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Valdebenito S, Eugenin E, Oberhauser A. SPR spectroscopic analysis of myosin binding to wild type and mutant UNC45B. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001131. [PMID: 38404916 PMCID: PMC10884834 DOI: 10.17912/micropub.biology.001131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/27/2024]
Abstract
UNC45B is a multidomain molecular chaperone that is essential for the proper folding and function of myosin. It has previously been demonstrated that the UCS domain is responsible for the chaperoning function of UNC45B and that removing its client-binding loop leads to a significant change in its solution conformation and a reduced chaperoning function. Here, we report the direct quantification of affinities of myosin binding to wild type and mutant UNC45B using surface plasmon resonance (SPR) spectroscopy. We found that deletion of the client-binding loop in UNC45B resulted in a dramatic decrease in myosin affinity.
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Affiliation(s)
- Silvana Valdebenito
- The University of Texas Medical Branch at Galveston, Galveston, Texas, United States
| | - Eliseo Eugenin
- The University of Texas Medical Branch at Galveston, Galveston, Texas, United States
| | - Andres Oberhauser
- The University of Texas Medical Branch at Galveston, Galveston, Texas, United States
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2
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Hamada N, Longo ML. Charged hybrid block copolymer-lipid-cholesterol vesicles: pH, ionic environment, and composition dependence of phase transitions. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184026. [PMID: 35952852 DOI: 10.1016/j.bbamem.2022.184026] [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: 06/20/2022] [Revised: 07/23/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
The impacts of pH, salt concentration (expressed as Debye length), and composition on the phase behavior of hybrid block copolymer-lipid-cholesterol bilayers incorporating carboxyl-terminated poly(butadiene)-block-poly(ethylene oxide) copolymer (PBdPEO1800(-)) or/and non-carboxyl-terminated PBdPEO (PBdPEO1800 or/and PBdPEO950), egg sphingomyelin (egg SM), and cholesterol were examined using fluorescence spectroscopy of laurdan. Laurdan emission spectra were decomposed into three lognormal curves as functions of energy. The ratio of the area of the mid-energy peak to the sum of the areas of all three peaks was evaluated as vesicles were cooled, yielding temperature breakpoint values (Tbreak) expected to be within the range of the phase transition temperature. Tbreak values displayed dependence on pH, Debye length, and vesicle composition consistent with an electrostatic repulsion contribution to vesicle phase behavior. Increased pH and Debye length, for which a greater dissociated fraction of PBdPEO1800(-) and a greater energy of electrostatic repulsion would be expected, resulted in Tbreak values as much as 10 °C less than at low pH or short Debye lengths. Additionally, at Debye lengths comparable to those at physiologically relevant ionic strength, Tbreak at pH 5.9 was observed to be slightly higher than at pH 7.0 for vesicles containing 50 mol% PBdPEO1800(-). Electrostatic effects observed for hybrid vesicles incorporating significant amounts of carboxyl-terminated polymer may have the ability to drive phase separation in response to pH drops-such as those observed after endocytosis-in physiologically relevant conditions, suggesting the utility of such materials for drug delivery.
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Affiliation(s)
- Naomi Hamada
- Department of Chemical Engineering, University of California Davis, Davis, CA 95616, United States
| | - Marjorie L Longo
- Department of Chemical Engineering, University of California Davis, Davis, CA 95616, United States.
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3
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Hamada N, Longo ML. Characterization of phase separation phenomena in hybrid lipid/block copolymer/cholesterol bilayers using laurdan fluorescence with log-normal multipeak analysis. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183887. [PMID: 35150645 DOI: 10.1016/j.bbamem.2022.183887] [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: 11/18/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Phase separation phenomena in hybrid lipid/block copolymer/cholesterol bilayers combining polybutadiene-block-polyethylene oxide (PBdPEO), egg sphingomyelin (egg SM), and cholesterol were studied with fluorescence spectroscopy and microscopy for comparison to lipid bilayers composed of palmitoyl oleoyl phosphatidylcholine (POPC), egg SM, and cholesterol. Laurdan emission spectra were decomposed into three lognormal curves. The temperature dependence of the ratios of the areas of the middle and lowest energy peaks revealed temperature break-point (Tbreak) values that were in better agreement, compared to generalized polarization inflection temperatures, with phase transition temperatures in giant unilamellar vesicles (GUVs). Agreement between GUV and spectroscopy results was further improved for hybrid vesicles by using the ratio of the area of the middle peak to the sum of the areas all three peaks to find the Tbreak values. For the hybrid vesicles, trends at Tbreak are hypothesized to be correlated with the mechanisms by which the phase transition takes place, supported by the compositional range as well as the morphologies of domains observed in GUVs. Low miscibility of PBdPEO and egg SM is suggested by the finding of relatively high Tbreak values at cholesterol contents greater than 30 mol%. Further, GUV phase behavior suggests stronger partitioning of cholesterol into PBdPEO than into POPC, and less miscibility of PBdPEO than POPC with egg SM. These results, summarized using a heat-map, contribute to the limited body of knowledge regarding the effect of cholesterol on hybrid membranes, with potential application toward the development of such materials for drug delivery or membrane protein reconstitution.
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Affiliation(s)
- Naomi Hamada
- Department of Chemical Engineering, University of California Davis, Davis, CA 95616, United States
| | - Marjorie L Longo
- Department of Chemical Engineering, University of California Davis, Davis, CA 95616, United States.
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4
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Photophysical Properties of BADAN Revealed in the Study of GGBP Structural Transitions. Int J Mol Sci 2021; 22:ijms222011113. [PMID: 34681772 PMCID: PMC8540541 DOI: 10.3390/ijms222011113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 01/14/2023] Open
Abstract
The fluorescent dye BADAN (6-bromoacetyl-2-dimetylaminonaphtalene) is widely used in various fields of life sciences, however, the photophysical properties of BADAN are not fully understood. The study of the spectral properties of BADAN attached to a number of mutant forms of GGBP, as well as changes in its spectral characteristics during structural changes in proteins, allowed to shed light on the photophysical properties of BADAN. It was shown that spectral properties of BADAN are determined by at least one non-fluorescent and two fluorescent isomers with overlapping absorbing bands. It was found that BADAN fluorescence is determined by the unsolvated "PICT" (planar intramolecular charge transfer state) and solvated "TICT" (twisted intramolecular charge transfer state) excited states. While "TICT" state can be formed both as a result of the "PICT" state solvation and as a result of light absorption by the solvated ground state of the dye. BADAN fluorescence linked to GGBP/H152C apoform is quenched by Trp 183, but this effect is inhibited by glucose intercalation. New details of the changes in the spectral characteristics of BADAN during the unfolding of the protein apo and holoforms have been obtained.
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5
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Trends in the Design of Intensity-Based Optical Fiber Biosensors (2010-2020). BIOSENSORS-BASEL 2021; 11:bios11060197. [PMID: 34203715 PMCID: PMC8232210 DOI: 10.3390/bios11060197] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/29/2022]
Abstract
There exists an increasing interest in monitoring low concentrations of biochemical species, as they allow the early-stage detection of illnesses or the monitoring of the environment quality. Thus, both companies and research groups are focused on the development of accurate, fast and highly sensitive biosensors. Optical fiber sensors have been widely employed for these purposes because they provide several advantages for their use in point-of-care and real-time applications. In particular, this review is focused on optical fiber biosensors based on luminescence and absorption. Apart from the key parameters that determine the performance of a sensor (limit of detection, sensibility, cross-sensibility, etc.), other features are analyzed, such as the optical fiber dimensions, the sensing set ups and the fiber functionalization. The aim of this review is to have a comprehensive insight of the different aspects that must be taken into account when working with this kind of sensors.
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6
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Puff N, Staneva G, Angelova MI, Seigneuret M. Improved Characterization of Raft-Mimicking Phase-Separation Phenomena in Lipid Bilayers Using Laurdan Fluorescence with Log-Normal Multipeak Analysis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4347-4356. [PMID: 32233510 DOI: 10.1021/acs.langmuir.0c00412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The study of biomimetic model membrane systems undergoing liquid-ordered (Lo)-liquid-disordered (Ld) phase separation using spectroscopic methods has played an important role in understanding the properties of lipid rafts in plasma membranes. In particular, the membrane-associated fluorescence probe Laurdan has proved to be a very efficient reporter of Lo-Ld phase separation in lipid bilayers using the general polarization (GP) parameter. A limitation of the GP approach is that it monitors only global average packing so that the contribution of each phase remains undetermined. The decomposition of Laurdan emission spectra has been proposed as an additional approach to overcoming this limitation. Here, further developments of this method for the study of Lo-Ld phase separation are described here for Laurdan in sphingomyelin-phosphatidylcholine-cholesterol large unilamellar vesicles. Lipid compositions corresponding to homogeneous Lo or Ld phases as well as undergoing thermally induced Lo-Ld phase separation were investigated. In addition, the occurrence of phase separation was checked by the fluorescence imaging of giant unilamellar vesicles. Decomposition into three log-normal components is used to show that an intermediate energy component is specifically associated with the occurrence of the Lo phase, with a small contribution from this component occurring above the phase-separation temperature being attributable to phase fluctuations. The ratio RX of the relative area of this intermediate-energy peak to that of the low-energy peak is shown to provide a straightforward index of Lo-Ld phase separation as a function of temperature, which is occasionally more sensitive than GP. It is also shown that RX can be used in conjunction with GP to gain further insight into Lo-Ld, the phase-separation processes. This latter feature is illustrated by the influence of the alcohol butanol on the Lo-Ld phase separation in sphingomyelin-phosphatidylcholine-cholesterol bilayers by showing that the effect of the alcohol occurs specifically at the onset of the phase separation, indicating a line tension mechanism. It is proposed that the three components of log-normal decomposition approaching Laurdan emission spectra provide a useful improvement for characterizing Lo-Ld phase-separation phenomena.
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Affiliation(s)
- Nicolas Puff
- Sorbonne Université, Faculté des Sciences et Ingénierie, UFR 925 Physique, Paris F-75005, France
- Université Paris Diderot - Paris 7, Université de Paris, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, Paris F-75013, France
| | - Galya Staneva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Miglena I Angelova
- Sorbonne Université, Faculté des Sciences et Ingénierie, UFR 925 Physique, Paris F-75005, France
- Université Paris Diderot - Paris 7, Université de Paris, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, Paris F-75013, France
| | - Michel Seigneuret
- Université Paris Diderot - Paris 7, Université de Paris, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, Paris F-75013, France
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7
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Wolf A, Dragelj J, Wonneberg J, Stellmacher J, Balke J, Woelke AL, Hodoscek M, Knapp EW, Alexiev U. The redox-coupled proton-channel opening in cytochrome c oxidase. Chem Sci 2020. [DOI: 10.1039/c9sc06463j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The interplay of cytochrome c oxidase's cofactor electrostatics, long-range conformational changes, H-bond rearrangement, and water dynamics enables transient proton-channel activation.
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Affiliation(s)
- Alexander Wolf
- Physics Department
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | - Jovan Dragelj
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | | | | | - Jens Balke
- Physics Department
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | - Anna Lena Woelke
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
- Department of Chemistry
| | - Milan Hodoscek
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
- National Institute of Chemistry
| | - Ernst Walter Knapp
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | - Ulrike Alexiev
- Physics Department
- Freie Universität Berlin
- 14195 Berlin
- Germany
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8
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Wolf A, Wonneberg J, Balke J, Alexiev U. Electronation-dependent structural change at the proton exit side of cytochrome c oxidase as revealed by site-directed fluorescence labeling. FEBS J 2019; 287:1232-1246. [PMID: 31597007 DOI: 10.1111/febs.15084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/17/2019] [Accepted: 10/04/2019] [Indexed: 02/05/2023]
Abstract
Cytochrome c oxidase (CcO), the terminal enzyme of the respiratory chain of mitochondria and many aerobic prokaryotes that function as a redox-coupled proton pump, catalyzes the reduction of molecular oxygen to water. As part of the respiratory chain, CcO contributes to the proton motive force driving ATP synthesis. While many aspects of the enzyme's catalytic mechanisms have been established, a clear picture of the proton exit pathway(s) remains elusive. Here, we aim to gain insight into the molecular mechanisms of CcO through the development of a new homologous mutagenesis/expression system in Paracoccus denitrificans, which allows mutagenesis of CcO subunits 1, 2, and 3. Our system provides true single thiol-reactive CcO variants in a three-subunit base variant with unique labeling sites for the covalent attachment of reporter groups sensitive to nanoenvironmental factors like protonation, polarity, and hydration. To this end, we exchanged six residues on both membrane sides of CcO for cysteines. We show redox-dependent wetting changes at the proton uptake channel and increased polarity at the proton exit side of CcO upon electronation. We suggest an electronation-dependent conformational change to play a role in proton exit from CcO.
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Affiliation(s)
- Alexander Wolf
- Institute of Experimental Physics, Freie Universität Berlin, Germany
| | - Juliane Wonneberg
- Institute of Experimental Physics, Freie Universität Berlin, Germany
| | - Jens Balke
- Institute of Experimental Physics, Freie Universität Berlin, Germany
| | - Ulrike Alexiev
- Institute of Experimental Physics, Freie Universität Berlin, Germany
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9
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Raghuraman H, Chatterjee S, Das A. Site-Directed Fluorescence Approaches for Dynamic Structural Biology of Membrane Peptides and Proteins. Front Mol Biosci 2019; 6:96. [PMID: 31608290 PMCID: PMC6774292 DOI: 10.3389/fmolb.2019.00096] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Membrane proteins mediate a number of cellular functions and are associated with several diseases and also play a crucial role in pathogenicity. Due to their importance in cellular structure and function, they are important drug targets for ~60% of drugs available in the market. Despite the technological advancement and recent successful outcomes in determining the high-resolution structural snapshot of membrane proteins, the mechanistic details underlining the complex functionalities of membrane proteins is least understood. This is largely due to lack of structural dynamics information pertaining to different functional states of membrane proteins in a membrane environment. Fluorescence spectroscopy is a widely used technique in the analysis of functionally-relevant structure and dynamics of membrane protein. This review is focused on various site-directed fluorescence (SDFL) approaches and their applications to explore structural information, conformational changes, hydration dynamics, and lipid-protein interactions of important classes of membrane proteins that include the pore-forming peptides/proteins, ion channels/transporters and G-protein coupled receptors.
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Affiliation(s)
- H. Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, Kolkata, India
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10
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Fonin A, Kuznetsova I, Turoverov K. Spectral properties of BADAN in solutions with different polarities. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.01.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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11
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Puff N, Watanabe C, Seigneuret M, Angelova MI, Staneva G. Lo/Ld phase coexistence modulation induced by GM1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2105-14. [DOI: 10.1016/j.bbamem.2014.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 04/30/2014] [Accepted: 05/03/2014] [Indexed: 01/31/2023]
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12
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Fonin AV, Stepanenko OV, Povarova OI, Volova CA, Philippova EM, Bublikov GS, Kuznetsova IM, Demchenko AP, Turoverov KK. Spectral characteristics of the mutant form GGBP/H152C of D-glucose/D-galactose-binding protein labeled with fluorescent dye BADAN: influence of external factors. PeerJ 2014; 2:e275. [PMID: 24711960 PMCID: PMC3970809 DOI: 10.7717/peerj.275] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/26/2014] [Indexed: 11/22/2022] Open
Abstract
The mutant form GGBP/H152C of the D-glucose/D-galactose-binding protein with the solvatochromic dye BADAN linked to cysteine residue Cys 152 can be used as a potential base for a sensitive element of glucose biosensor system. We investigated the influence of various external factors on the physical-chemical properties of GGBP/H152C-BADAN and its complex with glucose. The high affinity (Kd = 8.5 µM) and high binding rate of glucose make GGBP/H152C-BADAN a good candidate to determine the sugar content in biological fluids extracted using transdermal techniques. It was shown that changes in the ionic strength and pH of solution within the physiological range did not have a significant influence on the fluorescent characteristics of GGBP/H152C-BADAN. The mutant form GGBP/H152C has relatively low resistance to denaturation action of GdnHCl and urea. This result emphasizes the need to find more stable proteins for the creation of a sensitive element for a glucose biosensor system.
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Affiliation(s)
- Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia
| | - Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia
| | - Olga I Povarova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia
| | - Catherine A Volova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia ; Department of Biology, St. Petersburg State University , St. Petersburg , Russia
| | - Elizaveta M Philippova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia ; Department of Physical Electronics, St. Petersburg State Polytechnical University , St. Petersburg , Russia
| | - Grigory S Bublikov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia ; Department of Biophysics, St. Petersburg State Polytechnical University , St. Petersburg , Russia
| | - Alexander P Demchenko
- Laboratory of Nanobiotechnologies, Palladin Institute of Biochemistry of the National Academy of Sciences of Ukraine , Kiev , Ukraine
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia ; Department of Biophysics, St. Petersburg State Polytechnical University , St. Petersburg , Russia
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13
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Reverse micelles as a tool for probing solvent modulation of protein dynamics: Reverse micelle encapsulated hemoglobin. Chem Phys 2013; 430:88-97. [PMID: 24039330 DOI: 10.1016/j.chemphys.2013.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Hydration waters impact protein dynamics. Dissecting the interplay between hydration waters and dynamics requires a protein that manifests a broad range of dynamics. Proteins in reverse micelles (RMs) have promise as tools to achieve this objective because the water content can be manipulated. Hemoglobin is an appropriate tool with which to probe hydration effects. We describe both a protocol for hemoglobin encapsulation in reverse micelles and a facile method using PEG and cosolvents to manipulate water content. Hydration properties are probed using the water-sensitive fluorescence from Hb bound pyranine and covalently attached Badan. Protein dynamics are probed through ligand recombination traces derived from photodissociated carbonmonoxy hemoglobin on a log scale that exposes the potential role of both α and β solvent fluctuations in modulating protein dynamics. The results open the possibility of probing hydration level phenomena in this system using a combination of NMR and optical probes.
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14
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Abstract
Ion channels, as membrane proteins, are the sensors of the cell. They act as the first line of communication with the world beyond the plasma membrane and transduce changes in the external and internal environments into unique electrical signals to shape the responses of excitable cells. Because of their importance in cellular communication, ion channels have been intensively studied at the structural and functional levels. Here, we summarize the diverse approaches, including molecular and cellular, chemical, optical, biophysical, and computational, used to probe the structural and functional rearrangements that occur during channel activation (or sensitization), inactivation (or desensitization), and various forms of modulation. The emerging insights into the structure and function of ion channels by multidisciplinary approaches allow the development of new pharmacotherapies as well as new tools useful in controlling cellular activity.
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Affiliation(s)
- Wei-Guang Li
- Neuroscience Division, Department of Biochemistry and Molecular Cell Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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15
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Krepkiy D, Gawrisch K, Swartz KJ. Structural interactions between lipids, water and S1-S4 voltage-sensing domains. J Mol Biol 2012; 423:632-47. [PMID: 22858867 PMCID: PMC3616881 DOI: 10.1016/j.jmb.2012.07.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 07/17/2012] [Accepted: 07/20/2012] [Indexed: 10/28/2022]
Abstract
Membrane proteins serve crucial signaling and transport functions, yet relatively little is known about their structures in membrane environments or how lipids interact with these proteins. For voltage-activated ion channels, X-ray structures suggest that the mobile voltage-sensing S4 helix would be exposed to the membrane, and functional studies reveal that lipid modification can profoundly alter channel activity. Here, we use solid-state NMR to investigate structural interactions of lipids and water with S1-S4 voltage-sensing domains and to explore whether lipids influence the structure of the protein. Our results demonstrate that S1-S4 domains exhibit extensive interactions with lipids and that these domains are heavily hydrated when embedded in a membrane. We also find evidence for preferential interactions of anionic lipids with S1-S4 domains and that these interactions have lifetimes on the timescale of ≤ 10(-3)s. Arg residues within S1-S4 domains are well hydrated and are positioned in close proximity to lipids, exhibiting local interactions with both lipid headgroups and acyl chains. Comparative studies with a positively charged lipid lacking a phosphodiester group reveal that this lipid modification has only modest effects on the structure and hydration of S1-S4 domains. Taken together, our results demonstrate that Arg residues in S1-S4 voltage-sensing domains reside in close proximity to the hydrophobic interior of the membrane yet are well hydrated, a requirement for carrying charge and driving protein motions in response to changes in membrane voltage.
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Affiliation(s)
- Dmitriy Krepkiy
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892 USA
| | - Klaus Gawrisch
- Laboratory of Membrane Biochemistry and Biophysics, National Institute of Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892 USA
| | - Kenton J. Swartz
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892 USA
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16
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Yan B, Hong Y, Chen T, Reinhard BM. Monitoring enzymatic degradation of pericellular matrices through SERS stamping. NANOSCALE 2012; 4:3917-25. [PMID: 22659641 PMCID: PMC3461839 DOI: 10.1039/c2nr30747b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We introduce a surface enhanced Raman spectroscopy (SERS) stamping approach for acquiring cell-surface specific vibrational spectra of individual living cells under physiological conditions. The SERS stamping approach utilizes a nanostructured metal surface on top of a lithographically defined piston that can be translated in 3-dimensions with nanometer resolution to contact living cells in solution with a pristine metal surface. We applied this approach to characterize the chemical composition of the cellular surface of living MCF7 breast cancer cells and to monitor its change upon addition of the enzyme hyaluronidase, which degrades major constituents of the pericellular matrix. Although the cell surface spectra show significant cell-to-cell fluctuations, a statistical barcode analysis of the spectra ensembles reveals systematic changes in the cell surface SERS spectra upon addition of hyaluronidase, which are consistent with a thinning of the pericellular matrix.
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Affiliation(s)
- Bo Yan
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02215, USA.
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17
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Lee JS, Feijen J. Polymersomes for drug delivery: Design, formation and characterization. J Control Release 2012; 161:473-83. [DOI: 10.1016/j.jconrel.2011.10.005] [Citation(s) in RCA: 533] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/04/2011] [Accepted: 10/06/2011] [Indexed: 01/06/2023]
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18
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An epifluorescence microscopy method for generalized polarization imaging. Biochem Biophys Res Commun 2011; 415:686-90. [PMID: 22079294 DOI: 10.1016/j.bbrc.2011.10.138] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 10/28/2011] [Indexed: 12/17/2022]
Abstract
Generalized polarization (GP) microscopy represents an excellent tool to study lipid-lipid and lipid-protein interactions in situ and in vitro. Here, we present an efficient and cost effective method to perform GP microscopy using a standard light-emitting diode (LED) epifluorescence microscope equipped with a digital color camera.
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Lee JS, Koehorst RBM, van Amerongen H, Feijen J. Time-resolved fluorescence and fluorescence anisotropy of fluorescein-labeled poly(N-isopropylacrylamide) incorporated in polymersomes. J Phys Chem B 2011; 115:13162-7. [PMID: 21995555 DOI: 10.1021/jp207072q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The phase behavior of fluorescein isothiocyanate (FITC) labeled poly(N-isopropylacrylamide) (PNIPAAm) incorporated in polymersomes (Ps) was studied by monitoring the fluorescence lifetime (FL) and the time-resolved fluorescence anisotropy (TRFA) as a function of temperature at pH 7.4. Ps containing FITC-labeled PNIPAAm with a diameter less than 200 nm were prepared by injecting a THF solution of poly(ethylene glycol)-b-poly(d,l-lactide) (mPEG-PDLLA) and FITC tagged PNIPAAm (FITC-N) into phosphate buffered saline (PBS, pH 7.4). Solutions of free FITC (2 μM) and FITC-N (2 μM) in PBS were used as controls. The polarized fluorescence decay curves of FITC were fitted with one rotational correlation time (θ(1)) and the corresponding amplitude (β(1)), while those for FITC-N were fitted with two rotational correlation times (θ(1,2)) and their corresponding amplitudes (β(1,2)). Short rotational correlation times, θ(1), correspond with the rotation of the FITC molecule itself, whereas θ(2) corresponds to FITC-segmental rotation. FITC-N encapsulated in Ps (FITC-N/Ps) showed a decrease of the rotational motion upon increasing the temperature. The long rotational correlation time (θ(2)) of FITC-N increased 3 fold, going from 15 to 40 °C, reflecting a reduced rotational mobility. The residual anisotropy (β(∞)) of FITC-N/Ps at pH 7.4 showed a gradual increase, going from 15 to 25 °C followed by a gradual decrease at higher temperatures. These results are explained by a transition from coil to globule, a gradual increase of intermolecular aggregation, and possibly phase separation and hydrogel formation.
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Affiliation(s)
- Jung Seok Lee
- Department of Polymer Chemistry and Biomaterials, Institute for Biomedical Technology and Technical Medicine, MIRA, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
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Interaction between sodium dodecyl sulfate and membrane reconstituted aquaporins: A comparative study of spinach SoPIP2;1 and E. coli AqpZ. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2600-7. [DOI: 10.1016/j.bbamem.2011.05.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 05/27/2011] [Accepted: 05/31/2011] [Indexed: 01/13/2023]
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21
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Wong WT, Chan KC, So PK, Yap HK, Chung WH, Leung YC, Wong KY, Zhao Y. Increased structural flexibility at the active site of a fluorophore-conjugated beta-lactamase distinctively impacts its binding toward diverse cephalosporin antibiotics. J Biol Chem 2011; 286:31771-80. [PMID: 21705325 DOI: 10.1074/jbc.m110.198895] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Ω-loop at the active site of β-lactamases exerts significant impact on the kinetics and substrate profile of these enzymes by forming part of the substrate binding site and posing as steric hindrance toward bulky substrates. Mutating certain residues on the Ω-loop has been a general strategy for molecular evolution of β-lactamases to expand their hydrolytic activity toward extended-spectrum antibiotics through a mechanism believed to involve enhanced structural flexibility of the Ω-loop. Yet no structural information is available that demonstrates such flexibility or its relation to substrate profile and enzyme kinetics. Here we report an engineered β-lactamase that contains an environment-sensitive fluorophore conjugated near its active site to probe the structural dynamics of the Ω-loop and to detect the binding of diverse substrates. Our results show that this engineered β-lactamase has improved binding kinetics and positive fluorescence signal toward oxyimino-cephalosporins, but shows little such effect to non-oxyimino-cephalosporins. Structural studies reveal that the Ω-loop adopts a less stabilized structure, and readily undergoes conformational change to accommodate the binding of bulky oxyimino-cephalosporins while no such change is observed for non-oxyimino-cephalosporins. Mutational studies further confirm that this substrate-induced structural change is directly responsible for the positive fluorescence signal specific to oxyimino-cephalosporins. Our data provide mechanistic evidence to support the long-standing model that the evolutionary strategy of mutating the Ω-loop leads to increased structural flexibility of this region, which in turn facilitates the binding of extended spectrum β-lactam antibiotics. The oxyimino-cephalosporin-specific fluorescence profile of our engineered β-lactamase also demonstrates the possibility of designing substrate-selective biosensing systems.
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Affiliation(s)
- Wai-Ting Wong
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
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22
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Lomize AL, Pogozheva I, Mosberg HI. Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects. J Chem Inf Model 2011; 51:918-29. [PMID: 21438609 PMCID: PMC3089899 DOI: 10.1021/ci2000192] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new implicit solvation model was developed for calculating free energies of transfer of molecules from water to any solvent with defined bulk properties. The transfer energy was calculated as a sum of the first solvation shell energy and the long-range electrostatic contribution. The first term was proportional to solvent accessible surface area and solvation parameters (σ(i)) for different atom types. The electrostatic term was computed as a product of group dipole moments and dipolar solvation parameter (η) for neutral molecules or using a modified Born equation for ions. The regression coefficients in linear dependencies of solvation parameters σ(i) and η on dielectric constant, solvatochromic polarizability parameter π*, and hydrogen-bonding donor and acceptor capacities of solvents were optimized using 1269 experimental transfer energies from 19 organic solvents to water. The root-mean-square errors for neutral compounds and ions were 0.82 and 1.61 kcal/mol, respectively. Quantification of energy components demonstrates the dominant roles of hydrophobic effect for nonpolar atoms and of hydrogen-bonding for polar atoms. The estimated first solvation shell energy outweighs the long-range electrostatics for most compounds including ions. The simplicity and computational efficiency of the model allows its application for modeling of macromolecules in anisotropic environments, such as biological membranes.
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Affiliation(s)
- Andrei L. Lomize
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St., Ann Arbor, MI, 48109-1065, USA
| | - Irina Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St., Ann Arbor, MI, 48109-1065, USA
| | - Henry I Mosberg
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St., Ann Arbor, MI, 48109-1065, USA
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Fluorescence Probing in Structurally Anisotropic Materials. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY III 2011. [DOI: 10.1007/978-3-642-18035-4_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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24
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Powe AM, Das S, Lowry M, El-Zahab B, Fakayode SO, Geng ML, Baker GA, Wang L, McCarroll ME, Patonay G, Li M, Aljarrah M, Neal S, Warner IM. Molecular Fluorescence, Phosphorescence, and Chemiluminescence Spectrometry. Anal Chem 2010; 82:4865-94. [DOI: 10.1021/ac101131p] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Aleeta M. Powe
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Susmita Das
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Mark Lowry
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Bilal El-Zahab
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Sayo O. Fakayode
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Maxwell L. Geng
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Gary A. Baker
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Lin Wang
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Matthew E. McCarroll
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Gabor Patonay
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Min Li
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Mohannad Aljarrah
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Sharon Neal
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Isiah M. Warner
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
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Tremblay ML, Banks AW, Rainey JK. The predictive accuracy of secondary chemical shifts is more affected by protein secondary structure than solvent environment. JOURNAL OF BIOMOLECULAR NMR 2010; 46:257-270. [PMID: 20213252 DOI: 10.1007/s10858-010-9400-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 02/17/2010] [Indexed: 05/28/2023]
Abstract
Biomolecular NMR spectroscopy frequently employs estimates of protein secondary structure using secondary chemical shift (Deltadelta) values, measured as the difference between experimental and random coil chemical shifts (RCCS). Most published random coil data have been determined in aqueous conditions, reasonable for non-membrane proteins, but potentially less relevant for membrane proteins. Two new RCCS sets are presented here, determined in dimethyl sulfoxide (DMSO) and chloroform:methanol:water (4:4:1 by volume) at 298 K. A web-based program, CS-CHEMeleon, has been implemented to determine the accuracy of secondary structure assessment by calculating and comparing Deltadelta values for various RCCS datasets. Using CS-CHEMeleon, Deltadelta predicted versus experimentally determined secondary structures were compared for large datasets of membrane and non-membrane proteins as a function of RCCS dataset, Deltadelta threshold, nucleus, localized parameter averaging and secondary structure type. Optimized Deltadelta thresholds are presented both for published and for the DMSO and chloroform:methanol:water derived RCCS tables. Despite obvious RCCS variations between datasets, prediction of secondary structure was consistently similar. Strikingly, predictive accuracy seems to be most dependent upon the type of secondary structure, with helices being the most accurately predicted by Deltadelta values using five different RCCS tables. We suggest caution when using Deltadelta-based restraints in structure calculations as the underlying dataset may be biased. Comparative assessment of multiple RCCS datasets should be performed, and resulting Deltadelta-based restraints weighted appropriately relative to other experimental restraints.
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Affiliation(s)
- Marie-Laurence Tremblay
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, B3H 1X5, Canada
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26
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Holt A, Koehorst RBM, Rutters-Meijneke T, Gelb MH, Rijkers DTS, Hemminga MA, Killian JA. Tilt and rotation angles of a transmembrane model peptide as studied by fluorescence spectroscopy. Biophys J 2010; 97:2258-66. [PMID: 19843458 DOI: 10.1016/j.bpj.2009.07.042] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 07/23/2009] [Accepted: 07/24/2009] [Indexed: 12/15/2022] Open
Abstract
In this study the membrane orientation of a tryptophan-flanked model peptide, WALP23, was determined by using peptides that were labeled at different positions along the sequence with the environmentally sensitive fluorescent label BADAN. The fluorescence properties, reflecting the local polarity, were used to determine the tilt and rotation angles of the peptide based on an ideal alpha-helix model. For WALP23 inserted in dioleoylphosphatidylcholine (DOPC), an estimated tilt angle of the helix with respect to the bilayer normal of 24 degrees +/- 5 degrees was obtained. When the peptides were inserted into bilayers with different acyl chain lengths or containing different concentrations of cholesterol, small changes in tilt angle were observed as response to hydrophobic mismatch, whereas the rotation angle appeared to be independent of lipid composition. In all cases, the tilt angles were significantly larger than those previously determined from (2)H NMR experiments, supporting recent suggestions that the relatively long timescale of (2)H NMR measurements may result in an underestimation of tilt angles due to partial motional averaging. It is concluded that although the fluorescence technique has a rather low resolution and limited accuracy, it can be used to resolve the discrepancies observed between previous (2)H NMR experiments and molecular-dynamics simulations.
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Affiliation(s)
- Andrea Holt
- Chemical Biology and Organic Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
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Stopar D, Koehorst RB, Spruijt RB, Hemminga MA. Asymmetric dipping of bacteriophage M13 coat protein with increasing lipid bilayer thickness. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:2217-21. [DOI: 10.1016/j.bbamem.2009.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 08/12/2009] [Accepted: 08/17/2009] [Indexed: 11/29/2022]
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Profiling of dynamics in protein-lipid-water systems: a time-resolved fluorescence study of a model membrane protein with the label BADAN at specific membrane depths. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:647-56. [PMID: 19760185 PMCID: PMC2841254 DOI: 10.1007/s00249-009-0538-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 08/19/2009] [Accepted: 08/26/2009] [Indexed: 12/03/2022]
Abstract
Profiles of lipid-water bilayer dynamics were determined from picosecond time-resolved fluorescence spectra of membrane-embedded BADAN-labeled M13 coat protein. For this purpose, the protein was labeled at seven key positions. This places the label at well-defined locations from the water phase to the center of the hydrophobic acyl chain region of a phospholipid model membrane, providing us with a nanoscale ruler to map membranes. Analysis of the time-resolved fluorescence spectroscopic data provides the characteristic time constant for the twisting motion of the BADAN label, which is sensitive to the local flexibility of the protein–lipid environment. In addition, we obtain information about the mobility of water molecules at the membrane–water interface. The results provide an unprecedented nanoscale profiling of the dynamics and distribution of water in membrane systems. This information gives clear evidence that the actual barrier of membranes for ions and aqueous solvents is located at the region of carbonyl groups of the acyl chains.
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Viruses: incredible nanomachines. New advances with filamentous phages. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:541-50. [PMID: 19680644 PMCID: PMC2841255 DOI: 10.1007/s00249-009-0523-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 07/06/2009] [Accepted: 07/09/2009] [Indexed: 12/11/2022]
Abstract
During recent decades, bacteriophages have been at the cutting edge of new developments in molecular biology, biophysics, and, more recently, bionanotechnology. In particular filamentous viruses, for example bacteriophage M13, have a virion architecture that enables precision building of ordered and defect-free two and three-dimensional structures on a nanometre scale. This could not have been possible without detailed knowledge of coat protein structure and dynamics during the virus reproduction cycle. The results of the spectroscopic studies conducted in our group compellingly demonstrate a critical role of membrane embedment of the protein both during infectious entry of the virus into the host cell and during assembly of the new virion in the host membrane. The protein is effectively embedded in the membrane by a strong C-terminal interfacial anchor, which together with a simple tilt mechanism and a subtle structural adjustment of the extreme end of its N terminus provides favourable thermodynamical association of the protein in the lipid bilayer. This basic physicochemical rule cannot be violated and any new bionanotechnology that will emerge from bacteriophage M13 should take this into account.
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Saxl T, Khan F, Matthews DR, Zhi ZL, Rolinski O, Ameer-Beg S, Pickup J. Fluorescence lifetime spectroscopy and imaging of nano-engineered glucose sensor microcapsules based on glucose/galactose-binding protein. Biosens Bioelectron 2009; 24:3229-34. [PMID: 19442507 DOI: 10.1016/j.bios.2009.04.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Revised: 03/26/2009] [Accepted: 04/06/2009] [Indexed: 01/14/2023]
Abstract
We aimed to develop microsensors for eventual glucose monitoring in diabetes, based on fluorescence lifetime changes in glucose/galactose-binding protein (GBP) labelled with the environmentally sensitive fluorophore dye, badan. A mutant of GBP was labelled with badan near the binding site, the protein adsorbed to microparticles of CaCO(3) as templates and encapsulated in alternating nano-layers of poly-L-lysine and heparin. We used fluorescence lifetime imaging (FLIM) with two-photon excitation and time-correlated single-photon counting to visualize the lifetime changes in the capsules. Addition of glucose increased the mean lifetime of GBP-badan by a maximum of approximately 2 ns. Analysis of fluorescence decay curves was consistent with two GBP states, a short-lifetime component (approximately 0.8 ns), likely representing the open form of the protein with no bound glucose, and a long-lifetime component (approximately 3.1 ns) representing the closed form with bound glucose and where the lobes of GBP have closed round the dye creating a more hydrophobic environment. FLIM demonstrated that increasing glucose increased the fractional proportion of the long-lifetime component. We conclude that fluorescence lifetime-based glucose sensing using GBP encapsulated with nano-engineered layer-by-layer films is a glucose monitoring technology suitable for development in diabetes management.
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Affiliation(s)
- Tania Saxl
- Metabolic Unit, King's College London School of Medicine, Guy's Hospital, London, UK.
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