1
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Souroullas K, Manoli A, Itskos G, Apostolou T, Papademas P. Fluorescence of Intrinsic Milk Chromophores as a Novel Verification Method of UV-C Treatment of Milk. Foods 2024; 13:2887. [PMID: 39335816 PMCID: PMC11431347 DOI: 10.3390/foods13182887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/26/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
The European Food Safety Authority (EFSA) has approved the use of a 1045 J/L UV-C dose as an adjunct to pasteurization to increase the shelf life and vitamin D3 content of milk. However, there are no verification methods analogous to the alkaline phosphatase test for pasteurized milk to ensure that the desired UV-C dose has been correctly applied. The aim is to develop a real-time in-line detector based on fluorescence spectroscopy. In this study, 22 different UV-C doses (ranging from 0 to 2000 J/L) were applied to milk to assess the impact of photooxidation on intrinsic photosensitive chromophores. Fluorescence spectroscopy (90°-angle) was employed as the method of analysis for monitoring the changes in the fluorescence spectra of chromophores in milk without sample pretreatment. Three important chromophore areas (CAs) were identified: CA 1 (riboflavin), CA 3 (vitamin A and dityrosine) and CA 4 (tryptophan), with statistically significant changes at around 1045 J/L and 1500 J/L. The findings of our preliminary study support our hypothesis that the fluorescence of intrinsic chromophores can be used as verification of the applied UV-C dose.
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Affiliation(s)
- Kallis Souroullas
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol 3036, Cyprus
| | - Andreas Manoli
- Experimental Condensed Matter Physics Laboratory, Department of Physics, University of Cyprus, Nicosia 1678, Cyprus
| | - Grigorios Itskos
- Experimental Condensed Matter Physics Laboratory, Department of Physics, University of Cyprus, Nicosia 1678, Cyprus
| | | | - Photis Papademas
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol 3036, Cyprus
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2
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Masse MM, Guzman-Luna V, Varela AE, Mahfuza Shapla U, Hutchinson RB, Srivastava A, Wei W, Fuchs AM, Cavagnero S. Nascent chains derived from a foldable protein sequence interact with specific ribosomal surface sites near the exit tunnel. Sci Rep 2024; 14:12324. [PMID: 38811604 PMCID: PMC11137106 DOI: 10.1038/s41598-024-61274-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/03/2024] [Indexed: 05/31/2024] Open
Abstract
In order to become bioactive, proteins must be translated and protected from aggregation during biosynthesis. The ribosome and molecular chaperones play a key role in this process. Ribosome-bound nascent chains (RNCs) of intrinsically disordered proteins and RNCs bearing a signal/arrest sequence are known to interact with ribosomal proteins. However, in the case of RNCs bearing foldable protein sequences, not much information is available on these interactions. Here, via a combination of chemical crosslinking and time-resolved fluorescence-anisotropy, we find that nascent chains of the foldable globin apoHmp1-140 interact with ribosomal protein L23 and have a freely-tumbling non-interacting N-terminal compact region comprising 63-94 residues. Longer RNCs (apoHmp1-189) also interact with an additional yet unidentified ribosomal protein, as well as with chaperones. Surprisingly, the apparent strength of RNC/r-protein interactions does not depend on nascent-chain sequence. Overall, foldable nascent chains establish and expand interactions with selected ribosomal proteins and chaperones, as they get longer. These data are significant because they reveal the interplay between independent conformational sampling and nascent-protein interactions with the ribosomal surface.
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Affiliation(s)
- Meranda M Masse
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Valeria Guzman-Luna
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Angela E Varela
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ummay Mahfuza Shapla
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Rachel B Hutchinson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Food Science, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Aniruddha Srivastava
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- McGaw Medical Center, Northwestern University, Chicago, IL, 60611, USA
| | - Wanting Wei
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- AIDS Vaccine Research Laboratory, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Andrew M Fuchs
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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3
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Masse M, Hutchinson RB, Morgan CE, Allaman HJ, Guan H, Yu EW, Cavagnero S. Mapping Protein-Protein Interactions at Birth: Single-Particle Cryo-EM Analysis of a Ribosome-Nascent Globin Complex. ACS CENTRAL SCIENCE 2024; 10:385-401. [PMID: 38435509 PMCID: PMC10906257 DOI: 10.1021/acscentsci.3c00777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 03/05/2024]
Abstract
Interactions between ribosome-bound nascent chains (RNCs) and ribosomal components are critical to elucidate the mechanism of cotranslational protein folding. Nascent protein-ribosome contacts within the ribosomal exit tunnel were previously assessed mostly in the presence of C-terminal stalling sequences, yet little is known about contacts taking place in the absence of these strongly interacting motifs. Further, there is nearly no information about ribosomal proteins (r-proteins) interacting with nascent chains within the outer surface of the ribosome. Here, we combine chemical cross-linking, single-particle cryo-EM, and fluorescence anisotropy decays to determine the structural features of ribosome-bound apomyoglobin (apoMb). Within the ribosomal exit tunnel core, interactions are similar to those identified in previous reports. However, once the RNC enters the tunnel vestibule, it becomes more dynamic and interacts with ribosomal RNA (rRNA) and the L23 r-protein. Remarkably, on the outer surface of the ribosome, RNCs interact mainly with a highly conserved nonpolar patch of the L23 r-protein. RNCs also comprise a compact and dynamic N-terminal region lacking contact with the ribosome. In all, apoMb traverses the ribosome and interacts with it via its C-terminal region, while N-terminal residues sample conformational space and form a compact subdomain before the entire nascent protein sequence departs from the ribosome.
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Affiliation(s)
- Meranda
M. Masse
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Rachel B. Hutchinson
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Christopher E. Morgan
- Department
of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Heather J. Allaman
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Hongqing Guan
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Edward W. Yu
- Department
of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Silvia Cavagnero
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
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4
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Gooran N, Kopra K. Fluorescence-Based Protein Stability Monitoring-A Review. Int J Mol Sci 2024; 25:1764. [PMID: 38339045 PMCID: PMC10855643 DOI: 10.3390/ijms25031764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.
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Affiliation(s)
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland;
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5
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Addabbo RM, Hutchinson RB, Allaman HJ, Dalphin MD, Mecha MF, Liu Y, Staikos A, Cavagnero S. Critical Beginnings: Selective Tuning of Solubility and Structural Accuracy of Newly Synthesized Proteins by the Hsp70 Chaperone System. J Phys Chem B 2023; 127:3990-4014. [PMID: 37130318 PMCID: PMC10829761 DOI: 10.1021/acs.jpcb.2c08485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Proteins are particularly prone to aggregation immediately after release from the ribosome, and it is therefore important to elucidate the role of chaperones during these key steps of protein life. The Hsp70 and trigger factor (TF) chaperone systems interact with nascent proteins during biogenesis and immediately post-translationally. It is unclear, however, whether these chaperones can prevent formation of soluble and insoluble aggregates. Here, we address this question by monitoring the solubility and structural accuracy of globin proteins biosynthesized in an Escherichia coli cell-free system containing different concentrations of the bacterial Hsp70 and TF chaperones. We find that Hsp70 concentrations required to grant solubility to newly synthesized proteins are extremely sensitive to client-protein sequence. Importantly, Hsp70 concentrations yielding soluble client proteins are insufficient to prevent formation of soluble aggregates. In fact, for some aggregation-prone protein variants, avoidance of soluble-aggregate formation demands Hsp70 concentrations that exceed cellular levels in E. coli. In all, our data highlight the prominent role of soluble aggregates upon nascent-protein release from the ribosome and show the limitations of the Hsp70 chaperone system in the case of highly aggregation-prone proteins. These results demonstrate the need to devise better strategies to prevent soluble-aggregate formation upon release from the ribosome.
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Affiliation(s)
- Rayna M. Addabbo
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Rachel B. Hutchinson
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Heather J. Allaman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Matthew D. Dalphin
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Miranda F. Mecha
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Yue Liu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Alexios Staikos
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Silvia Cavagnero
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
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6
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Dehghan Niestanak V, Unsworth LD. Detailing Protein-Bound Uremic Toxin Interaction Mechanisms with Human Serum Albumin in the Pursuit of Designing Competitive Binders. Int J Mol Sci 2023; 24:ijms24087452. [PMID: 37108613 PMCID: PMC10139063 DOI: 10.3390/ijms24087452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Chronic kidney disease is the gradual progression of kidney dysfunction and involves numerous co-morbidities, one of the leading causes of mortality. One of the primary complications of kidney dysfunction is the accumulation of toxins in the bloodstream, particularly protein-bound uremic toxins (PBUTs), which have a high affinity for plasma proteins. The buildup of PBUTs in the blood reduces the effectiveness of conventional treatments, such as hemodialysis. Moreover, PBUTs can bind to blood plasma proteins, such as human serum albumin, alter their conformational structure, block binding sites for other valuable endogenous or exogenous substances, and exacerbate the co-existing medical conditions associated with kidney disease. The inadequacy of hemodialysis in clearing PBUTs underscores the significance of researching the binding mechanisms of these toxins with blood proteins, with a critical analysis of the methods used to obtain this information. Here, we gathered the available data on the binding of indoxyl sulfate, p-cresyl sulfate, indole 3-acetic acid, hippuric acid, 3-carboxyl-4-methyl-5-propyl-2-furan propanoic acid, and phenylacetic acid to human serum albumin and reviewed the common techniques used to investigate the thermodynamics and structure of the PBUT-albumin interaction. These findings can be critical in investigating molecules that can displace toxins on HSA and improve their clearance by standard dialysis or designing adsorbents with greater affinity for PBUTs than HSA.
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Affiliation(s)
- Vida Dehghan Niestanak
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB T6G 2G4, Canada
| | - Larry D Unsworth
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada
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7
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Villar SF, Dalla-Rizza J, Möller MN, Ferrer-Sueta G, Malacrida L, Jameson DM, Denicola A. Fluorescence Lifetime Phasor Analysis of the Decamer-Dimer Equilibrium of Human Peroxiredoxin 1. Int J Mol Sci 2022; 23:5260. [PMID: 35563654 PMCID: PMC9100220 DOI: 10.3390/ijms23095260] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/22/2022] Open
Abstract
Protein self-assembly is a common feature in biology and is often required for a myriad of fundamental processes, such as enzyme activity, signal transduction, and transport of solutes across membranes, among others. There are several techniques to find and assess homo-oligomer formation in proteins. Naturally, all these methods have their limitations, meaning that at least two or more different approaches are needed to characterize a case study. Herein, we present a new method to study protein associations using intrinsic fluorescence lifetime with phasors. In this case, the method is applied to determine the equilibrium dissociation constant (KD) of human peroxiredoxin 1 (hPrx1), an efficient cysteine-dependent peroxidase, that has a quaternary structure comprised of five head-to-tail homodimers non-covalently arranged in a decamer. The hPrx1 oligomeric state not only affects its activity but also its association with other proteins. The excited state lifetime of hPrx1 has distinct values at high and low concentrations, suggesting the presence of two different species. Phasor analysis of hPrx1 emission lifetime allowed for the identification and quantification of hPrx1 decamers, dimers, and their mixture at diverse protein concentrations. Using phasor algebra, we calculated the fraction of hPrx1 decamers at different concentrations and obtained KD (1.1 × 10-24 M4) and C0.5 (1.36 μM) values for the decamer-dimer equilibrium. The results were validated and compared with size exclusion chromatography. In addition, spectral phasors provided similar results despite the small differences in emission spectra as a function of hPrx1 concentration. The phasor approach was shown to be a highly sensitive and quantitative method to assess protein oligomerization and an attractive addition to the biophysicist's toolkit.
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Affiliation(s)
- Sebastián F. Villar
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (S.F.V.); (J.D.-R.); (M.N.M.); (G.F.-S.)
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
| | - Joaquín Dalla-Rizza
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (S.F.V.); (J.D.-R.); (M.N.M.); (G.F.-S.)
| | - Matías N. Möller
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (S.F.V.); (J.D.-R.); (M.N.M.); (G.F.-S.)
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
| | - Gerardo Ferrer-Sueta
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (S.F.V.); (J.D.-R.); (M.N.M.); (G.F.-S.)
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
| | - Leonel Malacrida
- Advanced Bioimaging Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay;
- Departamento de Fisiopatología, Hospital de Clínicas, Universidad de la República, Montevideo 11600, Uruguay
| | - David M. Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Ana Denicola
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (S.F.V.); (J.D.-R.); (M.N.M.); (G.F.-S.)
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
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8
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Ma Y, Zhu M, Zhang Y, Gao E, Wu S. A multiemissive lanthanide metal-organic framework for selective detection of L-tryptophan. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.120928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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9
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Yahav G, Weber Y, Duadi H, Pawar S, Fixler D. Classification of fluorescent anisotropy decay based on the distance approach in the frequency domain. OPTICS EXPRESS 2022; 30:6176-6192. [PMID: 35209559 DOI: 10.1364/oe.453108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Frequency-domain (FD) fluorometry is a widely utilized tool to probe unique features of complex biological structures, which may serve medical diagnostic purposes. The conventional data analysis approaches used today to extract the fluorescence intensity or fluorescence anisotropy (FA) decay data suffer from several drawbacks and are inherently limited by the characteristics and complexity of the decay models. This paper presents the squared distance (D2) technique, which categorized samples based on the direct frequency response data (FRD) of the FA decay. As such, it improves the classification ability of the FD measurements of the FA decay as it avoids any distortion that results from the challenged translation into time domain data. This paper discusses the potential use of the D2 approach to classify biological systems. Mathematical formulation of D2 technique adjusted to the FRD of the FA decay is described. In addition, it validates the D2 approach using 2 simulated data sets of 6 groups with similar widely and closely spaced FA decay data as well as in experimental data of 4 samples of a fluorophore-solvent (fluorescein-glycerol) system. In the simulations, the classification accuracy was above 95% for all 6 groups. In the experimental data, the classification accuracy was 100%. The D2 approach can help classify samples whose FA decay data are difficult to extract making FA in the FD a realistic diagnostic tool. The D2 approach offers an advanced method for sorting biological samples with differences beyond the practical temporal resolution limit in a reliable and efficient manner based on the FRD of their time-resolved fluorescence measurements thereby achieving better diagnostic quality in a shorter time.
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10
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Diffusional microfluidics for protein analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2021.116508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Sun HX, Zhou J, Zhang Z, He M, He LC, Du L, Xie MJ, Zhao QH. Anion-controlled Zn(II) coordination polymers with 1-(tetrazo-5-yl)-3-(triazo-1-yl) benzene as an assembling ligand: synthesis, characterization, and efficient detection of tryptophan in water. Dalton Trans 2021; 50:18044-18052. [PMID: 34826320 DOI: 10.1039/d1dt03045k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tryptophan regulates and participates in various physiological systems in the human body, and its excessive intake has harmful effects. Therefore, detecting and monitoring tryptophan in water and distinguishing it from other amino acids are necessary. In addition to their excellent luminescence, coordination polymer-based sensors have good stability and high sensitivity and selectivity for sensing applications. In this work, two luminescent coordination polymers (CPs), [Zn(ttb)Cl]n (1) and [Zn2(ttb)2(OH)(NO3)]n (2), were obtained through the solvothermal reaction of different Zn(II) salts with a rarely studied multidentate N-donor ligand, 1-(tetrazo-5-yl)-3-(triazo-1-yl) benzene (Httb). Crystallographic investigations revealed that the structure of 1 exhibits a 2D fes net with Cl- anions acting as terminal charge balancers, and that of 2 features a 3D ant net with NO3- anions in a rare monodentate bridging (μ2-O-η1:η1) mode. In terms of stability tests, 2 has better thermal and water stability than 1. Although both show good fluorescence performance, specific tryptophan detection, and excellent anti-interference ability, 2 has higher KSV (111 852.6 M-1), a lower limit of detection (LOD = 23.6 nM), and a better recovery rate than 1. Cytotoxicity experiments proved that 2 has extremely low toxicity and thus has great potential for in vivo detection. Therefore, CP 2 is a suitable candidate for advanced practical applications for the efficient sensing of tryptophan in water. The luminescence of the ligands was also calculated using DFT theory and further discussed through experiments. The quenching mechanism that occurs after tryptophan addition was explored through Hirshfeld surface analysis.
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Affiliation(s)
- Han-Xu Sun
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China.
| | - Jie Zhou
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China.
| | - Zhen Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China.
| | - Mei He
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China.
| | - Lian-Cheng He
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China.
| | - Lin Du
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China.
| | - Ming-Jin Xie
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China.
| | - Qi-Hua Zhao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China.
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12
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Aslankoohi N, Mequanint K. Intrinsically fluorescent bioactive glass-poly(ester amide) hybrid microparticles for dual drug delivery and bone repair. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 128:112288. [PMID: 34474839 DOI: 10.1016/j.msec.2021.112288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/27/2021] [Accepted: 06/26/2021] [Indexed: 12/19/2022]
Abstract
The bone extracellular matrix (ECM) is a composite scaffold having inorganic hydroxyapatite and organic collagen fibers. Synthetic bone repair scaffolds that mimic the chemical composition of the native ECM and capable of delivering therapeutics are beneficial. In this study, we prepared intrinsically fluorescent organic-inorganic hybrid microparticle biomaterials by sol-gel process. Unlike the conventional Stöber process which requires an alkaline condition for microparticle formation, an acidic condition in the presence of a biodegradable poly(ester amide) (PEA) polymer was used to prepare silica and tertiary bioactive glass hybrids. During their preparation, one or two model drugs were loaded in the microparticles. Our results showed that a gelation temperature between 40 °C-60 °C and the inclusion of PEA were critical for microparticle formation. Unexpectedly, the hybrid microparticles were fluorescent with tunable emission by changing the excitation wavelengths ranging from 300 to 565 nm for potential multiplex imaging. Gene expression studies showed that the hybrid materials induce osteogenic differentiation of 10T1/2 cells without adding exogenous biochemical factors. The bioactivity of the inorganic phase and the dual drug release from homogenous, biodegradable, biocompatible, osteoinductive, and intrinsically fluorescent microparticles may offer a unique platform for bone regeneration and therapy.
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Affiliation(s)
- Neda Aslankoohi
- School of Biomedical Engineering, The University of Western Ontario, London, Ontario N6A 5B9, Canada
| | - Kibret Mequanint
- School of Biomedical Engineering, The University of Western Ontario, London, Ontario N6A 5B9, Canada; Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, Ontario N6A 5B9, Canada.
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13
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Gorokhov VV, Korvatovsky BN, Knox PP, Grishanova NP, Goryachev SN, Pashchenko VZ, Rubin AB. Temperature Dependence of Tryptophan Fluorescence Lifetime as an Indicator of Its Microenvironment Dynamics. DOKL BIOCHEM BIOPHYS 2021; 498:170-176. [PMID: 34189644 DOI: 10.1134/s1607672921030030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 11/23/2022]
Abstract
The spectral-kinetic characteristics of the fluorescence of the tryptophan molecule in an aqueous solution and in the composition of a protein (albumin) were studied in the temperature range from -170 to 25°C. To explain the observed changes in the spectra and the tryptophan fluorescence lifetime with temperature, a model of transitions between the excited and ground states involving a charge-transfer state was used, which takes into account the nonlinear nature of the dynamics of these transitions. In these processes, an important role is played by the interaction of tryptophan molecules with its microenvironment, as well as rearrangements in the system of hydrogen bonds of the water-protein matrix surrounding the tryptophan molecule.
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Affiliation(s)
| | | | - P P Knox
- Moscow State University, Moscow, Russia
| | | | | | | | - A B Rubin
- Moscow State University, Moscow, Russia
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14
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Hutchinson RB, Chen X, Zhou N, Cavagnero S. Fluorescence Anisotropy Decays and Microscale-Volume Viscometry Reveal the Compaction of Ribosome-Bound Nascent Proteins. J Phys Chem B 2021; 125:6543-6558. [PMID: 34110829 PMCID: PMC8741338 DOI: 10.1021/acs.jpcb.1c04473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This work introduces a technology that combines fluorescence anisotropy decay with microscale-volume viscometry to investigate the compaction and dynamics of ribosome-bound nascent proteins. Protein folding in the cell, especially when nascent chains emerge from the ribosomal tunnel, is poorly understood. Previous investigations based on fluorescence anisotropy decay determined that a portion of the ribosome-bound nascent protein apomyoglobin (apoMb) forms a compact structure. This work, however, could not assess the size of the compact region. The combination of fluorescence anisotropy with microscale-volume viscometry, presented here, enables identifying the size of compact nascent-chain subdomains using a single fluorophore label. Our results demonstrate that the compact region of nascent apoMb contains 57-83 amino acids and lacks residues corresponding to the two native C-terminal helices. These amino acids are necessary for fully burying the nonpolar residues in the native structure, yet they are not available for folding before ribosome release. Therefore, apoMb requires a significant degree of post-translational folding for the generation of its native structure. In summary, the combination of fluorescence anisotropy decay and microscale-volume viscometry is a powerful approach to determine the size of independently tumbling compact regions of biomolecules. This technology is of general applicability to compact macromolecules linked to larger frameworks.
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Affiliation(s)
| | - Xi Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ningkun Zhou
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
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15
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Jadavi S, Bianchini P, Cavalleri O, Dante S, Canale C, Diaspro A. Correlative nanoscopy: A multimodal approach to molecular resolution. Microsc Res Tech 2021; 84:2472-2482. [PMID: 33955625 PMCID: PMC8518117 DOI: 10.1002/jemt.23800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/11/2021] [Indexed: 11/24/2022]
Abstract
Atomic force microscopy (AFM) is a nano‐mechanical tool uniquely suited for biological studies at the molecular scale. AFM operation is based on mechanical interaction between the tip and the sample, a mechanism of contrast capable of measuring different information, including surface topography, mechanical, and electrical properties. However, the lack of specificity highlights the need to integrate AFM data with other techniques providing compositional hints. In particular, optical microscopes based on fluorescence as a mechanism of contrast can access the local distribution of specific molecular species. The coupling between AFM and super‐resolved fluorescence microscopy solves the resolution mismatch between AFM and conventional fluorescence optical microscopy. Recent advances showed that also the inherently label‐free imaging capabilities of the AFM are fundamental to complement the fluorescence images. In this review, we have presented a brief historical view on correlative microscopy, and, finally, we have summarized the progress of correlative AFM‐super‐resolution microscopy in biological research.
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Affiliation(s)
- Samira Jadavi
- DIFILAB, Department of Physics, University of Genova, Genova, Italy.,Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Genova, Italy
| | - Paolo Bianchini
- Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Genova, Italy
| | | | - Silvia Dante
- Materials Characterization Facility, Istituto Italiano di Tecnologia, Genova, Italy
| | - Claudio Canale
- DIFILAB, Department of Physics, University of Genova, Genova, Italy
| | - Alberto Diaspro
- DIFILAB, Department of Physics, University of Genova, Genova, Italy.,Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Genova, Italy
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16
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Paschenko VZ, Gorokhov VV, Korvatovsky BN, Knox PP, Grishanova NP, Goryachev SN. A Study of the Temperature Dependence of Tryptophan Fluorescence Lifetime in the Range of –170 to +20°С in Various Solvents. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921030143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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17
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Zhang Y, Herling TW, Kreida S, Peter QAE, Kartanas T, Törnroth-Horsefield S, Linse S, Knowles TPJ. A microfluidic strategy for the detection of membrane protein interactions. LAB ON A CHIP 2020; 20:3230-3238. [PMID: 32744557 DOI: 10.1039/d0lc00205d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Membrane proteins perform a vast range of vital biological functions and are the gatekeepers for exchange of information and matter between the intracellular and extracellular environment. However, membrane protein interactions can be challenging to characterise in a quantitative manner due to the low solubility and large size of the membrane protein complex with associated lipid or detergent molecules. Here, we show that measurements of the changes in charge and diffusivity on the micron scale allow for non-disruptive studies of membrane protein interactions in solution. The approach presented here uses measurements of key physical properties of membrane proteins and their ligands to characterise the binding equilibrium parameters. We demonstrate this approach for human aquaporins (AQPs), key membrane proteins in the regulation of water homeostasis in cells. We perform quantitative measurements to characterise the interactions between two full-length AQP isoforms and the regulatory protein, calmodulin (CaM), and show that CaM selectively binds AQP0. Through direct measurements of the diffusivity and mobility in an external electric field, the diffusion coefficients and electrophoretic mobilities are determined for the individual components and the resulting AQP0-CaM complex. Furthermore, we obtain directly the binding equilibrium parameters and effective charge of each component. These results open up a route towards the use of microfluidics as a general platform in protein science and open up new possibilities for the characterisation of membrane protein interactions in solution.
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Affiliation(s)
- Yuewen Zhang
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Therese W Herling
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Stefan Kreida
- Department of Biochemistry and Structural Biology, Lund University, Lund, 221 00, Sweden.
| | - Quentin A E Peter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Tadas Kartanas
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | | | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund, 221 00, Sweden.
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. and Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK
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18
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Datta R, Heaster TM, Sharick JT, Gillette AA, Skala MC. Fluorescence lifetime imaging microscopy: fundamentals and advances in instrumentation, analysis, and applications. JOURNAL OF BIOMEDICAL OPTICS 2020; 25:1-43. [PMID: 32406215 PMCID: PMC7219965 DOI: 10.1117/1.jbo.25.7.071203] [Citation(s) in RCA: 326] [Impact Index Per Article: 81.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/24/2020] [Indexed: 05/18/2023]
Abstract
SIGNIFICANCE Fluorescence lifetime imaging microscopy (FLIM) is a powerful technique to distinguish the unique molecular environment of fluorophores. FLIM measures the time a fluorophore remains in an excited state before emitting a photon, and detects molecular variations of fluorophores that are not apparent with spectral techniques alone. FLIM is sensitive to multiple biomedical processes including disease progression and drug efficacy. AIM We provide an overview of FLIM principles, instrumentation, and analysis while highlighting the latest developments and biological applications. APPROACH This review covers FLIM principles and theory, including advantages over intensity-based fluorescence measurements. Fundamentals of FLIM instrumentation in time- and frequency-domains are summarized, along with recent developments. Image segmentation and analysis strategies that quantify spatial and molecular features of cellular heterogeneity are reviewed. Finally, representative applications are provided including high-resolution FLIM of cell- and organelle-level molecular changes, use of exogenous and endogenous fluorophores, and imaging protein-protein interactions with Förster resonance energy transfer (FRET). Advantages and limitations of FLIM are also discussed. CONCLUSIONS FLIM is advantageous for probing molecular environments of fluorophores to inform on fluorophore behavior that cannot be elucidated with intensity measurements alone. Development of FLIM technologies, analysis, and applications will further advance biological research and clinical assessments.
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Affiliation(s)
- Rupsa Datta
- Morgridge Institute for Research, Madison, Wisconsin, United States
| | - Tiffany M. Heaster
- Morgridge Institute for Research, Madison, Wisconsin, United States
- University of Wisconsin, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | - Joe T. Sharick
- Morgridge Institute for Research, Madison, Wisconsin, United States
| | - Amani A. Gillette
- Morgridge Institute for Research, Madison, Wisconsin, United States
- University of Wisconsin, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | - Melissa C. Skala
- Morgridge Institute for Research, Madison, Wisconsin, United States
- University of Wisconsin, Department of Biomedical Engineering, Madison, Wisconsin, United States
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19
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Knox PP, Gorokhov VV, Korvatovsky BN, Grishanova NP, Goryachev SN, Paschenko VZ. Specific features of the temperature dependence of tryptophan fluorescence lifetime in the temperature range of −170–20 °C. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Poursoleiman A, Karimi-Jafari MH, Zolmajd-Haghighi Z, Bagheri M, Haertlé T, Behbehani GR, Ghasemi A, Stroylova YY, Muronetz VI, Saboury AA. Polymyxins interaction to the human serum albumin: A thermodynamic and computational study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 217:155-163. [PMID: 30933779 DOI: 10.1016/j.saa.2019.03.077] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 03/18/2019] [Accepted: 03/22/2019] [Indexed: 06/09/2023]
Abstract
Polymyxin B and E (colistin), are a group of cationic charged cyclic antibiotic lipopeptides that are frequently used in the clinics to treat infections caused by the multidrug-resistant gram-negative bacteria. Since the interactions with the blood plasma drug-transport proteins may play a critical role in determining their pharmacological and pharmacokinetic profiles, we studied the binding properties of polymyxins to the human serum albumin (HSA) under simulated physiological conditions by the combination of biophysical approaches, such as isothermal titration calorimetry (ITC), fluorescence anisotropy, circular dichroism (CD) buttressed by computational studies. The HSA binding to the polymyxins was relatively strong (Ka ≈ 1.0 × 107 M-1). Molecular docking indicated that polymyxins bind to the cleft of HSA between domains I and III via the electrostatic interactions. This evidence was further confirmed by the entropy-driven interaction for the polymyxins bound HSA. Far UV-CD experiments showed that the secondary structure of HSA doesn't alter and its stable structure is preserved. Collectively, these investigations revealed that the polymyxins bind preferentially to the partially unfolded intermediate forms of the protein structure; however, HSA molecule does not undergo any significant conformational changes upon binding. This is promising as it may limit the unfavorable side effects of the medicine. On the whole, the results provide quantitative and qualitative insight of the binding interaction between HSA and polymyxins, which is important in understanding their effect as therapeutic agents.
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Affiliation(s)
- A Poursoleiman
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - M H Karimi-Jafari
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Z Zolmajd-Haghighi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - M Bagheri
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - T Haertlé
- Poznan University of Life Sciences, Department of Animal Nutrition, Poznan, Poland; Biopolymers, Interactions, Assemblies, UR 1268, Institute National de la Recherche Agronomique, Nantes, France
| | - G Rezaei Behbehani
- Chemistry Department, Imam Khomeini International University, Qazvin, Iran
| | - A Ghasemi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Y Y Stroylova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - V I Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - A A Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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21
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Knox PP, Korvatovskiy BN, Gorokhov VV, Goryachev SN, Mamedov MD, Paschenko VZ. Comparison of tryptophan fluorescence lifetimes in cyanobacterial photosystem I frozen in the light and in the dark. PHOTOSYNTHESIS RESEARCH 2019; 139:441-448. [PMID: 30353420 DOI: 10.1007/s11120-018-0595-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/09/2018] [Indexed: 06/08/2023]
Abstract
The dependence on temperature of tryptophan fluorescence lifetime in trimeric photosystem I (PSI) complexes from cyanobacteria Synechocystis sp. PCC 6803 during the heating of pre-frozen to - 180 °C in the dark or in the light-activated preparations has been studied. Fluorescence lifetime in samples frozen in the light was longer than in samples frozen in the dark. For samples in 65% glycerol at λreg = 335 nm and at 20 °C, the lifetime of components were as follows: τ1 ≈ 1.2 ns, τ2 ≈ 4.9 ns, and τ3 ≈ 20 ns. The contribution of the first component was negligible. To analyze the contribution of components 2 and 3 derived from frozen-thawed samples, two temperature ranges from - 180 to - 90 °C and above - 90 °C are considered. In doing so, the contributions of these components appear antiphase course to each other. The dependence on temperature of these contributions is explained by the influence of the microconformational protein dynamics on the tryptophan fluorescence lifetime. In the present work, a comparative analysis of temperature-dependent conformational dynamics and electron transfer in cyanobacterial PSI (Schlodder et al., in Biochemistry 37:9466-9476, 1998) and Rhodobacter sphaeroides reaction center complexes (Knox et al., in J Photochem Photobiol B 180:140-148, 2018) was also carried out.
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Affiliation(s)
- Peter P Knox
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Boris N Korvatovskiy
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Vladimir V Gorokhov
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Sergey N Goryachev
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Mahir D Mamedov
- A.N. Belozersky Institute of Physical-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Vladimir Z Paschenko
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, Moscow, Russia, 119991.
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22
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Characterization of esterase activity from an Acetomicrobium hydrogeniformans enzyme with high structural stability in extreme conditions. Extremophiles 2018; 22:781-793. [DOI: 10.1007/s00792-018-1038-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/09/2018] [Indexed: 01/06/2023]
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23
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Velocity-resolved kinetics of site-specific carbon monoxide oxidation on platinum surfaces. Nature 2018; 558:280-283. [DOI: 10.1038/s41586-018-0188-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 04/16/2018] [Indexed: 11/08/2022]
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24
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Sun J, Jiang J, Pan H, Li J. Additive-Free Pd-Catalysed C-2 Arylation of Tryptophan Derivatives with Diaryliodonium Salts. JOURNAL OF CHEMICAL RESEARCH 2018. [DOI: 10.3184/174751918x15232701502261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An efficient, mild and Pd-catalysed C-2 arylation of Fmoc-L-tryptophan with diaryliodonium salts has been developed, giving easy access to C-2 arylated tryptophan derivatives. This protocol tolerates a variety of functional groups and proceeds smoothly in high yields without any additives. In addition, the chemoseletive C–H arylation with unsymmetrical salts is described.
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Affiliation(s)
- Jian Sun
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, P.R. China
| | - Jun Jiang
- National Engineering Research Center for Process Development of Active Pharmaceutical Ingredients, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P.R. China
| | - Heng Pan
- National Engineering Research Center for Process Development of Active Pharmaceutical Ingredients, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P.R. China
| | - Jianjun Li
- National Engineering Research Center for Process Development of Active Pharmaceutical Ingredients, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P.R. China
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, P.R. China
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25
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Weiss-Errico MJ, Miksovska J, O’Shea KE. β-Cyclodextrin Reverses Binding of Perfluorooctanoic Acid to Human Serum Albumin. Chem Res Toxicol 2018; 31:277-284. [DOI: 10.1021/acs.chemrestox.8b00002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Mary Jo Weiss-Errico
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Kevin E. O’Shea
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
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26
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Knox PP, Gorokhov VV, Korvatovskiy BN, Lukashev EP, Goryachev SN, Paschenko VZ, Rubin AB. The effect of light and temperature on the dynamic state of Rhodobacter sphaeroides reaction centers proteins determined from changes in tryptophan fluorescence lifetime and P +Q A- recombination kinetics. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 180:140-148. [PMID: 29413697 DOI: 10.1016/j.jphotobiol.2018.01.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/22/2018] [Accepted: 01/29/2018] [Indexed: 11/26/2022]
Abstract
The temperature dependencies of the rate of dark recombination of separated charges between the photoactive bacteriochlorophyll and the primary quinone acceptor (QA) in photosynthetic reaction centers (RCs) of the purple bacteria Rhodobacter sphaeroides (Rb. sphaeroides) were investigated. Measurements were performed in water-glycerol and trehalose environments after freezing to -180 °C in the dark and under actinic light with subsequent heating. Simultaneously, the RC tryptophanyl fluorescence lifetime in the spectral range between 323 and 348 nm was measured under these conditions. A correlation was found between the temperature dependencies of the functional and dynamic parameters of RCs in different solvent mixtures. For the first time, differences in the average fluorescence lifetime of tryptophanyl residues were measured between RCs frozen in the dark and in the actinic light. The obtained results can be explained by the RC transitions between different conformational states and the dynamic processes in the structure of the hydrogen bonds of RCs. We assumed that RCs exist in two main microconformations - "fast" and "slow", which are characterized by different rates of P+ and QA- recombination reactions. The "fast" conformation is induced in frozen RCs in the dark, while the "slow" conformation of RC occurs when the RC preparation is frozen under actinic light. An explanation of the temperature dependencies of tryptophan fluorescence lifetimes in RC proteins was made under the assumption that temperature changes affect mainly the electron transfer from the indole ring of the tryptophan molecule to the nearest amide or carboxyl groups.
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Affiliation(s)
- Peter P Knox
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir V Gorokhov
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Boris N Korvatovskiy
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Eugene P Lukashev
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Sergey N Goryachev
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir Z Paschenko
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Andrew B Rubin
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
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27
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Gorokhov VV, Knox PP, Korvatovskiy BN, Seifullina NK, Goryachev SN, Paschenko VZ. Temperature Dependence of Tryptophan Fluorescence Lifetime in Aqueous Glycerol and Trehalose Solutions. BIOCHEMISTRY (MOSCOW) 2018; 82:1269-1275. [PMID: 29223153 DOI: 10.1134/s0006297917110049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The temperature dependences of tryptophan fluorescence decay kinetics in aqueous glycerol and 1 M trehalose solutions were examined. The fluorescence decay kinetics were recorded in the spectral region of 292.5-417.5 nm with nanosecond time resolution. The kinetics curves were approximated by the sum of three exponential terms, and the spectral distribution (DAS) of these components was determined. An antisymbatic course of fluorescence decay times of two (fast and medium) components in the temperature range from -60 to +10°C was observed. The third (slow) component showed only slight temperature dependence. The antisymbatic behavior of fluorescence lifetimes of the fast and medium components was explained on the assumption that some of the excited tryptophan molecules are transferred from a short-wavelength B-form with short fluorescence lifetime to a long-wavelength R-form with an intermediate fluorescence lifetime. This transfer occurred in the indicated temperature range.
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Affiliation(s)
- V V Gorokhov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia.
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28
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Zhang J, Huang Y, Yue D, Cui Y, Yang Y, Qian G. A luminescent turn-up metal–organic framework sensor for tryptophan based on singlet–singlet Förster energy transfer. J Mater Chem B 2018; 6:5174-5180. [DOI: 10.1039/c8tb01592a] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A highly stable MOF, ZJU-108, was synthesized with Zn2+ and 6-(4-pyridyl)-terephthalic acid (H2pta) as construction units, and it exhibits an impressive turn-on luminescence enhancement response to tryptophan.
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Affiliation(s)
- Jun Zhang
- State Key Laboratory of Silicon Materials
- Cyrus Tang Center for Sensor Materials and Applications
- School of Materials Science and Engineering
- Zhejiang University
- Hangzhou 310027
| | - Yike Huang
- State Key Laboratory of Silicon Materials
- Cyrus Tang Center for Sensor Materials and Applications
- School of Materials Science and Engineering
- Zhejiang University
- Hangzhou 310027
| | - Dan Yue
- State Key Laboratory of Silicon Materials
- Cyrus Tang Center for Sensor Materials and Applications
- School of Materials Science and Engineering
- Zhejiang University
- Hangzhou 310027
| | - Yuanjing Cui
- State Key Laboratory of Silicon Materials
- Cyrus Tang Center for Sensor Materials and Applications
- School of Materials Science and Engineering
- Zhejiang University
- Hangzhou 310027
| | - Yu Yang
- State Key Laboratory of Silicon Materials
- Cyrus Tang Center for Sensor Materials and Applications
- School of Materials Science and Engineering
- Zhejiang University
- Hangzhou 310027
| | - Guodong Qian
- State Key Laboratory of Silicon Materials
- Cyrus Tang Center for Sensor Materials and Applications
- School of Materials Science and Engineering
- Zhejiang University
- Hangzhou 310027
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29
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Lopes JLS, Yoneda JS, Martins JM, DeMarco R, Jameson DM, Castro AM, Bossolan NRS, Wallace BA, Araujo APU. Environmental Factors Modulating the Stability and Enzymatic Activity of the Petrotoga mobilis Esterase (PmEst). PLoS One 2016; 11:e0158146. [PMID: 27351338 PMCID: PMC4924860 DOI: 10.1371/journal.pone.0158146] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/11/2016] [Indexed: 01/20/2023] Open
Abstract
Enzymes isolated from thermophilic organisms found in oil reservoirs can find applications in many fields, including the oleochemical, pharmaceutical, bioenergy, and food/dairy industries. In this study, in silico identification and recombinant production of an esterase from the extremophile bacteria Petrotoga mobilis (designated PmEst) were performed. Then biochemical, bioinformatics and structural characterizations were undertaken using a combination of synchrotron radiation circular dichroism (SRCD) and fluorescence spectroscopies to correlate PmEst stability and hydrolytic activity on different substrates. The enzyme presented a high Michaelis-Menten constant (KM 0.16 mM) and optimum activity at ~55°C for p-nitrophenyl butyrate. The secondary structure of PmEst was preserved at acid pH, but not under alkaline conditions. PmEst was unfolded at high concentrations of urea or guanidine through apparently different mechanisms. The esterase activity of PmEst was preserved in the presence of ethanol or propanol and its melting temperature increased ~8°C in the presence of these organic solvents. PmEst is a mesophilic esterase with substrate preference towards short-to medium-length acyl chains. The SRCD data of PmEst is in agreement with the prediction of an α/β protein, which leads us to assume that it displays a typical fold of esterases from this family. The increased enzyme stability in organic solvents may enable novel applications for its use in synthetic biology. Taken together, our results demonstrate features of the PmEst enzyme that indicate it may be suitable for applications in industrial processes, particularly, when the use of polar organic solvents is required.
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Affiliation(s)
- Jose L. S. Lopes
- Instituto de Física, Universidade de São Paulo, São Paulo, Brazil
| | - Juliana S. Yoneda
- Instituto de Física, Universidade de São Paulo, São Paulo, Brazil
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Julia M. Martins
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Ricardo DeMarco
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - David M. Jameson
- Department of Cell and Molecular Biology, University of Hawai’i at Manoa, Hawaii, United States of America
| | - Aline M. Castro
- Biotechnology Division, Research and Development Center, Petrobras, Brazil
| | - Nelma R. S. Bossolan
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - B. A. Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Ana P. U. Araujo
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
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Banerjee S, Baiardi A, Bloino J, Barone V. Temperature Dependence of Radiative and Nonradiative Rates from Time-Dependent Correlation Function Methods. J Chem Theory Comput 2016; 12:774-86. [DOI: 10.1021/acs.jctc.5b01017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shiladitya Banerjee
- Scuola Normale Superiore, piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Consiglio Nazionale
delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Alberto Baiardi
- Scuola Normale Superiore, piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Julien Bloino
- Scuola Normale Superiore, piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Consiglio Nazionale
delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, piazza
dei Cavalieri 7, I-56126 Pisa, Italy
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31
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Bartoccini F, Bartolucci S, Mari M, Piersanti G. A simple, modular synthesis of C4-substituted tryptophan derivatives. Org Biomol Chem 2016; 14:10095-10100. [DOI: 10.1039/c6ob01791f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A straightforward, rapid, versatile, regio- and chemoselective approach for the synthesis of C4-substituted tryptophan derivatives is reported.
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Affiliation(s)
- F. Bartoccini
- Department of Biomolecular Sciences
- University of Urbino “Carlo Bo”
- 61029 Urbino
- Italy
| | - S. Bartolucci
- Department of Biomolecular Sciences
- University of Urbino “Carlo Bo”
- 61029 Urbino
- Italy
| | - M. Mari
- Department of Biomolecular Sciences
- University of Urbino “Carlo Bo”
- 61029 Urbino
- Italy
| | - G. Piersanti
- Department of Biomolecular Sciences
- University of Urbino “Carlo Bo”
- 61029 Urbino
- Italy
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32
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Peng W, Ding F, Xie Y. Biointeractions of C.I. Acid Red 2 and its structural analogues with transporter albumin: Fluorescence, circular dichroism, and ligand docking approaches. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 154:40-50. [DOI: 10.1016/j.jphotobiol.2015.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 11/08/2015] [Accepted: 11/24/2015] [Indexed: 02/02/2023]
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33
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Ding F, Peng W. Biological activity of natural flavonoids as impacted by protein flexibility: an example of flavanones. MOLECULAR BIOSYSTEMS 2015; 11:1119-33. [PMID: 25673513 DOI: 10.1039/c4mb00662c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Naturally multifunctional Rutaceae hesperidin and its aglycone hesperetin have a great variety of biopharmaceutical activities, e.g. anti-cancer, anti-inflammatory, antioxidant and antitumor; however, the influence of the molecular structures of hesperidin and hesperetin, and in particular, the structural properties such as flexibility and dynamic features of protein on the biological activities of these bioactive compounds remains ambiguous. In the present study, the biomolecular recognition of crucial biopolymer - albumin from human serum (HSA) with Rutaceae, the recognition differences between HSA-hesperidin and HSA-hesperetin, the key elements that lead to the discrepancies as well as the structural characters of protein to the recognition processes were comparatively examined by employing biophysical approaches at the molecular scale. The results illustrated distinctly that (1) aglycone hesperetin can form stronger noncovalent bonds with HSA and possess higher recognition stability as compared with hesperidin. This phenomenon suggest that the introduction of glycoside structure into flavanone may possibly not be able to increase the noncovalent recognition of flavanone by a biopolymer, and conversely, this event will probably decrease the recognition capacity. (2) Although hesperidin and hesperetin can be located within subdomains IIA and IIIA, respectively, the conformational stability of flavanones in subdomain IIA is greater than subdomain IIIA; as a result, the recognition ability of subdomain IIIA with flavanones is patently lesser than subdomain IIA. These discrepancies likely originate from the unique characteristics of the respective cavity, or more specifically, subdomain IIA is basically a closed space, whereas subdomain IIIA is a semi-open region. Meanwhile, the detailed analyses of root-mean-square fluctuation interpreted the recognition of flavanones by subdomain IIA on HSA, which would evoke larger conformational alterations in several amino acid residues, and the similar phenomenon also resides in subdomain IIIA, which signifies that the flexible characteristics of different binding patches in protein may possess fairly notable effects on the HSA-flavanones recognition. Moreover, the integral structural changes of HSA exhibit some disparities on account of the dissimilarities of recognition capability to the protein-flavanone biointeractions, and all these conclusions received further forceful supports from fluorescence and circular dichroism experiments in solution. Perhaps the work emerged herein could not only help us to better evaluate the bioavailability of natural flavanones with or without glycoside, but to understand the sketches of the three-dimensional structure trait of certain biomacromolecules for the medicinal properties of flavonoids in the human body.
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Affiliation(s)
- Fei Ding
- College of Agriculture and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China.
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34
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Zhu Y, Bauer M, Ackermann L. Late-Stage Peptide Diversification by Bioorthogonal Catalytic CH Arylation at 23 °C in H2O. Chemistry 2015; 21:9980-3. [DOI: 10.1002/chem.201501831] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 12/12/2022]
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35
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Hierrezuelo JM, Carnero Ruiz C. Exploring the affinity binding of alkylmaltoside surfactants to bovine serum albumin and their effect on the protein stability: A spectroscopic approach. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2015; 53:156-65. [PMID: 26042703 DOI: 10.1016/j.msec.2015.04.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/23/2015] [Accepted: 04/21/2015] [Indexed: 12/18/2022]
Abstract
Steady-state and time-resolved fluorescence together with circular dichroism (CD) spectroscopic studies was performed to examine the interactions between bovine serum albumin (BSA) and two alkylmaltoside surfactants, i.e. n-decyl-β-D-maltoside (β-C10G2) and n-dodecyl-β-D-maltoside (β-C12G2), having identical structures but different tail lengths. Changes in the intrinsic fluorescence of BSA from static as well as dynamic measurements revealed a weak protein-surfactant interaction and gave the corresponding binding curves, suggesting that the binding mechanism of surfactants to protein is essentially cooperative in nature. The behavior of both surfactants is similar, so that the differences detected were attributed to the more hydrophobic nature of β-C12G2, which favors the adsorption of micelle-like aggregates onto the protein surface. These observations were substantially demonstrated by data derived from synchronous, three-dimensional and anisotropy fluorescence experiments. Changes in the secondary structure of the protein induced by the interaction with surfactants were analyzed by CD to determine the contents of α-helix and β-strand. It was noted that whereas the addition of β-C10G2 appears to stabilize the secondary structure of the protein, β-C12G2 causes a marginal denaturation of BSA for a protein:surfactant molar ratio as high as 1 to 100.
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Affiliation(s)
- J M Hierrezuelo
- Department of Applied Physics II, Engineering School, University of Malaga, 29071 Malaga, Spain
| | - C Carnero Ruiz
- Department of Applied Physics II, Engineering School, University of Malaga, 29071 Malaga, Spain.
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36
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Lopes JLS, Araujo APU, Jameson DM. Investigation of the conformational flexibility of DGAT1 peptides using tryptophan fluorescence. Methods Appl Fluoresc 2015; 3:025003. [PMID: 29148488 DOI: 10.1088/2050-6120/3/2/025003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The conformational behavior of synthetic peptides corresponding to the putative binding sites of the diacylglycerol acyltransferase 1 enzyme (a polytopic integral membrane protein) was investigated using steady-state and time-resolved fluorescence spectroscopies. Three small linear peptides with 13, 15 and 22 amino acid residues, containing one, two and three Trp residues, respectively, were studied in aqueous solution, in the absence and presence of model membranes. The high flexibility and unordered conformation of the peptides in solution were confirmed by the low Trp polarization values, the high accessibility to water-soluble quencher, and the fast rotational correlation times of the Trp residues. However, upon binding to the lipid systems, the Trp residues were incorporated within the acyl hydrophobic core and their lifetimes and rotational correlation times increased. Phasor plots were employed to analyze intensity decay of peptide-lipid binding and provided a trajectory, in phasor space, that lies along a line connecting the points of the free and bound peptide. This trajectory was analyzed to determine the association constant of the peptide to the model membrane.
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Affiliation(s)
- Jose L S Lopes
- Institute of Physics of Sao Carlos, University of Sao Paulo, Sao Carlos, SP, Brazil. Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI, USA
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37
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Pham K, Dhulipala G, Gonzalez WG, Gerstman BS, Regmi C, Chapagain PP, Miksovska J. Ca2+ and Mg2+ modulate conformational dynamics and stability of downstream regulatory element antagonist modulator. Protein Sci 2015; 24:741-51. [PMID: 25627705 DOI: 10.1002/pro.2646] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 01/25/2015] [Indexed: 11/09/2022]
Abstract
Downstream Regulatory Element Antagonist Modulator (DREAM) belongs to the family of neuronal calcium sensors (NCS) that transduce the intracellular changes in Ca(2+) concentration into a variety of responses including gene expression, regulation of Kv channel activity, and calcium homeostasis. Despite the significant sequence and structural similarities with other NCS members, DREAM shows several features unique among NCS such as formation of a tetramer in the apo-state, and interactions with various intracellular biomacromolecules including DNA, presenilin, Kv channels, and calmodulin. Here we use spectroscopic techniques in combination with molecular dynamics simulation to study conformational changes induced by Ca(2+) /Mg(2+) association to DREAM. Our data indicate a minor impact of Ca(2+) association on the overall structure of the N- and C-terminal domains, although Ca(2+) binding decreases the conformational heterogeneity as evident from the decrease in the fluorescence lifetime distribution in the Ca(2+) bound forms of the protein. Time-resolved fluorescence data indicate that Ca(2+) binding triggers a conformational transition that is characterized by more efficient quenching of Trp residue. The unfolding of DREAM occurs through an partially unfolded intermediate that is stabilized by Ca(2+) association to EF-hand 3 and EF-hand 4. The native state is stabilized with respect to the partially unfolded state only in the presence of both Ca(2+) and Mg(2+) suggesting that, under physiological conditions, Ca(2+) free DREAM exhibits a high conformational flexibility that may facilitate its physiological functions.
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Affiliation(s)
- Khoa Pham
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199
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38
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Ionic Liquids Increase the Catalytic Efficiency of a Lipase (Lip1) From an Antarctic Thermophilic Bacterium. Lipids 2014; 50:49-55. [DOI: 10.1007/s11745-014-3973-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/06/2014] [Indexed: 10/24/2022]
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39
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Zasedateleva OA, Vasiliskov VA, Surzhikov SA, Sazykin AY, Putlyaeva LV, Schwarz AM, Kuprash DV, Rubina AY, Barsky VE, Zasedatelev AS. UV fluorescence of tryptophan residues effectively measures protein binding to nucleic acid fragments immobilized in gel elements of microarrays. Biotechnol J 2014; 9:1074-80. [DOI: 10.1002/biot.201300556] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Revised: 05/04/2014] [Accepted: 06/11/2014] [Indexed: 12/13/2022]
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40
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Montecinos-Franjola F, James NG, Concha-Marambio L, Brunet JE, Lagos R, Monasterio O, Jameson DM. Single tryptophan mutants of FtsZ: nucleotide binding/exchange and conformational transitions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1193-200. [PMID: 24704635 DOI: 10.1016/j.bbapap.2014.03.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 03/24/2014] [Accepted: 03/26/2014] [Indexed: 11/27/2022]
Abstract
Cell division protein FtsZ cooperatively self-assembles into straight filaments when bound to GTP. A set of conformational changes that are linked to FtsZ GTPase activity are involved in the transition from straight to curved filaments that eventually disassemble. In this work, we characterized the fluorescence of single Trp mutants as a reporter of the predicted conformational changes between the GDP- and GTP-states of Escherichia coli FtsZ. Steady-state fluorescence characterization showed the Trp senses different environments and displays low solvent accessibility. Time-resolved fluorescence data indicated that the main conformational changes in FtsZ occur at the interaction surface between the N and C domains, but also minor rearrangements were detected in the bulk of the N domain. Surprisingly, despite its location near the bottom protofilament interface at the C domain, the Trp 275 fluorescence lifetime did not report changes between the GDP and GTP states. The equilibrium unfolding of FtsZ features an intermediate that is stabilized by the nucleotide bound in the N-domain as well as by quaternary protein-protein interactions. In this context, we characterized the unfolding of the Trp mutants using time-resolved fluorescence and phasor plot analysis. A novel picture of the structural transition from the native state in the absence of denaturant, to the solvent-exposed unfolded state is presented. Taken together our results show that conformational changes between the GDP and GTP states of FtsZ, such as those observed in FtsZ unfolding, are restricted to the interaction surface between the N and C domains.
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Affiliation(s)
- Felipe Montecinos-Franjola
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800024, Chile.
| | - Nicholas G James
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu 96813, HI, USA.
| | - Luis Concha-Marambio
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800024, Chile.
| | - Juan E Brunet
- Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
| | - Rosalba Lagos
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800024, Chile.
| | - Octavio Monasterio
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800024, Chile.
| | - David M Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu 96813, HI, USA.
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Abstract
Frequency domain fluorometry is a widely utilized tool in the physical, chemical, and biological sciences. This chapter focuses on the theory of the method and the practical aspects required to carry out intensity decay, i.e., lifetime measurements on a modern frequency domain fluorometer. Several chemical/biological systems are utilized to illustrate data acquisition protocols. Data analysis procedures and methodologies are also discussed.
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Affiliation(s)
- Carissa M Vetromile
- Department Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
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42
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James NG, Jameson DM. Steady-state fluorescence polarization/anisotropy for the study of protein interactions. Methods Mol Biol 2014; 1076:29-42. [PMID: 24108621 DOI: 10.1007/978-1-62703-649-8_2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Fluorescence methods are often employed for the characterization of molecular interactions. In particular, polarization/anisotropy studies are widely utilized in the life sciences as they allow quantification of protein interactions in the micro- and nanomolar concentration range. Herein we shall briefly describe the theoretical aspects of polarization/anisotropy and outline an experiment for determination of the dissociation constant for a protein-ligand complex.
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Affiliation(s)
- Nicholas G James
- Department Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
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43
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Deacon LJ, Billones H, Galyean AA, Donaldson T, Pennacchio A, Iozzino L, D'Auria S, Dattelbaum JD. Tryptophan-scanning mutagenesis of the ligand binding pocket in Thermotoga maritima arginine-binding protein. Biochimie 2013; 99:208-14. [PMID: 24370478 DOI: 10.1016/j.biochi.2013.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 12/11/2013] [Indexed: 11/28/2022]
Abstract
The Thermotoga maritima arginine binding protein (TmArgBP) is a member of the periplasmic binding protein superfamily. As a highly thermostable protein, TmArgBP has been investigated for the potential to serve as a protein scaffold for the development of fluorescent protein biosensors. To establish a relationship between structural dynamics and ligand binding capabilities, we constructed single tryptophan mutants to probe the arginine binding pocket. Trp residues placed around the binding pocket reveal a strong dependence on fluorescence emission of the protein with arginine for all but one of the mutants. Using these data, we calculated dissociation constants of 1.9-3.3 μM for arginine. Stern-Volmer quenching analysis demonstrated that the protein undergoes a large conformational change upon ligand binding, which is a common feature of this protein superfamily. While still active at room temperature, time-resolved intensity and anisotropy decay data suggest that the protein exists as a highly rigid structure under these conditions. Interestingly, TmArgBP exists as a dimer at room temperature in both the presence and absence of arginine, as determined by asymmetric flow field flow fractionation (AF4) and supported by native gel-electrophoresis and time-resolved anisotropy. Our data on dynamics and stability will contribute to our understanding of hyperthermophilic proteins and their potential biotechnological applications.
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Affiliation(s)
- Lindsay J Deacon
- Department of Chemistry, University of Richmond, Richmond, VA 23173, USA
| | - Hilbert Billones
- Department of Chemistry, University of Richmond, Richmond, VA 23173, USA
| | - Anne A Galyean
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Teraya Donaldson
- Department of Chemistry, University of Richmond, Richmond, VA 23173, USA
| | - Anna Pennacchio
- Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Luisa Iozzino
- Department of Chemistry, University of Richmond, Richmond, VA 23173, USA; Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Sabato D'Auria
- Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
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44
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Jameson DM, Vetromile CM, James NG. Investigations of protein–protein interactions using time-resolved fluorescence and phasors. Methods 2013; 59:278-86. [DOI: 10.1016/j.ymeth.2013.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 01/10/2013] [Accepted: 01/11/2013] [Indexed: 11/28/2022] Open
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45
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Mocz G, Ross JA. Fluorescence techniques in analysis of protein-ligand interactions. Methods Mol Biol 2013; 1008:169-210. [PMID: 23729253 DOI: 10.1007/978-1-62703-398-5_7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fluorescence spectroscopy may serve as a universal tool for the study of protein-ligand interactions. Applications of fluorometry have made use of various aspects of fluorescence such as intensity, emission and excitation spectra, lifetime, quantum yield, polarization state, and anisotropy, as well as energy transfer and other electronic phenomena. An experimentalist has to consider each of these characteristics carefully, frequently in combination with each other, for the analysis of protein-ligand complexes and for the determination of binding constants. Most of the available techniques are of a rather general nature and a wealth of possibilities exists for their utilization. In this chapter we will provide a short survey of selected techniques that can be used for measuring binding constants and probing protein-ligand interactions. Basic principles and phenomena are discussed followed by experimental considerations and examples of binding constant determination. Emphasis is placed on steady-state techniques that employ the use of intrinsic protein fluorescence, labeled ligands, as well as anisotropy and resonance energy transfer.
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Affiliation(s)
- Gabor Mocz
- Pacific Biosciences Research Center, University of Hawaii, Honolulu, HI, USA
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46
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Montecinos-Franjola F, Ross JA, Sánchez SA, Brunet JE, Lagos R, Jameson DM, Monasterio O. Studies on the dissociation and urea-induced unfolding of FtsZ support the dimer nucleus polymerization mechanism. Biophys J 2012; 102:2176-85. [PMID: 22824282 DOI: 10.1016/j.bpj.2012.03.064] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 01/31/2012] [Accepted: 03/12/2012] [Indexed: 01/23/2023] Open
Abstract
FtsZ is a major protein in bacterial cytokinesis that polymerizes into single filaments. A dimer has been proposed to be the nucleating species in FtsZ polymerization. To investigate the influence of the self-assembly of FtsZ on its unfolding pathway, we characterized its oligomerization and unfolding thermodynamics. We studied the assembly using size-exclusion chromatography and fluorescence spectroscopy, and the unfolding using circular dichroism and two-photon fluorescence correlation spectroscopy. The chromatographic analysis demonstrated the presence of monomers, dimers, and tetramers with populations dependent on protein concentration. Dilution experiments using fluorescent conjugates revealed dimer-to-monomer and tetramer-to-dimer dissociation constants in the micromolar range. Measurements of fluorescence lifetimes and rotational correlation times of the conjugates supported the presence of tetramers at high protein concentrations and monomers at low protein concentrations. The unfolding study demonstrated that the three-state unfolding of FtsZ was due to the mainly dimeric state of the protein, and that the monomer unfolds through a two-state mechanism. The monomer-to-dimer equilibrium characterized here (K(d) = 9 μM) indicates a significant fraction (~10%) of stable dimers at the critical concentration for polymerization, supporting a role of the dimeric species in the first steps of FtsZ polymerization.
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Affiliation(s)
- Felipe Montecinos-Franjola
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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47
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Characterization of Förster resonance energy transfer in a botulinum neurotoxin protease assay. Anal Biochem 2011; 413:43-9. [DOI: 10.1016/j.ab.2011.01.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 01/28/2011] [Accepted: 01/29/2011] [Indexed: 11/22/2022]
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48
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Ross JA, Chen Y, Müller J, Barylko B, Wang L, Banks HB, Albanesi JP, Jameson DM. Dimeric endophilin A2 stimulates assembly and GTPase activity of dynamin 2. Biophys J 2011; 100:729-737. [PMID: 21281588 DOI: 10.1016/j.bpj.2010.12.3717] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 12/02/2010] [Accepted: 12/14/2010] [Indexed: 10/18/2022] Open
Abstract
Endophilin, which participates in membrane vesiculation during receptor-mediated endocytosis, is a ∼40 kDa SH3 domain-containing protein that binds to the proline/arginine-rich domain of dynamin, a ∼100 kDa GTPase that is essential for endocytic membrane scission. It has been suggested that endophilin is monomeric in the cytoplasm and dimerizes only after it binds to membranes (or perhaps to dimers or tetramers of dynamin). To clarify this issue, we studied the oligomeric state of endophilin both in vitro using analytical ultracentrifugation and fluorescence anisotropy, and in living cells using two-photon fluorescence fluctuation spectroscopy. We analyzed the fluctuation data using the Q-analysis method, which allowed us to determine the intrinsic brightness of the labeled protein complexes and hence its aggregation state in the cytoplasmic regions of the cell. Although a relatively high K(d) (∼5-15 μM) was observed in vitro, the cell measurements indicate that endophilin is dimeric in the cytoplasm, even at submicromolar concentrations. We also demonstrate that endophilin significantly enhances the assembly of dynamin, and that this enhancement is proportional to the fraction of dimeric endophilin that is present. Moreover, there is correlation between the concentrations of endophilin that promote dynamin self-assembly and those that stimulate dynamin GTPase activity. These findings support the view that endophilin-dynamin interactions play an important role in endocytosis.
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Affiliation(s)
- Justin A Ross
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Yan Chen
- Physics Department, University of Minnesota, Minneapolis, Minnesota
| | - Joachim Müller
- Physics Department, University of Minnesota, Minneapolis, Minnesota
| | - Barbara Barylko
- Pharmacology Department, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Lei Wang
- Pharmacology Department, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Hunter B Banks
- Pharmacology Department, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Joseph P Albanesi
- Pharmacology Department, University of Texas Southwestern Medical Center, Dallas, Texas
| | - David M Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii.
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Zakharov MN, Ulloor J, Bhasin S, Ross JA, Narula NS, Bakhit M, Pillai BK, Kumar R, Jameson DM, Jasuja R. Guanidinium chloride-induced spectral perturbations of 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid confound interpretation of data on molten globule states. Anal Biochem 2011; 416:126-8. [PMID: 21569754 DOI: 10.1016/j.ab.2011.04.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 04/09/2011] [Accepted: 04/12/2011] [Indexed: 11/18/2022]
Abstract
We describe limitations in the use of 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) to examine unfolding intermediates associated with guanidinium chloride (GuHCl)-induced protein denaturation. Several studies have used alterations in fluorescence emission of bis-ANS to quantify the population of "molten globule" states. Our findings indicate that the observed changes in bis-ANS spectroscopic properties could originate from the interactions of bis-ANS and GuHCl and the aggregation of the dye at higher GuHCl concentrations. We posit that in the absence of additional complementary structural or spectroscopic measurements, the use of bis-ANS emission alone to monitor protein conformations can be misleading.
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Affiliation(s)
- M N Zakharov
- Section of Endocrinology, Diabetes, and Nutrition, Boston University School of Medicine, Boston, MA 02118, USA
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Štefl M, James NG, Ross JA, Jameson DM. Applications of phasors to in vitro time-resolved fluorescence measurements. Anal Biochem 2011; 410:62-9. [PMID: 21078290 PMCID: PMC3065364 DOI: 10.1016/j.ab.2010.11.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 11/05/2010] [Accepted: 11/07/2010] [Indexed: 11/28/2022]
Abstract
The phasor method of treating fluorescence lifetime data provides a facile and convenient approach to characterize lifetime heterogeneity and to detect the presence of excited state reactions such as solvent relaxation and Förster resonance energy transfer. The method uses a plot of M sin(Φ) versus M cos(Φ), where M is the modulation ratio and Φ is the phase angle taken from frequency domain fluorometry. A principal advantage of the phasor method is that it provides a model-less approach to time-resolved data amenable to visual inspection. Although the phasor approach has been recently applied to fluorescence lifetime imaging microscopy, it has not been used extensively for cuvette studies. In the current study, we explore the applications of the method to in vitro samples. The phasors of binary and ternary mixtures of fluorescent dyes demonstrate the utility of the method for investigating complex mixtures. Data from excited state reactions, such as dipolar relaxation in membrane and protein systems and also energy transfer from the tryptophan residue to the chromophore in enhanced green fluorescent protein, are also presented.
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Affiliation(s)
- Martin Štefl
- J. Heyrovský Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Department of Biophysical Chemistry, Dolejškova 3, Prague 18223, Czech Republic
| | - Nicholas G. James
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St., BSB222, Honolulu, Hawaii 96813
| | - Justin A. Ross
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St., BSB222, Honolulu, Hawaii 96813
| | - David M. Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St., BSB222, Honolulu, Hawaii 96813
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