Analysis of fluorescence quenching of ribosome-bound virginiamycin S.

Giambattista, M. Di; Ide, G; Engelborghs, Yves; Cocito, Carlo

doi:10.1016/s0021-9258(20)82145-0

Cited by 22 publications

(18 citation statements)

References 32 publications

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“…This implies the inaccessibility of a fraction of fluorophores to the quencher. Hence, a modified Stern–Volmer equation or, more generally, the Lehrer equation (eq ) was used as the sample contains more than one fluorophore with different accessibilities. − where F 0 and F are the fluorescence intensities without and with quencher, K SV is the Stern–Volmer constant, [Q] is the concentration of the quencher, and α is the fraction of accessible fluorophores. The Lehrer plot is shown in Figure , and the fraction of accessible fluorophores (α) was determined from the intercepts, as given in Table .…”

Section: Resultsmentioning

confidence: 99%

A Fluorescence Lifetime Imaging Microscopy Supported Investigation on Temperature-Dependent Penetration of Dopamine in a 1,2-Ditetradecanoyl-sn-glycero-3-phospho-(1′-rac-glycerol) Lipid Bilayer

Das

Purkayastha

2017

Langmuir

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Distribution of dopamine, an essential neurotransmitter in mammalian central and peripheral nervous systems, in a lipid bilayer and at the surface of 1,2-ditetradecanoyl-sn-glycero-3-phospho-(1'-rac-glycerol) vesicles has been studied herein. To track the progress of dopamine through different regions of the lipid vesicle, these were synthesized using 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD)-labeled phospholipid molecules tagged to either the headgroup (NBDPE) or the acyl chain (NBDPG). Dopamine-induced quenching of NBD fluorescence in the lipid vesicles demonstrates that dopamine has a preference to diffuse into the lipid bilayer. The change in the excited state lifetime obtained for NBDPG clearly indicates the preference in dopamine binding. The propositions were supported by fluorescence lifetime imaging microscopy.

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Section: Resultsmentioning

confidence: 99%

A Fluorescence Lifetime Imaging Microscopy Supported Investigation on Temperature-Dependent Penetration of Dopamine in a 1,2-Ditetradecanoyl-sn-glycero-3-phospho-(1′-rac-glycerol) Lipid Bilayer

Das

Purkayastha

2017

Langmuir

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“…The intrinsic fluorescence of tryptophan is sensitive to changes in the polarity of the medium and therefore can provide useful information on the tertiary structure of proteins (Di Giambattista et al 1984). Therefore, monitoring the microenvironment of tryptophan residues can facilitates the understanding of subtle conformational changes in proteins.…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, monitoring the microenvironment of tryptophan residues can facilitates the understanding of subtle conformational changes in proteins. The accessibility of tryptophan moieties within a protein can be monitored through fluorescence quenching (Di Giambattista et al 1984, Samworth et al 1988, Jamir and Seshagirirao 2018, Papadopoulou et al 2005). Acrylamide and succinimide are both neutral quenchers and can potentially quench tryptophan residues located in different microenvironments.…”

Section: Resultsmentioning

confidence: 99%

“…However, as succinimide is a bulkier molecule, it cannot access the tryptophan residues located in the interior of proteins. Succinimide can only access the superficially and partially buried tryptophan residues (Di Giambattista et al 1984). Anionic (I -) and cationic (Cs + ) quenchers were also used to obtain information on the microenvironment of the tryptophan residues.…”

Section: Resultsmentioning

confidence: 99%

“…Anionic (I -) and cationic (Cs + ) quenchers were also used to obtain information on the microenvironment of the tryptophan residues. Quenching accessibility of ionic quenchers depends on the charged environment in the spatial vicinity of the tryptophan residues (Di Giambattista et al 1984). Fluorescence quenching parameters were obtained from Stern-Volmer and modified Stern-Volmer plots (Figure 7C-D).…”

Section: Resultsmentioning

confidence: 99%

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cpSRP43 is both highly flexible and stable: Structural insights using a combined experimental and computational approach

Benton

Furr

Kumar

et al. 2022

Preprint

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The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light-harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. Nuclear-encoded LHCPs are synthesized in the cytoplasm then imported into the chloroplast. Upon emergence into the stroma, LHCPs form a soluble transit complex with the cpSRP heterodimer, which is composed of cpSRP43 and cpSRP54, a 54 kDa subunit homologous to the universally conserved GTPase in cytosolic SRP pathways. cpSRP43 is irreplaceable as a chaperone to LHCPs in their translocation to the thylakoid membrane and remarkable in its ability to dissolve aggregates of LHCPs without the need for external energy input. In previous studies, cpSRP43 has demonstrated significant flexibility and interdomain dynamics. However, the high flexibility and structural dynamics of cpSRP43 is yet unexplained by current crystal structures of cpSRP43. This is due, in part, to the fact that free full length cpSRP43 is so flexible that it is unable to crystalize. In this study, we explore the structural stability of cpSRP43 under different conditions using various biophysical techniques and find that this protein is concurrently highly stable and flexible. This conclusion is interesting considering that stable proteins typically possess a non-dynamic structure. Molecular dynamics (MD) simulations which correlated with data from biophysical experimentation were used to explain the basis of the extraordinary stability of cpSRP43. This combination of biophysical data and microsecond-level MD simulations allows us to obtain a detailed perspective of the conformational landscape of these proteins.

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