will lay the foundation to inform the design of antibody drugs broadly and engineer novel CDR-H3 peptide scaffolds as therapeutics.
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Affiliation(s)
- Guangkuan Zhao
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Alexis D. Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - R. Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
| | - Stéphane P. Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
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40
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Yagi S, Tagami S. An ancestral fold reveals the evolutionary link between RNA polymerase and ribosomal proteins. Nat Commun 2024; 15:5938. [PMID: 39025855 PMCID: PMC11258233 DOI: 10.1038/s41467-024-50013-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 06/25/2024] [Indexed: 07/20/2024] Open
Abstract
Numerous molecular machines are required to drive the central dogma of molecular biology. However, the means by which these numerous proteins emerged in the early evolutionary stage of life remains enigmatic. Many of them possess small β-barrel folds with different topologies, represented by double-psi β-barrels (DPBBs) conserved in DNA and RNA polymerases, and similar but topologically distinct six-stranded β-barrel RIFT or five-stranded β-barrel folds such as OB and SH3 in ribosomal proteins. Here, we discover that the previously reconstructed ancient DPBB sequence could also adopt a β-barrel fold named Double-Zeta β-barrel (DZBB), as a metamorphic protein. The DZBB fold is not found in any modern protein, although its structure shares similarities with RIFT and OB. Indeed, DZBB could be transformed into them through simple engineering experiments. Furthermore, the OB designs could be further converted into SH3 by circular-permutation as previously predicted. These results indicate that these β-barrels diversified quickly from a common ancestor at the beginning of the central dogma evolution.
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Affiliation(s)
- Sota Yagi
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Faculty of Human Sciences, Waseda University, 2-579-15, Mikajima, Tokorozawa, Saitama, 359-1192, Japan.
| | - Shunsuke Tagami
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Graduate School of Medicine, Science and Technology, Shinshu University, 3-1-1 Asahi, Matsumoto City, Nagano, 390-8621, Japan.
- International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM²), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
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41
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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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42
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Rodina N, Hornung S, Sarkar R, Suladze S, Peters C, Schmid PWN, Niu Z, Haslbeck M, Buchner J, Kapurniotu A, Reif B. Modulation of Alzheimer's Disease Aβ40 Fibril Polymorphism by the Small Heat Shock Protein αB-Crystallin. J Am Chem Soc 2024; 146:19077-19087. [PMID: 38973199 PMCID: PMC11258688 DOI: 10.1021/jacs.4c03504] [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: 03/11/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/09/2024]
Abstract
Deposition of amyloid plaques in the brains of Alzheimer's disease (AD) patients is a hallmark of the disease. AD plaques consist primarily of the beta-amyloid (Aβ) peptide but can contain other factors such as lipids, proteoglycans, and chaperones. So far, it is unclear how the cellular environment modulates fibril polymorphism and how differences in fibril structure affect cell viability. The small heat-shock protein (sHSP) alpha-B-Crystallin (αBC) is abundant in brains of AD patients, and colocalizes with Aβ amyloid plaques. Using solid-state NMR spectroscopy, we show that the Aβ40 fibril seed structure is not replicated in the presence of the sHSP. αBC prevents the generation of a compact fibril structure and leads to the formation of a new polymorph with a dynamic N-terminus. We find that the N-terminal fuzzy coat and the stability of the C-terminal residues in the Aβ40 fibril core affect the chemical and thermodynamic stability of the fibrils and influence their seeding capacity. We believe that our results yield a better understanding of how sHSP, such as αBC, that are part of the cellular environment, can affect fibril structures related to cell degeneration in amyloid diseases.
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Affiliation(s)
- Natalia Rodina
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
- Helmholtz-Zentrum
München (HMGU), Deutsches Forschungszentrum für Gesundheit
und Umwelt, Institute of Structural Biology (STB), Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Simon Hornung
- Division
of Peptide Biochemistry, TUM School of Life Sciences, Technical University of Munich, Emil-Erlenmeyer-Forum 5, Freising 85354, Germany
| | - Riddhiman Sarkar
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
- Helmholtz-Zentrum
München (HMGU), Deutsches Forschungszentrum für Gesundheit
und Umwelt, Institute of Structural Biology (STB), Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Saba Suladze
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
| | - Carsten Peters
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
| | - Philipp W. N. Schmid
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
| | - Zheng Niu
- School
of Pharmacy, Henan University, Kaifeng, Henan 475004, China
| | - Martin Haslbeck
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
| | - Johannes Buchner
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
| | - Aphrodite Kapurniotu
- Division
of Peptide Biochemistry, TUM School of Life Sciences, Technical University of Munich, Emil-Erlenmeyer-Forum 5, Freising 85354, Germany
| | - Bernd Reif
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
- Helmholtz-Zentrum
München (HMGU), Deutsches Forschungszentrum für Gesundheit
und Umwelt, Institute of Structural Biology (STB), Ingolstädter Landstr. 1, Neuherberg 85764, Germany
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43
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Shekhar S, Meena R, Lal J, Yadav M, Kant R, Reddy DN. Stabilizing Bifurcated Hydrogen Bond in 8-Aminoquinoline Appended Peptides. Chem Asian J 2024; 19:e202400248. [PMID: 38701035 DOI: 10.1002/asia.202400248] [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: 03/06/2024] [Revised: 04/21/2024] [Accepted: 05/03/2024] [Indexed: 05/05/2024]
Abstract
The hydrogen bonding interaction between an amide N-H and the amide N of the preceding residue is prevalent in proline-containing proteins and peptides. However, the N-H⋅⋅⋅N hydrogen bonding interaction is rare in non-prolyl natural peptides due to restricted dihedral angles. Herein, we stabilize this type of interaction in 8-aminoquinoline appended non-prolyl peptides through bifurcated N⋅⋅⋅H⋅⋅⋅N hydrogen bond. The 8-aminoquinoline-incorporated model peptides 2 a-i were designed, synthesized, and the crystal structures of 2 a-c and 2 i were solved. Analysis of crystal data reveals that the amide N-H of aminoquinoline is involved in bifurcated hydrogen bonding interaction with the nitrogen of the preceding amino acid residue and the nitrogen in quinoline. Analysis of crystal packing, Hirshfeld surface and fingerprint plots confirms that the intermolecular O⋅⋅⋅H contacts significantly contribute to stabilizing bifurcated N⋅⋅⋅H⋅⋅⋅N hydrogen bonding interaction. Furthermore, NMR experiments and CD spectroscopy were conducted to examine the preferred conformation in solution, and the data corroborate with the crystal structure conformation.
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Affiliation(s)
- Shashank Shekhar
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
| | - Rachana Meena
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
| | - Jhajan Lal
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
| | - Mukul Yadav
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
| | - Ruchir Kant
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, 226031, Lucknow, India
| | - Damodara N Reddy
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
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44
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Pispas I, Spiliopoulos N, Papagiannopoulos A. Biocompatible Preparation of Beta-Lactoglobulin/Chondroitin Sulfate Carrier Nanoparticles and Modification of Their Colloidal and Hydropathic Properties by Tween 80. Polymers (Basel) 2024; 16:1995. [PMID: 39065312 PMCID: PMC11280915 DOI: 10.3390/polym16141995] [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: 06/25/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The electrostatic complexation of the protein beta-lactoglobulin (β-LG) with the anionic polysaccharide chondroitin sulfate (CS) and the subsequent stabilization by thermal treatment were studied to achieve the well-defined nanoparticles (NPs). The formation of the well-defined NPs was obtained at pH 4 with a hydrodynamic radius from 60 to 80 nm. NP aggregation was observed at pH 1.5 because of the loss of the anionic charge of chondroitin sulfate on the surface of the NPs. After thermal treatment, the NPs exhibited stability against a pH increase to pH 7 while a stronger aggregation at pH 1.5 was observed. Core-shell structures were found at pH 7 after thermal treatment, indicating a possible mechanism of partial disintegration. The addition of Tween 80 (T80) before thermal treatment led to the formation of T80 self-assemblies inside the NPs. This caused an increase in the hydrophobicity of the inner and outer surfaces of the NPs as it was observed by fluorescence spectroscopy. The ζ-potential of the complexes and NPs was about -20 mV while the presence of T80 did not affect it. FTIR spectra verified changes of the secondary structure of β-LG in its complexes with CS and T80. The thermally treated NPs exhibited high surface and overall hydrophobicity and stability in high salinity and biocompatible solutions. The thermally treated NPs showed colloidal and physicochemical stability for 1 month, which were enhanced by the addition of T80. Due to the nature of the precursors and their colloidal properties, the NPs are highly promising for applications as biocompatible drug delivery nanocarriers while T80 acts as an agent to modify their properties.
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Affiliation(s)
- Ioannis Pispas
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece;
| | | | - Aristeidis Papagiannopoulos
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece;
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45
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Loffredo M, Casciaro B, Bellavita R, Troiano C, Brancaccio D, Cappiello F, Merlino F, Galdiero S, Fabrizi G, Grieco P, Stella L, Carotenuto A, Mangoni ML. Strategic Single-Residue Substitution in the Antimicrobial Peptide Esc(1-21) Confers Activity against Staphylococcus aureus, Including Drug-Resistant and Biofilm Phenotype. ACS Infect Dis 2024; 10:2403-2418. [PMID: 38848266 PMCID: PMC11250030 DOI: 10.1021/acsinfecdis.4c00130] [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: 02/19/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/09/2024]
Abstract
Staphylococcus aureus, a bacterium resistant to multiple drugs, is a significant cause of illness and death worldwide. Antimicrobial peptides (AMPs) provide an excellent potential strategy to cope with this threat. Recently, we characterized a derivative of the frog-skin AMP esculentin-1a, Esc(1-21) (1) that is endowed with potent activity against Gram-negative bacteria but poor efficacy against Gram-positive strains. In this study, three analogues of peptide 1 were designed by replacing Gly8 with α-aminoisobutyric acid (Aib), Pro, and dPro (2-4, respectively). The single substitution Gly8 → Aib8 in peptide 2 makes it active against the planktonic form of Gram-positive bacterial strains, especially Staphylococcus aureus, including multidrug-resistant clinical isolates, with an improved biostability without resulting in cytotoxicity to mammalian cells. Moreover, peptide 2 showed a higher antibiofilm activity than peptide 1 against both reference and clinical isolates of S. aureus. Peptide 2 was also able to induce rapid bacterial killing, suggesting a membrane-perturbing mechanism of action. Structural analysis of the most active peptide 2 evidenced that the improved biological activity of peptide 2 is the consequence of a combination of higher biostability, higher α helical content, and ability to reduce membrane fluidity and to adopt a distorted helix, bent in correspondence of Aib8. Overall, this study has shown how a strategic single amino acid substitution is sufficient to enlarge the spectrum of activity of the original peptide 1, and improve its biological properties for therapeutic purposes, thus paving the way to optimize AMPs for the development of new broad-spectrum anti-infective agents.
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Affiliation(s)
- Maria
Rosa Loffredo
- Department
of Biochemical Sciences, Laboratory Affiliated to Istituto Pasteur
Italia-Fondazione Cenci Bolognetti, Sapienza
University of Rome, 00185 Rome, Italy
| | - Bruno Casciaro
- Department
of Biochemical Sciences, Laboratory Affiliated to Istituto Pasteur
Italia-Fondazione Cenci Bolognetti, Sapienza
University of Rome, 00185 Rome, Italy
| | - Rosa Bellavita
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
| | - Cassandra Troiano
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133 Rome, Italy
| | - Diego Brancaccio
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
| | - Floriana Cappiello
- Department
of Biochemical Sciences, Laboratory Affiliated to Istituto Pasteur
Italia-Fondazione Cenci Bolognetti, Sapienza
University of Rome, 00185 Rome, Italy
| | - Francesco Merlino
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
| | - Stefania Galdiero
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
| | - Giancarlo Fabrizi
- Department
of Chemistry and Technology of Drugs, “Department of Excellence
2018−2022”, Sapienza University
of Rome, 00185 Rome, Italy
| | - Paolo Grieco
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
| | - Lorenzo Stella
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133 Rome, Italy
| | - Alfonso Carotenuto
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
| | - Maria Luisa Mangoni
- Department
of Biochemical Sciences, Laboratory Affiliated to Istituto Pasteur
Italia-Fondazione Cenci Bolognetti, Sapienza
University of Rome, 00185 Rome, Italy
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46
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Matsuo T, Yamamoto S, Matsuo K. Phospholipid-induced secondary structural changes of lysozyme polymorphic amyloid fibrils studied using vacuum-ultraviolet circular dichroism. Phys Chem Chem Phys 2024; 26:18943-18952. [PMID: 38952218 DOI: 10.1039/d4cp00965g] [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: 07/03/2024]
Abstract
The hallmark of amyloidosis, such as Alzheimer's disease and Parkinson's disease, is the deposition of amyloid fibrils in various internal organs. The onset of the disease is related to the strength of cytotoxicity caused by toxic amyloid species. Furthermore, amyloid fibrils show polymorphism, where some types of fibrils are cytotoxic while others are not. It is thus essential to understand the molecular mechanism of cytotoxicity, part of which is caused by the interaction between amyloid polymorphic fibrils and cell membranes. Here, using amyloid polymorphs of hen egg white lysozyme, which is associated with hereditary systemic amyloidosis, showing different levels of cytotoxicity and liposomes of DMPC and DMPG, changes in the secondary structure of the polymorphs and the structural state of phospholipid membranes caused by the interaction were investigated using vacuum-ultraviolet circular dichroism (VUVCD) and Laurdan fluorescence measurements, respectively. Analysis has shown that the more cytotoxic polymorph increases the antiparallel β-sheet content and causes more disorder in the membrane structure while the other less cytotoxic polymorph shows the opposite structural changes and causes less structural disorder in the membrane. These results suggest a close correlation between the structural properties of amyloid fibrils and the degree of structural disorder of phospholipid membranes, both of which are involved in the fundamental process leading to amyloid cytotoxicity.
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Affiliation(s)
- Tatsuhito Matsuo
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Chiba, 263-8555, Japan.
| | - Seigi Yamamoto
- Laboratory of Evolutionary Oncology, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima, Japan
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47
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Merlino F, Marzano S, Zizza P, D’Aria F, Grasso N, Carachino A, Iachettini S, Biroccio A, Fonzo SD, Grieco P, Randazzo A, Amato J, Pagano B. Unlocking the potential of protein-derived peptides to target G-quadruplex DNA: from recognition to anticancer activity. Nucleic Acids Res 2024; 52:6748-6762. [PMID: 38828773 PMCID: PMC11229374 DOI: 10.1093/nar/gkae471] [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: 04/15/2024] [Revised: 05/11/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024] Open
Abstract
Noncanonical nucleic acid structures, particularly G-quadruplexes, have garnered significant attention as potential therapeutic targets in cancer treatment. Here, the recognition of G-quadruplex DNA by peptides derived from the Rap1 protein is explored, with the aim of developing novel peptide-based G-quadruplex ligands with enhanced selectivity and anticancer activity. Biophysical techniques were employed to assess the interaction of a peptide derived from the G-quadruplex-binding domain of the protein with various biologically relevant G-quadruplex structures. Through alanine scanning mutagenesis, key amino acids crucial for G-quadruplex recognition were identified, leading to the discovery of two peptides with improved G-quadruplex-binding properties. However, despite their in vitro efficacy, these peptides showed limited cell penetration and anticancer activity. To overcome this challenge, cell-penetrating peptide (CPP)-conjugated derivatives were designed, some of which exhibited significant cytotoxic effects on cancer cells. Interestingly, selected CPP-conjugated peptides exerted potent anticancer activity across various tumour types via a G-quadruplex-dependent mechanism. These findings underscore the potential of peptide-based G-quadruplex ligands in cancer therapy and pave the way for the development of novel therapeutic strategies targeting these DNA structures.
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Affiliation(s)
- Francesco Merlino
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Pasquale Zizza
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Federica D’Aria
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Nicola Grasso
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Alice Carachino
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Sara Iachettini
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Annamaria Biroccio
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Silvia Di Fonzo
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste 34149, Italy
| | - Paolo Grieco
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
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48
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Flores-Fernandez JM, Pesch V, Sriraman A, Chimal-Juarez E, Amidian S, Wang X, Duckering C, Fang A, Reithofer S, Ma L, Cortez LM, Sim VL, Tamgüney G, Wille H. Rational design of structure-based vaccines targeting misfolded alpha-synuclein conformers of Parkinson's disease and related disorders. Bioeng Transl Med 2024; 9:e10665. [PMID: 39036077 PMCID: PMC11256163 DOI: 10.1002/btm2.10665] [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: 07/24/2023] [Revised: 02/28/2024] [Accepted: 03/22/2024] [Indexed: 07/23/2024] Open
Abstract
Synucleinopathies, including Parkinson's disease (PD), multiple system atrophy (MSA), and dementia with Lewy bodies (DLB), are neurodegenerative disorders caused by the accumulation of misfolded alpha-synuclein protein. Developing effective vaccines against synucleinopathies is challenging due to the difficulty of stimulating an immune-specific response against alpha-synuclein without causing harmful autoimmune reactions, selectively targeting only pathological forms of alpha-synuclein. Previous attempts using linear peptides and epitopes without control of the antigen structure failed in clinical trials. The immune system was unable to distinguish between native alpha-synuclein and its amyloid form. The prion domain of the fungal HET-s protein was selected as a scaffold to introduce select epitopes from the surface of alpha-synuclein fibrils. Four vaccine candidates were generated by introducing specific amino acid substitutions onto the surface of the scaffold protein. The approach successfully mimicked the stacking of the parallel in-register beta-sheet structure seen in alpha-synuclein fibrils. All vaccine candidates induced substantial levels of IgG antibodies that recognized pathological alpha-synuclein fibrils derived from a synucleinopathy mouse model. Furthermore, the antisera recognized pathological alpha-synuclein aggregates in brain lysates from patients who died from DLB, MSA, or PD, but did not recognize linear alpha-synuclein peptides. Our approach, based on the rational design of vaccines using the structure of alpha-synuclein amyloid fibrils and strict control over the exposed antigen structure used for immunization, as well as the ability to mimic aggregated alpha-synuclein, provides a promising avenue toward developing effective vaccines against alpha-synuclein fibrils.
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Affiliation(s)
- Jose Miguel Flores-Fernandez
- Centre for Prions and Protein Folding Diseases University of Alberta Edmonton Alberta Canada
- Department of Biochemistry University of Alberta Edmonton Alberta Canada
- Department of Research and Innovation Universidad Tecnológica de Oriental Oriental Puebla Mexico
| | - Verena Pesch
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich GmbH Jülich Germany
| | - Aishwarya Sriraman
- Centre for Prions and Protein Folding Diseases University of Alberta Edmonton Alberta Canada
- Department of Biochemistry University of Alberta Edmonton Alberta Canada
| | - Enrique Chimal-Juarez
- Centre for Prions and Protein Folding Diseases University of Alberta Edmonton Alberta Canada
- Present address: Indiana University School of Medicine Stark Neurosciences Research Institute Indianapolis Indiana USA
| | - Sara Amidian
- Centre for Prions and Protein Folding Diseases University of Alberta Edmonton Alberta Canada
- Department of Biochemistry University of Alberta Edmonton Alberta Canada
| | - Xiongyao Wang
- Centre for Prions and Protein Folding Diseases University of Alberta Edmonton Alberta Canada
- Present address: School of Materials Science and Engineering Harbin Institute of Technology Weihai Shandong China
| | - Caleb Duckering
- Centre for Prions and Protein Folding Diseases University of Alberta Edmonton Alberta Canada
- Department of Biochemistry University of Alberta Edmonton Alberta Canada
| | - Andrew Fang
- Centre for Prions and Protein Folding Diseases University of Alberta Edmonton Alberta Canada
- Department of Biochemistry University of Alberta Edmonton Alberta Canada
| | - Sara Reithofer
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich GmbH Jülich Germany
| | - Liang Ma
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich GmbH Jülich Germany
| | - Leonardo M Cortez
- Centre for Prions and Protein Folding Diseases University of Alberta Edmonton Alberta Canada
- Department of Medicine University of Alberta Edmonton Alberta Canada
| | - Valerie L Sim
- Centre for Prions and Protein Folding Diseases University of Alberta Edmonton Alberta Canada
- Department of Medicine University of Alberta Edmonton Alberta Canada
- Neuroscience and Mental Health Institute, University of Alberta Edmonton Alberta Canada
| | - Gültekin Tamgüney
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich GmbH Jülich Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf Düsseldorf Germany
| | - Holger Wille
- Centre for Prions and Protein Folding Diseases University of Alberta Edmonton Alberta Canada
- Department of Biochemistry University of Alberta Edmonton Alberta Canada
- Neuroscience and Mental Health Institute, University of Alberta Edmonton Alberta Canada
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49
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Cimmino L, Diaferia C, Rosa M, Morelli G, Rosa E, Accardo A. Hybrid peptide-PNA monomers as building blocks for the fabrication of supramolecular aggregates. J Pept Sci 2024; 30:e3573. [PMID: 38471735 DOI: 10.1002/psc.3573] [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] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/14/2024]
Abstract
Advantages like biocompatibility, biodegradability and tunability allowed the exploitation of peptides and peptidomimetics as versatile therapeutic or diagnostic agents. Because of their selectivity towards transmembrane receptors or cell membranes, peptides have also been identified as suitable molecules able to deliver in vivo macromolecules, proteins or nucleic acids. However, after the identification of the homodimer diphenylalanine (FF) as an aggregative motif inside the Aβ1-42 polypeptide, short and ultrashort peptides have been studied as building blocks for the fabrication of supramolecular, ordered nanostructures for applications in biotechnological, biomedical and industrial fields. In this perspective, many hybrid molecules that combine FF with other chemical entities have been synthesized and characterized. Two novel hybrid derivatives (tFaF and cFgF), in which the FF homodimer is alternated with the peptide-nucleic acid (PNA) heterodimer "g-c" (guanine-cytosine) or "a-t" (adenine-thymine) and their dimeric forms (tFaF)2 and (cFgF)2 were synthesized. The structural characterization performed by circular dichroism (CD), Fourier transform infrared (FTIR) and fluorescence spectroscopies highlighted the capability of all the FF-PNA derivatives to self-assemble into β-sheet structures. As a consequence of this supramolecular organization, the resulting aggregates also exhibit optoelectronic properties already reported for other similar nanostructures. This photoemissive behavior is promising for their potential applications in bioimaging.
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Affiliation(s)
| | - Carlo Diaferia
- Department of Pharmacy and CIRPeB, Research Centre on Bioactive Peptides "Carlo Pedone", University of Naples "Federico II", Naples, Italy
| | - Mariangela Rosa
- Department of Pharmacy and CIRPeB, Research Centre on Bioactive Peptides "Carlo Pedone", University of Naples "Federico II", Naples, Italy
| | - Giancarlo Morelli
- Department of Pharmacy and CIRPeB, Research Centre on Bioactive Peptides "Carlo Pedone", University of Naples "Federico II", Naples, Italy
| | - Elisabetta Rosa
- Department of Pharmacy and CIRPeB, Research Centre on Bioactive Peptides "Carlo Pedone", University of Naples "Federico II", Naples, Italy
| | - Antonella Accardo
- Department of Pharmacy and CIRPeB, Research Centre on Bioactive Peptides "Carlo Pedone", University of Naples "Federico II", Naples, Italy
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50
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Ikeda K, Sugiura Y, Nakao H, Nakano M. Thermodynamics of oligomerization and Helix-to-sheet structural transition of amyloid β-protein on anionic phospholipid vesicles. Biophys Chem 2024; 310:107248. [PMID: 38653174 DOI: 10.1016/j.bpc.2024.107248] [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: 02/14/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Understanding oligomerization and aggregation of the amyloid-β protein is important to elucidate the pathological mechanisms of Alzheimer's disease, and lipid membranes play critical roles in this process. In addition to studies reported by other groups, our group has also reported that the negatively-charged lipid bilayers with a high positive curvature induced α-helix-to-β-sheet conformational transitions of amyloid-β-(1-40) upon increase in protein density on the membrane surface and promoted amyloid fibril formation of the protein. Herein, we investigated detailed mechanisms of the conformational transition and oligomer formation of the amyloid-β protein on the membrane surface. Changes in the fractions of the three protein conformers (free monomer, membrane-bound α-helix-rich conformation, and β-sheet-rich conformation) were determined from the fluorescent spectral changes of the tryptophan probe in the protein. The helix-to-sheet structural transition on the surface was described by a thermodynamic model of octamer formation driven by entropic forces including hydrophobic interactions. These findings provide useful information for understanding the self-assembly of amyloidogenic proteins on lipid membrane surfaces.
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Affiliation(s)
- Keisuke Ikeda
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan.
| | - Yuuki Sugiura
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Hiroyuki Nakao
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Minoru Nakano
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
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