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Article ; Online: Isospectral intermediates in the photochemical reaction cycle of anion channelrhodopsin GtACR1.

Schleissner, Pamela / Szundi, Istvan / Chen, Eefei / Li, Hai / Spudich, John L / Kliger, David S

2023 Volume 122, Issue 20, Page(s) 4091–4103

Abstract: The most effective tested optogenetic tools available for neuronal silencing are the light-gated anion channel proteins found in the cryptophyte alga Guillardia theta (GtACRs). Molecular mechanisms of GtACRs, including the photointermediates responsible ... ...

Abstract	The most effective tested optogenetic tools available for neuronal silencing are the light-gated anion channel proteins found in the cryptophyte alga Guillardia theta (GtACRs). Molecular mechanisms of GtACRs, including the photointermediates responsible for the open channel state, are of great interest for understanding their exceptional conductance. In this study, the photoreactions of GtACR1 and its D234N, A75E, and S97E mutants were investigated using multichannel time-resolved absorption spectroscopy. For each of the proteins, the analysis showed two early microsecond transitions between K-like and L-like forms and two late millisecond recovery steps. Spectral forms associated with potential molecular intermediates of the proteins were derived and their evolutions in time were analyzed. The results indicate the presence of isospectral intermediates in the photocycles and expand the range of potential intermediates responsible for the open channel state.
MeSH term(s)	Channelrhodopsins/metabolism ; Anions/metabolism ; Cryptophyta/metabolism ; Optogenetics/methods ; Light
Chemical Substances	Channelrhodopsins ; Anions
Language	English
Publishing date	2023-09-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2023.09.009
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Article ; Online: Pump-Probe Circular Dichroism Spectroscopy of Cyanobacteriochrome TePixJ Yields: Insights into Its Photoconversion.

Clinger, Jonathan A / Chen, Eefei / Kliger, David S / Phillips, George N

The journal of physical chemistry. B

2020 Volume 125, Issue 1, Page(s) 202–210

Abstract: The bilin-containing photoreceptor TePixJ, a member of the cyanobacteriochrome (CBCR) family of phytochromes, switches between blue-light-absorbing and green-light-absorbing states in order to drive phototaxis ... ...

Abstract	The bilin-containing photoreceptor TePixJ, a member of the cyanobacteriochrome (CBCR) family of phytochromes, switches between blue-light-absorbing and green-light-absorbing states in order to drive phototaxis in
MeSH term(s)	Bacterial Proteins ; Circular Dichroism ; Cyanobacteria ; Light ; Photoreceptors, Microbial ; Phytochrome
Chemical Substances	Bacterial Proteins ; Photoreceptors, Microbial ; Phytochrome (11121-56-5)
Language	English
Publishing date	2020-12-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.0c04822
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Article ; Online: Time-Resolved Linear Dichroism Measurements of Carbonmonoxy Myoglobin as a Probe of the Microviscosity in Crowded Environments.

Chen, Eefei / Kliger, David S

The journal of physical chemistry. B

2017 Volume 121, Issue 29, Page(s) 7064–7074

Abstract: The distribution of viscosities in living cells is heterogeneous because of the different sizes and natures of macromolecular components. When thinking about protein folding/function processes in such an environment, the relevant (micro)viscosity at the ... ...

Abstract	The distribution of viscosities in living cells is heterogeneous because of the different sizes and natures of macromolecular components. When thinking about protein folding/function processes in such an environment, the relevant (micro)viscosity at the micrometer length scale is necessarily distinguished from the bulk (macro)viscosity. The concentration dependencies of microviscosities are determined by a number of factors, such as electrostatic interactions, van der Waals forces, and excluded volume effects. To explore such factors, the rotational diffusion time of myoglobin in the presence of varying concentrations of macromolecules that differ in molecular weight (dextran 6000, 10 000, and 70 000), shape (dextran versus Ficoll), size, and surface charge is measured with time-resolved linear dichroism spectroscopy. The results of these studies offer simple empirically determined linear and exponential functions useful for predicting microviscosities as a function of concentration for these macromolecular crowders that are typically used to study crowding effects on protein folding. To understand how relevant these microviscosity measurements are to intracellular environments, the TRLD results are discussed in the context of studies that measure viscosity in cells.
MeSH term(s)	Circular Dichroism ; Molecular Weight ; Myoglobin/chemistry ; Particle Size ; Protein Folding ; Static Electricity ; Viscosity
Chemical Substances	Myoglobin
Language	English
Publishing date	2017-07-13
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.7b04107
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Article ; Online: Styrene-maleic acid copolymer effects on the function of the GPCR rhodopsin in lipid nanoparticles.

Szundi, Istvan / Pitch, Stephanie G / Chen, Eefei / Farrens, David L / Kliger, David S

Biophysical journal

2021 Volume 120, Issue 20, Page(s) 4337–4348

Abstract: Styrene-maleic acid (SMA) copolymers solubilize biological membranes to form lipid nanoparticles (SMALPs) that contain membrane proteins surrounded by native lipids, thus enabling the use of a variety of biophysical techniques for structural and ... ...

Abstract	Styrene-maleic acid (SMA) copolymers solubilize biological membranes to form lipid nanoparticles (SMALPs) that contain membrane proteins surrounded by native lipids, thus enabling the use of a variety of biophysical techniques for structural and functional studies. The question of whether SMALPs provide a truly natural environment or SMA solubilization affects the functional properties of membrane proteins, however, remains open. We address this question by comparing the photoactivation kinetics of rhodopsin, a G-protein-coupled receptor in the disk membranes of rod cells, in native membrane and SMALPs prepared at different molar ratios between SMA(3:1) and rhodopsin. Time-resolved absorption spectroscopy combined with complex kinetic analysis reveals kinetic and mechanistic differences between the native membrane and SMA-stabilized environment. The results suggest a range of molar ratios for nanoparticles suitable for kinetic studies.
MeSH term(s)	Kinetics ; Lipid Bilayers ; Lipids ; Maleates ; Nanoparticles ; Polystyrenes ; Rhodopsin
Chemical Substances	Lipid Bilayers ; Lipids ; Maleates ; Polystyrenes ; Rhodopsin (9009-81-8) ; maleic acid (91XW058U2C)
Language	English
Publishing date	2021-09-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2021.09.012
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Article: Time-Resolved Linear Dichroism Measurements of Carbonmonoxy Myoglobin as a Probe of the Microviscosity in Crowded Environments

Chen, Eefei / Kliger David S

Journal of physical chemistry. 2017 July 27, v. 121, no. 29

2017

Abstract	The distribution of viscosities in living cells is heterogeneous because of the different sizes and natures of macromolecular components. When thinking about protein folding/function processes in such an environment, the relevant (micro)viscosity at the micrometer length scale is necessarily distinguished from the bulk (macro)viscosity. The concentration dependencies of microviscosities are determined by a number of factors, such as electrostatic interactions, van der Waals forces, and excluded volume effects. To explore such factors, the rotational diffusion time of myoglobin in the presence of varying concentrations of macromolecules that differ in molecular weight (dextran 6000, 10â¯000, and 70â¯000), shape (dextran versus Ficoll), size, and surface charge is measured with time-resolved linear dichroism spectroscopy. The results of these studies offer simple empirically determined linear and exponential functions useful for predicting microviscosities as a function of concentration for these macromolecular crowders that are typically used to study crowding effects on protein folding. To understand how relevant these microviscosity measurements are to intracellular environments, the TRLD results are discussed in the context of studies that measure viscosity in cells.
Keywords	dextran ; ficoll ; molecular weight ; myoglobin ; prediction ; protein folding ; spectroscopy ; van der Waals forces ; viscosity
Language	English
Dates of publication	2017-0727
Size	p. 7064-7074.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021%2Facs.jpcb.7b04107
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Functional integrity of membrane protein rhodopsin solubilized by styrene-maleic acid copolymer.

Pitch, Stephanie G / Yao, Weekie / Szundi, Istvan / Fay, Jonathan / Chen, Eefei / Shumate, Anthony / Kliger, David S / Farrens, David L

Biophysical journal

2021 Volume 120, Issue 16, Page(s) 3508–3515

Abstract: Membrane proteins often require solubilization to study their structure or define the mechanisms underlying their function. In this study, the functional properties of the membrane protein rhodopsin in its native lipid environment were investigated after ...

Abstract	Membrane proteins often require solubilization to study their structure or define the mechanisms underlying their function. In this study, the functional properties of the membrane protein rhodopsin in its native lipid environment were investigated after being solubilized with styrene-maleic acid (SMA) copolymer. The static absorption spectra of rhodopsin before and after the addition of SMA were recorded at room temperature to quantify the amount of membrane protein solubilized. The samples were then photobleached to analyze the functionality of rhodopsin upon solubilization. Samples with low or high SMA/rhodopsin ratios were compared to find a threshold in which the maximal amount of active rhodopsin was solubilized from membrane suspensions. Interestingly, whereas the highest SMA/rhodopsin ratios yielded the most solubilized rhodopsin, the rhodopsin produced under these conditions could not reach the active (Meta II) state upon photoactivation. The results confirm that SMA is a useful tool for membrane protein research, but SMA added in excess can interfere with the dynamics of protein activation.
MeSH term(s)	Lipids ; Maleates ; Membrane Proteins ; Rhodopsin
Chemical Substances	Lipids ; Maleates ; Membrane Proteins ; Rhodopsin (9009-81-8) ; maleic acid (91XW058U2C)
Language	English
Publishing date	2021-05-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2021.05.008
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Article ; Online: First Synthesis of Mn-Doped Cesium Lead Bromide Perovskite Magic Sized Clusters at Room Temperature.

Xu, Ke / Vickers, Evan T / Luo, Binbin / Allen, A'Lester C / Chen, Eefei / Roseman, Graham / Wang, Qihui / Kliger, David S / Millhauser, Glenn L / Yang, Wenjing / Li, Xueming / Zhang, Jin Zhong

The journal of physical chemistry letters

2020 Volume 11, Issue 3, Page(s) 1162–1169

Abstract: ... Mn-doped ... ...

Abstract	Mn-doped CsPbBr
Language	English
Publishing date	2020-01-28
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.9b03700
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Article ; Online: Deconstructing time-resolved optical rotatory dispersion kinetic measurements of cytochrome c folding: from molten globule to the native state.

Chen, Eefei / Kliger, David S

Methods in molecular biology (Clifton, N.J.)

2012 Volume 895, Page(s) 405–419

Abstract: The far-UV time-resolved optical rotatory dispersion (TRORD) technique has contributed significantly to our understanding of nanosecond secondary structure kinetics in protein folding and function reactions. For reduced cytochrome c, protein folding ... ...

Abstract	The far-UV time-resolved optical rotatory dispersion (TRORD) technique has contributed significantly to our understanding of nanosecond secondary structure kinetics in protein folding and function reactions. For reduced cytochrome c, protein folding kinetics have been probed largely from the unfolded to the native state. Here we provide details about sample preparation and the TRORD apparatus and measurements for studying folding from a partly unfolded state to the native secondary structure conformation of reduced cytochrome c.
MeSH term(s)	Circular Dichroism ; Cytochromes c/chemistry ; Kinetics ; Phase Transition ; Protein Denaturation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sodium Dodecyl Sulfate/chemistry ; Surface-Active Agents/chemistry ; Titrimetry
Chemical Substances	Surface-Active Agents ; Sodium Dodecyl Sulfate (368GB5141J) ; Cytochromes c (9007-43-6)
Language	English
Publishing date	2012
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-61779-927-3_23
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Article ; Online: Microviscosity in E. coli Cells from Time-Resolved Linear Dichroism Measurements.

Chen, Eefei / Esquerra, Raymond M / Meléndez, Philipp A / Chandrasekaran, Sita S / Kliger, David S

The journal of physical chemistry. B

2018 Volume 122, Issue 49, Page(s) 11381–11389

Abstract: A protein's folding or function depends on its mobility through the viscous environment that is defined by the presence of macromolecules throughout the cell. The relevant parameter for this mobility is microviscosity-the viscosity on a time and distance ...

Abstract	A protein's folding or function depends on its mobility through the viscous environment that is defined by the presence of macromolecules throughout the cell. The relevant parameter for this mobility is microviscosity-the viscosity on a time and distance scale that is important for protein folding/function movements. A quasi-null, ultrasensitive time-resolved linear dichroism (TRLD) spectroscopy is proving to be a useful tool for measurements of viscosity on this scale, with previous in vitro studies reporting on the microviscosities of crowded environments mimicked by high concentrations of different macromolecules. This study reports the microviscosity experienced by myoglobin in the E. coli cell's heterogeneous cytoplasm by using TRLD to measure rotational diffusion times. The results show that photolyzed deoxyMb ensembles randomize through environment-dependent rotational diffusion with a lifetime of 34 ± 6 ns. This value corresponds to a microviscosity of 2.82 ± 0.42 cP, which is consistent with previous reports of cytoplasmic viscosity in E. coli. The results of these TRLD studies in E. coli (1) provide a measurement of myoglobin mobility in the cytoplasm, (2) taken together with in vitro TRLD studies yield new insights into the nature of the cytoplasmic environment in cells, and (3) demonstrate the feasibility of TRLD as a probe of intracellular viscosity.
MeSH term(s)	Circular Dichroism ; Cytoplasm/chemistry ; Diffusion ; Escherichia coli/chemistry ; Escherichia coli/cytology ; Myoglobin/chemistry ; Time Factors ; Viscosity
Chemical Substances	Myoglobin
Language	English
Publishing date	2018-08-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.8b07362
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Article ; Online: Venus

Kim, Youngchan / Puhl, Henry L / Chen, Eefei / Taumoefolau, Grace H / Nguyen, Tuan A / Kliger, David S / Blank, Paul S / Vogel, Steven S

Biophysical journal

2019 Volume 116, Issue 10, Page(s) 1918–1930

Abstract: Fluorescent proteins (FPs) have revolutionized cell biology by allowing genetic tagging of specific proteins inside living cells. In conjunction with Förster's resonance energy transfer (FRET) measurements, FP-tagged proteins can be used to study protein- ...

Abstract	Fluorescent proteins (FPs) have revolutionized cell biology by allowing genetic tagging of specific proteins inside living cells. In conjunction with Förster's resonance energy transfer (FRET) measurements, FP-tagged proteins can be used to study protein-protein interactions and estimate distances between tagged proteins. FRET is mediated by weak Coulombic dipole-dipole coupling of donor and acceptor fluorophores that behave independently, with energy hopping discretely and incoherently between fluorophores. Stronger dipole-dipole coupling can mediate excitonic coupling in which excitation energy is distributed near instantaneously between coherently interacting excited states that behave as a single quantum entity. The interpretation of FP energy transfer measurements to estimate separation often assumes that donors and acceptors are very weakly coupled and therefore use a FRET mechanism. This assumption is considered reasonable as close fluorophore proximity, typically associated with strong excitonic coupling, is limited by the FP β-barrel structure. Furthermore, physiological temperatures promote rapid vibrational dephasing associated with a rapid decoherence of fluorophore-excited states. Recently, FP dephasing times that are 50 times slower than traditional organic fluorophores have been measured, raising the possibility that evolution has shaped FPs to allow stronger than expected coupling under physiological conditions. In this study, we test if excitonic coupling between FPs is possible at physiological temperatures. FRET and excitonic coupling can be distinguished by monitoring spectral changes associated with fluorophore dimerization. The weak coupling mediating FRET should not cause a change in fluorophore absorption, whereas strong excitonic coupling causes Davydov splitting. Circular dichroism spectroscopy revealed Davydov splitting when the yellow FP Venus
MeSH term(s)	HEK293 Cells ; Humans ; Luminescent Proteins/chemistry ; Models, Molecular ; Protein Multimerization ; Protein Structure, Quaternary ; Temperature
Chemical Substances	Luminescent Proteins
Language	English
Publishing date	2019-04-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2019.04.014
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