Solvation Dynamics of a Protein in the Pre Molten Globule State

Samaddar, Soma; Mandal, Amit Kumar; Mondal, Sudip Kumar; Sahu, Kalyanasis; Bhattacharyya, Kankan; Roy, Siddhartha

doi:10.1021/jp064136g

Cited by 32 publications

(29 citation statements)

References 38 publications

(67 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…23 Samaddar et al studied solvation dynamics in the pre-molten globule state of GlnRS. 24 They observed that the solvation time is of the order, native > molten globule > premolten globule.…”

Section: Solvation Dynamics In Proteins and Dnamentioning

confidence: 99%

Ultrafast Dynamics in Biological Systems and in Nano-Confined Environments

Sahu

Mondal

Ghosh

et al. 2007

Bulletin of the Chemical Society of Japan

Self Cite

View full text Add to dashboard Cite

Ultrafast chemical dynamics in a nano-confined system is very different from that in a bulk liquid. In this account, we give an overview on recent femtosecond study on dynamics of ultrafast chemical processes in the nanocavity of a biological system. Dynamics in a biological system crucially depends on the location of the fluorescent probe. We show that one can study solvation dynamics in different regions (i.e. spatially resolve) by variation of the excitation wavelength. We discuss two interesting cases of how structure affects dynamics. First, solvation dynamics of two protein folding intermediates of cytochrome c is found to be differ significantly in the ultrafast initial part (<20 ps). Second, methyl substitution of the OH group in a cyclodextrin is shown to slow down the initial part of solvation dynamics quite dramatically. The most interesting observation is the discovery of the ultraslow component of solvation dynamics which is 100-1000 times slower compared to bulk water. The electron-and proton-transfer processes in a nano-confined system are found to be markedly retarded because of slow solvation and structural constraints. Close proximity of the reactants in a confined system is expected to accelerate dynamics of bi-molecular processes. This is illustrated by ultrafast fluorescence resonance energy transfer (FRET) in %1 ps time scale between a donor and an acceptor in a micelle. Finally, it is demonstrated that the decay of fluorescence anisotropy provides structural information (e.g. size of a cyclodextrin inclusion complex) and may be used to detect formation of a nano-aggregate.

show abstract

Section: Solvation Dynamics In Proteins and Dnamentioning

confidence: 99%

Ultrafast Dynamics in Biological Systems and in Nano-Confined Environments

Sahu

Mondal

Ghosh

et al. 2007

Bulletin of the Chemical Society of Japan

Self Cite

View full text Add to dashboard Cite

show abstract

“…1,2,17−19 These photophysics are strongly medium-dependent, presumably due to the molecular dipole moment increasing upon excitation and specific solvation, including hydrogen bonding. 2,19 The dyes are frequently used as probes of polarity and dynamics of the local environment in proteins 1,20,21 as well as micelles and membranes, 1,2,17,18 by measuring stationary and time-resolved fluorescence spectra. 1 The environmental dependence of Badan fluorescence lifetimes was employed, for example, in a glucose sensor.…”

Section: Introductionmentioning

confidence: 99%

Fluorescence Quenching of (Dimethylamino)naphthalene Dyes Badan and Prodan by Tryptophan in Cytochromes P450 and Micelles

et al. 2014

View full text Add to dashboard Cite

Fluorescence of 2-(N,N-dimethylamino)-6-propionylnaphthalene dyes Badan and Prodan is quenched by tryptophan in Brij 58 micelles as well as in two cytochrome P450 proteins (CYP102, CYP119) with Badan covalently attached to a cysteine residue. Formation of nonemissive complexes between a dye molecule and tryptophan accounts for about 76% of the fluorescence intensity quenching in micelles, the rest is due to diffusive encounters. In the absence of tryptophan, fluorescence of Badan-labeled cytochromes decays with triexponential kinetics characterized by lifetimes of about 100 ps, 700–800 ps, and 3 ns. Site mutation of a histidine residue in the vicinity of the Badan label by tryptophan results in shortening of all three decay lifetimes. The relative amplitude of the fastest component increases at the expense of the two slower ones. The average quenching rate constants are 4.5 × 108 s–1 (CYP102) and 3.7 × 108 s–1 (CYP119), at 288 K. Cyclic voltammetry of Prodan in MeCN shows a reversible reduction peak at −1.85 V vs NHE that becomes chemically irreversible and shifts positively upon addition of water. A quasireversible reduction at −0.88 V was observed in an aqueous buffer (pH 7.3). The excited-state reduction potential of Prodan (and Badan) is estimated to vary from about +0.6 V (vs NHE) in polar aprotic media (MeCN) to approximately +1.6 V in water. Tryptophan quenching of Badan/Prodan fluorescence in CYPs and Brij 58 micelles is exergonic by ≤0.5 V and involves tryptophan oxidation by excited Badan/Prodan, coupled with a fast reaction between the reduced dye and water. Photoreduction is a new quenching mechanism for 2-(N,N-dimethylamino)-6-propionylnaphthalene dyes that are often used as solvatochromic polarity probes, FRET donors and acceptors, as well as reporters of solvation dynamics.

show abstract

“…In view of the fundamental relationship between protein solvation and dynamics, it is important to understand the dynamical and energetic changes in the protein solvating layer that accompany the folding or unfolding process (38,39). Recent studies with fluorescent probes attached to the protein surfaces and dynamic lightscattering experiments have elucidated differences in solvation times between the fully denatured, ''premolten'' globule, molten globule, and native states (3,4). Molecular dynamics simulations have been used to point out clear differences in the secondary structure dependence of solvation dynamics between the native and a hypothetical molten globule state of the protein HP-36 (46).…”

Section: Introductionmentioning

confidence: 99%

Hydration Dynamics in a Partially Denatured Ensemble of the Globular Protein Human α-Lactalbumin Investigated with Molecular Dynamics Simulations

Sengupta

Jaud

Tobias

2008

Biophysical Journal

View full text Add to dashboard Cite

Atomistic molecular dynamics simulations are used to probe changes in the nature and subnanosecond dynamical behavior of solvation waters that accompany partial denaturation of the globular protein, human alpha-lactalbumin. A simulated ensemble of subcompact conformers, similar to the molten globule state of human alpha-lactalbumin, demonstrates a marginal increase in the amount of surface solvation relative to the native state. This increase is accompanied by subtle but distinct enhancement in surface water dynamics, less favorable protein-water interactions, and a marginal decrease in the anomalous behavior of solvation water dynamics. The extent of solvent influx is not proportional to the increased surface area, and the partially denatured conformers are less uniformly solvated compared to their native counterpart. The observed solvation in partially denatured conformers is lesser in extent compared to earlier experimental estimates in molten globule states, and is consistent with more recent descriptions based on nuclear magnetic relaxation dispersion studies.

show abstract

Solvation Dynamics of a Protein in the Pre Molten Globule State

Cited by 32 publications

References 38 publications

Ultrafast Dynamics in Biological Systems and in Nano-Confined Environments

Ultrafast Dynamics in Biological Systems and in Nano-Confined Environments

Fluorescence Quenching of (Dimethylamino)naphthalene Dyes Badan and Prodan by Tryptophan in Cytochromes P450 and Micelles

Hydration Dynamics in a Partially Denatured Ensemble of the Globular Protein Human α-Lactalbumin Investigated with Molecular Dynamics Simulations

Contact Info

Product

Resources

About