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Ran C, Pu K. Molecularly generated light and its biomedical applications. Angew Chem Int Ed Engl 2024; 63:e202314468. [PMID: 37955419 DOI: 10.1002/anie.202314468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/01/2023] [Accepted: 11/10/2023] [Indexed: 11/14/2023]
Abstract
Molecularly generated light, referred to here as "molecular light", mainly includes bioluminescence, chemiluminescence, and Cerenkov luminescence. Molecular light possesses unique dual features of being both a molecule and a source of light. Its molecular nature enables it to be delivered as molecules to regions deep within the body, overcoming the limitations of natural sunlight and physically generated light sources like lasers and LEDs. Simultaneously, its light properties make it valuable for applications such as imaging, photodynamic therapy, photo-oxidative therapy, and photobiomodulation. In this review article, we provide an updated overview of the diverse applications of molecular light and discuss the strengths and weaknesses of molecular light across various domains. Lastly, we present forward-looking perspectives on the potential of molecular light in the realms of molecular imaging, photobiological mechanisms, therapeutic applications, and photobiomodulation. While some of these perspectives may be considered bold and contentious, our intent is to inspire further innovations in the field of molecular light applications.
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Affiliation(s)
- Chongzhao Ran
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Kanyi Pu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 637459, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 308232, Singapore, Singapore
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Cheng Q, He X, Feng A, Ouyang W, Hu Y, Feng J, Zhang L, Yin H, Zheng L. Characteristics of dissolved organic matter during the cyanobacterial degradation in Chaohu Lake, China. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2024; 89:887-903. [PMID: 38423607 PMCID: wst_2024_031 DOI: 10.2166/wst.2024.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The actual DOM in Chaohu Lake was used to feed cyanobacterial to explore the changes of microbial communities, fluorescence spectral characteristics and molecular composition of DOM during the degradation of cyanobacteria. It is found that cyanobacterial grow periodically depending on the concentration of nutrients with the decreasing concentration of nutrient salts. Both Bacteroidetes and Actinobacteria have strong correlation with algae growth. Bacteroidetes has a positive correlation with algae growth, relationship on the contrary, Actinobacteria has a negative relationship. The humus-like components in the four groups are similar, but the protein-like component (C3) shows periodic changes with the life process of cyanobacteria. The average molecular weight of each sample detected by Orbitrap high-resolution mass spectrometer increases slightly and the DOM increase aromaticity in the end. In this study, the molecule of Carboxyl-Rich Alicyclic Molecules (CRAM) is difficult to be done by photodegradation and biodegradation in the early periods, but some molecules of CRAM are selectively degraded by microorganisms in the final period. The growth of cyanobacterial lead to increasing the concentration of protein-like and carbohydrate-like molecule of DOM in the water. In the final stage, the molecule group of CHO disappear significantly and the molecule group of heteroatomic group increase.
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Affiliation(s)
- Qiao Cheng
- Anhui Province Engineering Laboratory for Mine Ecological Remediation, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China E-mail:
| | - Xi He
- Anhui Province Engineering Laboratory for Mine Ecological Remediation, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Airong Feng
- Instruments' Center for Physical Science, University of Science and Technology of China, Hefei 230026, China
| | - Wenjuan Ouyang
- Chinese Academy of Sciences, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing 400714, China
| | - Yanyun Hu
- Instruments' Center for Physical Science, University of Science and Technology of China, Hefei 230026, China
| | - Jingwei Feng
- Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, School of Civil and Hydraulic Engineering, Hefei University of Technology, Hefei 230009, China
| | - Liu Zhang
- Anhui Research Academy for Environmental Science, Hefei 230071, China
| | - Hao Yin
- Instruments' Center for Physical Science, University of Science and Technology of China, Hefei 230026, China
| | - Liugen Zheng
- Anhui Province Engineering Laboratory for Mine Ecological Remediation, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
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Coutinho A, Poveda JA, Renart ML. Conformational Dynamic Studies of Prokaryotic Potassium Channels Explored by Homo-FRET Methodologies. Methods Mol Biol 2024; 2796:35-72. [PMID: 38856894 DOI: 10.1007/978-1-0716-3818-7_3] [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] [Indexed: 06/11/2024]
Abstract
Fluorescence techniques have been widely used to shed light over the structure-function relationship of potassium channels for the last 40-50 years. In this chapter, we describe how a Förster resonance energy transfer between identical fluorophores (homo-FRET) approach can be applied to study the gating behavior of the prokaryotic channel KcsA. Two different gates have been described to control the K+ flux across the channel's pore, the helix-bundle crossing and the selectivity filter, located at the opposite sides of the channel transmembrane section. Both gates can be studied individually or by using a double-reporter system. Due to its homotetrameric structural arrangement, KcsA presents a high degree of symmetry that fulfills the first requisite to calculate intersubunit distances through this technique. The results obtained through this work have helped to uncover the conformational plasticity of the selectivity filter under different experimental conditions and the importance of its allosteric coupling to the opening of the activation (inner) gate. This biophysical approach usually requires low protein concentration and presents high sensitivity and reproducibility, complementing the high-resolution structural information provided by X-ray crystallography, cryo-EM, and NMR studies.
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Affiliation(s)
- Ana Coutinho
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Elche, Spain
| | - María Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Elche, Spain.
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Mondal A, Dolui S, Dhabal S, Kundu S, Das L, Bhattacharjee A, Maiti NC. Structure specific neuro-toxicity of α-synuclein oligomer. Int J Biol Macromol 2023; 253:126683. [PMID: 37666396 DOI: 10.1016/j.ijbiomac.2023.126683] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Parkinson's disease (PD) is linked to α-synuclein (aS) aggregation and deposition of amyloid in the substantia nigra region of the brain tissues. In the current investigation we produced two distinct classes of aS oligomer of differed protein conformation, stability and compared their toxic nature to cultured neuronal cells. Lyophilized oligomer (LO) was produced in storage of aS at-20 °C for 7 days and it was enriched with loosely hold molten globule like structure with residues having preferences for α-helical conformational space. The size of the oligomer was 4-5.5 nm under AFM. This kind of oligomer exhibited potential toxicity towards neuronal cell lines and did not transform into compact β-sheet rich amyloid fiber even after incubation at 37 °C for several days. Formation of another type of oligomer was often observed in the lag phase of aS fibrillation that often occurred at an elevated temperature (37 °C). This kind of heat induced oligomer (IO) was more hydrophobic and relatively less toxic to neuronal cells compared to lyophilized oligomer (LO). Importantly, initiation of hydrophobic zipping of aS caused the transformation of IO into thermodynamically stable β-sheet rich amyloid fibril. On the other hand, the presence of molten globule like conformation in LO, rendered greater toxicity to cultured neuronal cells.
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Affiliation(s)
- Animesh Mondal
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Department of Zoology, Government General Degree College-Mangalkote, Purba Bardhaman, West Bengal 713132, India.
| | - Sandip Dolui
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Sukhamoy Dhabal
- Department of Biotechnology, National Institute of Technology-Durgapur, Mahatma Gandhi Rd, A-Zone, Durgapur, West Bengal 713209, India
| | - Shubham Kundu
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Lopamudra Das
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Ashish Bhattacharjee
- Department of Biotechnology, National Institute of Technology-Durgapur, Mahatma Gandhi Rd, A-Zone, Durgapur, West Bengal 713209, India
| | - Nakul C Maiti
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India.
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Santana PA, Álvarez CA, Valenzuela S, Manchego A, Guzmán F, Tirapegui C, Ahumada M. Stability of ACE2 Peptide Mimetics and Their Implications on the Application for SARS-CoV2 Detection. BIOSENSORS 2023; 13:bios13040473. [PMID: 37185548 PMCID: PMC10136198 DOI: 10.3390/bios13040473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023]
Abstract
The SARS-CoV-2 worldwide outbreak prompted the development of several tools to detect and treat the disease. Among the new detection proposals, the use of peptides mimetics has surged as an alternative to avoid the use of antibodies, of which there has been a shortage during the COVID-19 pandemic. However, the use of peptides in detection systems still presents some questions to be answered, mainly referring to their stability under different environmental conditions. In this work, we synthesized an ACE2 peptide mimic and evaluated its stability in different pH, salinity, polarity, and temperature conditions. Further, the same conditions were assessed when using the ability of the peptide mimic to detect the recombinant SARS-CoV-2 spike protein in a biotin-streptavidin-enzyme-linked assay. Finally, we also tested the capacity of the peptide to detect SARS-CoV-2 from patients' samples. The results indicate that the peptide is structurally sensitive to the medium conditions, with relevance to the pH, where basic pH favored its performance when used as a SARS-CoV-2 detector. Further, the proposed peptide mimic was able to detect SARS-CoV-2 comparably to RT-qPCR results. Therefore, the present study promotes knowledge advancement, particularly in terms of stability considerations, in the application of peptide mimics as a replacement for antibodies in detection systems.
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Affiliation(s)
- Paula A Santana
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, el Llano Subercaseaux 2801, San Miguel, Santiago 8910272, Chile
| | - Claudio A Álvarez
- Laboratorio de Fisiología y Genética Marina, Centro de Estudios Avanzados en Zonas Áridas, Larrondo 1281, Coquimbo 1780000, Chile
- Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo 1780000, Chile
| | - Santiago Valenzuela
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, el Llano Subercaseaux 2801, San Miguel, Santiago 8910272, Chile
| | - Alberto Manchego
- Laboratorio de Microbiología, Facultad de Medicina Veterinaria y Parasitología Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 3673, Peru
| | - Fanny Guzmán
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
| | - Cristian Tirapegui
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, el Llano Subercaseaux 2801, San Miguel, Santiago 8910272, Chile
| | - Manuel Ahumada
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Camino La Piramide 5750, Huechuraba, Santiago 8910272, Chile
- Centro de Nanotecnología Aplicada, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Camino La Piramide 5750, Huechuraba, Santiago 8910272, Chile
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Carlier L, Samson D, Khemtemourian L, Joliot A, Fuchs PFJ, Lequin O. Anionic lipids induce a fold-unfold transition in the membrane-translocating Engrailed homeodomain. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184030. [PMID: 35988722 DOI: 10.1016/j.bbamem.2022.184030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/17/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Homeoprotein transcription factors have the property of interacting with membranes through their DNA-binding homeodomain, which is involved in unconventional internalization and secretion. Both processes depend on membrane-translocating events but their detailed molecular mechanisms are still poorly understood. We have previously characterized the conformational properties of Engrailed 2 homeodomain (EnHD) in aqueous solution and in micelles as membrane-mimetic environments. In the present study, we used small isotropic lipid bicelles as a more relevant membrane-mimetic model to characterize the membrane-bound state of EnHD. We show that lipid bicelles, in contrast to micelles, adequately reproduce the requirement of anionic lipids in the membrane binding and conformational transition of EnHD. The fold-unfold transition of EnHD induced by anionic lipids was characterized by NMR using 1H, 13C, 15N chemical shifts, nuclear Overhauser effects, residual dipolar couplings, intramolecular and intermolecular paramagnetic relaxation enhancements induced by site-directed spin-label or paramagnetic lipid probe, respectively. A global unpacking of EnHD helices is observed leading to a loss of the native fold. However, near-native propensities of EnHD backbone conformation are maintained in membrane environment, including not only the three helices but also the turn connecting helices H2 and H3. NMR and coarse-grained molecular dynamics simulations reveal that the EnHD adopts a shallow insertion in the membrane, with the three helices oriented parallel to the membrane. EnHD explores extended conformations and closed U-shaped conformations, which are stabilized by anionic lipid recruitment.
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Affiliation(s)
- Ludovic Carlier
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, 4 place Jussieu, F-75005 Paris, France.
| | - Damien Samson
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, 4 place Jussieu, F-75005 Paris, France
| | - Lucie Khemtemourian
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, 4 place Jussieu, F-75005 Paris, France
| | - Alain Joliot
- INSERM U932, Institut Curie Centre de Recherche, PSL University, France
| | - Patrick F J Fuchs
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, 4 place Jussieu, F-75005 Paris, France; Université Paris Cité, UFR Sciences du Vivant, F-75013 Paris, France
| | - Olivier Lequin
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, 4 place Jussieu, F-75005 Paris, France.
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Molecular Events behind the Selectivity and Inactivation Properties of Model NaK-Derived Ion Channels. Int J Mol Sci 2022; 23:ijms23169246. [PMID: 36012519 PMCID: PMC9409022 DOI: 10.3390/ijms23169246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/10/2022] [Accepted: 08/14/2022] [Indexed: 11/17/2022] Open
Abstract
Y55W mutants of non-selective NaK and partly K+-selective NaK2K channels have been used to explore the conformational dynamics at the pore region of these channels as they interact with either Na+ or K+. A major conclusion is that these channels exhibit a remarkable pore conformational flexibility. Homo-FRET measurements reveal a large change in W55–W55 intersubunit distances, enabling the selectivity filter (SF) to admit different species, thus, favoring poor or no selectivity. Depending on the cation, these channels exhibit wide-open conformations of the SF in Na+, or tight induced-fit conformations in K+, most favored in the four binding sites containing NaK2K channels. Such conformational flexibility seems to arise from an altered pattern of restricting interactions between the SF and the protein scaffold behind it. Additionally, binding experiments provide clues to explain such poor selectivity. Compared to the K+-selective KcsA channel, these channels lack a high affinity K+ binding component and do not collapse in Na+. Thus, they cannot properly select K+ over competing cations, nor reject Na+ by collapsing, as K+-selective channels do. Finally, these channels do not show C-type inactivation, likely because their submillimolar K+ binding affinities prevent an efficient K+ loss from their SF, thus favoring permanently open channel states.
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Maity D, Oh Y, Gremer L, Hoyer W, Magzoub M, Hamilton AD. Cucurbit[7]uril Inhibits Islet Amyloid Polypeptide Aggregation by Targeting N Terminus Hot Segments and Attenuates Cytotoxicity. Chemistry 2022; 28:e202200456. [DOI: 10.1002/chem.202200456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Debabrata Maity
- Department of Chemistry New York University New York NY 10003 USA
- Present Address: Department of Organic Synthesis and Process Chemistry CSIR-Indian Institute of Chemical Technology (CSIR-IICT) Hyderabad 500007 India
| | - Yujeong Oh
- Biology Program New York University Abu Dhabi P.O. Box 129188, Saadiyat Island Campus Abu Dhabi United Arab Emirates
| | - Lothar Gremer
- Institut für Physikalische Biologie Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich 52425 Jülich Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich 52425 Jülich Germany
| | - Mazin Magzoub
- Biology Program New York University Abu Dhabi P.O. Box 129188, Saadiyat Island Campus Abu Dhabi United Arab Emirates
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Claro B, González-Freire E, Granja JR, Garcia-Fandiño R, Gallová J, Uhríková D, Fedorov A, Coutinho A, Bastos M. Partition of antimicrobial D-L-α-cyclic peptides into bacterial model membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2022; 1864:183729. [PMID: 34506796 DOI: 10.1016/j.bbamem.2021.183729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/30/2021] [Accepted: 08/11/2021] [Indexed: 11/29/2022]
Abstract
Fluorescence spectroscopy is used to characterize the partition of three second-generation D,L-α-cyclic peptides to two lipid model membranes. The peptides have proven antimicrobial activity, particularly against Gram positive bacteria, and the model membranes are formed of either with 1,2-dimyristoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DMPG) or its mixture with 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine (DMPE), at a molar ratio of (1:1). The peptide's intrinsic fluorescence was used in the Steady State and/or Time Resolved Fluorescence Spectroscopy experiments, showing that the peptides bind to the membranes, and the extent of their partition is thereof quantified. The peptide-induced membrane leakage was followed using an encapsulated fluorescent dye. Overall, the partition is mainly driven by electrostatics, but also involves hydrophobic interactions. The introduction of a hydrocarbon tail in one of the residues of the parent peptide, CPR, adjacent to the tryptophan (Trp) residue, significantly improves the partition of the modified peptides, CPRT10 and CPRT14, to both membrane systems. Further, we show that the length of the tail is the main distinguishing factor for the extension of the partition process. The parent peptide induces very limited leakage, at odds with the peptides with tail, that promote fast leakage, increasing in most cases with peptide concentration, and being almost complete for the highest peptide concentration and negatively charged membranes. Overall, the results help the unravelling of the antimicrobial action of these peptides and are well in line with their proven high antimicrobial activity.
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Affiliation(s)
- Bárbara Claro
- CIQUP, Centro de Investigação em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Eva González-Freire
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Juan R Granja
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Rebeca Garcia-Fandiño
- CIQUP, Centro de Investigação em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal; Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Jana Gallová
- Faculty of Pharmacy, Comenius University in Bratislava, 832 32 Bratislava, Slovak Republic
| | - Daniela Uhríková
- Faculty of Pharmacy, Comenius University in Bratislava, 832 32 Bratislava, Slovak Republic
| | - Aleksander Fedorov
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Ana Coutinho
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; Department of Chemistry and Biochemistry, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
| | - Margarida Bastos
- CIQUP, Centro de Investigação em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
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Rossi G, Durek J, Ojha S, Schlüter OK. Fluorescence-based characterisation of selected edible insect species: Excitation emission matrix (EEM) and parallel factor (PARAFAC) analysis. Curr Res Food Sci 2021; 4:862-872. [PMID: 34917946 PMCID: PMC8646056 DOI: 10.1016/j.crfs.2021.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/08/2021] [Indexed: 12/01/2022] Open
Abstract
Fluorescence spectroscopy coupled with chemometric tools is a powerful analytical method, largely used for rapid food quality and safety evaluations. However, its potential has not yet been explored in the novel food sector. In the present study, excitation emission matrices (EEMs) of 15 insect powders produced by milling insects belonging to 5 Orthoptera species (Acheta domesticus, Gryllus assimilis, Gryllus bimaculatus, Locusta migratoria, Schistocerca gregaria) from 3 different origins were investigated. Parallel factor (PARAFAC) analysis performed on the overall averaged dataset was validated for five components, highlighting the presence of five different fluorescence peaks. The presence of these peaks was confirmed on each species, suggesting that fluorescence compounds of edible insects are the same in several species. PARAFAC analysis performed on the overall averaged dataset after alternatively adding the EEM recorded from one standard compound allowed to speculate that edible insects fluorescence raises from mixtures of: tryptophan + tyrosine (PARAFAC component-1), tryptophan + tyrosine + tocopherol (PARAFAC component-2), collagen + pyridoxine + pterins (PARAFAC component-3). This study suggests that fluorescence spectroscopy may represent a powerful method for investigating composition and quality of insect-based foods. Fluorescence landscape of edible insects comprises of 5 different peaks. Similar fluorescence compounds are present among several Orthoptera species. Fluorescence peaks of edible insects result from several chemical molecules. Fluorescence intensity of edible insects depends on their species and origin.
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Affiliation(s)
- G Rossi
- Quality and Safety of Food and Feed, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | - J Durek
- Quality and Safety of Food and Feed, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | - S Ojha
- Quality and Safety of Food and Feed, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | - O K Schlüter
- Quality and Safety of Food and Feed, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany.,Department of Agricultural and Food Sciences, University of Bologna, Piazza Goidanich 60, 47521, Cesena, Italy
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11
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Díaz-García C, Renart ML, Poveda JA, Giudici AM, González-Ros JM, Prieto M, Coutinho A. Probing the Structural Dynamics of the Activation Gate of KcsA Using Homo-FRET Measurements. Int J Mol Sci 2021; 22:ijms222111954. [PMID: 34769384 PMCID: PMC8584343 DOI: 10.3390/ijms222111954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/18/2021] [Accepted: 10/29/2021] [Indexed: 12/16/2022] Open
Abstract
The allosteric coupling between activation and inactivation processes is a common feature observed in K+ channels. Particularly, in the prokaryotic KcsA channel the K+ conduction process is controlled by the inner gate, which is activated by acidic pH, and by the selectivity filter (SF) or outer gate, which can adopt non-conductive or conductive states. In a previous study, a single tryptophan mutant channel (W67 KcsA) enabled us to investigate the SF dynamics using time-resolved homo-Förster Resonance Energy Transfer (homo-FRET) measurements. Here, the conformational changes of both gates were simultaneously monitored after labelling the G116C position with tetramethylrhodamine (TMR) within a W67 KcsA background. At a high degree of protein labeling, fluorescence anisotropy measurements showed that the pH-induced KcsA gating elicited a variation in the homo-FRET efficiency among the conjugated TMR dyes (TMR homo-FRET), while the conformation of the SF was simultaneously tracked (W67 homo-FRET). The dependence of the activation pKa of the inner gate with the ion occupancy of the SF unequivocally confirmed the allosteric communication between the two gates of KcsA. This simple TMR homo-FRET based ratiometric assay can be easily extended to study the conformational dynamics associated with the gating of other ion channels and their modulation.
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Affiliation(s)
- Clara Díaz-García
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Maria Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
- Correspondence: (M.L.R.); (A.C.)
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - Ana Marcela Giudici
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - José M. González-Ros
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - Manuel Prieto
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Ana Coutinho
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: (M.L.R.); (A.C.)
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12
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Lopes-de-Campos D, Pereira-Leite C, Fontaine P, Coutinho A, Prieto M, Sarmento B, Jakobtorweihen S, Nunes C, Reis S. Interface-Mediated Mechanism of Action-The Root of the Cytoprotective Effect of Immediate-Release Omeprazole. J Med Chem 2021; 64:5171-5184. [PMID: 33847502 DOI: 10.1021/acs.jmedchem.1c00251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Omeprazole is usually administered under an enteric coating. However, there is a Food and Drug Administration-approved strategy that enables its release in the stomach. When locally absorbed, omeprazole shows a higher efficacy and a cytoprotective effect, whose mechanism was still unknown. Therefore, we aimed to assess the effect of the absorption route on the gastric mucosa. 2D and 3D models of dipalmitoylphosphatidylcholine (DPPC) at different pH values (5.0 and 7.4) were used to mimic different absorption conditions. Several experimental techniques, namely, fluorescence studies, X-ray scattering methodologies, and Langmuir monolayers coupled with microscopy, X-ray diffraction, and infrared spectroscopy techniques, were combined with molecular dynamics simulations. The results showed that electrostatic and hydrophobic interactions between omeprazole and DPPC rearranged the conformational state of DPPC. Omeprazole intercalates among DPPC molecules, promoting domain formation with untilted phospholipids. Hence, the local release of omeprazole enables its action as a phospholipid-like drug, which can reinforce and protect the gastric mucosa.
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Affiliation(s)
- Daniela Lopes-de-Campos
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Catarina Pereira-Leite
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Philippe Fontaine
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, BP48, 91192 Gif-sur-Yvette, France
| | - Ana Coutinho
- IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal.,Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Manuel Prieto
- IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Bruno Sarmento
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IINFACTS, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Instituto Universitário de Ciências da Saúde, 4585-116 Gandra, Portugal
| | - Sven Jakobtorweihen
- Institute of Thermal Separation Processes, Hamburg University of Technology, 21073 Hamburg, Germany
| | - Cláudia Nunes
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Salette Reis
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
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13
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Membrane binding properties of the C-terminal segment of retinol dehydrogenase 8. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183605. [PMID: 33766534 DOI: 10.1016/j.bbamem.2021.183605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/01/2021] [Accepted: 03/12/2021] [Indexed: 12/18/2022]
Abstract
Light absorption by rhodopsin leads to the release of all-trans retinal (ATRal) in the lipid phase of photoreceptor disc membranes. Retinol dehydrogenase 8 (RDH8) then reduces ATRal into all-trans retinol, which is the first step of the visual cycle. The membrane binding of RDH8 has been postulated to be mediated by one or more palmitoylated cysteines located in its C-terminus. Different peptide variants of the C-terminus of RDH8 were thus used to obtain information on the mechanism of membrane binding of this enzyme. Steady-state and time-resolved fluorescence measurements were performed using short and long C-terminal segments of bovine RDH8, comprising one or two tryptophan residues. The data demonstrate that the amphipathic alpha helical structure of the first portion of the C-terminus of RDH8 strongly contributes to its membrane binding, which is also favored by palmitoylation of at least one of the cysteines located in the last portion of the C-terminus.
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Yu J, Yang J, Seok C, Song WJ. Symmetry-related residues as promising hotspots for the evolution of de novo oligomeric enzymes. Chem Sci 2021; 12:5091-5101. [PMID: 34168770 PMCID: PMC8179601 DOI: 10.1039/d0sc06823c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Directed evolution has provided us with great opportunities and prospects in the synthesis of tailor-made proteins. It, however, often requires at least mid to high throughput screening, necessitating more effective strategies for laboratory evolution. We herein demonstrate that protein symmetry can be a versatile criterion for searching for promising hotspots for the directed evolution of de novo oligomeric enzymes. The randomization of symmetry-related residues located at the rotational axes of artificial metallo-β-lactamase yields drastic effects on catalytic activities, whereas that of non-symmetry-related, yet, proximal residues to the active site results in negligible perturbations. Structural and biochemical analysis of the positive hits indicates that seemingly trivial mutations at symmetry-related spots yield significant alterations in overall structures, metal-coordination geometry, and chemical environments of active sites. Our work implicates that numerous artificially designed and natural oligomeric proteins might have evolutionary advantages of propagating beneficial mutations using their global symmetry. Symmetry-related residues located at the rotational axes can be promising hotspots for the evolution of de novo oligomeric enzymes even though they are distantly located from the active site pocket.![]()
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Affiliation(s)
- Jaeseung Yu
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
| | - Jinsol Yang
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
| | - Chaok Seok
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
| | - Woon Ju Song
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
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15
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Screening of novel excipients for freeze-dried protein formulations. Eur J Pharm Biopharm 2021; 160:55-64. [PMID: 33508435 DOI: 10.1016/j.ejpb.2021.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/16/2021] [Accepted: 01/17/2021] [Indexed: 11/22/2022]
Abstract
The typical excipients used as bulking agents and lyoprotectants for freeze-drying are usually limited to only a few selected substances, such as sucrose and mannitol. Considering the sheer diversity amongst proteins, it is doubtful that this limited choice should, in every case, provide the best possible option in order to achieve the most stable product. In this work, a screening of 12 proteins with 64 excipients was conducted in order to increase the knowledge space of potential excipients. Three critical quality attributes (CQAs) of the freeze-dried products, namely the solid state, the cake appearance and the protein integrity based on changes in tryptophan fluorescence were investigated by high throughput X-ray powder diffraction, image analysis and intrinsic fluorescence spectroscopy, respectively. It was found, that in some cases the excipient had a dominating influence on the CQAs, whilst in other cases the CQAs were primarily protein dependent, or that the CQAs were dependent on the combination of both. In the course of this investigation, a general view of potentially relevant excipients, and their interplay with various proteins, was obtained, thereby furthermore paving the way for the use of novel freeze-drying excipients.
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16
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Giudici AM, Díaz-García C, Renart ML, Coutinho A, Prieto M, González-Ros JM, Poveda JA. Tetraoctylammonium, a Long Chain Quaternary Ammonium Blocker, Promotes a Noncollapsed, Resting-Like Inactivated State in KcsA. Int J Mol Sci 2021; 22:ijms22020490. [PMID: 33419017 PMCID: PMC7825302 DOI: 10.3390/ijms22020490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/28/2020] [Accepted: 01/01/2021] [Indexed: 02/06/2023] Open
Abstract
Alkylammonium salts have been used extensively to study the structure and function of potassium channels. Here, we use the hydrophobic tetraoctylammonium (TOA+) to shed light on the structure of the inactivated state of KcsA, a tetrameric prokaryotic potassium channel that serves as a model to its homologous eukaryotic counterparts. By the combined use of a thermal denaturation assay and the analysis of homo-Förster resonance energy transfer in a mutant channel containing a single tryptophan (W67) per subunit, we found that TOA+ binds the channel cavity with high affinity, either with the inner gate open or closed. Moreover, TOA+ bound at the cavity allosterically shifts the equilibrium of the channel's selectivity filter conformation from conductive to an inactivated-like form. The inactivated TOA+-KcsA complex exhibits a loss in the affinity towards permeant K+ at pH 7.0, when the channel is in its closed state, but maintains the two sets of K+ binding sites and the W67-W67 intersubunit distances characteristic of the selectivity filter in the channel resting state. Thus, the TOA+-bound state differs clearly from the collapsed channel state described by X-ray crystallography and claimed to represent the inactivated form of KcsA.
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Affiliation(s)
- Ana Marcela Giudici
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
| | - Clara Díaz-García
- Institute for Bioengineering and Bioscience (IBB), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (A.C.); (M.P.)
| | - Maria Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
| | - Ana Coutinho
- Institute for Bioengineering and Bioscience (IBB), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (A.C.); (M.P.)
- Departamento de Química e Bioquímica, Faculty of Sciences, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Manuel Prieto
- Institute for Bioengineering and Bioscience (IBB), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (A.C.); (M.P.)
| | - José M. González-Ros
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
- Correspondence: (J.M.G.-R.); (J.A.P.); Tel.: +34-966-658-757 (J.M.G.-R.); +34-966-658-466 (J.A.P.)
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
- Correspondence: (J.M.G.-R.); (J.A.P.); Tel.: +34-966-658-757 (J.M.G.-R.); +34-966-658-466 (J.A.P.)
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17
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Xiong Y, Shi C, Li L, Tang Y, Zhang X, Liao S, Zhang B, Sun C, Ren C. A review on recent advances in amino acid and peptide-based fluorescence and its potential applications. NEW J CHEM 2021. [DOI: 10.1039/d1nj02230j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescence is widely used to detect functional groups and ions, and peptides are used in various fields due to their excellent biological activity.
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Affiliation(s)
- Yingshuo Xiong
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Changxin Shi
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Lingyi Li
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Yuanhan Tang
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Xin Zhang
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Sisi Liao
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Beibei Zhang
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Changmei Sun
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Chunguang Ren
- Yantai Institute of Materia Medica, Yantai 264000, China
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18
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Starosta R, Santos FC, de Almeida RF. Human and bovine serum albumin time-resolved fluorescence: Tryptophan and tyrosine contributions, effect of DMSO and rotational diffusion. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128805] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Quantitative analysis of weakly bound insulin oligomers in solution using polarized multidimensional fluorescence spectroscopy. Anal Chim Acta 2020; 1138:18-29. [PMID: 33161979 DOI: 10.1016/j.aca.2020.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/31/2020] [Accepted: 09/04/2020] [Indexed: 12/28/2022]
Abstract
Being able to measure the size and distribution of oligomers in solution is a critical issue in the manufacture and stability of insulin and other protein formulations. Measuring oligomers reliably can however be complicated, due to their fragile self-assembled structures, which are held together by weak forces. This can cause issues in chromatographic based methods, where dissociation or re-equilibration of oligomer populations can occur e.g. upon dilution in a different eluting buffer, but also for light scattering based methods like dynamic light scattering (DLS) where the size difference involved (often less than a factor 3) does not allow mixtures of oligomers to be resolved. Intrinsic fluorescence offers an attractive alternative as it is non-invasive, sensitive but also because it contains scattered light when implemented via excitation emission matrix (EEM) measurements, that is sensitive to changes in particle size. Here, using insulin at formulation level concentrations, we show for the first time how EEM can both discriminate and quantify the proportion of oligomeric states in solution. This was achieved by using the Rayleigh scatter (RS) band and the fluorescence signal contained in EEM. After validating size changes with DLS, we show in particular how the volume under the RS band correlated linearly with protein/oligomer molecular weight, in agreement with the Debye-Zimm relationship. This was true for the RS data from both EEM and polarized EEM (pEEM) measurements, the latter providing a stronger scatter signal, more sensitive to particle size changes. The fluorescence signal was then used with multivariate curve resolution (MCR) to quantify more precisely the soluble oligomer composition of insulin solutions. In conditions that promoted the formation of mainly one type of oligomer (monomer, dimer, or hexamer), pEEM-MCR helped identify the presence of small amounts of other oligomeric forms, while in conditions that were previously said to favour the insulin tetramer, we show that in the presence of zinc, these insulin samples were instead a heterogenous mixture composed of mostly dimers and hexamers. These MCR results correlated in all cases with the observed discrimination by principal component analysis (PCA), and deviations observed in the RS data. In conclusion, using pEEM scatter and emission components with chemometric data analysis provides a unique analytical method for characterising and monitoring changes in the soluble oligomeric state of proteins.
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20
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Díaz-García C, Hornos F, Giudici AM, Cámara-Artigas A, Luque-Ortega JR, Arbe A, Rizzuti B, Alfonso C, Forwood JK, Iovanna JL, Gómez J, Prieto M, Coutinho A, Neira JL. Human importin α3 and its N-terminal truncated form, without the importin-β-binding domain, are oligomeric species with a low conformational stability in solution. Biochim Biophys Acta Gen Subj 2020; 1864:129609. [PMID: 32234409 DOI: 10.1016/j.bbagen.2020.129609] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/13/2020] [Accepted: 03/26/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Eukaryotic cells have a continuous transit of macromolecules between the cytoplasm and the nucleus. Several carrier proteins are involved in this transport. One of them is importin α, which must form a complex with importin β to accomplish its function, by domain-swapping its 60-residue-long N terminus. There are several human isoforms of importin α; among them, importin α3 has a particularly high flexibility. METHODS We studied the conformational stability of intact importin α3 (Impα3) and its truncated form, where the 64-residue-long, N-terminal importin-β-binding domain (IBB) has been removed (ΔImpα3), in a wide pH range, with several spectroscopic, biophysical, biochemical methods and with molecular dynamics (MD). RESULTS Both species acquired native-like structure between pH 7 and 10.0, where Impα3 was a dimer (with an apparent self-association constant of ~10 μM) and ΔImpα3 had a higher tendency to self-associate than the intact species. The acquisition of secondary, tertiary and quaternary structure, and the burial of hydrophobic patches, occurred concomitantly. Both proteins unfolded irreversibly at physiological pH, by using either temperature or chemical denaturants, through several partially folded intermediates. The MD simulations support the presence of these intermediates. CONCLUSIONS The thermal stability of Impα3 at physiological pH was very low, but was higher than that of ΔImpα3. Both proteins were stable in a narrow pH range, and they unfolded at physiological pH populating several intermediate species. GENERAL SIGNIFICANCE The low conformational stability explains the flexibility of Impα3, which is needed to carry out its recognition of complex cargo sequences.
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Affiliation(s)
- Clara Díaz-García
- iBB- Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal
| | - Felipe Hornos
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | | | - Ana Cámara-Artigas
- Departamento de Química y Física, Research Center CIAIMBITAL, Universidad de Almería- ceiA3, 04120 Almería, Spain
| | - Juan Román Luque-Ortega
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Arantxa Arbe
- Centro de Física de Materiales (CFM) (CSIC-UPV/EHU), Materials Physics Center (MPC), 20018 San Sebastián, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Via P. Bucci, Cubo 31 C, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Juan L Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
| | - Javier Gómez
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | - Manuel Prieto
- iBB- Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal
| | - Ana Coutinho
- iBB- Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal; Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1649-004 Lisboa, Portugal
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain.
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Importance of Hypericin-Bcl2 interactions for biological effects at subcellular levels. Photodiagnosis Photodyn Ther 2019; 28:38-52. [PMID: 31430575 DOI: 10.1016/j.pdpdt.2019.08.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/18/2019] [Accepted: 08/12/2019] [Indexed: 02/06/2023]
Abstract
Hypericin (Hyp) is a naturally occurring compound used as photosensitizer in photodynamic therapy and diagnosis. Recently, we have shown that Hyp presence alone, without illumination, resulted in substantial biological effects at several sub-cellular levels. Hyp induced changes in cellular ultrastructure, mitochondria function and metabolism, and distribution of Bcl2 proteins in malignant and non-malignant cells. The molecular mechanisms that underlie Hyp light-independent effects are still elusive. We have hypothesized that Bcl2-Hyp interactions might be one possible mechanism. We performed molecular docking studies to determine the Hyp-Bcl2 interaction profile. Based on the interaction profiles small Bcl2 peptide segments were selected for further study. We designed small peptides corresponding to Bcl2 BH3 and BH1 domains and tested the binding of Hyp and Bcl2 known inhibitor, ABT263, to the peptides in computer modeling and in vitro binding studies. We employed endogenous tryptophan and tyrosine in the BH3 and BH1 peptides, respectively, and their fluorescent properties to show interaction with Hyp and ABT263. Overall, our results indicate that Hyp can interact with Bcl2 protein at its BH3-BH1 hydrophobic groove, and this interaction may trigger changes in intracellular distribution of Bcl2 proteins. In addition, our computer modeling results suggest that Hyp also interacts with other anti-apoptotic members of Bcl2 family similar to the known BH3 mimetics. Our findings are novel and might contribute to understanding Hyp light-independent effects. In addition, they may substantiate the therapeutic use of Hyp as a BH3 mimetic molecule to enhance other cancer treatments.
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22
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Hall L, Donovan E, Araya M, Idowa E, Jiminez-Segovia I, Folck A, Wells CD, Kimble-Hill AC. Identification of Specific Lysines and Arginines That Mediate Angiomotin Membrane Association. ACS OMEGA 2019; 4:6726-6736. [PMID: 31179409 PMCID: PMC6547806 DOI: 10.1021/acsomega.9b00165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/28/2019] [Indexed: 05/17/2023]
Abstract
The family of Angiomotin (Amot) proteins regulate several biological pathways associated with cellular differentiation, proliferation, and migration. These adaptor proteins target proteins to the apical membrane, actin fibers, or the nucleus. A major function of the Amot coiled-coil homology (ACCH) domain is to initiate protein interactions with the cellular membrane, particularly those containing phosphatidylinositol lipids. The work presented in this article uses several ACCH domain lysine/arginine mutants to probe the relative importance of individual residues for lipid binding. This identified four lysine and three arginine residues that mediate full lipid binding. Based on these findings, three of these residues were mutated to glutamates in the Angiomotin 80 kDa splice form and were incorporated into human mammary cell lines. Results show that mutating three of these residues in the context of full-length Angiomotin reduced the residence of the protein at the apical membrane. These findings provide new insight into how the ACCH domain mediates lipid binding to enable Amot proteins to control epithelial cell growth.
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Affiliation(s)
- Le’Celia Hall
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Emily Donovan
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Michael Araya
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Eniola Idowa
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Ilse Jiminez-Segovia
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Anthony Folck
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Clark D. Wells
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Ann C. Kimble-Hill
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
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Conformational plasticity in the KcsA potassium channel pore helix revealed by homo-FRET studies. Sci Rep 2019; 9:6215. [PMID: 30996281 PMCID: PMC6470172 DOI: 10.1038/s41598-019-42405-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/29/2019] [Indexed: 11/24/2022] Open
Abstract
Potassium channels selectivity filter (SF) conformation is modulated by several factors, including ion-protein and protein-protein interactions. Here, we investigate the SF dynamics of a single Trp mutant of the potassium channel KcsA (W67) using polarized time-resolved fluorescence measurements. For the first time, an analytical framework is reported to analyze the homo-Förster resonance energy transfer (homo-FRET) within a symmetric tetrameric protein with a square geometry. We found that in the closed state (pH 7), the W67-W67 intersubunit distances become shorter as the average ion occupancy of the SF increases according to cation type and concentration. The hypothesis that the inactivated SF at pH 4 is structurally similar to its collapsed state, detected at low K+, pH 7, was ruled out, emphasizing the critical role played by the S2 binding site in the inactivation process of KcsA. This homo-FRET approach provides complementary information to X-ray crystallography in which the protein conformational dynamics is usually compromised.
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24
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Neira JL, Díaz-García C, Prieto M, Coutinho A. The C-terminal SAM domain of p73 binds to the N terminus of MDM2. Biochim Biophys Acta Gen Subj 2019; 1863:760-770. [DOI: 10.1016/j.bbagen.2019.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/25/2019] [Accepted: 01/31/2019] [Indexed: 01/10/2023]
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25
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Nouchikian L, Roque C, Song JY, Rahman N, Ausar SF. An intrinsic fluorescence method for the determination of protein concentration in vaccines containing aluminum salt adjuvants. Vaccine 2018; 36:5738-5746. [PMID: 30107994 DOI: 10.1016/j.vaccine.2018.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/12/2018] [Accepted: 08/03/2018] [Indexed: 12/14/2022]
Abstract
Determination of protein concentration in vaccines containing aluminum salt adjuvant typically necessitates desorption of the protein prior to analysis. Here we describe a method based on the intrinsic fluorescence of tyrosine and tryptophan that requires no desorption of proteins. Adjuvanted formulations of three model Bordetella pertussis antigens were excited at 280 nm and their emission spectra collected from 290 to 400 nm. Emission spectra of protein antigens in the presence of aluminum salt adjuvants were able to be detected, the effects of adjuvants on the spectra were analyzed, and linear regressions were calculated. The fluorescence method proved to be very sensitive with a limit of quantification between 0.4 and 4.4 µg/mL and limit of linearity between 100 and 200 µg/mL, across the formulations tested. The fluorescence method was found to be influenced by adjuvant presence, type of adjuvant, adjuvant concentration, buffer and pH conditions. The method also demonstrated ability to monitor the percent adsorption of antigens to the adjuvants. Furthermore, intrinsic fluorescence showed good correlation with micro-Kjeldahl elemental assay in quantifying protein concentration. Being a non-invasive, quick and sensitive method, intrinsic fluorescence has the potential to be utilized as a high throughput tool for vaccine development and conceivably implemented in-line, using in-line fluorimeters, to monitor antigen concentration during formulation processing.
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Affiliation(s)
- Lucienne Nouchikian
- BioProcess Research and Development, Sanofi Pasteur, 1755 Steeles Ave West, Toronto, Ontario M3R 3T4, Canada
| | - Cristopher Roque
- BioProcess Research and Development, Sanofi Pasteur, 1755 Steeles Ave West, Toronto, Ontario M3R 3T4, Canada
| | - Jimmy Y Song
- BioProcess Research and Development, Sanofi Pasteur, 1755 Steeles Ave West, Toronto, Ontario M3R 3T4, Canada
| | - Nausheen Rahman
- BioProcess Research and Development, Sanofi Pasteur, 1755 Steeles Ave West, Toronto, Ontario M3R 3T4, Canada
| | - Salvador F Ausar
- BioProcess Research and Development, Sanofi Pasteur, 1755 Steeles Ave West, Toronto, Ontario M3R 3T4, Canada.
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26
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Stubenrauch JA, Mevissen C, Schulte MF, Bochenek S, Albrecht M, Subramanian PS. Highly specific “sensing” of tryptophan by a luminescent europium(III) complex. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2016. [DOI: 10.1515/znb-2016-0096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The europium(III) complex 1-Cl3 (S,S-2,2′-(((1,10-phenanthroline-2,9-diyl)bis(methanylylidene))bis(azanylylidene))bis(3-methylbutanamide)europiumtrichloride) undergoes, only in the presence of the amino acid tryptophan, a change of emission at 615 nm. In the presence of few equivalents of tryptophan, emission of the europium complex is enhanced while it disappears upon addition of large amounts. This behavior can be assigned to displacement of the sensitizing phenanthroline ligand of 1-Cl2•Trp in the latter case.
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Affiliation(s)
- Jan A. Stubenrauch
- Institut für Organische Chemie, RWTH Aachen, Landoltweg 1, 52074 Aachen, Germany
| | - Christian Mevissen
- Institut für Organische Chemie, RWTH Aachen, Landoltweg 1, 52074 Aachen, Germany
| | - Marie F. Schulte
- Institut für Organische Chemie, RWTH Aachen, Landoltweg 1, 52074 Aachen, Germany
| | - Steffen Bochenek
- Institut für Organische Chemie, RWTH Aachen, Landoltweg 1, 52074 Aachen, Germany
| | - Markus Albrecht
- Institut für Organische Chemie, RWTH Aachen, Landoltweg 1, 52074 Aachen, Germany
| | - Palani S. Subramanian
- Central Salt and Marine Chemicals, Research Institute (CSRI), Bhavnagar, 364 002, Gujarat, India
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27
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Liebau J, Pettersson P, Szpryngiel S, Mäler L. Membrane Interaction of the Glycosyltransferase WaaG. Biophys J 2016; 109:552-63. [PMID: 26244737 DOI: 10.1016/j.bpj.2015.06.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 06/17/2015] [Accepted: 06/19/2015] [Indexed: 11/30/2022] Open
Abstract
The glycosyltransferase WaaG is involved in the synthesis of lipopolysaccharides that constitute the outer leaflet of the outer membrane in Gram-negative bacteria such as Escherichia coli. WaaG has been identified as a potential antibiotic target, and inhibitor scaffolds have previously been investigated. WaaG is located at the cytosolic side of the inner membrane, where the enzyme catalyzes the transfer of the first outer-core glucose to the inner core of nascent lipopolysaccharides. Here, we characterized the binding of WaaG to membrane models designed to mimic the inner membrane of E. coli. Based on the crystal structure, we identified an exposed and largely α-helical 30-residue sequence, with a net positive charge and several aromatic amino acids, as a putative membrane-interacting region of WaaG (MIR-WaaG). We studied the peptide corresponding to this sequence, along with its bilayer interactions, using circular dichroism, fluorescence quenching, fluorescence anisotropy, and NMR. In the presence of dodecylphosphocholine, MIR-WaaG was observed to adopt a three-dimensional structure remarkably similar to the segment in the crystal structure. We found that the membrane interaction of WaaG is conferred at least in part by MIR-WaaG and that electrostatic interactions play a key role in binding. Moreover, we propose a mechanism of anchoring WaaG to the inner membrane of E. coli, where the central part of MIR-WaaG inserts into one leaflet of the bilayer. In this model, electrostatic interactions as well as surface-exposed Tyr residues bind WaaG to the membrane.
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Affiliation(s)
- Jobst Liebau
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Pontus Pettersson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Scarlett Szpryngiel
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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Melo AM, Fedorov A, Prieto M, Coutinho A. Exploring homo-FRET to quantify the oligomer stoichiometry of membrane-bound proteins involved in a cooperative partition equilibrium. Phys Chem Chem Phys 2015; 16:18105-17. [PMID: 24722583 DOI: 10.1039/c4cp00060a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The establishment of protein-protein interactions between membrane-bound proteins is associated with several biological functions and dysfunctions. Here, an analytical framework that uses energy homo transfer to directly probe quantitatively the oligomerization state of membrane-bound proteins engaged in a three-state cooperative partition is presented. Briefly, this model assumes that monomeric protein molecules partition into the bilayer surface and reversibly assemble into oligomers with k subunits. A general equation relating the overall steady-state fluorescence anisotropy of the sample to its fractional labeling was derived by considering explicitly that the anisotropy of mixed oligomers containing i-labeled monomers is inversely proportional to the number of labeled subunits per oligomer (Runnels and Scarlata limit). This method was very robust in describing the electrostatic interaction of Alexa Fluor 488 fluorescently labeled lysozyme (Lz-A488) with phosphatidylserine-containing membranes. The pronounced decrease detected in the fluorescence anisotropy of Lz-A488 always correlated with the system reaching a high membrane surface density of the protein (at a low lipid-to-protein (L/P) molar ratio). The occurrence of energy homo transfer-induced fluorescence depolarization was further confirmed by measuring the anisotropy decays of Lz-A488 under these conditions. A global analysis of the steady-state anisotropy data obtained under a wide range of experimental conditions (variable anionic lipid content of the liposomes, L/P molar ratios and protein fractional labeling) confirmed that membrane-bound Lz-A488 assembled into oligomeric complexes, possibly with a stoichiometry of k = 6 ± 1. This study illustrates that even in the presence of a coupled partition-oligomerization equilibrium, steady-state anisotropy measurements provide a simple and reliable tool to monitor the self-assembly of membrane-bound proteins.
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Affiliation(s)
- Ana M Melo
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
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29
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Ammari F, Bendoula R, Jouan-Rimbaud Bouveresse D, Rutledge DN, Roger JM. 3D front face solid-phase fluorescence spectroscopy combined with Independent Components Analysis to characterize organic matter in model soils. Talanta 2014; 125:146-52. [DOI: 10.1016/j.talanta.2014.02.049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/13/2014] [Accepted: 02/20/2014] [Indexed: 11/16/2022]
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30
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Xu Q, Lu Y, Jing L, Cai L, Zhu X, Xie J, Hu X. Specific binding and inhibition of 6-benzylaminopurine to catalase: multiple spectroscopic methods combined with molecular docking study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 123:327-335. [PMID: 24412785 DOI: 10.1016/j.saa.2013.12.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 12/05/2013] [Accepted: 12/05/2013] [Indexed: 06/03/2023]
Abstract
6-Benzylaminopurine (6-BA) is a kind of cytokinin which could regulate the activities of the antioxidant defense system of plants. In this work, its interaction with and inhibition of beef liver catalase have been systematically investigated using spectroscopic, isothermal titration calorimetric and molecular docking methods under physiological conditions. The fluorescence quenching of beef liver catalase (BLC) by 6-BA is due to the formation of 6-BA-BLC complex. Hydrogen bonds and van der Waals interactions play major roles in stabilizing the complex. The Stern-Volmer quenching constant, binding constant, the corresponding thermodynamic parameters and binding numbers were measured. The results of UV-vis absorption, three-dimensional fluorescence, synchronous fluorescence and circular dichroism spectroscopic results demonstrate that the binding of 6-BA results in the micro-environment change around tyrosine (Tyr) and tryptophan (Trp) residues of BLC. The BLC-mediated conversion of H2O2 to H2O and O2, in the presence and absence of 6-BA, was also studied. Lineweaver-Burk plot indicates a noncompetitive type of inhibition. Molecular docking study was used to find the binding sites.
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Affiliation(s)
- Qin Xu
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China.
| | - Yanni Lu
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Longyun Jing
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Lijuan Cai
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Xinfeng Zhu
- College of Information Technology, Yangzhou University, Yangzhou 225127, China
| | - Ju Xie
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Xiaoya Hu
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China.
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31
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Supramolecular structure of membrane-associated polypeptides by combining solid-state NMR and molecular dynamics simulations. Biophys J 2012; 103:29-37. [PMID: 22828329 DOI: 10.1016/j.bpj.2012.05.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 04/30/2012] [Accepted: 05/07/2012] [Indexed: 02/02/2023] Open
Abstract
Elemental biological functions such as molecular signal transduction are determined by the dynamic interplay between polypeptides and the membrane environment. Determining such supramolecular arrangements poses a significant challenge for classical structural biology methods. We introduce an iterative approach that combines magic-angle spinning solid-state NMR spectroscopy and atomistic molecular dynamics simulations for the determination of the structure and topology of membrane-bound systems with a resolution and level of accuracy difficult to obtain by either method alone. Our study focuses on the Shaker B ball peptide that is representative for rapid N-type inactivating domains of voltage-gated K(+) channels, associated with negatively charged lipid bilayers.
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32
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Dupuy F, Morero R. Microcin J25 membrane interaction: Selectivity toward gel phase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1764-71. [DOI: 10.1016/j.bbamem.2011.02.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 02/14/2011] [Accepted: 02/22/2011] [Indexed: 10/18/2022]
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33
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Fang J, Zhang X, Cai Y, Wei Y. Small Globular Protein Motif Forms Particulate Hydrogel under Various pH Conditions. Biomacromolecules 2011; 12:1578-84. [DOI: 10.1021/bm101571r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jun Fang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Xiaoning Zhang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yuguang Cai
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yinan Wei
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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34
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De Almeida RFM, Loura LMS, Prieto M, Watts A, Fedorov A, Barrantes FJ. Structure and dynamics of the γM4 transmembrane domain of the acetylcholine receptor in lipid bilayers: insights into receptor assembly and function. Mol Membr Biol 2009; 23:305-15. [PMID: 16923724 DOI: 10.1080/09687860600703613] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A 28-mer peptide (gammaM4) corresponding to the fourth transmembrane segment of the nicotinic acetylcholine receptor (AChR) gamma-subunit, with a single tryptophan residue (Trp6), was reconstituted into lipid bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), loaded with either high or low amounts of cholesterol, i.e., in the conjugated liquid-ordered and liquid-disordered phases, respectively, at room temperature. By making use of the Trp intrinsic fluorescence, both steady-state and time-resolved fluorescence techniques were employed, namely, red-edge excitation shift effect, decay-associated spectra (DAS), and time-resolved anisotropy. The results obtained here, together with previous studies on the same reconstituted peptide, indicate that: (i) Trp6 is strongly anchored in the bilayer with a defined transverse location; (ii) the modifications in the measured DAS are related to the complex result of a self-quenching process on the decay parameters; (iii) the wobbling movement of the indole moiety of Trp6 is fast but severely restricted in amplitude; and, (iv) in the liquid-ordered phase, the bilayer properties and the tilt angle of the peptide enhance peptide-peptide interactions, with the formation of peptide rich patches and possibly some anti-parallel helix-helix aggregates, showing different dynamics from that of the peptide in the liquid-disordered phase where the peptide is randomly distributed.
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Affiliation(s)
- Rodrigo F M De Almeida
- Centro de Química e Bioquímica, Faculdade de Ciências de Lisboa, Campo Grande, Lisboa, Portugal.
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35
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Teplova M, Patel DJ. Structural insights into RNA recognition by the alternative-splicing regulator muscleblind-like MBNL1. Nat Struct Mol Biol 2008; 15:1343-51. [PMID: 19043415 DOI: 10.1038/nsmb.1519] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Accepted: 10/27/2008] [Indexed: 12/21/2022]
Abstract
Muscleblind-like (MBNL) proteins, regulators of developmentally programmed alternative splicing, harbor tandem CCCH zinc-finger (ZnF) domains that target pre-mRNAs containing YGCU(U/G)Y sequence elements (where Y is a pyrimidine). In myotonic dystrophy, reduced levels of MBNL proteins lead to aberrant alternative splicing of a subset of pre-mRNAs. The crystal structure of MBNL1 ZnF3/4 bound to r(CGCUGU) establishes that both ZnF3 and ZnF4 target GC steps, with site-specific recognition mediated by a network of hydrogen bonds formed primarily with main chain groups of the protein. The relative alignment of ZnF3 and ZnF4 domains is dictated by the topology of the interdomain linker, with a resulting antiparallel orientation of bound GC elements, supportive of a chain-reversal loop trajectory for MBNL1-bound pre-mRNA targets. We anticipate that MBNL1-mediated targeting of looped RNA segments proximal to splice-site junctions could contribute to pre-mRNA alternative-splicing regulation.
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Affiliation(s)
- Marianna Teplova
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 439 East 67th Street, New York, NY 10021, USA
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36
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Pastor I, Prieto M, Mateo CR. Effect of Sol−Gel Confinement on the Structural Dynamics of the Enzyme Bovine Cu,Zn Superoxide Dismutase. J Phys Chem B 2008; 112:15021-8. [DOI: 10.1021/jp805368s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Isabel Pastor
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202-Elche, Spain, and Centro de Química-Física Molecular and IN- Institute of Nanosciences and Nanotechnology, Instituto Superior Técnico, Av. Rovisco Pais, P-1049-001, Lisboa, Portugal
| | - Manuel Prieto
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202-Elche, Spain, and Centro de Química-Física Molecular and IN- Institute of Nanosciences and Nanotechnology, Instituto Superior Técnico, Av. Rovisco Pais, P-1049-001, Lisboa, Portugal
| | - C. Reyes Mateo
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202-Elche, Spain, and Centro de Química-Física Molecular and IN- Institute of Nanosciences and Nanotechnology, Instituto Superior Técnico, Av. Rovisco Pais, P-1049-001, Lisboa, Portugal
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37
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Guillén J, Pérez-Berná AJ, Moreno MR, Villalaín J. A second SARS-CoV S2 glycoprotein internal membrane-active peptide. Biophysical characterization and membrane interaction. Biochemistry 2008; 47:8214-24. [PMID: 18616295 DOI: 10.1021/bi800814q] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV) envelope spike (S) glycoprotein, a class I viral fusion protein, is responsible for the fusion between the membranes of the virus and the target cell. The S2 domain of protein S has been suggested to have two fusion peptides, one located at its N-terminus, downstream of the furin cleavage, and another, more internal, located immediately upstream of the HR1. Therefore, we have carried out a study of the binding and interaction with model membranes of a peptide corresponding to segment 873-888 of the SARS-CoV S glycoprotein, peptide SARS IFP, as well as the structural changes taking place in both the phospholipid and the peptide induced by the binding of the peptide to the membrane. We demonstrate that SARS IFP peptide binds to and interacts with phospholipid model membranes and shows a higher affinity for negatively charged phospholipids than for zwitterionic ones. SARS IFP peptide specifically decreases the mobility of the phospholipid acyl chains of negatively charged phospholipids and adopts different conformations in the membrane depending upon their composition. These data support its role in SARS-mediated membrane fusion and suggest that the regions where this peptide resides might assist the fusion peptide and/or the pretransmembrane segment of the SARS-CoV spike glycoprotein in the fusion process.
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Affiliation(s)
- Jaime Guillén
- Instituto de Biología Molecular y Celular, Campus de Elche, Universidad Miguel Hernández, E-03202 Elche-Alicante, Spain
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Yang CM, Li X, Wei W, Li Y, Duan Z, Zheng J, Huang T. Dissecting the General Physicochemical Properties of Noncovalent Interactions Involving Tyrosine Side Chain as a Second-Shell Ligand in Biomolecular Metal-Binding Site Mimetics: An Experimental Study Combining Fluorescence,13C NMR Spectroscopy and ESI Mass Spectrometry. Chemistry 2007; 13:3120-30. [PMID: 17201001 DOI: 10.1002/chem.200600661] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Detailed physicochemical features inherent in the dynamic cation-pi interactions of aromatic amino acid side chains in the secondary coordination spheres around metal ions were extracted and mapped by intrinsic tyrosine fluorescence titration experiments with two homologous, artificially engineered metal-binding scaffolds which mimic metal-binding sites in metalloproteins. A newly formulated method for the treatment of fluorescence titration data allows straightforward assessment of both the magnitudes and properties of metal-chelation-assisted cation-aromatic interactions (K2) underlying a proposed two-step metallosupramolecular association process. The unprecedented linear platform-motif correlations between the two contrasting scaffolds in their changes in tyrosine fluorescence on binding of 3d metal cations help to elucidate the properties of general cation-arene recognition corresponding to the metal-responsive characteristics of the second-shell Tyr residue surrounding the metal-binding sites in the supramolecular context, and thereby define a new noncovalent design principle for metal-ion recognition in aqueous solution. As supported by NMR spectroscopic and ESI-MS analyses and molecular mechanics force field calculations, the systematic study exemplifies the concept of using steady-state tyrosine fluorescence as a powerful tool for comprehensive descriptions of cation-pi interactions in the extended environment of a metal-binding site. We established that the physicochemical properties pertaining to indirect metal-arene interactions are highly dependent on the electronic properties of the metal ions. This work suggests that second-shell cation-pi interactions may play more diverse roles, including modulation of structure, reactivity, and function of metal-binding sites, than the previously well-established direct cation-pi interactions involving hard cations (e.g., alkali metal ions). Moreover, such a study will continue to complement theoretical predications and/or the early experimental investigations in organic solvents.
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Affiliation(s)
- Chi Ming Yang
- Neurochemistry and Physical Organic Chemistry, Nankai University, Tianjin 300071, China.
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39
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From Lipid Phases to Membrane Protein Organization: Fluorescence Methodologies in the Study of Lipid-Protein Interactions. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/3-540-28435-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Lopes SCDN, Fedorov A, Castanho MARB. Cholesterol modulates maculosin's orientation in model systems of biological membranes. Relevance towards putative molecular recognition. Steroids 2004; 69:825-30. [PMID: 15582538 DOI: 10.1016/j.steroids.2004.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2004] [Revised: 09/10/2004] [Accepted: 10/04/2004] [Indexed: 10/26/2022]
Abstract
Fluorescence techniques were used to study (1) the extent of insertion of the bioactive cyclic dipeptide cyclo(l-tyrosyl-l-prolyl), maculosin, in model systems of membranes of 1, 2-palmitoyl-sn-glycero-3-phosphatidyl choline (DPPC) or 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl choline (POPC), (2) its in-depth location in those lipidic membranes, and (3) the influence of cholesterol on the dipeptides's location and orientation. Partition into lipidic bilayers is extensive, mainly for liquid crystalline phase membranes (K(p)=1.3x10(4)). Maculosin locates at the lipid head groups level regardless of the membrane system. Nevertheless, its orientation is lipid phase dependent. When maculosin was inserted in liquid crystalline phase bilayers, its phenolic ring was perpendicular to the membrane surface, whereas it changed orientation when inserted in gel phase membranes. Cholesterol was able to reverse the lipid phase influence on maculosin's orientation.
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Affiliation(s)
- Sílvia C D N Lopes
- Centro de Química-Física Molecular, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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Affiliation(s)
- Donald W Hilgemann
- Department of Physiology, University of Texas Southwestern, Dallas, TX 75235, USA.
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