Dmitri Toptygin - Academia.edu (original) (raw)

Papers by Dmitri Toptygin

Broadband lasers simultaneously generating a large number of longitudinal cavity modes are extrem... more Broadband lasers simultaneously generating a large number of longitudinal cavity modes are extremely sensitive to frequency-selective absorption by the media in the laser cavity. The spectroscopic technique based on this phenomenon is known as intracavity laser spectroscopy. The technique is capable of detecting absorption coefficients in the range of 10-10 cm-1. The sensitivity limit has been shown to result from

Radiative decay rate depends on the efficiency of coupling between the emission dipole and the el... more Radiative decay rate depends on the efficiency of coupling between the emission dipole and the electromagnetic field. Therefore, in optically discontinuous and/or anisotropic environments the radiative rate is dependent on the orientation of the emission dipole. Single-bilayer phospholipid membranes are interesting systems for the study of this phenomenon because in these systems the functional dependence of the radiative rate is

The journal of physical chemistry. B, 2015

Intrinsically disordered protein regions and many other biopolymers lack the three-dimensional st... more Intrinsically disordered protein regions and many other biopolymers lack the three-dimensional structure that could be determined by X-ray crystallography or NMR, which encourages the application of alternative experimental methods. Time-resolved resonance energy transfer data are often used to measure distances between two fluorophores attached to a flexible biopolymer. This is complicated by the rotational and translational diffusion of the fluorophores and by nonmonoexponential donor decay in the absence of the acceptor. Equation IDA(t) = ID(t)·F(t) is derived here, which is applicable regardless of whether ID(t) is monoexponential. ID(t) and IDA(t) are the δ-excitation donor emission decays in the absence and in the presence of the acceptor; F(t) contains information about energy transfer, donor-acceptor distance distribution, and diffusion dynamics. It is shown that in the absence of rotational and translational diffusion, F(t) is a continuous distribution of exponentials, wher...

IEEE Symposium Conference Record Nuclear Science 2004., 2004

The MiniBooNE neutrino detector at Fermilab (FNAL) is filled with 250,000 gallons of pure mineral... more The MiniBooNE neutrino detector at Fermilab (FNAL) is filled with 250,000 gallons of pure mineral oil. The principal signal for MiniBooNE is light observed in a prompt Cherenkov cone. Scattering and fluorescence modify our detection of this light. Scintillation is also created by ionization in the oil. Studies of fluorescence of this oil have been carried out over a wide spectrum of exciting light and time resolved fluorescence with a narrower range of excitation. Polarized scattering measurements have been carried out at longer wavelengths. Time resolved and spectrally resolved scintillation has been studied with a 200 MeV Proton beam at the Indiana University Cyclotron Facility. Results of these studies will be reported.

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Methods in Enzymology, 1997

The Journal of Physical Chemistry B, 2006

The B1 domain of Streptococcal protein G (GB1) is a small, thermostable protein containing a sing... more The B1 domain of Streptococcal protein G (GB1) is a small, thermostable protein containing a single tryptophan residue. We recorded time-resolved fluorescence of the wild-type GB1 and its 5-fluorotryptophan (5FTrp) variant at more than 30 emission wavelengths between 300 and 470 nm. The time-resolved emission spectra reveal no signs of heterogeneity, but show a time-dependent red shift characteristic of microscopic dielectric relaxation. This is true for both 5FTrp and unmodified Trp in GB1. The time-dependent red shifts in the fluorescence of 5FTrp and unmodified Trp are essentially identical, confirming that the shift is caused by the relaxation of the protein matrix rather than by the fluorophore itself. The total amplitude (but not the rate) of the time-dependent red shift depends on the fluorophore, specifically, on the magnitude of the vector difference between its excited state and ground state electric dipole moments; for 5FTrp this is estimated to be about 88% of that for the unmodified Trp. The decay of the excited state fluorophore population is not monoexponential for either fluorophore; however, the deviation from the monoexponential decay law is larger in the case of unmodified Trp. The relaxation dynamics of GB1 was found to be considerably faster than that of other proteins studied previously, consistent with the small size, tightly packed core, and high thermodynamic stability of GB1.

$Research paper thumbnail of Effect of the Solvent Refractive Index on the Excited-State Lifetime of a Single Tryptophan Residue in a Protein$

The Journal of Physical Chemistry B, 2002

ABSTRACT Excited-state lifetime and quantum yield of a fluorophore are determined by the radiativ... more ABSTRACT Excited-state lifetime and quantum yield of a fluorophore are determined by the radiative and nonradiative decay rates. There is an extensive literature about factors affecting the nonradiative decay rate. In this paper we demonstrate that the radiative decay rate for a tryptophan residue in a protein depends on the refractive index of the solvent, whether the residue is solvent-exposed or buried. We describe the theory of the refractive index effect and show that the theoretical prediction agrees with experimental data. The radiative decay rate for an electric dipole emitter embedded in a small dielectric ellipsoid of a refractive index n1 varies with the refractive index n0 of the surrounding dielectric fluid according to the law kr = γν3fcfn05[n02 + (n12 − n02)LM]-2, where γ is a constant factor, LM is determined by the ellipsoid axis ratio and the transition moment orientation, ν3fcf = ∫Fλ(λ) dλ/∫λ3Fλ(λ) dλ, and Fλ(λ) represents the corrected emission spectrum. The radiative decay rate of the only tryptophan residue in the E21W mutant of the IIAGlc protein of the phosphotransferase system of Escherichia coli varies in accordance with this law. Whether the refractive index of water is adjusted by the addition of glycerol or sucrose, the ratios kr/ν3fcf graphed versus the solvent refractive index fall on the same curve, which confirms that the effect is due to the refractive index rather than a specific chemical interaction. The emission spectrum and ν3fcf of a tryptophan residue may be sensitive to solvent polarity; therefore the radiative decay rate may be sensitive to both solvent polarity and refractive index, whereas the ratio kr/ν3fcf is sensitive to the refractive index only.

The Journal of Physical Chemistry B, 2001

... if the difference is preserved for the duration that equals or exceeds experimental time reso... more ... if the difference is preserved for the duration that equals or exceeds experimental time resolution (in time-resolved measurements) or ... 22 Several possible origins of heterogeneous fluorescence emission from tryptophan residues in proteins have been discussed in the literature. ...

The Journal of Physical Chemistry B, 1998

ABSTRACT In this study NorFES, an undecapeptide containing an amino acid sequence recognized by t... more ABSTRACT In this study NorFES, an undecapeptide containing an amino acid sequence recognized by the serine protease elastase, was covalently labeled with two xanthenes, one on each side of its cleavage site, to serve as a tool for examination of intramolecular resonance dipole−dipole interactions. To this end using all possible combinations from the group of xanthenes including fluorescein, tetramethylrhodamine, and rhodamine-X, three heterobichromophoric and three homobichromophoric NorFES derivatives were synthesized; their absorption and fluorescence spectra were measured both before and after cleavage by elastase. In the heterobichromophoric substrates the fluorescence of the fluorophore that would be the nominal donor in a Förster model system was quenched. Since the fluorescence intensity of the nominal acceptor in these substrates was also decreased, these data were not consistent with the Förster model. Rather, spectra for all six doubly labeled peptides could be explained by delocalization of excitation over each substrate's two fluorophores. Thus, by taking into account dipole−dipole interactions between two dyes placed in close proximity to each other, the spectral properties observed could not be ascribed to the monomeric components but were the unique optical signature of each ground-state dimer.

The Journal of Physical Chemistry B, 1997

... Dmitri D. Toptygin and Ludwig Brand*. Biology Department, Johns Hopkins University, 3400 Nort... more ... Dmitri D. Toptygin and Ludwig Brand*. Biology Department, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218. ... Tomomi Koshiyama, Naomi Kawaba, Tatsuo Hikage, Masanobu Shirai, Yuki Miura, Cheng-Yuan Huang, Koichiro Tanaka, Yoshihito ...

The Journal of Physical Chemistry B, 2010

How a biological system responds to a charge shift is a challenging question directly relevant to... more How a biological system responds to a charge shift is a challenging question directly relevant to biological function. Time-resolved fluorescence of a tryptophan residue reflects protein and solvent response to the difference in pi-electron density between the excited and the ground state. In this study we use molecular dynamics to calculate the time-dependent spectral shift (TDSS) in the fluorescence of Trp-43 in GB1 protein. A new computational method for separating solvent, protein, and fluorophore contributions to TDSS is applied to 100 nonequilibrium trajectories for GB1 in TIP3P water. The results support several nontrivial conclusions. Both longitudinal and transverse relaxation modes of bulk solvent contribute to the TDSS in proteins. All relaxation components slower than the transverse relaxation of bulk solvent have significant contributions from both protein and solvent, with a negative correlation between them. Five exponential terms in the TDSS of GB1 are well separated by their relaxation times. A 0.036 ps term is due to both solvent (60%) and protein (40%). Two exponential terms represent longitudinal (tau(L) approximately = 0.4 ps) and transverse (tau(D) approximately = 5.6 ps) relaxation modes of TIP3P water. A 131 ps term is attributable to a small change in the tertiary structure, with the alpha-helix moving 0.2 A away from the beta-strand containing Trp-43. A 2580 ps term is due to the change in the conformation of the Glu-42 side chain that brings its carboxyl group close to the positively charged end of the excited fluorophore. Interestingly, water cancels 60% of the TDSS resulting from this conformational change.

Proceedings of the National Academy of Sciences, 1996

Xanthene dyes are known to form dimers with spectral characteristics that have been interpreted i... more Xanthene dyes are known to form dimers with spectral characteristics that have been interpreted in terms of exciton theory. A unique aspect of H-type dimers is the fluorescence quenching that accompanies their formation. Using the principles of exciton theory as a guide, a series of protease substrates was synthesized with a xanthene dye on each side of the cleavage site. To bring the attached dyes into spatial proximity to form a dimer, the molecular design included structure determinant regions in the amino acid sequence. In addition, chromophores were chosen such that changes in absorption spectra indicative of exciton splitting were anticipated. Cleavage of the peptides by a protease resulted in disruption of the dimers and indeed significant absorption spectral changes were observed. Furthermore, substrate cleavage was accompanied by at least an order of magnitude increase in fluorescence intensity. This has allowed determination of intracellular elastase activity using a fluorescence microscope equipped with standard optics.

Journal of the American Chemical Society, 2009

The eye lens crystallin proteins are subject to UV irradiation throughout life, and the photochem... more The eye lens crystallin proteins are subject to UV irradiation throughout life, and the photochemistry of damage proceeds through the excited state; thus, their tryptophan (Trp) fluorescence lifetimes are physiologically important properties. The time resolved fluorescence spectra of single Trps in human γDand γS-crystallins have been measured with both an upconversion spectrophotofluorometer on the 300fs to 100ps time scale, and a time correlated single photon counting apparatus on the 100ps to 10ns time scale, respectively. Three Trps in each wild type protein were replaced by phenylalanine, leading to single-Trp mutants: W68-only and W156-only of HγD-and W72-only and W162-only of HγS-crystallin. These proteins exhibit similar ultrafast signatures: positive definite decay associated spectra (DAS) for 50 -65ps decay constants that indicate dominance of fast, heterogeneous quenching. The quenched population (judged by amplitude) of this DAS differs among mutants. Trps 68, 156 in human γDand Trp72 in human γS-crystallin are buried, but water can reach amide oxygen and ring HE1 atoms through narrow channels. QM-MM simulations of quenching by electron transfer predict heterogeneous decay times from 50-500 ps that agree with our experimental results. Further analysis of apparent radiative lifetimes allow us to deduce that substantial subpopulations of Trp are fully quenched in even faster (sub-300 fs) processes for several of the mutants. The quenching of Trp fluorescence of human γDand γS-crystallin may protect them from ambient light induced photo damage.

Journal of Fluorescence, 1995

This article reviews the determination of orientational order parameters in non-macroscopically o... more This article reviews the determination of orientational order parameters in non-macroscopically oriented membranes from the data obtained with the fluorescent probe all-trans-1,6-diphenyl-1,3,5-hexatriene (DPH). Special attention is paid to the effect of microheterogeneity in the probe environment on the recovered values of the order parameters. An effort is made to accommodate new findings in the existing picture of orientational order in membranes.

Journal of the American Chemical Society, 2006

The complete time-resolved fluorescence of tryptophan in the proteins monellin and IIA(Glc) has b... more The complete time-resolved fluorescence of tryptophan in the proteins monellin and IIA(Glc) has been investigated, using both an upconversion spectrophotofluorometer with 150 fs time resolution and a time-correlated single photon counting apparatus on the 100 ps to 20 ns time scale. In monellin, the fluorescence decay displays multiexponential character with decay times of 1.2 and 16 ps, and 0.6, 2.2, and 4.2 ns. In contrast, IIA(Glc) exhibited no component between 1.2 ps and 0.1 ns. For monellin, surprisingly, the 16 ps fluorescence component was found to have positive amplitude even at longer wavelengths (e.g., 400 nm). In conjunction with quantum mechanical simulation of tryptophan in monellin, the experimental decay associated spectra (DAS) and time-resolved emission spectra (TRES) indicate that this fluorescence decay time should be ascribed to a highly quenched conformer. Recent models (Peon, J.; et al. Proc. Natl.Acad. Sci. U.S.A. 2002, 99, 10964) invoked exchange-coupled rel...

Chemical Physics Letters, 2000

... and multiple states of lower energy. The energy of a state can be represented as a sum of ele... more ... and multiple states of lower energy. The energy of a state can be represented as a sum of electronic and vibrational energies: (1). Indexes n and m enumerateelectronic and vibrational states. The energy of the photon emitted ...

Chemical Physics Letters, 1997

There is striking dissimilarity among the absorption spectra of rhodamine dimers reported by diff... more There is striking dissimilarity among the absorption spectra of rhodamine dimers reported by different authors. To address this issue, we measured the absorption spectra of aqueous solutions of rhodamine 6G over a wide range of concentrations. The lack of an isosbestic point near 508 nm indicates the presence of at least three species. Data analysis using the program spectrabind described

Biophysical Journal, 2012

Biophysical Journal, 2011

decreases thinning out time, keeping thinning out time more consistent (~30min). Lipid solution w... more decreases thinning out time, keeping thinning out time more consistent (~30min). Lipid solution was deposited in a small aperture fabricated on a PDMS film and was frozen before use. Upon thawing a lipid bilayer is spontaneously reconstructed with the mean formation time of~30 min with high success rate (>80%). We also show potential applications with lipid bilayers created in a PDMS film due to its versatility 3292-Pos Board B397 Studying noise properties of ion currents in nanopores can improve detection limits for nanopore sensors as well as give insight into behavior of transport at the nanoscale. We focused on the 1/ftalpha noise that is observed in the low frequency regime of the ion current power spectra with the exponent al-pha~1. We found that 1/f noise in single conically shaped nanopores in polymer films and glass nanopipettes exhibits asymmetric noise properties with respect to voltage polarity which are not observed for cylindrical and silicon nitride nanopores. The noise asymmetry is shown by the normalized power spectra, which present the noise amplitude at a given frequency, typically 1 Hz for these measurements, divided by the ion current squared. The conically shaped structures rectify the ion current and the currents for the forward bias exhibit noise that increases with voltage in an exponential manner, and are weakly KCl concentration dependent. The normalized noise of currents in the reverse bias is typically voltage-independent but increases with the increase of KCl concentration. The difference in noise properties of the currents is most pronounced when the pore diameter is comparable to the thickness of the electrical double-layer. We discuss two models, which could explain the observed effects: (i) presence of air bubbles, and (ii) crowding of ions at the pore entrance. Fluorescence Spectroscopy III 3293-Pos Board B398 Tryptophan Fluorescence from G. Weber to the Present Ludwig Brand. Gregorio Weber (Symposium on Light and Life, W.D. McElroy and Glass, B.