1
|
Brahma R, Raghuraman H. Characterization of a novel MgtE homolog and its structural dynamics in membrane mimetics. Biophys J 2024; 123:1968-1983. [PMID: 38042987 PMCID: PMC11309985 DOI: 10.1016/j.bpj.2023.11.3402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/03/2023] [Accepted: 11/30/2023] [Indexed: 12/04/2023] Open
Abstract
Magnesium (Mg2+) is the most abundant divalent cation in the cell and is critical for numerous cellular processes. Despite its importance, the mechanisms of intracellular Mg2+ transport and its regulation are poorly understood. MgtE is the main Mg2+ transport system in almost half of bacterial species and is an ortholog of mammalian SLC41A1 transporters, which are implicated in neurodegenerative diseases and cancer. To date, only MgtE from Thermus thermophilus (MgtETT) has been extensively characterized, mostly in detergent micelles, and gating-related structural dynamics in biologically relevant membranes are scarce. The MgtE homolog from Bacillus firmus (MgtEBF) is unique since it lacks the entire Mg2+-sensing N-domain but has conserved structural motifs in the TM-domain for Mg2+ transport. In this work, we have successfully purified this novel homolog in a stable and functional form, and ColabFold structure prediction analysis suggests a homodimer. Further, microscale thermophoresis experiments show that MgtEBF binds Mg2+ and ATP, similar to MgtETT. Importantly, we show that, despite lacking the N-domain, MgtEBF mediates Mg2+ transport function in the presence of an inwardly directed Mg2+ gradient in reconstituted proteoliposomes. Furthermore, comparison of the organization and dynamics of Trp residues in the TM-domain of MgtEBF in membrane mimetics, in apo- and Mg2+-bound forms, suggests that the cytoplasmic binding of Mg2+ might involve modest gating-related conformational changes at the TM-domain. Overall, our results show that the gating-related structural dynamics (hydration dynamics, conformational heterogeneity) of the full-length MgtEBF is significantly changed in functionally pertinent membrane environment, emphasizing the importance of lipid-protein interactions in MgtE gating mechanisms.
Collapse
Affiliation(s)
- Rupasree Brahma
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - H Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Training School Complex, Mumbai, India.
| |
Collapse
|
2
|
Dong Y, Bai W, Zhang Y, Zhang L, Liu D, Gao F. Computationally-efficient linear scheme for overlap time-gating spatial frequency domain diffuse optical tomography using an analytical diffusion model. BIOMEDICAL OPTICS EXPRESS 2024; 15:3654-3669. [PMID: 38867798 PMCID: PMC11166425 DOI: 10.1364/boe.523972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 06/14/2024]
Abstract
Time-domain (TD) spatial frequency domain (SFD) diffuse optical tomography (DOT) potentially enables laminar tomography of both the absorption and scattering coefficients. Its full time-resolved-data scheme is expected to enhance performances of the image reconstruction but poses heavy computational costs and also susceptible signal-to-noise ratio (SNR) limits, as compared to the featured-data one. We herein propose a computationally-efficient linear scheme of TD-SFD-DOT, where an analytical solution to the TD phasor diffusion equation for semi-infinite geometry is derived and used to formulate the Jacobian matrices with regard to overlap time-gating data of the time-resolved measurement for improved SNR and reduced redundancy. For better contrasting the absorption and scattering and widely adapted to practically-available resources, we develop an algebraic-reconstruction-technique-based two-step linear inversion procedure with support of a balanced memory-speed strategy and multi-core parallel computation. Both simulations and phantom experiments are performed to validate the effectiveness of the proposed TD-SFD-DOT method and show an achieved tomographic reconstruction at a relative depth resolution of ∼4 mm.
Collapse
Affiliation(s)
- Yihan Dong
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Wenxing Bai
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Yaru Zhang
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Limin Zhang
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Dongyuan Liu
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| |
Collapse
|
3
|
Assefa GT, Botha JL, van Heerden B, Kyeyune F, Krüger TPJ, Gwizdala M. ApcE plays an important role in light-induced excitation energy dissipation in the Synechocystis PCC6803 phycobilisomes. PHOTOSYNTHESIS RESEARCH 2024; 160:17-29. [PMID: 38407779 PMCID: PMC11006782 DOI: 10.1007/s11120-024-01078-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/18/2024] [Indexed: 02/27/2024]
Abstract
Phycobilisomes (PBs) play an important role in cyanobacterial photosynthesis. They capture light and transfer excitation energy to the photosynthetic reaction centres. PBs are also central to some photoprotective and photoregulatory mechanisms that help sustain photosynthesis under non-optimal conditions. Amongst the mechanisms involved in excitation energy dissipation that are activated in response to excessive illumination is a recently discovered light-induced mechanism that is intrinsic to PBs and has been the least studied. Here, we used single-molecule spectroscopy and developed robust data analysis methods to explore the role of a terminal emitter subunit, ApcE, in this intrinsic, light-induced mechanism. We isolated the PBs from WT Synechocystis PCC 6803 as well as from the ApcE-C190S mutant of this strain and compared the dynamics of their fluorescence emission. PBs isolated from the mutant (i.e., ApcE-C190S-PBs), despite not binding some of the red-shifted pigments in the complex, showed similar global emission dynamics to WT-PBs. However, a detailed analysis of dynamics in the core revealed that the ApcE-C190S-PBs are less likely than WT-PBs to enter quenched states under illumination but still fully capable of doing so. This result points to an important but not exclusive role of the ApcE pigments in the light-induced intrinsic excitation energy dissipation mechanism in PBs.
Collapse
Affiliation(s)
- Gonfa Tesfaye Assefa
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Joshua L Botha
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Bertus van Heerden
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), Stellenbosch, South Africa
| | - Farooq Kyeyune
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
- Department of Physics, Faculty of Science, Kyambogo University, P.O. Box 1, Kyambogo, Kampala, Uganda
| | - Tjaart P J Krüger
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), Stellenbosch, South Africa
| | - Michal Gwizdala
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, 08860, Spain.
| |
Collapse
|
4
|
Das A, Bysack A, Raghuraman H. Cholesterol modulates the structural dynamics of the paddle motif loop of KvAP voltage sensor. Curr Res Struct Biol 2024; 7:100137. [PMID: 38500801 PMCID: PMC10945132 DOI: 10.1016/j.crstbi.2024.100137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 03/20/2024] Open
Abstract
KvAP is a prokaryotic Kv channel, which has been widely used as a model system to understand voltage- and lipid-dependent gating mechanisms. In phospholipid membranes, the KvAP-VSD adopts the activated/'Up' conformation, whereas the presence of non-phospholipids in membranes favours the structural transition to resting/'Down' state. The S3b-S4 paddle motif loop of KvAP-VSD is functionally important as this participates in protein-protein interactions and is the target for animal toxins. In this study, we have monitored the modulatory role of cholesterol - the physiologically-relevant non-phospholipid - on the organization and dynamics of the S3b-S4 loop of the isolated KvAP-VSD in membranes by site-directed fluorescence approaches using the environmental sensitivity of 7-nitrobenz-2-oxa-1,3-diazol-4-yl-ethylenediamine (NBD) fluorescence. Our results show that cholesterol alters the dynamic nature (rotational and hydration dynamics) of S3b-S4 loop in a segmental fashion, i.e., the residues 110 to 114 and 115 to 117 behave differently in the presence of cholesterol, which is accompanied by considerable change in conformational heterogeneity. Further, quantitative depth measurements using the parallax quenching method reveal that the sensor loop is located at the shallow interfacial region of cholesterol-containing membranes, suggesting that the sensor loop organization is not directly correlated with S4 helix movement. Our results clearly show that cholesterol-induced changes in bilayer properties may not be the predominant factor for the sensor loop's altered structural dynamics, but can be attributed to the conformational change of the KvAP-VSD in cholesterol-containing membranes. Overall, these results are relevant for gating mechanisms, particularly the lipid-dependent gating, of Kv channels in membranes.
Collapse
Affiliation(s)
- Anindita Das
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400 094, India
| | - Arpan Bysack
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400 094, India
| | - H. Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400 094, India
| |
Collapse
|
5
|
Waly SMA, Benniston AC, Harriman A. Deducing the conformational space for an octa-proline helix. Chem Sci 2024; 15:1657-1671. [PMID: 38303943 PMCID: PMC10829019 DOI: 10.1039/d3sc05287g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024] Open
Abstract
A molecular dyad, PY-P8-PER, comprising a proline octamer sandwiched between pyrene and perylene terminals has been synthesized in order to address the dynamics of electronic energy transfer (EET) along the oligo-proline chain. A simple pyrene-based control compound equipped with a bis-proline attachment serves as a reference for spectroscopic studies. The N-H NMR signal at the terminal pyrene allows distinction between cis and trans amides and, although the crystal structure for the control has the trans conformation, temperature-dependent NMR studies provide clear evidence for trans/cis isomerisation in D6-DMSO. Polar solvents tend to stabilise the trans structure for the pyrene amide group, even for longer oligo-proline units. Circular dichroism shows that the proline spacer for PY-P8-PER exists mainly in the all-trans geometry in methanol. Preferential excitation of the pyrene chromophore is possible at wavelengths in the 320-350 nm range and, for the dyad, is followed by efficacious EET to the perylene emitter. The probability for intramolecular EET, obtained from analysis of steady-state spectroscopic data, is ca. 80-90% in solvents of disparate polarity. Comparison with the Förster critical distance suggests the terminals are ca. 18 Å apart. Time-resolved fluorescence spectroscopy, in conjunction with DFT calculations, indicates the dyad exists as a handful of conformers displaying a narrow range of EET rates. Optimisation of a distributive model allows accurate simulation of the EET dynamics in terms of reasonable structures based on isomerisation of certain amide groups.
Collapse
Affiliation(s)
- Sara M A Waly
- Molecular Photonics Laboratory, Bedson Building, School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Andrew C Benniston
- Molecular Photonics Laboratory, Bedson Building, School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Anthony Harriman
- Molecular Photonics Laboratory, Bedson Building, School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
| |
Collapse
|
6
|
Blum D, Reuter M, Schliebs W, Tomaschewski J, Erdmann R, Wagner R. Membrane binding and pore forming insertion of PEX5 into horizontal lipid bilayer. Biol Chem 2023; 404:157-167. [PMID: 36260915 DOI: 10.1515/hsz-2022-0183] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/29/2022] [Indexed: 11/15/2022]
Abstract
The assembly of the peroxisomal translocon involves the transition of a soluble form of the peroxisomal targeting receptor PEX5 into a membrane-bound form, which becomes an integral membrane component of the import pore for peroxisomal matrix proteins. How this transition occurs is still a mystery. We addressed this question using a artificial horizontal bilayer in combination with fluorescence time-correlated single photon counting (TCSPC) and electrophysiological channel recording. Purified human isoform PEX5L and truncated PEX5L(1-335) lacking the cargo binding domain were selectively labeled with thiol-reactive Atto-dyes. Diffusion coefficients of labeled protein in solution show that PEX5L is monomeric with a rather compact spherical conformation, while the truncated protein appeared in a more extended conformation. Labeled PEX5L and the truncated PEX5L(1-335) bind stably to horizontal bilayer thereby accumulating around 100-fold. The diffusion coefficients of the membrane-bound PEX5L forms are 3-4 times lower than in solution, indicating the formation of larger complexes. Electrophysiological single channel recording shows that membrane-bound labeled and non-labeled PEX5L, but not the truncated PEX5L(1-335), can form ion conducting membrane channels. The data suggest that PEX5L is the pore-forming component of the oligomeric peroxisomal translocon and that spontaneous PEX5L membrane surface binding might be an important step in its assembly.
Collapse
Affiliation(s)
- Daniel Blum
- MOLIFE Research Center, Jacobs, University Bremen, D-28759 Bremen, Germany
| | - Maren Reuter
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Wolfgang Schliebs
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Jana Tomaschewski
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Ralf Erdmann
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Richard Wagner
- MOLIFE Research Center, Jacobs, University Bremen, D-28759 Bremen, Germany
| |
Collapse
|
7
|
Brahma R, Das A, Raghuraman H. Site-directed fluorescence approaches to monitor the structural dynamics of proteins using intrinsic Trp and labeled with extrinsic fluorophores. STAR Protoc 2022; 3:101200. [PMID: 35252885 PMCID: PMC8889417 DOI: 10.1016/j.xpro.2022.101200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Comprehensive understanding of a protein's function depends on having reliable, sophisticated tools to study protein structural dynamics in physiologically-relevant conditions. Here, we present an effective, robust step-by-step protocol to monitor the structural dynamics (including hydration dynamics) of a protein utilizing various site-directed fluorescence (SDFL) approaches. This protocol should be widely applicable for studying soluble proteins, intrinsically-disordered proteins, and membrane proteins. For complete details on the use and execution of this protocol, please refer to Das et al. (2020), Das and Raghuraman (2021), and Chatterjee et al. (2021).
Collapse
Affiliation(s)
- Rupasree Brahma
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata 700 064, India
| | - Anindita Das
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata 700 064, India
| | - H. Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata 700 064, India
| |
Collapse
|
8
|
Fazel M, Jazani S, Scipioni L, Vallmitjana A, Gratton E, Digman MA, Pressé S. High Resolution Fluorescence Lifetime Maps from Minimal Photon Counts. ACS PHOTONICS 2022; 9:1015-1025. [PMID: 35847830 PMCID: PMC9278809 DOI: 10.1021/acsphotonics.1c01936] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) may reveal subcellular spatial lifetime maps of key molecular species. Yet, such a quantitative picture of life necessarily demands high photon budgets at every pixel under the current analysis paradigm, thereby increasing acquisition time and photodamage to the sample. Motivated by recent developments in computational statistics, we provide a direct means to update our knowledge of the lifetime maps of species of different lifetimes from direct photon arrivals, while accounting for experimental features such as arbitrary forms of the instrument response function (IRF) and exploiting information from empty laser pulses not resulting in photon detection. Our ability to construct lifetime maps holds for arbitrary lifetimes, from short lifetimes (comparable to the IRF) to lifetimes exceeding interpulse times. As our method is highly data efficient, for the same amount of data normally used to determine lifetimes and photon ratios, working within the Bayesian paradigm, we report direct blind unmixing of lifetimes with subnanosecond resolution and subpixel spatial resolution using standard raster scan FLIM images. We demonstrate our method using a wide range of simulated and experimental data.
Collapse
Affiliation(s)
- Mohamadreza Fazel
- Center
for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Sina Jazani
- Center
for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Lorenzo Scipioni
- Department
of Biomedical Engineering, University of
California Irvine, Irvine, California 92697, United States
- Laboratory
of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Alexander Vallmitjana
- Department
of Biomedical Engineering, University of
California Irvine, Irvine, California 92697, United States
- Laboratory
of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Enrico Gratton
- Department
of Biomedical Engineering, University of
California Irvine, Irvine, California 92697, United States
- Laboratory
of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Michelle A. Digman
- Department
of Biomedical Engineering, University of
California Irvine, Irvine, California 92697, United States
- Laboratory
of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Steve Pressé
- Center
for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Science, Arizona State University, Tempe, Arizona 85287, United States
- E-mail:
| |
Collapse
|
9
|
Waly SM, Karlsson JKG, Waddell PG, Benniston AC, Harriman A. Light-Harvesting Crystals Formed from BODIPY-Proline Biohybrid Conjugates: Antenna Effects and Excitonic Coupling. J Phys Chem A 2022; 126:1530-1541. [PMID: 35230124 PMCID: PMC9097531 DOI: 10.1021/acs.jpca.2c00035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A boron dipyrromethene (BODIPY) derivative
bearing a cis-proline residue at the meso-position crystallizes
in the form of platelets with strong (i.e., ΦF =
0.34) red fluorescence, but the absorption and emission spectra differ
markedly from those for dilute solutions. A key building block for
the crystal is a pseudo-dimer where hydrogen bonding
aligns the proline groups and separates the terminal chromophores
by ca. 25 Å. Comparison with a covalently linked bichromophore
suggests that one-dimensional (1D) excitonic coupling between the
terminals is too small to perturb the optical properties. However,
accretion of the pseudo-dimer forms narrow channels
possessing a high density of chromophores. The resultant absorption
spectrum exhibits strong excitonic splitting, which can be explained
quantitatively using the extended dipole approach and allowing for
coupling between ca. 30 BODIPY units. Fluorescence, which decays with
a lifetime of 2.2 ns, is assigned to a delocalized and (slightly)
super-radiant BODIPY dimer situated at the interface and populated
via electronic energy transfer from the interior.
Collapse
|
10
|
Chen W, Lu W, Wolynes PG, Komives E. Single-molecule conformational dynamics of a transcription factor reveals a continuum of binding modes controlling association and dissociation. Nucleic Acids Res 2021; 49:11211-11223. [PMID: 34614173 PMCID: PMC8565325 DOI: 10.1093/nar/gkab874] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/10/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022] Open
Abstract
Binding and unbinding of transcription factors to DNA are kinetically controlled to regulate the transcriptional outcome. Control of the release of the transcription factor NF-κB from DNA is achieved through accelerated dissociation by the inhibitor protein IκBα. Using single-molecule FRET, we observed a continuum of conformations of NF-κB in free and DNA-bound states interconverting on the subseconds to minutes timescale, comparable to in vivo binding on the seconds timescale, suggesting that structural dynamics directly control binding kinetics. Much of the DNA-bound NF-κB is partially bound, allowing IκBα invasion to facilitate DNA dissociation. IκBα induces a locked conformation where the DNA-binding domains of NF-κB are too far apart to bind DNA, whereas a loss-of-function IκBα mutant retains the NF-κB conformational ensemble. Overall, our results suggest a novel mechanism with a continuum of binding modes for controlling association and dissociation of transcription factors.
Collapse
Affiliation(s)
- Wei Chen
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Wei Lu
- Center for Theoretical Biological Physics, Departments of Chemistry, Physics, and Biosciences, Rice University, Houston, Texas 77005, USA
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Departments of Chemistry, Physics, and Biosciences, Rice University, Houston, Texas 77005, USA
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| |
Collapse
|
11
|
Syed A, Mishra S, Jayanty S. 7,7-bis(N, N-diethylethylenediamino)-8,8-dicyanoquinodimethane: Effect of Ethyl Moiety on the Photophysical Property besides Thermal Stability. J Fluoresc 2021; 32:115-124. [PMID: 34599730 DOI: 10.1007/s10895-021-02830-0] [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: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 11/26/2022]
Abstract
Tetracyanoquinodimethane (TCNQ) on reaction with primary/secondary amines sequels in mono/di-substituted TCNQ adducts known as diaminodicyanoquinodimethanes (DADQ's) possessing astounding optical or non-linear optical characteristics. Crucially, the subtle choice of amine contributes to the outcome of molecular material aspects. Herein, we present a comprehensive investigation of 7,7-bis(N,N-diethylethylenediamino)-8,8-dicyanoquinodimethane (BDEDDQ); manifesting the impact of ethyl group (existing on the di-substituted nitrogen of N,N-diethylethylenediamine (DEED)); on the crystal structure, optical property and thermal stability. Crystallography study revealed supramolecular self-assemblies among molecular dipoles emanating fluorescence enhancement in the solid state compared to solutions. Quantum yields were primarily ~0.2 to 0.4% in solutions and ~56% in the solid. Stokes shift was noticed to be more in solutions (~90 nm) than solid (~67 nm), suggesting excess vibrational relaxations in solutions. Differential scanning calorimetry revealed ~182 °C as the melting temperature. The heat capacity of solid was found to be 5.03 mJs-1. Thermogravimetric analysis conveyed single stage decomposition process initiated by the two amine side chains. Scanning electron microscopy of films prepared by drop casting solutions imparted divergent morphological features, due to different rates of evaporation accompanied by varied growth kinetics. Accordingly, in this paper we have demonstrated the utilization of simple N,N-diethylethylenediamine (DEED) to successfully generate a noteworthy blue emissive molecular material exhibiting semiconducting feature besides reasonable thermal stability.
Collapse
Affiliation(s)
- Anwarhussaini Syed
- Department of Chemistry, Birla Institute of Technology and Science-Hyderabad Campus, Medchal Dist. Hyderabad - 500078, Telangana State, Jawaharnagar, Shameerpet, Kapra Mandal, India
| | - Sabyashachi Mishra
- Department of Chemistry, Kharagpur and Centre for Computational and Data Sciences, Indian Institute of Technology, Indian Institute of Technology Kharagpur, 721302, Kharagpur, West Bengal, India
| | - Subbalakshmi Jayanty
- Department of Chemistry, Birla Institute of Technology and Science-Hyderabad Campus, Medchal Dist. Hyderabad - 500078, Telangana State, Jawaharnagar, Shameerpet, Kapra Mandal, India.
| |
Collapse
|
12
|
Zimányi L, Sipos Á, Sarlós F, Nagypál R, Groma GI. Machine-learning model selection and parameter estimation from kinetic data of complex first-order reaction systems. PLoS One 2021; 16:e0255675. [PMID: 34370771 PMCID: PMC8352076 DOI: 10.1371/journal.pone.0255675] [Citation(s) in RCA: 3] [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: 02/18/2021] [Accepted: 07/22/2021] [Indexed: 11/28/2022] Open
Abstract
Dealing with a system of first-order reactions is a recurrent issue in chemometrics, especially in the analysis of data obtained by spectroscopic methods applied on complex biological systems. We argue that global multiexponential fitting, the still common way to solve such problems, has serious weaknesses compared to contemporary methods of sparse modeling. Combining the advantages of group lasso and elastic net-the statistical methods proven to be very powerful in other areas-we created an optimization problem tunable from very sparse to very dense distribution over a large pre-defined grid of time constants, fitting both simulated and experimental multiwavelength spectroscopic data with high computational efficiency. We found that the optimal values of the tuning hyperparameters can be selected by a machine-learning algorithm based on a Bayesian optimization procedure, utilizing widely used or novel versions of cross-validation. The derived algorithm accurately recovered the true sparse kinetic parameters of an extremely complex simulated model of the bacteriorhodopsin photocycle, as well as the wide peak of hypothetical distributed kinetics in the presence of different noise levels. It also performed well in the analysis of the ultrafast experimental fluorescence kinetics data detected on the coenzyme FAD in a very wide logarithmic time window. We conclude that the primary application of the presented algorithms-implemented in available software-covers a wide area of studies on light-induced physical, chemical, and biological processes carried out with different spectroscopic methods. The demand for this kind of analysis is expected to soar due to the emerging ultrafast multidimensional infrared and electronic spectroscopic techniques that provide very large and complex datasets. In addition, simulations based on our methods could help in designing the technical parameters of future experiments for the verification of particular hypothetical models.
Collapse
Affiliation(s)
- László Zimányi
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Áron Sipos
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Ferenc Sarlós
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Rita Nagypál
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
- Doctoral School of Physics, University of Szeged, Szeged, Hungary
| | - Géza I. Groma
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| |
Collapse
|
13
|
Mukherjee T, Soppina V, Ludovic R, Mély Y, Klymchenko AS, Collot M, Kanvah S. Live-cell imaging of the nucleolus and mapping mitochondrial viscosity with a dual function fluorescent probe. Org Biomol Chem 2021; 19:3389-3395. [PMID: 33555275 DOI: 10.1039/d0ob02378g] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Visualization of sub-cellular organelles allows the determination of various cellular processes and the underlying mechanisms. Herein, we report a fluorescent probe, bearing push-pull substituents emitting at 600 nm and its application in cellular imaging. The probe shows dual imaging of mitochondria and nucleoli and maps mitochondrial viscosity in live cells under various physiological variations and show minimum cytotoxicity. Nucleolar staining is confirmed by RNAase digestion.
Collapse
Affiliation(s)
- Tarushyam Mukherjee
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar 382355, India.
| | - Virupakshi Soppina
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar 382355, India.
| | - Richert Ludovic
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Mayeul Collot
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Sriram Kanvah
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar 382355, India.
| |
Collapse
|
14
|
Das A, Raghuraman H. Conformational heterogeneity of the voltage sensor loop of KvAP in micelles and membranes: A fluorescence approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183568. [PMID: 33529577 DOI: 10.1016/j.bbamem.2021.183568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/06/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
KvAP is a tetrameric voltage-gated potassium channel that is composed of a pore domain and a voltage-sensing domain (VSD). The VSD is crucial for sensing transmembrane potential and gating. At 0 mV, the VSD adopts an activated conformation in both n-octylglucoside (OG) micelles and phospholipid membranes. Importantly, gating-modifier toxins that bind at S3b-S4 loop of KvAP-VSD exhibit pronounced differences in binding affinity in these membrane-mimetic systems. However, the conformational heterogeneity of this functionally-important sensor loop in membrane mimetics is poorly understood, and is the focus of this work. In this paper, we establish, using intrinsic fluorescence of the uniquely positioned W70 in KvAP-VSD and environment-sensitive NBD (7-nitrobenz-2-oxa-1,3-diazol-4-yl-ethylenediamine) fluorescence of the labelled S3b-S4 loop, that the surface charge of the membrane does not significantly affect the topology and structural dynamics of the sensor loop in membranes. Importantly, the dynamic variability of the sensor loop is preserved in both zwitterionic (POPC) and anionic (POPC/POPG) membranes. Further, the lifetime distribution analysis for the NBD-labelled residues by maximum entropy method (MEM) demonstrates that, in contrast to micelles, the membrane environment not only reduces the relative discrete population of sensor loop conformations, but also broadens the lifetime distribution peaks. Overall, our results strongly suggest that the conformational heterogeneity of the sensor loop is significantly altered in membranes and this correlates well with its environmental heterogeneity. This constitutes the first report demonstrating that MEM-lifetime distribution could be a powerful tool to distinguish changes in conformational heterogeneity in potassium channels with similar architecture and topology.
Collapse
Affiliation(s)
- Anindita Das
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India
| | - H Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India.
| |
Collapse
|
15
|
Chatterjee S, Brahma R, Raghuraman H. Gating-related Structural Dynamics of the MgtE Magnesium Channel in Membrane-Mimetics Utilizing Site-Directed Tryptophan Fluorescence. J Mol Biol 2020; 433:166691. [PMID: 33203509 DOI: 10.1016/j.jmb.2020.10.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/25/2022]
Abstract
Magnesium is the most abundant divalent cation present in the cell, and an abnormal Mg2+ homeostasis is associated with several diseases in humans. However, among ion channels, the mechanisms of intracellular regulation and transport of Mg2+ are poorly understood. MgtE is a homodimeric Mg2+-selective channel and is negatively regulated by high intracellular Mg2+ concentration where the cytoplasmic domain of MgtE acts as a Mg2+ sensor. Most of the previous biophysical studies on MgtE have been carried out in detergent micelles and the information regarding gating-related structural dynamics of MgtE in physiologically-relevant membrane environment is scarce. In this work, we monitored the changes in gating-related structural dynamics, hydration dynamics and conformational heterogeneity of MgtE in micelles and membranes using the intrinsic site-directed Trp fluorescence. For this purpose, we have engineered six single-Trp mutants in the functional Trp-less background of MgtE to obtain site-specific information on the gating-related structural dynamics of MgtE in membrane-mimetic systems. Our results indicate that Mg2+-induced gating might involve the possibility of a 'conformational wave' from the cytosolic N-domain to transmembrane domain of MgtE. Although MgtE is responsive to Mg2+-induced gating in both micelles and membranes, the organization and dynamics of MgtE is substantially altered in physiologically important phospholipid membranes compared to micelles. This is accompanied by significant changes in hydration dynamics and conformational heterogeneity. Overall, our results highlight the importance of lipid-protein interactions and are relevant for understanding gating mechanism of magnesium channels in general, and MgtE in particular.
Collapse
Affiliation(s)
- Satyaki Chatterjee
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India
| | - Rupasree Brahma
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India
| | - H Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India.
| |
Collapse
|
16
|
Chen Y, Liu J, Zhang X, Blough NV. Time-Resolved Fluorescence Spectra of Untreated and Sodium Borohydride-Reduced Chromophoric Dissolved Organic Matter. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:12109-12118. [PMID: 32845124 DOI: 10.1021/acs.est.0c03135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Time-resolved fluorescence spectra of chromophoric dissolved organic matter (CDOM) from different sources were acquired using UV (280 and 375 nm) and visible light (440 and 640 nm) excitation to probe the structural basis of the emission properties of CDOM. Emission decays were faster at the blue and red edges, particularly at the red edge, relative to those acquired from 480 to 550 nm. Based on the lifetime distribution and multiexponential analysis of the emission decays recorded at different time resolution, current findings demonstrate that the components recovered based on a superposition model have no defined physical meaning. A substantial increase in steady-state fluorescence intensity and only small changes (<30%) of amplitude-weighted average lifetime caused by sodium borohydride reduction suggest that intramolecular fluorescence quenching occurs mainly through formation of ground state charge-transfer interactions. Short-lived species (lifetime < 100 ps) dominate the emission decays over wavelengths from 400 to 800 nm, particularly under excitation at long wavelengths (440 and 640 nm). Compared to locally excited (LE) states, the contribution of charge-transfer excited (ECT) states and other short-lived species to the steady-state emission is small because of their very rapid nonradiative relaxation. This study suggests that a careful choice of observation wavelength is needed to distinguish LE states from ECT states.
Collapse
Affiliation(s)
- Yuan Chen
- Department of Environmental Science, School of Resources and Environmental Science, Wuhan University, Wuhan 430079, P. R. China
| | - Juan Liu
- Department of Environmental Science, School of Resources and Environmental Science, Wuhan University, Wuhan 430079, P. R. China
| | - Xu Zhang
- Department of Environmental Science, School of Resources and Environmental Science, Wuhan University, Wuhan 430079, P. R. China
| | - Neil V Blough
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| |
Collapse
|
17
|
Panigrahi SK, Mishra AK. Total Emission Time Resolved Decay: a Method for Measurement and Resolution of Broad-Band Emission. J Fluoresc 2020; 30:1085-1094. [PMID: 32632718 DOI: 10.1007/s10895-020-02581-4] [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: 04/11/2020] [Accepted: 06/26/2020] [Indexed: 10/23/2022]
Abstract
This article reports a time-resolved fluorescence data acquisition technique termed as "Total Emission Time Resolved Decay" (TETRD). TETRD is recorded by using zero-order diffraction of emission grating in TCSPC instrument. TETRD decay curve has entire wavelength dependent decay information buried in it. Cut-off filters are used to avoid scattering contamination. Two existing approaches are used for analysing the interconnected TETRD data. (i) First, global analysis: for discretely decaying multiple components, TETRD dataset is analyzed using global analysis. The normalized pre-exponentials (αi) and relative amplitudes (fi) recovered from global analysis reflect the individual component emission more faithfully and resembles with steady-state spectral data as well. (ii) Second, stretched exponential fitting (StrEF): for continuous lifetime distribution systems, StrEF (I(t) = I0 exp[-(t/τ)1/h]) has been used to analyse TETRD data. The average lifetime (τ) of StrEF matches well with the average lifetime of multi-exponential fitting, the heterogeneity factor (h) of StrEF is an additional parameter, which informs about local heterogeneity in the system. It is shown that the lifetimes obtained with TETRD matches well with the lifetimes obtained using conventional time resolved emission spectra (TRES). TETRD holds advantage in rapid data acquisition and facilitates inclusion of another variable (like concentration, solvent composition, pH, excitation wavelength etc.) into experimental design. Further, with the use of an appropriate data analysis tool, the multi-component decay profiles can be resolved conveniently.
Collapse
|
18
|
Beckwith JS, Rumble CA, Vauthey E. Data analysis in transient electronic spectroscopy – an experimentalist's view. INT REV PHYS CHEM 2020. [DOI: 10.1080/0144235x.2020.1757942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Joseph S. Beckwith
- Department of Physical Chemistry, University of Geneva, Geneva, Switzerland
| | | | - Eric Vauthey
- Department of Physical Chemistry, University of Geneva, Geneva, Switzerland
| |
Collapse
|
19
|
Romei MG, Lin CY, Mathews II, Boxer SG. Electrostatic control of photoisomerization pathways in proteins. Science 2020; 367:76-79. [PMID: 31896714 DOI: 10.1126/science.aax1898] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/04/2019] [Accepted: 10/31/2019] [Indexed: 12/23/2022]
Abstract
Rotation around a specific bond after photoexcitation is central to vision and emerging opportunities in optogenetics, super-resolution microscopy, and photoactive molecular devices. Competing roles for steric and electrostatic effects that govern bond-specific photoisomerization have been widely discussed, the latter originating from chromophore charge transfer upon excitation. We systematically altered the electrostatic properties of the green fluorescent protein chromophore in a photoswitchable variant, Dronpa2, using amber suppression to introduce electron-donating and electron-withdrawing groups to the phenolate ring. Through analysis of the absorption (color), fluorescence quantum yield, and energy barriers to ground- and excited-state isomerization, we evaluate the contributions of sterics and electrostatics quantitatively and demonstrate how electrostatic effects bias the pathway of chromophore photoisomerization, leading to a generalized framework to guide protein design.
Collapse
Affiliation(s)
- Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
20
|
Paterson KA, Arlt J, Jones AC. Dynamic and static quenching of 2-aminopurine fluorescence by the natural DNA nucleotides in solution. Methods Appl Fluoresc 2020; 8:025002. [PMID: 32000159 DOI: 10.1088/2050-6120/ab71c3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
2-aminopurine (2AP) is a responsive fluorescent base analogue that is used widely as a probe of the local molecular environment in DNA. The ability of 2AP to report changes in local conformation and base-stacking interactions arises from the efficient quenching of its fluorescence by the natural DNA bases. However, the mechanism of this inter-base quenching remains imperfectly understood. Two previous studies of the collisional quenching of 2AP by the natural bases, in different buffer solutions, showed that dynamic quenching efficiency depends on the identity of the natural base, but disagreed on the relative quenching efficiencies of the bases. We report a comprehensive investigation of inter-base quenching of 2AP by the natural nucleoside monophosphates (NMPs), replicating the buffer conditions used in the previous studies. Using time-resolved fluorescence measurements to distinguish between dynamic and static quenching, we find that the dynamic quenching rate constants of the different bases show a consistent trend across both buffers, and this is in line with a charge-transfer mechanism. Time-resolved measurements also provide insight into static quenching, revealing formation of 2AP-NMP ground-state complexes in which 2AP displays a very short fluorescence lifetime, comparable to that seen in oligonucleotides. In these complexes, the dependence of the rate of quenching on the partner base also supports a charge-transfer mechanism.
Collapse
Affiliation(s)
- Kyle A Paterson
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | | | | |
Collapse
|
21
|
Chandra A, Jana K, Moorthy JN. One-Pot Synthesis of 4-Carboalkoxy-Substituted Benzo[ h]coumarins from α- and β-Naphthols and Their Excited-State Properties. ACS OMEGA 2020; 5:207-218. [PMID: 31956767 PMCID: PMC6963932 DOI: 10.1021/acsomega.9b02489] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/14/2019] [Indexed: 05/27/2023]
Abstract
One-pot synthesis has been developed for 4-carboethoxybenzo[h]coumarins starting from α-/β-naphthols. Accordingly, diverse 4-carboethoxybenzocoumarins can be synthesized in moderate-to-excellent (31-75%) isolated yields. The synthesis involves initial oxidation of naphthols to the intermediary 1,2-naphthoquinones with 2-iodoxybenzoic acid followed by a cascade of reactions, namely, Wittig olefination, Michael addition, β-elimination, and cyclization. Furthermore, we have comprehensively investigated the excited-state properties of differently substituted 4-carboalkoxybenzo[h]coumarins. It is shown that they exhibit low to high fluorescence quantum yields (1-36%) and excited-state lifetimes (ca. 1-7 ns) depending on the substitution pattern and solvent employed.
Collapse
|
22
|
Identification of pyrene in complex sample matrix using time-resolved fluorescence measurement coupled with PARAFAC analysis. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.111991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
23
|
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.
Collapse
Affiliation(s)
- H. Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, Kolkata, India
| | | | | |
Collapse
|
24
|
Griffin SR, Biechele-Speziale JA, Smith CJ, You-Dow X, White JK, Zhang SW, Novak J, Liu Z, Simpson GJ. Iterative Non-Negative Matrix Factorization Filter for Blind Deconvolution in Photon/Ion Counting. Anal Chem 2019; 91:5286-5294. [PMID: 30856314 DOI: 10.1021/acs.analchem.9b00120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A digital filter based on non-negative matrix factorization (NMF) enables blind deconvolution of temporal information from large data sets, simultaneously recovering both photon arrival times and the instrument impulse response function (IRF). In general, the measured digital signals produced by modern analytical instrumentation are convolved by the corresponding IRFs, which can complicate quantitative analyses. Common examples include photon counting (PC), chromatography, super resolution imaging, fluorescence imaging, and mass spectrometry. Scintillation counting, in particular, provides a signal-to-noise advantage in measurements of low intensity signals, but has a limited dynamic range due to pulse overlap. This limitation can complicate the interpretation of data by masking temporal and amplitude information on the underlying detected signal. Typical methods for deconvolution of the photon events require advanced knowledge of the IRF, which is not generally trivial to obtain. In this work, a sliding window approach was developed to perform NMF one pixel at a time on short segments of large (e.g., 25 million point) data sets. Using random initial guesses for the IRF, the NMF filter simultaneously recovered both the deconvolved photon arrival times and the IRF. Applying the NMF filter to the analysis of triboluminescence (TL) data traces of active pharmaceutical ingredients enabled discrimination between different hypothesized physical origins of the signal.
Collapse
Affiliation(s)
- Scott R Griffin
- Purdue University , West Lafayette , Indiana 47906 , United States
| | | | - Casey J Smith
- Purdue University , West Lafayette , Indiana 47906 , United States
| | - Ximeng You-Dow
- Merck & Co., Inc. , Kenilworth , New Jersey 07033 , United States
| | - Julia K White
- Purdue University , West Lafayette , Indiana 47906 , United States
| | - Si-Wei Zhang
- Merck & Co., Inc. , Kenilworth , New Jersey 07033 , United States
| | - Julie Novak
- Merck & Co., Inc. , Kenilworth , New Jersey 07033 , United States
| | - Zhen Liu
- Merck & Co., Inc. , Kenilworth , New Jersey 07033 , United States
| | - Garth J Simpson
- Purdue University , West Lafayette , Indiana 47906 , United States
| |
Collapse
|
25
|
Collot M, Bou S, Fam TK, Richert L, Mély Y, Danglot L, Klymchenko AS. Probing Polarity and Heterogeneity of Lipid Droplets in Live Cells Using a Push–Pull Fluorophore. Anal Chem 2018; 91:1928-1935. [DOI: 10.1021/acs.analchem.8b04218] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mayeul Collot
- Laboratoire de Biophotonique et Pathologies, Faculté de Pharmacie, UMR 7021 CNRS, Université de Strasbourg, 74, Route du Rhin, 67401 Cedex, Illkirch, France
| | - Sophie Bou
- Laboratoire de Biophotonique et Pathologies, Faculté de Pharmacie, UMR 7021 CNRS, Université de Strasbourg, 74, Route du Rhin, 67401 Cedex, Illkirch, France
| | - Tkhe Kyong Fam
- Laboratoire de Biophotonique et Pathologies, Faculté de Pharmacie, UMR 7021 CNRS, Université de Strasbourg, 74, Route du Rhin, 67401 Cedex, Illkirch, France
| | - Ludovic Richert
- Laboratoire de Biophotonique et Pathologies, Faculté de Pharmacie, UMR 7021 CNRS, Université de Strasbourg, 74, Route du Rhin, 67401 Cedex, Illkirch, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pathologies, Faculté de Pharmacie, UMR 7021 CNRS, Université de Strasbourg, 74, Route du Rhin, 67401 Cedex, Illkirch, France
| | - Lydia Danglot
- Institut Jacques Monod, University Paris Diderot, Sorbonne Paris Cité, CNRS UMR 7592, 75013 Paris, France
- Membrane Traffic in Healthy and Diseased Brain, INSERM U894, Institute of Psychiatry and Neuroscience of Paris, 102 rue de la Santé, 75 014 Paris, France
| | - Andrey S. Klymchenko
- Laboratoire de Biophotonique et Pathologies, Faculté de Pharmacie, UMR 7021 CNRS, Université de Strasbourg, 74, Route du Rhin, 67401 Cedex, Illkirch, France
| |
Collapse
|
26
|
Affiliation(s)
- David J S Birch
- Photophysics Group, Department of Physics, University of Strathclyde, Scottish Universities Physics Alliance, Glasgow G4 0NG, Scotland, United Kingdom
| |
Collapse
|