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Xu J, Zhang X, Zhong J, Huang S, Wang S, Zhai H. Surface-active agent enhanced FRET effect Cu-doped NH 2-MIL-88(Fe) for highly sensitive detection of 3-nitro-L-tyrosine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 316:124315. [PMID: 38688213 DOI: 10.1016/j.saa.2024.124315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/11/2024] [Accepted: 04/18/2024] [Indexed: 05/02/2024]
Abstract
In this study, Cu-doped NH2-MIL-88(Fe) metal-organic frameworks (MOF) were synthesized via a one-step method. Characterization techniques such as XPS, XRD and FTIR confirmed the successful incorporation of Cu2+ into NH2-MIL-88(Fe), naming this MOF as NH2-MIL-88(Fe)@Cu2+. This MOF was employed to develop a highly sensitive fluorescence sensing platform for detecting 3-nitro-L-tyrosine(3-NT). The potential for fluorescence resonance energy transfer (FRET) was suggested by the spectral overlap between NH2-MIL-88(Fe)@Cu2+'s emission and 3-NT's UV absorption. To augment this effect, cationic surfactant hexadecyltrimethylammonium bromide (CTAB), which self-assembled into nanostructured microspheres above its critical micelle concentration, was utilized. The charged surface of these microspheres, formed by the self-assembly of CTAB, is bound to the MOF surface through electrostatic force and simultaneously attracts 3-NT. Adjusting the solution's pH strengthened the interaction between NH2-MIL-88(Fe)@Cu2+ and 3-NT, thereby enhancing their mutual FRET interaction. Experimental results indicated that CTAB's introduction markedly improved the FRET effects, potentially converting a weak FRET into a strong one and enhancing detection sensitivity and accuracy. Under optimal conditions, NH2-MIL-88(Fe)@Cu2+ detected 3-NT within 0-30 μM range, with a limit of detection (LOD, S/N = 3) of 41.1 nM. Finally, the applicability of the sensor is tested by calibrating measurements in fetal bovine serum samples, achieving good performance in terms of sensitivity, selectivity and reproducibility. This research provides a method for efficient and highly sensitive 3-NT detection and insights into the FRET effect between MOF and target molecules, likely advancing related fields and inspiring future fluorescence sensor designs.
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Affiliation(s)
- Jin Xu
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Xiaohui Zhang
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jiapeng Zhong
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Siying Huang
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Shumei Wang
- Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Haiyun Zhai
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou 510006, China.
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2
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Dey A, Patil A, Arumugam S, Maiti S. Single-Molecule Maps of Membrane Insertion by Amyloid-β Oligomers Predict Their Toxicity. J Phys Chem Lett 2024; 15:6292-6298. [PMID: 38855822 DOI: 10.1021/acs.jpclett.4c01048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The interaction of small Amyloid-β (Aβ) oligomers with the lipid membrane is an important component of the pathomechanism of Alzheimer's disease (AD). However, oligomers are heterogeneous in size. How each type of oligomer incorporates into the membrane, and how that relates to their toxicity, is unknown. Here, we employ a single molecule technique called Q-SLIP (Quencher-induced Step Length Increase in Photobleaching) to measure the membrane insertion of each monomeric unit of individual oligomers of Aβ42, Aβ40, and Aβ40-F19-Cyclohexyl alanine (Aβ40-F19Cha), and correlate it with their toxicity. We observe that the N-terminus of Aβ42 inserts close to the center of the bilayer, the less toxic Aβ40 inserts to a shallower depth, and the least toxic Aβ40-F19Cha has no specific distribution. This oligomer-specific map provides a mechanistic representation of membrane-mediated Aβ toxicity and should be a valuable tool for AD research.
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Affiliation(s)
- Arpan Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Abhishek Patil
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC 3800, Australia
| | - Senthil Arumugam
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC 3800, Australia
- European Molecular Biological Laboratory Australia (EMBL Australia), Monash University, Clayton/Melbourne, VIC 3800, Australia
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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3
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Tutkus M, Lundgaard CV, Veshaguri S, Tønnesen A, Hatzakis N, Rasmussen SGF, Stamou D. Probing Activation and Conformational Dynamics of the Vesicle-Reconstituted β 2 Adrenergic Receptor at the Single-Molecule Level. J Phys Chem B 2024; 128:2124-2133. [PMID: 38391238 PMCID: PMC10926102 DOI: 10.1021/acs.jpcb.3c08349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
G-protein-coupled receptors (GPCRs) are structurally flexible membrane proteins that mediate a host of physiological responses to extracellular ligands like hormones and neurotransmitters. Fine features of their dynamic structural behavior are hypothesized to encode the functional plasticity seen in GPCR activity, where ligands with different efficacies can direct the same receptor toward different signaling phenotypes. Although the number of GPCR crystal structures is increasing, the receptors are characterized by complex and poorly understood conformational landscapes. Therefore, we employed a fluorescence microscopy assay to monitor conformational dynamics of single β2 adrenergic receptors (β2ARs). To increase the biological relevance of our findings, we decided not to reconstitute the receptor in detergent micelles but rather lipid membranes as proteoliposomes. The conformational dynamics were monitored by changes in the intensity of an environmentally sensitive boron-dipyrromethene (BODIPY 493/503) fluorophore conjugated to an endogenous cysteine (located at the cytoplasmic end of the sixth transmembrane helix of the receptor). Using total internal reflection fluorescence microscopy (TIRFM) and a single small unilamellar liposome assay that we previously developed, we followed the real-time dynamic properties of hundreds of single β2ARs reconstituted in a native-like environment─lipid membranes. Our results showed that β2AR-BODIPY fluctuates between several states of different intensity on a time scale of seconds, compared to BODIPY-lipid conjugates that show almost entirely stable fluorescence emission in the absence and presence of the full agonist BI-167107. Agonist stimulation changes the β2AR dynamics, increasing the population of states with higher intensities and prolonging their durations, consistent with bulk experiments. The transition density plot demonstrates that β2AR-BODIPY, in the absence of the full agonist, interconverts between states of low and moderate intensity, while the full agonist renders transitions between moderate and high-intensity states more probable. This redistribution is consistent with a mechanism of conformational selection and is a promising first step toward characterizing the conformational dynamics of GPCRs embedded in a lipid bilayer.
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Affiliation(s)
- Marijonas Tutkus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio Ave. 7, LT-10257 Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Saulėtekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Christian V Lundgaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Salome Veshaguri
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Asger Tønnesen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Nikos Hatzakis
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
- Department of Chemistry and Nanoscience Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Søren G F Rasmussen
- Department of Neuroscience and Pharmacology, Panum, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Dimitrios Stamou
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
- Center for Geometrically Engineered Cellular Systems, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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4
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Kyrychenko A, Ladokhin AS. Fluorescent Probes and Quenchers in Studies of Protein Folding and Protein-Lipid Interactions. CHEM REC 2024; 24:e202300232. [PMID: 37695081 PMCID: PMC11113672 DOI: 10.1002/tcr.202300232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/20/2023] [Indexed: 09/12/2023]
Abstract
Fluorescence spectroscopy provides numerous methodological tools for structural and functional studies of biological macromolecules and their complexes. All fluorescence-based approaches require either existence of an intrinsic probe or an introduction of an extrinsic one. Moreover, studies of complex systems often require an additional introduction of a specific quencher molecule acting in combination with a fluorophore to provide structural or thermodynamic information. Here, we review the fundamentals and summarize the latest progress in applications of different classes of fluorescent probes and their specific quenchers, aimed at studies of protein folding and protein-membrane interactions. Specifically, we discuss various environment-sensitive dyes, FRET probes, probes for short-distance measurements, and several probe-quencher pairs for studies of membrane penetration of proteins and peptides. The goals of this review are: (a) to familiarize the readership with the general concept that complex biological systems often require both a probe and a quencher to decipher mechanistic details of functioning and (b) to provide example of the immediate applications of the described methods.
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Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody sq., Kharkiv, 61022, Ukraine
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, United States
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5
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Jeong HJ. Quenchbodies That Enable One-Pot Detection of Antigens: A Structural Perspective. Bioengineering (Basel) 2023; 10:1262. [PMID: 38002387 PMCID: PMC10669387 DOI: 10.3390/bioengineering10111262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Quenchbody (Q-body) is a unique, reagentless, fluorescent antibody whose fluorescent intensity increases in an antigen-concentration-dependent manner. Q-body-based homogeneous immunoassay is superior to conventional immunoassays as it does not require multiple immobilization, reaction, and washing steps. In fact, simply mixing the Q-body and the sample containing the antigen enables the detection of the target antigen. To date, various Q-bodies have been developed to detect biomarkers of interest, including haptens, peptides, proteins, and cells. This review sought to describe the principle of Q-body-based immunoassay and the use of Q-body for various immunoassays. In particular, the Q-bodies were classified from a structural perspective to provide useful information for designing Q-bodies with an appropriate objective.
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Affiliation(s)
- Hee-Jin Jeong
- Department of Biological and Chemical Engineering, Hongik University, Sejong-si 30016, Republic of Korea
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6
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Tatsukawa H, Aoyama R, Hitomi K. Development of peptide-based biosensors for detecting cross-linking and deamidation activities of transglutaminases. Amino Acids 2023:10.1007/s00726-023-03272-7. [PMID: 37165293 DOI: 10.1007/s00726-023-03272-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 04/20/2023] [Indexed: 05/12/2023]
Abstract
Transglutaminases (TGs) are a protein family that catalyzes isopeptide bond formation between glutamine and lysine residues of various proteins. There are eight TG isozymes in humans, and each is involved in diverse biological phenomena due to their characteristic distribution. Abnormal activity of TG1 and TG2, which are major TG isozymes, is believed to cause various diseases, such as ichthyosis and celiac disease. To elucidate TGs' mechanisms of action and develop new therapeutic strategies, it is essential to develop bioprobes that can specifically examine the activity of each TG isozyme, which has not been sufficiently studied. We previously have identified several substrate peptide sequences containing Gln residues for each isozyme and developed a method to detect isozyme-specific activities by incorporating a labeled substrate peptide into lysine residues of proteins. We prepared the fluorescein isothiocyanate (FITC)-labeled Gln substrate peptide (FITC-K5 and FITC-T26) and Rhodamine B-labeled Lys substrate peptide (RhoB-Kpep). Each TG reaction specifically cross-linked these probe pairs, and the proximity of FITC and Rhodamine B significantly decreased the fluorescence intensity of FITC depending on the concentration and reaction time of each TG. In this study, we developed a peptide-based biosensor that quickly and easily measures TG isozyme-specific activity. This probe is expected to be helpful in elucidating TG's physiological and pathological functions and in developing compounds that modulate TG activity.
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Affiliation(s)
- Hideki Tatsukawa
- Cellular Biochemistry Lab., Graduate School of Pharmaceutical Sciences, Nagoya University, Tokai National Higher Education and Research System, Furo-cho, Chikusa, Nagoya, 464-8601, Japan.
| | - Ruriko Aoyama
- Cellular Biochemistry Lab., Graduate School of Pharmaceutical Sciences, Nagoya University, Tokai National Higher Education and Research System, Furo-cho, Chikusa, Nagoya, 464-8601, Japan
| | - Kiyotaka Hitomi
- Cellular Biochemistry Lab., Graduate School of Pharmaceutical Sciences, Nagoya University, Tokai National Higher Education and Research System, Furo-cho, Chikusa, Nagoya, 464-8601, Japan
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7
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Illumination of a progressive allosteric mechanism mediating the glycine receptor activation. Nat Commun 2023; 14:795. [PMID: 36781912 PMCID: PMC9925812 DOI: 10.1038/s41467-023-36471-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 02/02/2023] [Indexed: 02/15/2023] Open
Abstract
Pentameric ligand-gated ion channel mediate signal transduction at chemical synapses by transiting between resting and open states upon neurotransmitter binding. Here, we investigate the gating mechanism of the glycine receptor fluorescently labeled at the extracellular-transmembrane interface by voltage-clamp fluorometry (VCF). Fluorescence reports a glycine-elicited conformational change that precedes pore opening. Low concentrations of glycine, partial agonists or specific mixtures of glycine and strychnine trigger the full fluorescence signal while weakly activating the channel. Molecular dynamic simulations of a partial agonist bound-closed Cryo-EM structure show a highly dynamic nature: a marked structural flexibility at both the extracellular-transmembrane interface and the orthosteric site, generating docking properties that recapitulate VCF data. This work illuminates a progressive propagating transition towards channel opening, highlighting structural plasticity within the mechanism of action of allosteric effectors.
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8
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Fang B, Shen Y, Peng B, Bai H, Wang L, Zhang J, Hu W, Fu L, Zhang W, Li L, Huang W. Small‐Molecule Quenchers for Förster Resonance Energy Transfer: Structure, Mechanism, and Applications. Angew Chem Int Ed Engl 2022; 61:e202207188. [DOI: 10.1002/anie.202207188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Bin Fang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- State Key Laboratory of Solidification Processing School of Materials Science and Engineering Northwestern Polytechnical University 127 West Youyi Road Xi'an 710072 China
| | - Yu Shen
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Hua Bai
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Limin Wang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Jiaxin Zhang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Wenbo Hu
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Li Fu
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- State Key Laboratory of Solidification Processing School of Materials Science and Engineering Northwestern Polytechnical University 127 West Youyi Road Xi'an 710072 China
| | - Wei Zhang
- Teaching and Evaluation Center of Air Force Medical University Xi'an 710032 China
| | - Lin Li
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- The Institute of Flexible Electronics (IFE, Future Technologies) Xiamen University Xiamen 361005, Fujian China
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- The Institute of Flexible Electronics (IFE, Future Technologies) Xiamen University Xiamen 361005, Fujian China
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9
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Fang B, Shen Y, Peng B, Bai H, Wang L, Zhang J, Hu W, Fu L, Zhang W, Li L, Huang W. Small Molecule Quenchers for Förster Resonance Energy Transfer: Structure, Mechanism and Applications. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Bin Fang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Yu Shen
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Bo Peng
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Hua Bai
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Limin Wang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Jiaxin Zhang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Wenbo Hu
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Li Fu
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Wei Zhang
- Air Force Medical University Teaching and Evaluation Center CHINA
| | - Lin Li
- Nanjing Tech University Institute of Advanced Materials 30 South Puzhu Road 210008 Nanjing CHINA
| | - Wei Huang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
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10
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Sarkar A, Kumbhakar M. Inter-molecular Interaction Kinetics: Tale of Photon Anti-bunching and Bunching in Fluorescence Correlation Spectroscopy (FCS). Methods Appl Fluoresc 2022; 10. [PMID: 35817064 DOI: 10.1088/2050-6120/ac804b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/11/2022] [Indexed: 11/12/2022]
Abstract
Molecular interactions are fundamental to any chemical or biological processes, and their rates define the operational sequence and control for any desirable product. Here, we deliberate on a recently developed novel fluorescence spectroscopic method, which combines fluorescence photon anti-bunching, photon bunching, time-correlated single-photon counting (TCSPC), and steady-state fluorescence spectroscopy, to study composite chemical reactions with single molecule sensitivity. The proposed method captures the full picture of the multifaceted quenching kinetics, which involves static quenching by ground state complexation and collisional quenching in the excited state under dynamic exchange of fluorophore in a heterogeneous media, and which cannot be seen by steady-state or lifetime measurements alone. Photon correlation in fluorescence correlation spectroscopy (FCS) provides access to interrogate interaction dynamics from picosecond to seconds, stitching all possible stages of dye-quencher interaction in a micellar media. This is not possible with the limited time window available to conventional ensemble techniques like TCSPC, flash photolysis, transient absorption, stop-flow, etc. The basic premises of such unified global analysis and sanctity of extracted parameters critically depends on the minimum but precise description of reaction scheme, for which careful inspection of ensemble spectroscopy data for photo-physical behaviour is very important. Though in this contribution we discussed and demonstrated the merits of photon antibunching and bunching spectroscopy for dye-quencher interaction in cationic cetyltrimethylammonium bromide (CTAB) micellar solution by photo-induced electron transfer mechanism and the influence of micellar charge and microenvironment on the interaction kinetics, but in principal similar arguments are equally applicable to any other interaction mechanisms which alter fluorescence photon correlations, like Förster resonance energy transfer (FRET), proton transfer, isomerisation, etc.
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Affiliation(s)
- Aranyak Sarkar
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, CFB, C-139, Mumbai, Maharashtra, 400085, INDIA
| | - Manoj Kumbhakar
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, CFB, C-139, Mumbai, 400085, INDIA
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11
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Mahani M, Karimi-Mazidi P, Khakbaz F, Torkzadeh-Mahani M. Carbon quantum dots-Annexin V probe: photoinduced electron transfer mechanism, phosphatidylserine detection, and apoptotic cell imaging. Mikrochim Acta 2022; 189:69. [PMID: 35066672 DOI: 10.1007/s00604-021-05147-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 12/12/2021] [Indexed: 12/22/2022]
Abstract
An annexin V-based probe is designed and fabricated using carbon quantum dot as highly stable and biocompatible fluorescent crystals for real-time fluorescence imaging of apoptotic cells. Carbon quantum dots were synthesized, characterized, and conjugated to annexin V. The fluorescence of CQDs at 450 nm (excitation at 350 nm) is quenched due to the photoinduced electron transfer between "carbon quantum dots" and two amino acids (tyrosine and tryptophan) in the annexin structure as quencher. The probe shows very strong and bright fluorescence emission in the presence of phosphatidylserine on the outer layer of the apoptotic cell membrane. It was shown that using fluorescence spectroscopy, the probe can be applied to sensitive phosphatidylserine determination and using fluorescence microscopy, it is possible to monitor cell apoptosis in real time.
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Affiliation(s)
- Mohamad Mahani
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Graduate University of Advanced Technology, 7631818356, Kerman, Iran.
| | - Parisa Karimi-Mazidi
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Graduate University of Advanced Technology, 7631818356, Kerman, Iran
| | - Faeze Khakbaz
- Department of Nano Chemistry, Faculty of Chemistry, Shahid Bahonar University, Kerman, Iran
| | - Masoud Torkzadeh-Mahani
- Department of Biotechnology, Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
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12
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Vishvakarma V, Maiti S. Measuring the Size and Spontaneous Fluctuations of Amyloid Aggregates with Fluorescence Correlation Spectroscopy. Methods Mol Biol 2022; 2538:35-54. [PMID: 35951292 DOI: 10.1007/978-1-0716-2529-3_4] [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: 06/15/2023]
Abstract
Bacterial amyloids decorate the cell surface of many bacteria by forming functional amyloid fibers. These amyloids have structural and biochemical similarities with many disease-related amyloids in eukaryotes. Amyloid aggregation starts at the individual monomer level, and the end product is the amyloid fibril. The process of amyloid aggregation involves a continuous increase of the aggregate size, and therefore size is a critical parameter to measure in aggregation experiments. Also, our understanding of the aggregation process, and our ability to design interventions, can benefit from a measurement of the conformational dynamics of proteins undergoing aggregation. Fluorescence correlation spectroscopy (FCS) is perhaps the most sensitive and rapid technique available currently for this purpose. It can measure the average size and the size distribution of molecules and aggregates down to sub-nm length scales and can also measure fast nanosecond time-scale conformational dynamics, all in an equilibrium solution. FCS achieves this by measuring the fluorescence intensity fluctuations of freely diffusing protein molecules in an optically defined microscopic probe volume in a solution. Here, we present a set of instructions for effectively measuring the size and dynamics of amyloid aggregates with FCS.
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Affiliation(s)
- Vicky Vishvakarma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India.
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13
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Dey A, Vishvakarma V, Das A, Kallianpur M, Dey S, Joseph R, Maiti S. Single Molecule Measurements of the Accessibility of Molecular Surfaces. Front Mol Biosci 2021; 8:745313. [PMID: 34926574 PMCID: PMC8672140 DOI: 10.3389/fmolb.2021.745313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
An important measure of the conformation of protein molecules is the degree of surface exposure of its specific segments. However, this is hard to measure at the level of individual molecules. Here, we combine single molecule photobleaching (smPB, which resolves individual photobleaching steps of single molecules) and fluorescence quenching techniques to measure the accessibility of individual fluorescently labeled protein molecules to quencher molecules in solution. A quencher can reduce the time a fluorophore spends in the excited state, increasing its photostability under continuous irradiation. Consequently, the photo-bleaching step length would increase, providing a measure for the accessibility of the fluorophore to the solvent. We demonstrate the method by measuring the bleaching step-length increase in a lipid, and also in a lipid-anchored peptide (both labelled with rhodamine-B and attached to supported lipid bilayers). The fluorophores in both molecules are expected to be solvent-exposed. They show a near two-fold increase in the step length upon incubation with 5 mM tryptophan (a quencher of rhodamine-B), validating our approach. A population distribution plot of step lengths before and after addition of tryptophan show that the increase is not always homogenous. Indeed there are different species present with differential levels of exposure. We then apply this technique to determine the solvent exposure of membrane-attached N-terminus labelled amylin (h-IAPP, an amyloid associated with Type II diabetes) whose interaction with lipid bilayers is poorly understood. hIAPP shows a much smaller increase of the step length, signifying a lower level of solvent exposure of its N-terminus. Analysis of results from individual molecules and step length distribution reveal that there are at least two different conformers of amylin in the lipid bilayer. Our results show that our method (“Q-SLIP”, Quenching-induced Step Length increase in Photobleaching) provides a simple route to probe the conformational states of membrane proteins at a single molecule level.
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Affiliation(s)
- Arpan Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Vicky Vishvakarma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Anirban Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Mamata Kallianpur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Simli Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Roshni Joseph
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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14
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Gausterer JC, Schüßler C, Gabor F. The impact of calcium phosphate on FITC-BSA loading of sonochemically prepared PLGA nanoparticles for inner ear drug delivery elucidated by two different fluorimetric quantification methods. ULTRASONICS SONOCHEMISTRY 2021; 79:105783. [PMID: 34653915 PMCID: PMC8527049 DOI: 10.1016/j.ultsonch.2021.105783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 09/25/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
Although therapeutically active proteins are highly efficacious, their content in protective nanoparticles is often too low to elicit adequate plasma levels. A strategy to increase protein loading is the in-situ generation of calcium phosphate as a protein adsorbent. To verify this approach, a highly sensitive and reliable fluorimetric method for quantification of incorporated fluorescein-labelled bovine serum albumin (FITC-BSA) as a model protein drug was developed. Dequenching the fluorescein label by pronase E, which digests the protein backbone, and dissolving the nanoparticle matrix in acetonitrile enabled FITC-BSA quantification in the nanogram per milliliter range. This test was confirmed by a second assay involving alkaline hydrolysis of FITC-BSA and the matrix. Nanoparticles prepared with calcium phosphate contained 40 µg FITC-BSA/mg and nanoparticles without calcium phosphate only 15 µg FITC-BSA/mg, representing a 2.7-fold increase in model protein loading. In this work the nanoparticle preparation procedure was optimized in terms of size for administration in the inner ear, but the range of applications is not limited.
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Affiliation(s)
- Julia Clara Gausterer
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria.
| | - Clara Schüßler
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria
| | - Franz Gabor
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria.
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15
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Alston JJ, Soranno A, Holehouse AS. Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins. Methods 2021; 193:116-135. [PMID: 33831596 PMCID: PMC8713295 DOI: 10.1016/j.ymeth.2021.03.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 12/21/2022] Open
Abstract
Over the last two decades, intrinsically disordered proteins and protein regions (IDRs) have emerged from a niche corner of biophysics to be recognized as essential drivers of cellular function. Various techniques have provided fundamental insight into the function and dysfunction of IDRs. Among these techniques, single-molecule fluorescence spectroscopy and molecular simulations have played a major role in shaping our modern understanding of the sequence-encoded conformational behavior of disordered proteins. While both techniques are frequently used in isolation, when combined they offer synergistic and complementary information that can help uncover complex molecular details. Here we offer an overview of single-molecule fluorescence spectroscopy and molecular simulations in the context of studying disordered proteins. We discuss the various means in which simulations and single-molecule spectroscopy can be integrated, and consider a number of studies in which this integration has uncovered biological and biophysical mechanisms.
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Affiliation(s)
- Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110, MO, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis 63130, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110, MO, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis 63130, MO, USA.
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110, MO, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis 63130, MO, USA.
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16
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Sarkar A, Namboodiri V, Enderlein J, Kumbhakar M. Picosecond to Second Fluorescence Correlation Spectroscopy for Studying Solute Exchange and Quenching Dynamics in Micellar Media. J Phys Chem Lett 2021; 12:7641-7649. [PMID: 34351151 DOI: 10.1021/acs.jpclett.1c02021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Numerous studies have been devoted to understand the reaction kinetics in micelles, where the accessible kinetic time window is often limited by the dynamic range of the employed spectroscopic technique. This is usually accompanied by a selection of probes that comfortably explore time scales where slow solute exchange kinetics is negligible, as compared to the fast excited state reactions. This has led to an undervaluation of the role played by dynamic partitioning of hydrophilic solutes in microheterogeneous media. Here, we employ fluorescence correlation spectroscopy (FCS) and the zwitterionic dye Rhodamine 110 to quantitatively explore the impact of solute exchange on the photoinduced electron transfer between this dye and N,N-dimethylaniline in micellar media. Our study elucidates the coupling and interplay between the kinetics of photophysics, quenching, and solute exchange through a quantitative unified molecular-state quenching-kinetic model that describes the steady-state ensemble and FCS data from subnanosecond photon antibunching to millisecond diffusions.
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Affiliation(s)
- Aranyak Sarkar
- Radiation and Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Vinu Namboodiri
- Radiation and Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
| | - Jörg Enderlein
- III. Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Manoj Kumbhakar
- Radiation and Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
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17
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Ghosh A, Enderlein J. Advanced fluorescence correlation spectroscopy for studying biomolecular conformation. Curr Opin Struct Biol 2021; 70:123-131. [PMID: 34371261 DOI: 10.1016/j.sbi.2021.06.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 10/20/2022]
Abstract
We present the recent developments and advances in fluorescence correlation spectroscopy (FCS) and their application to the investigation of biomolecular conformations. In particular, we present and discuss three techniques: multichannel nanosecond FCS, photo-induced electron transfer FCS, and fluorescence lifetime correlation spectroscopy. We briefly describe each method and discuss recent applications to diverse biophysical studies of biomolecular conformation.
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Affiliation(s)
- Arindam Ghosh
- Third Institute of Physics, Biophysics, University of Göttingen, Friedrich Hund Platz 1 Göttingen, 37077, Germany
| | - Jörg Enderlein
- Third Institute of Physics, Biophysics, University of Göttingen, Friedrich Hund Platz 1 Göttingen, 37077, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Georg August University, Göttingen, 37077, Germany.
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18
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Ligand modulation of the conformational dynamics of the A 2A adenosine receptor revealed by single-molecule fluorescence. Sci Rep 2021; 11:5910. [PMID: 33723285 PMCID: PMC7960716 DOI: 10.1038/s41598-021-84069-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of transmembrane proteins, making them an important target for therapeutics. Activation of these receptors is modulated by orthosteric ligands, which stabilize one or several states within a complex conformational ensemble. The intra- and inter-state dynamics, however, is not well documented. Here, we used single-molecule fluorescence to measure ligand-modulated conformational dynamics of the adenosine A2A receptor (A2AR) on nanosecond to millisecond timescales. Experiments were performed on detergent-purified A2R in either the ligand-free (apo) state, or when bound to an inverse, partial or full agonist ligand. Single-molecule Förster resonance energy transfer (smFRET) was performed on detergent-solubilized A2AR to resolve active and inactive states via the separation between transmembrane (TM) helices 4 and 6. The ligand-dependent changes of the smFRET distributions are consistent with conformational selection and with inter-state exchange lifetimes ≥ 3 ms. Local conformational dynamics around residue 2296.31 on TM6 was measured using fluorescence correlation spectroscopy (FCS), which captures dynamic quenching due to photoinduced electron transfer (PET) between a covalently-attached dye and proximal aromatic residues. Global analysis of PET-FCS data revealed fast (150-350 ns), intermediate (50-60 μs) and slow (200-300 μs) conformational dynamics in A2AR, with lifetimes and amplitudes modulated by ligands and a G-protein mimetic (mini-Gs). Most notably, the agonist binding and the coupling to mini-Gs accelerates and increases the relative contribution of the sub-microsecond phase. Molecular dynamics simulations identified three tyrosine residues (Y112, Y2887.53, and Y2907.55) as being responsible for the dynamic quenching observed by PET-FCS and revealed associated helical motions around residue 2296.31 on TM6. This study provides a quantitative description of conformational dynamics in A2AR and supports the idea that ligands bias not only GPCR conformations but also the dynamics within and between distinct conformational states of the receptor.
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19
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Feng Y, Liu W, Mercadé-Prieto R, Chen XD. Dye-protein interactions between Rhodamine B and whey proteins that affect the photoproperties of the dye. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.113092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Kim H, Goh SH, Choi Y. Quenched cetuximab conjugate for fast fluorescence imaging of EGFR-positive lung cancers. Biomater Sci 2021; 9:456-462. [PMID: 32760993 DOI: 10.1039/d0bm01148g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cetuximab-dye conjugates have shown great potential for image-guided surgery of epidermal growth factor receptor (EGFR)-positive cancers in clinical trials. However, their long circulation half-life and prolonged generation of high background signals require the injection of antibody conjugates several days prior to imaging, which limits the clinical applications. Herein, we developed a cetuximab-ATTO655 conjugate (i.e., Q-Cetuximab) for fast and real-time fluorescence imaging of EGFR-positive lung cancers. The fluorescence intensity of Q-Cetuximab was quenched to just 6.9% of that of the unconjugated dye when only 2.14 ATTO655 dyes were conjugated to cetuximab. In vitro real-time cell imaging showed that EGFR-positive A549 cells emitted strong fluorescence at 10 min after Q-Cetuximab treatment in the absence of the washing step, implying target-specific activation of quenched Q-Cetuximab fluorescence upon binding with EGFR-positive cancer cells. When mice with orthotropic A549 tumors received intravenous injection of Q-Cetuximab, scattered microsized tumors in the lungs could be clearly identified from near-infrared fluorescence imaging with a tumor-to-background ratio of 4.28 at 8 h post-injection. For comparison, the cetuximab-Alexa647 conjugate (i.e., ON-Cetuximab), which does not show fluorescence quenching, was synthesized as an always-on type of probe. The ON-Cetuximab-treated mice expressed strong fluorescence throughout their body at 8 h post-injection; therefore, lung tumor sites could not be discriminated using fluorescence imaging. These results confirm the benefits of Q-Cetuximab for image-guided precision surgery of EGFR-positive lung cancers.
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Affiliation(s)
- Hyunjin Kim
- Research Institute, National Cancer Center, 323 Ilsanro, Goyang, Gyeonggi-do 10408, Republic of Korea.
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21
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Kim H, Kim HY, Lee EY, Choi BK, Jang H, Choi Y. A Quenched Annexin V-Fluorophore for the Real-Time Fluorescence Imaging of Apoptotic Processes In Vitro and In Vivo. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2002988. [PMID: 33344139 PMCID: PMC7740095 DOI: 10.1002/advs.202002988] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/19/2020] [Indexed: 05/14/2023]
Abstract
Annexin-based probes have long been used to study apoptotic cell death, which is of key importance to many areas of biological research, drug discovery, and clinical applications. Although apoptosis is a dynamic biological event with cell-to-cell variations, current annexin-based probes are impractical for monitoring apoptosis in real-time. Herein, a quenched annexin V-near-infrared fluorophore conjugate (Q-annexin V) is reported as the first OFF-ON annexin protein-based molecular sensor for real-time near-infrared fluorescence imaging of apoptosis. Q-annexin V is non-fluorescent in the extracellular region, due to photoinduced electron transfer interactions between the conjugated dye and amino acid quenchers (tryptophan and tyrosine). The probe becomes highly fluorescent when bound to phosphatidylserines on the outer layer of cell membranes during apoptosis, thereby enabling apoptosis to be monitored in real-time in 2D and 3D cell structures. In particular, Q-annexin V shows superior utility for in vivo apoptosis fluorescence imaging in animal models of cisplatin-induced acute kidney injury and cancer immune therapy, compared to the conventional polarity-sensitive pSIVA-IANBD or annexin V-Alexa647 conjugates.
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Affiliation(s)
- Hyunjin Kim
- Research InstituteNational Cancer Center323 Ilsan‐roGoyangGyeonggi10408Republic of Korea
| | - Hee Yeon Kim
- Research InstituteNational Cancer Center323 Ilsan‐roGoyangGyeonggi10408Republic of Korea
| | - Eun Young Lee
- Research InstituteNational Cancer Center323 Ilsan‐roGoyangGyeonggi10408Republic of Korea
| | - Boem Kyu Choi
- Research InstituteNational Cancer Center323 Ilsan‐roGoyangGyeonggi10408Republic of Korea
| | - Hyonchol Jang
- Research InstituteNational Cancer Center323 Ilsan‐roGoyangGyeonggi10408Republic of Korea
- Department of Cancer Biomedical ScienceNational Cancer Center Graduate School of Cancer Science and Policy323 Ilsan‐roGoyangGyeonggi10408Republic of Korea
| | - Yongdoo Choi
- Research InstituteNational Cancer Center323 Ilsan‐roGoyangGyeonggi10408Republic of Korea
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22
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Toledo PVO, Bernardinelli OD, Sabadini E, Petri DFS. The states of water in tryptophan grafted hydroxypropyl methylcellulose hydrogels and their effect on the adsorption of methylene blue and rhodamine B. Carbohydr Polym 2020; 248:116765. [PMID: 32919561 DOI: 10.1016/j.carbpol.2020.116765] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/27/2020] [Accepted: 07/11/2020] [Indexed: 11/28/2022]
Abstract
Tryptophan (Trp) decorated hydroxypropyl methylcellulose (HPMC) cryogels were prepared by a one-step reaction with citric acid. The increase of Trp content in the 3D network from 0 to 2.18 wt% increased the apparent density from 0.0267 g.cm-3 to 0.0381 g.cm-3 and the compression modulus from 94 kPa to 201 kPa, due to hydrophobic interactions between Trp molecules. The increase of Trp content in HPMC-Trp hydrogels increased the amount of non-freezing water, estimated from differential scanning calorimetry, and the amount of freezing water, which was determined by time-domain nuclear magnetic resonance. The adsorption capacity of methylene blue (MB) and rhodamine B (RB) on HPMC-Trp hydrogels increased with Trp content and the amount of freezing water. HPMC-Trp hydrogels could be recycled 6 times keeping the original adsorptive capacity. The diffusional constants of MB and RB tended to increase with Trp content. RB adsorbed on HPMC-Trp hydrogels presented a bathochromic shift of fluorescence.
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Affiliation(s)
- Paulo V O Toledo
- Fundamental Chemistry Department, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, Brazil.
| | - Oigres D Bernardinelli
- Department of Physicochemistry, Institute of Chemistry, University of Campinas (UNICAMP), 13083-970, Campinas, São Paulo, Brazil.
| | - Edvaldo Sabadini
- Department of Physicochemistry, Institute of Chemistry, University of Campinas (UNICAMP), 13083-970, Campinas, São Paulo, Brazil.
| | - Denise F S Petri
- Fundamental Chemistry Department, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, Brazil.
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23
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Enzian P, Schell C, Link A, Malich C, Pries R, Wollenberg B, Rahmanzadeh R. Optically Controlled Drug Release from Light-Sensitive Liposomes with the New Photosensitizer 5,10-DiOH. Mol Pharm 2020; 17:2779-2788. [PMID: 32543848 DOI: 10.1021/acs.molpharmaceut.9b01173] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The delivery of therapeutic drugs to a specific cellular site is a challenge in the treatment of different diseases. Liposomes have been widely studied as vehicles for drug delivery, and recent research begins to show the potential of the light-controlled opening of liposomes. Liposomes with photoactive molecules can release their cargo upon light irradiation for localized drug release. Light as an external trigger can be controlled temporally and spatially with high precision. In this study, we investigate the potential of light-sensitive liposomes with four photosensitizers and two lipid formulations for light-induced release. To investigate the permeabilization of the liposomes, calcein was encapsulated in high concentration inside the liposomes so that the calcein fluorescence is quenched. If calcein is released from the liposome, quenching is avoided, and the fluorescence increases. We demonstrated that liposomes with the sensitizers benzoporphyrine derivative monoacid (BPD), chlorine e6 (Ce6), Al(III) phthalocyanine chloride disulfonic acid (AlPcS2), and 5,10-di-(4-hydroxyphenyl)-15,20-diphenyl-21,23H-porphyrin (5,10-DiOH) release cargo effectively after irradiation. Liposomes with 5,10-DiOH showed a quicker release compared to the other sensitizers upon irradiation at 420 nm. Further, we observed through fractionated irradiation, that most of the release took place during light application, while the permeability of the liposome decreased shortly after light exposure. This effect was stronger with liposomes containing less cholesterol.
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Affiliation(s)
- Paula Enzian
- Institute of Biomedical Optics, University of Lübeck, Peter-Monnik-Weg 4, 23562 Lübeck, Germany
| | - Christian Schell
- Por-Lab, Porphyrin-Laboratories GmbH, Blauenkrog 15, 23684 Scharbeutz, Germany
| | - Astrid Link
- Institute of Biomedical Optics, University of Lübeck, Peter-Monnik-Weg 4, 23562 Lübeck, Germany
| | - Carina Malich
- Institute of Biomedical Optics, University of Lübeck, Peter-Monnik-Weg 4, 23562 Lübeck, Germany
| | - Ralph Pries
- Department of Otorhinolaryngology, Clinic for ENT and HNS, University Hospital of Schleswig-Holstein, Campus Luübeck, Ratzeburger Allee 160, 23538 Luübeck, Germany
| | - Barbara Wollenberg
- Department of Otorhinolaryngology, Clinic for ENT and HNS, University Hospital of Schleswig-Holstein, Campus Luübeck, Ratzeburger Allee 160, 23538 Luübeck, Germany
| | - Ramtin Rahmanzadeh
- Institute of Biomedical Optics, University of Lübeck, Peter-Monnik-Weg 4, 23562 Lübeck, Germany
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24
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Study of Interfacial Charge Transfer from an Electron Rich Organic Molecule to CdTe Quantum Dot by using Stern‐Volmer and Stochastic Kinetic Models. Chemphyschem 2020; 21:415-422. [DOI: 10.1002/cphc.201901159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 12/24/2019] [Indexed: 01/09/2023]
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25
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Beltrán A, Burguete MI, Galindo F, Luis SV. Synthesis of new fluorescent pyrylium dyes and study of their interaction with N-protected amino acids. NEW J CHEM 2020. [DOI: 10.1039/d0nj02033h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Six new fluorescent styrylpyrylium dyes have been synthesized and the collisional quenching taking place upon their interaction with Z-protected amino acids has been studied.
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Affiliation(s)
- Alicia Beltrán
- Universitat Jaume I
- Departamento de Química Inorgánica y Orgánica
- Avda. Vicente Sos Baynat s/n
- Castellón
- Spain
| | - M. Isabel Burguete
- Universitat Jaume I
- Departamento de Química Inorgánica y Orgánica
- Avda. Vicente Sos Baynat s/n
- Castellón
- Spain
| | - Francisco Galindo
- Universitat Jaume I
- Departamento de Química Inorgánica y Orgánica
- Avda. Vicente Sos Baynat s/n
- Castellón
- Spain
| | - Santiago V. Luis
- Universitat Jaume I
- Departamento de Química Inorgánica y Orgánica
- Avda. Vicente Sos Baynat s/n
- Castellón
- Spain
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26
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Kandula HN, Jee AY, Granick S. Robustness of FCS (Fluorescence Correlation Spectroscopy) with Quenchers Present. J Phys Chem A 2019; 123:10184-10189. [PMID: 31702916 DOI: 10.1021/acs.jpca.9b08273] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inspired by recent publications doubtful of the FCS technique, we scrutinize how irreversible ("static") and reversible ("dynamic") quenching can influence the interpretation of such data. Textbook presentations often emphasize only how to analyze data in extremes, the absence of quenching or the presence of substantial quenching. Here, we consider intermediate cases where the assessment of photophysics (static quenching, blinking-like triplet-state relaxation) influence on autocorrelation curves can be delicate if dye-labeled objects diffuse on comparably rapid time scales. We used the amino acid, tryptophan, as the quencher. As our example of small-molecule dye that diffuses rapidly, we mix the quencher with the fluorescence dye, Alexa 488. The translational diffusion coefficient, inferred from fit to the standard one-component Fickian diffusion model, speeds up without the loss of quality of fit, but quenching is reflected in the fact that the data become exceptionally noisy. This reflects the bidisperse population of quenched and unquenched dyes when the time scales overlap between the processes of translational diffusion, quenching, and blinking. As our example of the large-molecule dye-labeled object that diffuses relatively slowly, we mixed the quencher with dye-labeled BSA, bovine serum albumin. Diffusion, static quenching, and blinking time scales are now separated. In spite of quenching contribution to the autocorrelation function when the delay time is relatively short, the inferred translational diffusion coefficient now depends weakly on the presence of a quencher. We conclude that when the diffusing molecule is substantially slower to diffuse than the time scale of photophysical processes of the fluorescent dye to which it is attached, the influence of quenching is self-evident and the FCS autocorrelation curves give an appropriate diffusion coefficient if correct fitting functions are chosen in the analysis.
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Affiliation(s)
- Hima Nagamanasa Kandula
- Center for Soft and Living Matter , Institute for Basic Science (IBS) , Ulsan 44919 , South Korea
| | - Ah-Young Jee
- Center for Soft and Living Matter , Institute for Basic Science (IBS) , Ulsan 44919 , South Korea
| | - Steve Granick
- Center for Soft and Living Matter , Institute for Basic Science (IBS) , Ulsan 44919 , South Korea.,Department of Chemistry , Ulsan National Institute of Science and Technology (UNIST) , Ulsan 44919 , South Korea
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27
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Mühle S, Zhou M, Ghosh A, Enderlein J. Loop formation and translational diffusion of intrinsically disordered proteins. Phys Rev E 2019; 100:052405. [PMID: 31869980 DOI: 10.1103/physreve.100.052405] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Indexed: 06/10/2023]
Abstract
The conformational flexibility and dynamics of unfolded peptide chains is of major interest in the context of protein folding and protein functioning. The rate with which amino acids at different positions along the peptide chain meet sets an upper speed limit for protein folding. By using single-molecule photo-induced energy transfer spectroscopy, we have systematically measured end-to-end and end-to-internal site contact formation rates for several intrinsically disordered protein fragments (IDPs) (11 to 41 amino acids) and have also determined their hydrodynamic radius using dual-focus fluorescence correlation spectroscopy. For interpreting the measured values, we have developed a Brownian dynamics model (based on bead-rod chain dynamics in a thermal bath including hydrodynamic interactions) which quantitatively reproduces all measured data surprisingly well while requiring only two fit parameters. The model provides a complete picture of the peptides' dynamics and allows us to translate the experimental rates and radii into molecular properties of the peptides: We find a persistence length of l_{P}=5.2±1.9Å, a hydrodynamic radius of a=3.5±0.7Å per amino acid, and that excluded volume effects play an important role in the dynamics of IDPs.
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Affiliation(s)
- Steffen Mühle
- III. Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Man Zhou
- Biochemistry Department, Oxford University, South Parks Rd, Oxford OX1 3QU, United Kingdom
| | - Arindam Ghosh
- III. Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Jörg Enderlein
- III. Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany
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28
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Wang B, Wang P, Xie LH, Lin RB, Lv J, Li JR, Chen B. A stable zirconium based metal-organic framework for specific recognition of representative polychlorinated dibenzo-p-dioxin molecules. Nat Commun 2019; 10:3861. [PMID: 31455843 PMCID: PMC6712023 DOI: 10.1038/s41467-019-11912-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 08/09/2019] [Indexed: 11/29/2022] Open
Abstract
Polychlorinated dibenzo-p-dioxins (PCDDs), as a class of persistent and highly toxic organic pollutants, have been posing a great threat to human health and the environment. The sensing of these compounds is important but challenging. Here, we report a highly stable zirconium-based metal-organic framework (MOF), Zr6O4(OH)8(HCOO)2(CPTTA)2 (BUT-17) with one-dimensional hexagonal channels and phenyl-rich pore surfaces for the recognition and sensing of two representative PCDDs, 2,3-dichlorodibenzo-p-dioxin (BCDD) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), based on the fluorescence quenching. BUT-17 exhibits high sensing ability with the detection limits as low as 27 and 57 part per billion toward BCDD and TCDD, respectively, and is very selective as well without the interference of similar compounds. The recognition of BUT-17 toward BCDD is demonstrated by single-crystal structure of its guest-loaded phase, in which the fluorescence-quenched complexes form between the adsorbed BCDD molecules and the MOF host through π-π stacking and hydrogen bonding interactions.
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Affiliation(s)
- Bin Wang
- Beijing Key Laboratory for Green Catalysis and Separation and Department of Chemistry and Chemical Engineering, College of Environmental and Energy Engineering, Beijing University of Technology, 100124, Beijing, P. R. China
| | - Peilong Wang
- Institute of Quality Standards and Testing Technology for Agro-products, Chinese Academy of Agricultural Sciences, 100081, Beijing, P. R. China
| | - Lin-Hua Xie
- Beijing Key Laboratory for Green Catalysis and Separation and Department of Chemistry and Chemical Engineering, College of Environmental and Energy Engineering, Beijing University of Technology, 100124, Beijing, P. R. China
| | - Rui-Biao Lin
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249-0698, USA
| | - Jie Lv
- Beijing Key Laboratory for Green Catalysis and Separation and Department of Chemistry and Chemical Engineering, College of Environmental and Energy Engineering, Beijing University of Technology, 100124, Beijing, P. R. China
| | - Jian-Rong Li
- Beijing Key Laboratory for Green Catalysis and Separation and Department of Chemistry and Chemical Engineering, College of Environmental and Energy Engineering, Beijing University of Technology, 100124, Beijing, P. R. China.
| | - Banglin Chen
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249-0698, USA.
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29
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Chekmarev SF. How the dyes affect folding of small proteins in single-molecule FRET experiments: A simulation study. Biophys Chem 2019; 254:106243. [PMID: 31442765 DOI: 10.1016/j.bpc.2019.106243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 11/18/2022]
Abstract
A key question in the application of the single-molecule Förster resonance energy transfer (smFRET) technique to study protein folding is how the dyes affect the protein behavior. Understanding of these effects is particularly important for small proteins, for which the dyes, along with their linkers, can be comparable in size (mass) with the protein. Using a coarse-grained model, we simulated folding of BBL protein and two of its FRET constructs. The obtained results suggest that even for small proteins, such as the 45-residue BBL, the appearance of the excluded volume in the protein conformation space due to the presence of dyes does not change the overall picture of folding. At the same time, some deviations from folding of the original protein are observed, in particular, the FRET constructs fold considerably slower than the original protein because the protein collapse in the initial state of folding is slowed down due to the protein loading with relatively massive dyes.
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Affiliation(s)
- Sergei F Chekmarev
- Institute of Thermophysics, SB RAS, 630090 Novosibirsk, Russia; Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia.
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30
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Sharma A, Sarkar A, Goswami D, Bhattacharyya A, Enderlein J, Kumbhakar M. Determining Metal Ion Complexation Kinetics with Fluorescent Ligands by Using Fluorescence Correlation Spectroscopy. Chemphyschem 2019; 20:2093-2102. [PMID: 31240810 DOI: 10.1002/cphc.201900517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/25/2019] [Indexed: 11/08/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) has been extensively used to measure equilibrium binding constants (K) or association and dissociation rates in many reversible chemical reactions across chemistry and biology. For the majority of investigated reactions, the binding constant was on the order of ∼100 M-1 , with dissociation constants faster or equal to 103 s-1 , which ensured that enough association/dissociation events occur during the typical diffusion-determined transition time of molecules through the FCS detection volume. However, complexation reactions involving metal ions and chelating ligands exhibit equilibrium constants exceeding 104 M-1 . In the present paper, we explore the applicability of FCS for measuring reaction rates of such complexation reactions, and apply it to binding of iron, europium and uranyl ions to a fluorescent chelating ligand, calcein. For this purpose, we exploit the fact that the ligand fluorescence becomes strongly quenched after binding a metal ion, which results in strong intensity fluctuations that lead to a partial correlation decay in FCS. We also present measurements for the strongly radioactive ions of 241 Am3+ , where the extreme sensitivity of FCS allows us to work with sample concentrations and volumes that exhibit close to negligible radioactivity levels. A general discussion of the applicability of FCS to the investigation of metal-ligand binding reactions concludes our paper.
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Affiliation(s)
- Arjun Sharma
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.,Chemical Sciences, Homi Bhabha National Institute, Mumbai 400094, India
| | - Aranyak Sarkar
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.,Chemical Sciences, Homi Bhabha National Institute, Mumbai 400094, India
| | - Dibakar Goswami
- Chemical Sciences, Homi Bhabha National Institute, Mumbai 400094, India.,Bio-organic Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Arunasis Bhattacharyya
- Chemical Sciences, Homi Bhabha National Institute, Mumbai 400094, India.,Radiochemistry Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Manoj Kumbhakar
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.,Chemical Sciences, Homi Bhabha National Institute, Mumbai 400094, India
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31
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Beliu G, Kurz AJ, Kuhlemann AC, Behringer-Pliess L, Meub M, Wolf N, Seibel J, Shi ZD, Schnermann M, Grimm JB, Lavis LD, Doose S, Sauer M. Bioorthogonal labeling with tetrazine-dyes for super-resolution microscopy. Commun Biol 2019; 2:261. [PMID: 31341960 PMCID: PMC6642216 DOI: 10.1038/s42003-019-0518-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/27/2019] [Indexed: 12/28/2022] Open
Abstract
Genetic code expansion (GCE) technology allows the specific incorporation of functionalized noncanonical amino acids (ncAAs) into proteins. Here, we investigated the Diels-Alder reaction between trans-cyclooct-2-ene (TCO)-modified ncAAs, and 22 known and novel 1,2,4,5-tetrazine-dye conjugates spanning the entire visible wavelength range. A hallmark of this reaction is its fluorogenicity - the tetrazine moiety can elicit substantial quenching of the dye. We discovered that photoinduced electron transfer (PET) from the excited dye to tetrazine is the main quenching mechanism in red-absorbing oxazine and rhodamine derivatives. Upon reaction with dienophiles quenching interactions are reduced resulting in a considerable increase in fluorescence intensity. Efficient and specific labeling of all tetrazine-dyes investigated permits super-resolution microscopy with high signal-to-noise ratio even at the single-molecule level. The different cell permeability of tetrazine-dyes can be used advantageously for specific intra- and extracellular labeling of proteins and highly sensitive fluorescence imaging experiments in fixed and living cells.
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Affiliation(s)
- Gerti Beliu
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Andreas J. Kurz
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Alexander C. Kuhlemann
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Lisa Behringer-Pliess
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Mara Meub
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Natalia Wolf
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jürgen Seibel
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Zhen-Dan Shi
- Imaging Probe Development Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD 20850 USA
| | - Martin Schnermann
- Center for Cancer Research, Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702 USA
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147 USA
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147 USA
| | - Sören Doose
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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32
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Goluguri RR, Sen S, Udgaonkar J. Microsecond sub-domain motions and the folding and misfolding of the mouse prion protein. eLife 2019; 8:e44766. [PMID: 31025940 PMCID: PMC6516828 DOI: 10.7554/elife.44766] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 04/25/2019] [Indexed: 12/29/2022] Open
Abstract
Protein aggregation appears to originate from partially unfolded conformations that are sampled through stochastic fluctuations of the native protein. It has been a challenge to characterize these fluctuations, under native like conditions. Here, the conformational dynamics of the full-length (23-231) mouse prion protein were studied under native conditions, using photoinduced electron transfer coupled to fluorescence correlation spectroscopy (PET-FCS). The slowest fluctuations could be associated with the folding of the unfolded state to an intermediate state, by the use of microsecond mixing experiments. The two faster fluctuations observed by PET-FCS, could be attributed to fluctuations within the native state ensemble. The addition of salt, which is known to initiate the aggregation of the protein, resulted in an enhancement in the time scale of fluctuations in the core of the protein. The results indicate the importance of native state dynamics in initiating the aggregation of proteins.
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Affiliation(s)
- Rama Reddy Goluguri
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBengaluruIndia
| | - Sreemantee Sen
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBengaluruIndia
| | - Jayant Udgaonkar
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBengaluruIndia
- Indian Institute of Science Education and ResearchPuneIndia
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33
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Kim H, Cho MH, Choi HS, Lee BI, Choi Y. Zwitterionic near-infrared fluorophore-conjugated epidermal growth factor for fast, real-time, and target-cell-specific cancer imaging. Am J Cancer Res 2019; 9:1085-1095. [PMID: 30867817 PMCID: PMC6401407 DOI: 10.7150/thno.29719] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/26/2018] [Indexed: 12/31/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) is overexpressed in many types of cancers, which is associated with metastatic potential and poor prognosis in cancer patients. Therefore, development of EGFR-targeted sensitive imaging probes has been a challenge in tumor targeting, image-guided cancer surgery, patient-selective anti-EGFR therapy, and efficient targeted therapies. Methods: We synthesized a zwitterionic near-infrared fluorophore (ATTO655)-conjugated epidermal growth factor (EGF) as a novel activatable molecular probe. Fluorescence OFF/ON property and EGFR-targeting specificity of EGF-ATTO655 as well as its utility in real-time near-infrared (NIR) fluorescence imaging of EGFR-positive cancers were evaluated using in vitro and in vivo studies. Results: When conjugated to EGF, the fluorescence of ATTO655 quenched efficiently by photo-induced electron transfer (PET) mechanism between the conjugated dyes and nearby amino acid quenchers (tryptophan/tyrosine residues), which was stably maintained at physiological pH and in the presence of serum for at least 17 h. The fluorescence of EGF-ATTO655 turned on by receptor-mediated endocytosis and subsequent disintegration of EGF in EGFR-positive A431 cancer cells, thereby enabling specific and real-time fluorescence imaging of EGFR-positive cancer cells. Consequently, EGFR-positive tumors could be clearly visualized 3 h post-injection with a significantly high tumor-to-background ratio (TBR = 6.37). Conclusion: This PET mechanism-based OFF/ON type of EGF probe showed great potential for rapid, real-time, and target-cell-specific imaging of EGFR-overexpressing cancers in vitro and in vivo.
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34
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Kokkonen P, Sykora J, Prokop Z, Ghose A, Bednar D, Amaro M, Beerens K, Bidmanova S, Slanska M, Brezovsky J, Damborsky J, Hof M. Molecular Gating of an Engineered Enzyme Captured in Real Time. J Am Chem Soc 2018; 140:17999-18008. [DOI: 10.1021/jacs.8b09848] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Piia Kokkonen
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jan Sykora
- J. Heyrovsky Institute of Physical Chemistry of the ASCR, v. v. i., Dolejskova 3, 182 23 Prague 8, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Avisek Ghose
- J. Heyrovsky Institute of Physical Chemistry of the ASCR, v. v. i., Dolejskova 3, 182 23 Prague 8, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Mariana Amaro
- J. Heyrovsky Institute of Physical Chemistry of the ASCR, v. v. i., Dolejskova 3, 182 23 Prague 8, Czech Republic
| | - Koen Beerens
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Sarka Bidmanova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Michaela Slanska
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Martin Hof
- J. Heyrovsky Institute of Physical Chemistry of the ASCR, v. v. i., Dolejskova 3, 182 23 Prague 8, Czech Republic
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35
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Holmstrom ED, Holla A, Zheng W, Nettels D, Best RB, Schuler B. Accurate Transfer Efficiencies, Distance Distributions, and Ensembles of Unfolded and Intrinsically Disordered Proteins From Single-Molecule FRET. Methods Enzymol 2018; 611:287-325. [PMID: 30471690 PMCID: PMC8018263 DOI: 10.1016/bs.mie.2018.09.030] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Intrinsically disordered proteins (IDPs) sample structurally diverse ensembles. Characterizing the underlying distributions of conformations is a key step toward understanding the structural and functional properties of IDPs. One increasingly popular method for obtaining quantitative information on intramolecular distances and distributions is single-molecule Förster resonance energy transfer (FRET). Here we describe two essential elements of the quantitative analysis of single-molecule FRET data of IDPs: the sample-specific calibration of the single-molecule instrument that is required for determining accurate transfer efficiencies, and the use of state-of-the-art methods for inferring accurate distance distributions from these transfer efficiencies. First, we illustrate how to quantify the correction factors for instrument calibration with alternating donor and acceptor excitation measurements of labeled samples spanning a wide range of transfer efficiencies. Second, we show how to infer distance distributions based on suitably parameterized simple polymer models, and how to obtain conformational ensembles from Bayesian reweighting of molecular simulations or from parameter optimization in simplified coarse-grained models.
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Affiliation(s)
- Erik D Holmstrom
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Andrea Holla
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States.
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States.
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland; Department of Physics, University of Zurich, Zurich, Switzerland.
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36
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Pantazis A, Westerberg K, Althoff T, Abramson J, Olcese R. Harnessing photoinduced electron transfer to optically determine protein sub-nanoscale atomic distances. Nat Commun 2018; 9:4738. [PMID: 30413716 PMCID: PMC6226468 DOI: 10.1038/s41467-018-07218-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 10/16/2018] [Indexed: 11/29/2022] Open
Abstract
Proteins possess a complex and dynamic structure, which is influenced by external signals and may change as they perform their biological functions. We present an optical approach, distance-encoding photoinduced electron transfer (DEPET), capable of the simultaneous study of protein structure and function. An alternative to FRET-based methods, DEPET is based on the quenching of small conjugated fluorophores by photoinduced electron transfer: a reaction that requires contact of the excited fluorophore with a suitable electron donor. This property allows DEPET to exhibit exceptional spatial and temporal resolution capabilities in the range pertinent to protein conformational change. We report the first implementation of DEPET on human large-conductance K+ (BK) channels under voltage clamp. We describe conformational rearrangements underpinning BK channel sensitivity to electrical excitation, in conducting channels expressed in living cells. Finally, we validate DEPET in synthetic peptide length standards, to evaluate its accuracy in measuring sub- and near-nanometer intramolecular distances.
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Affiliation(s)
- Antonios Pantazis
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, UCLA, Los Angeles, CA, 90095, USA. .,Division of Neurobiology, Department of Clinical and Experimental Medicine (IKE), Linköping University, Linköping, 581 83, Sweden. .,Wallenberg Center for Molecular Medicine, Linköping University, Linköping, 581 83, Sweden.
| | - Karin Westerberg
- 0000 0001 0657 5612grid.417886.4Amgen, Thousand Oaks, CA 91320 USA
| | - Thorsten Althoff
- 0000 0000 9632 6718grid.19006.3eDepartment of Physiology, UCLA, Los Angeles, CA 90095 USA
| | - Jeff Abramson
- 0000 0000 9632 6718grid.19006.3eDepartment of Physiology, UCLA, Los Angeles, CA 90095 USA
| | - Riccardo Olcese
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, UCLA, Los Angeles, CA, 90095, USA. .,Department of Physiology, UCLA, Los Angeles, CA, 90095, USA.
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37
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Masureel M, Zou Y, Picard LP, van der Westhuizen E, Mahoney JP, Rodrigues JPGLM, Mildorf TJ, Dror RO, Shaw DE, Bouvier M, Pardon E, Steyaert J, Sunahara RK, Weis WI, Zhang C, Kobilka BK. Structural insights into binding specificity, efficacy and bias of a β 2AR partial agonist. Nat Chem Biol 2018; 14:1059-1066. [PMID: 30327561 PMCID: PMC6197491 DOI: 10.1038/s41589-018-0145-x] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 09/06/2018] [Indexed: 11/08/2022]
Abstract
Salmeterol is a partial agonist for the β2 adrenergic receptor (β2AR) and the first long-acting β2AR agonist to be widely used clinically for the treatment of asthma and chronic obstructive pulmonary disease. Salmeterol's safety and mechanism of action have both been controversial. To understand its unusual pharmacological action and partial agonism, we obtained the crystal structure of salmeterol-bound β2AR in complex with an active-state-stabilizing nanobody. The structure reveals the location of the salmeterol exosite, where sequence differences between β1AR and β2AR explain the high receptor-subtype selectivity. A structural comparison with the β2AR bound to the full agonist epinephrine reveals differences in the hydrogen-bond network involving residues Ser2045.43 and Asn2936.55. Mutagenesis and biophysical studies suggested that these interactions lead to a distinct active-state conformation that is responsible for the partial efficacy of G-protein activation and the limited β-arrestin recruitment for salmeterol.
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Affiliation(s)
- Matthieu Masureel
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yaozhong Zou
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Geneus Technologies, Ltd, Chengdu, Sichuan, People's Republic of China
| | - Louis-Philippe Picard
- Department of Biochemistry, Institute for Research in Immunology and Cancer, Université de Montreal, Montreal, Québec, Canada
| | - Emma van der Westhuizen
- Department of Biochemistry, Institute for Research in Immunology and Cancer, Université de Montreal, Montreal, Québec, Canada
- Monash Institute for Pharmaceutical Sciences, Monash University, Victoria, Australia
| | - Jacob P Mahoney
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - João P G L M Rodrigues
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | - Thomas J Mildorf
- D. E. Shaw Research, New York, NY, USA
- Dropbox, New York, NY, USA
| | - Ron O Dror
- D. E. Shaw Research, New York, NY, USA
- Department of Computer Science and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - David E Shaw
- D. E. Shaw Research, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Michel Bouvier
- Department of Biochemistry, Institute for Research in Immunology and Cancer, Université de Montreal, Montreal, Québec, Canada
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Structural Biology Research Center, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Structural Biology Research Center, VIB, Brussels, Belgium
| | - Roger K Sunahara
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - William I Weis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
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38
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Wang Q, London E. Lipid Structure and Composition Control Consequences of Interleaflet Coupling in Asymmetric Vesicles. Biophys J 2018; 115:664-678. [PMID: 30082033 DOI: 10.1016/j.bpj.2018.07.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 07/05/2018] [Accepted: 07/10/2018] [Indexed: 01/07/2023] Open
Abstract
Using Förster resonance energy transfer, raft/liquid-ordered-domain formation was assessed in asymmetric vesicles containing outer leaflets composed of high-Tm (melting temperature) saturated phosphatidylcholines (diC18:0PC, diC16:0PC, diC15:0PC, or diC14:0PC), low-Tm unsaturated dioleoylphosphatidylcholine (DOPC) and cholesterol, and inner leaflets composed of lipids that by themselves would not form ordered domains (DOPC and cholesterol). Ordered-domain formation in the outer leaflet was compared to that in symmetric vesicles with the same lipid composition as the asymmetric vesicle outer leaflets. The difference between ordered-domain thermal stability in asymmetric and symmetric vesicles was highly dependent on high-Tm PC acyl-chain length. At one extreme, in diC14:0PC-containing asymmetric vesicles, the outer leaflet did not segregate to form ordered domains over the entire experimental temperature range even though ordered domains formed in the symmetric vesicles, indicating the inner leaflet dominated outer-leaflet physical behavior in the asymmetric vesicles. At the other extreme, in diC18:0PC-containing asymmetric vesicles, ordered domains formed over the entire temperature range at which they were present in symmetric vesicles, indicating the inner leaflet did not dominate outer-leaflet physical behavior. DiC15:0PC- and diC16:0PC-containing vesicles exhibited intermediate behaviors. A different set of vesicles was prepared with high-Tm lipid sphingomyelin (SM) in place of saturated phosphatidylcholine, and the % SM was varied. The thermal stability of outer-leaflet ordered domains in asymmetric vesicles was found to decrease more than in symmetric vesicles as SM levels decreased, indicating that the inner leaflet increasingly dominated outer leaflet physical state as SM levels decreased. Overall, inhibition of outer-leaflet ordered-domain formation in asymmetric vesicles by inner-leaflet lipids decreased as the ability of outer-leaflet lipids to form an ordered state by themselves increased, i.e., when outer-leaflet high-Tm lipid content or acyl-chain length increased. This has implications for how ordered-domain formation may be controlled in vivo.
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Affiliation(s)
- Qing Wang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York
| | - Erwin London
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York.
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39
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Weißenstein A, Saha-Möller CR, Würthner F. Optical Sensing of Aromatic Amino Acids and Dipeptides by a Crown-Ether-Functionalized Perylene Bisimide Fluorophore. Chemistry 2018; 24:8009-8016. [DOI: 10.1002/chem.201800870] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Annike Weißenstein
- Universität Würzburg; Institut für Organische Chemie; Am Hubland 97074 Würzburg Germany
| | - Chantu R. Saha-Möller
- Universität Würzburg; Institut für Organische Chemie; Am Hubland 97074 Würzburg Germany
| | - Frank Würthner
- Universität Würzburg; Institut für Organische Chemie; Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC); Universität Würzburg; Theodor-Boveri-Weg 97074 Würzburg Germany
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40
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Jacob MH, D'Souza RN, Schwarzlose T, Wang X, Huang F, Haas E, Nau WM. Method-Unifying View of Loop-Formation Kinetics in Peptide and Protein Folding. J Phys Chem B 2018; 122:4445-4456. [PMID: 29617564 DOI: 10.1021/acs.jpcb.8b00879] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein folding can be described as a probabilistic succession of events in which the peptide chain forms loops closed by specific amino acid residue contacts, herein referred to as loop nodes. To measure loop rates, several photophysical methods have been introduced where a pair of optically active probes is incorporated at selected chain positions and the excited probe undergoes contact quenching (CQ) upon collision with the second probe. The quenching mechanisms involved triplet-triplet energy transfer, photoinduced electron transfer, and collision-induced fluorescence quenching, where the fluorescence of Dbo, an asparagine residue conjugated to 2,3-diazabicyclo[2.2.2]octane, is quenched by tryptophan. The discrepancy between the loop rates afforded from these three CQ techniques has, however, remained unresolved. In analyzing this discrepancy, we now report two short-distance FRET methods where Dbo acts as an energy acceptor in combination with tryptophan and naphtylalanine, two donors with largely different fluorescence lifetimes of 1.3 and 33 ns, respectively. Despite the different quenching mechanisms, the rates from FRET and CQ methods were, surprisingly, of comparable magnitude. This combination of FRET and CQ data led to a unifying physical model and to the conclusion that the rate of loop formation in folding reactions varies not only with the kind and number of residues that constitute the chain but also in particular with the size and properties of the residues that constitute the loop node.
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Affiliation(s)
- Maik H Jacob
- Department of Life Sciences and Chemistry , Jacobs University Bremen , Bremen 28759 , Germany
| | - Roy N D'Souza
- Department of Life Sciences and Chemistry , Jacobs University Bremen , Bremen 28759 , Germany
| | - Thomas Schwarzlose
- Department of Life Sciences and Chemistry , Jacobs University Bremen , Bremen 28759 , Germany
| | - Xiaojuan Wang
- Center for Biotechnology and Bioengineering , China University of Petroleum , Qingdao , Shandong , China 266580
| | - Fang Huang
- Center for Biotechnology and Bioengineering , China University of Petroleum , Qingdao , Shandong , China 266580
| | - Elisha Haas
- Department of Life Science , Bar Ilan University , Ramat Gan 5290002 , Israel
| | - Werner M Nau
- Department of Life Sciences and Chemistry , Jacobs University Bremen , Bremen 28759 , Germany.,Center for Biotechnology and Bioengineering , China University of Petroleum , Qingdao , Shandong , China 266580
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41
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Sharma A, Enderlein J, Kumbhakar M. Photon Antibunching Reveals Static and Dynamic Quenching Interaction of Tryptophan with Atto-655. J Phys Chem Lett 2017; 8:5821-5826. [PMID: 29125301 DOI: 10.1021/acs.jpclett.7b02430] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) of photoinduced electron transfer (PET) between the dye Atto-655 and the amino acid tryptophan has been extensively used for studying fast conformational dynamics of small disordered peptides and proteins. However, a precise understanding of the quenching mechanism and its exact rates that would explain ensemble as well as single-molecule spectroscopy results is still lacking. In this contribution, a general unified model for intermolecular PET between Atto-655 and tryptophan is developed, which involves ground-state complex formation, quenching sphere of action, and dynamic quenching at the single-molecule level. We present measurements of fluorescence antibunching, fluorescence lifetime, and steady-state fluorescence intensity and absorbance and demonstrate that our model is capable to describe all results in a global and coherent manner.
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Affiliation(s)
- Arjun Sharma
- Radiation & Photochemistry Division, Bhabha Atomic Research Center , Mumbai 400085, India
- Homi Bhabha National Institute , Training School Complex, , Anushaktinagar, Mumbai 400094, India
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University , 37077 Göttingen, Germany
| | - Manoj Kumbhakar
- Radiation & Photochemistry Division, Bhabha Atomic Research Center , Mumbai 400085, India
- Homi Bhabha National Institute , Training School Complex, , Anushaktinagar, Mumbai 400094, India
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42
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Zosel F, Haenni D, Soranno A, Nettels D, Schuler B. Combining short- and long-range fluorescence reporters with simulations to explore the intramolecular dynamics of an intrinsically disordered protein. J Chem Phys 2017; 147:152708. [DOI: 10.1063/1.4992800] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Franziska Zosel
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Dominik Haenni
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Center for Microscopy and Image Analysis, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Andrea Soranno
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department of Physics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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43
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Li S, Zhang H, Lu R, Yu A. Interaction between triethanolamine and singlet or triplet excited state of xanthene dyes in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 184:204-210. [PMID: 28499174 DOI: 10.1016/j.saa.2017.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 04/29/2017] [Accepted: 05/04/2017] [Indexed: 06/07/2023]
Abstract
Triethanolamine (TEOA) has been often used as a hole-scavenger in dye-sensitized semiconductor photocatalytic systems. However, the femtosecond time-resolved kinetics of the interaction between a sensitized dye and TEOA has not been reported in literatures. Herein, we selected four commonly used xanthene dyes, such as fluorescein, dibromofluorescein, eosin Y, and erythrosine B, and studied their ultrafast fluorescence quenching dynamics in the presence of TEOA in aqueous solution, respectively, by using both femtosecond transient absorption and time-resolved fluorescence measurements. We obtained the electron transfer rate from TEOA to each photoexcited xanthene dye in 2.0 M TEOA solution. We also obtained the intersystem crossing rate of each xanthene dye in aqueous solution with fluorescence quantum yield and lifetime measurements. Finally we found that TEOA mainly interacts with the singlet excited-state of fluorescein, dibromofluorescein, and eosin Y, and that TEOA can interact with both the singlet and triplet excited-states of erythrosine B in high concentration of TEOA aqueous solution.
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Affiliation(s)
- Shuang Li
- Department of Chemistry, Renmin University of China, Beijing 100872, PR China
| | - Huiyu Zhang
- Department of Chemistry, Renmin University of China, Beijing 100872, PR China
| | - Rong Lu
- Department of Chemistry, Renmin University of China, Beijing 100872, PR China.
| | - Anchi Yu
- Department of Chemistry, Renmin University of China, Beijing 100872, PR China.
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44
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Chandra A, Singh N. Biocompatible Fluorescent Carbon Dots for Ratiometric Intracellular pH Sensing. ChemistrySelect 2017. [DOI: 10.1002/slct.201701012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Anil Chandra
- Centre for Biomedical Engineering; Indian Institute of Technology Delhi, Hauz Khas; New Delhi-110016 India
| | - Neetu Singh
- Centre for Biomedical Engineering; Indian Institute of Technology Delhi, Hauz Khas; New Delhi-110016 India
- Biomedical Engineering Unit; All India Institute of Medical Sciences, Ansari Nagar; New Delhi-110029 India
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45
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Lin CW, Mensa B, Barniol-Xicota M, DeGrado WF, Gai F. Activation pH and Gating Dynamics of Influenza A M2 Proton Channel Revealed by Single-Molecule Spectroscopy. Angew Chem Int Ed Engl 2017; 56:5283-5287. [PMID: 28374543 PMCID: PMC5543805 DOI: 10.1002/anie.201701874] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Indexed: 12/17/2022]
Abstract
Because of its importance in viral replication, the M2 proton channel of the influenza A virus has been the focus of many studies. Although we now know a great deal about the structural architecture underlying its proton conduction function, we know little about its conformational dynamics, especially those controlling the rate of this action. Herein, we employ a single-molecule fluorescence method to assess the dynamics of the inter-helical channel motion of both full-length M2 and the transmembrane domain of M2. The rate of this motion depends not only on the identity of the channel and membrane composition but also on the pH in a sigmoidal manner. For the full-length M2 channel, the rate is increased from approximately 190 μs-1 at high pH to approximately 80 μs-1 at low pH, with a transition midpoint at pH 6.1. Because the latter value is within the range reported for the conducting pKa value of the His37 tetrad, we believe that this inter-helical motion accompanies proton conduction.
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Affiliation(s)
- Chun-Wei Lin
- Ultrafast Optical Processes Laboratory, Department of Chemistry, University of Pennsylvania, Philadelphia, 231 S. 34th Street, Philadelphia, PA, 19104, USA
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, San Francisco, CA, 94158-2517, USA
| | - Marta Barniol-Xicota
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, San Francisco, CA, 94158-2517, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, San Francisco, CA, 94158-2517, USA
| | - Feng Gai
- Ultrafast Optical Processes Laboratory, Department of Chemistry, University of Pennsylvania, Philadelphia, 231 S. 34th Street, Philadelphia, PA, 19104, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, 231 S. 34th Street, Philadelphia, PA, 19104, USA
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46
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Lin CW, Mensa B, Barniol-Xicota M, DeGrado WF, Gai F. Activation pH and Gating Dynamics of Influenza A M2 Proton Channel Revealed by Single-Molecule Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Chun-Wei Lin
- Ultrafast Optical Processes Laboratory; Department of Chemistry; University of Pennsylvania, Philadelphia; 231 S. 34th Street Philadelphia PA 19104 USA
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry; University of California San Francisco; 600 16th Street San Francisco CA 94158-2517 USA
| | - Marta Barniol-Xicota
- Department of Pharmaceutical Chemistry; University of California San Francisco; 600 16th Street San Francisco CA 94158-2517 USA
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry; University of California San Francisco; 600 16th Street San Francisco CA 94158-2517 USA
| | - Feng Gai
- Ultrafast Optical Processes Laboratory; Department of Chemistry; University of Pennsylvania, Philadelphia; 231 S. 34th Street Philadelphia PA 19104 USA
- Department of Chemistry; University of Pennsylvania, Philadelphia; 231 S. 34th Street Philadelphia PA 19104 USA
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47
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Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations. Proc Natl Acad Sci U S A 2017. [PMID: 28223518 DOI: 10.1073/pnas.1616672114.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Internal friction is an important contribution to protein dynamics at all stages along the folding reaction. Even in unfolded and intrinsically disordered proteins, internal friction has a large influence, as demonstrated with several experimental techniques and in simulations. However, these methods probe different facets of internal friction and have been applied to disparate molecular systems, raising questions regarding the compatibility of the results. To obtain an integrated view, we apply here the combination of two complementary experimental techniques, simulations, and theory to the same system: unfolded protein L. We use single-molecule Förster resonance energy transfer (FRET) to measure the global reconfiguration dynamics of the chain, and photoinduced electron transfer (PET), a contact-based method, to quantify the rate of loop formation between two residues. This combination enables us to probe unfolded-state dynamics on different length scales, corresponding to different parts of the intramolecular distance distribution. Both FRET and PET measurements show that internal friction dominates unfolded-state dynamics at low denaturant concentration, and the results are in remarkable agreement with recent large-scale molecular dynamics simulations using a new water model. The simulations indicate that intrachain interactions and dihedral angle rotation correlate with the presence of internal friction, and theoretical models of polymer dynamics provide a framework for interrelating the contribution of internal friction observed in the two types of experiments and in the simulations. The combined results thus provide a coherent and quantitative picture of internal friction in unfolded proteins that could not be attained from the individual techniques.
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48
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Karathanasis C, Fricke F, Hummer G, Heilemann M. Molecule Counts in Localization Microscopy with Organic Fluorophores. Chemphyschem 2017; 18:942-948. [PMID: 28196307 DOI: 10.1002/cphc.201601425] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Indexed: 11/08/2022]
Abstract
Single-molecule localization microscopy (SMLM) can be used to count fluorescently labeled molecules even when they are not individually resolved. We demonstrate SMLM molecule counting for nucleic acids labeled with the organic fluorophore Alexa Fluor 647 and imaged under photoswitching conditions. From the observed distributions of the number of fluorophore blinking events, we extract the number of fluorophores per spot using a statistical model. We validate the molecule counting method for single Alexa Fluor 647 fluorophores, and for trimers of Alexa Fluor 647 constructed on a DNA origami structure. This simple counting strategy enables quantitative super-resolution imaging with organic fluorophores.
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Affiliation(s)
- Christos Karathanasis
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Franziska Fricke
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany.,Institute of Biophysics, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
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49
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Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations. Proc Natl Acad Sci U S A 2017; 114:E1833-E1839. [PMID: 28223518 DOI: 10.1073/pnas.1616672114] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Internal friction is an important contribution to protein dynamics at all stages along the folding reaction. Even in unfolded and intrinsically disordered proteins, internal friction has a large influence, as demonstrated with several experimental techniques and in simulations. However, these methods probe different facets of internal friction and have been applied to disparate molecular systems, raising questions regarding the compatibility of the results. To obtain an integrated view, we apply here the combination of two complementary experimental techniques, simulations, and theory to the same system: unfolded protein L. We use single-molecule Förster resonance energy transfer (FRET) to measure the global reconfiguration dynamics of the chain, and photoinduced electron transfer (PET), a contact-based method, to quantify the rate of loop formation between two residues. This combination enables us to probe unfolded-state dynamics on different length scales, corresponding to different parts of the intramolecular distance distribution. Both FRET and PET measurements show that internal friction dominates unfolded-state dynamics at low denaturant concentration, and the results are in remarkable agreement with recent large-scale molecular dynamics simulations using a new water model. The simulations indicate that intrachain interactions and dihedral angle rotation correlate with the presence of internal friction, and theoretical models of polymer dynamics provide a framework for interrelating the contribution of internal friction observed in the two types of experiments and in the simulations. The combined results thus provide a coherent and quantitative picture of internal friction in unfolded proteins that could not be attained from the individual techniques.
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50
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Koley S, Ghosh S. Encapsulation and Residency of a Hydrophobic Dye within the Water-Filled Interior of a PAMAM Dendrimer Molecule. J Phys Chem B 2017; 121:1930-1940. [DOI: 10.1021/acs.jpcb.6b10176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Somnath Koley
- School of Chemical Sciences, National Institute of Science Education and Research, HBNI, Khurda 752050, Odisha, India
| | - Subhadip Ghosh
- School of Chemical Sciences, National Institute of Science Education and Research, HBNI, Khurda 752050, Odisha, India
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