David Talaga was born in Des Moines, Iowa. He grew up in Iowa, Illinois, New York, Michigan, and California, attending some eleven different schools for his primary education. In spite of a disjointed education, he developed an early love for science and etymology and read reference books for fun. David attended Damien High School in La Verne, California which is a Catholic Boys High School run by priests of the Congregation of the Sacred Hearts of Jesus and Mary. While there he was active in Model United Nations and proved himself a mediocre athlete in five different sports. His fascination with science continued, but he also became interested in education through his experiences tutoring math and science. He picked up computer programming first as a hobby and then through coursework. Shortly before he graduated in 1987 he won the Science Gold Medal in the regional Academic Olympiad and the Damien AP Physics Award.
David received his undergraduate degree in chemistry and mathematics from Occidental College and supplemented his interests with graduate courses from Caltech. He started working in the laboratory of Prof. Craney as a freshman, and continued there until his graduation in 1991. In the Craney lab, David studied the human erythrocyte protein glucose 6-phosphate dehydrogenase. This included isolation and purification of the enzyme from gallons of past-code human blood cells, performing inhibition kinetics studies and 31P NMR substrate binding studies. While at Occidental he served as vice president of the local chapter of the Alpha Chi Sigma chemistry fraternity. He worked at the Learning Resource Center as a Peer Advisor in General, Analytcal, and Physical Chemistry, and served as a Teaching Assistant for General Chemistry and Analytical Chemistry. He also served as a representative in student government. These experiences cemented his interest in research and teaching in physical chemistry.
David Talaga was seduced away from biochemistry by the beautiful symmetry of inorganic and organometallic molecules and joined the laboratory of Jeff Zink at UCLA to study for his PhD. At UCLA David studied high-resolution gas phase spectroscopy of inorganic complexes and chemical vapor deposition precursors. He also developed time-dependent quantum theoretical approaches to vibronic coupling effects on electronic and vibrational spectroscopy and filed his dissertation in the fall of 1996. In late 1996, David Talaga was awarded a NIH NRSA postdoctoral fellowship to train under Robin Hochstrasser at the University of Pennsylvania. At Penn, David returned to biophysical problems and worked on picosecond temperature jump methods for initiation of conformational changes and protein unfolding monitored using infrared spectroscopy. He also worked on single molecule FRET approaches to protein folding.
In 2000 David Talaga joined the faculty at Rutgers New Brunswick, where he is currently an Associate Professor of Chemistry and Chemical Biology. His research has focussed on amyloidogenesis, single molecule experiments and theory, and protein folding. He has recently been working on incorporating nanopore approaches to single protein folding, aggregation, and assembly.
Abstract: We combine atomic-force-microscopy particle-size-distribution measurements with earlier measurements on 1-anilino-8-naphthalene sulfonate, thioflavin T, and dynamic light scattering to develop a quantitative kinetic model for the aggregation of beta-lactoglobulin into amyloid. We directly compare our simulations to the population distributions provided by dynamic light scattering and atomic force microscopy. We combine species in the simulation according to structural type for comparison with fluorescence fingerprint results. The kinetic model of amyloidogenesis leads to an aggregation free-energy landscape. We define the roles of and propose a classification scheme for different oligomeric species based on their location in the aggregation free-energy landscape. We relate the different types of oligomers to the amyloid cascade hypothesis and the toxic oligomer hypothesis for amyloid-related diseases. We discuss existing kinetic mechanisms in terms of the different types of oligomers. We provide a possible resolution to the toxic oligomer-amyloid coincidence.
Abstract: Time-correlated single photon counting allows luminescence lifetime information to be determined on a single molecule level. This paper develops a formalism to allow information theory analysis of the ability of luminescence lifetime measurements to resolve states in a single molecule. It analyzes the information content of the photon stream and the fraction of that information that is relevant to the state determination problem. Experimental losses of information due to instrument response, digitization, and different types of background are calculated and a procedure to determine the optimal value of experimental parameters is demonstrated. This paper shows how to use the information theoretical formalism to evaluate the number of photons required to distinguish dyes that differ only by lifetime. It extends this idea to include distinguishing molecular states that differ in the electron transfer quenching or resonant energy transfer and shows how the differences between the lifetime of signal and background can help distinguish the dye position in an excitation beam.
Abstract: We use single silicon nitride nanopores to study folded, partially folded, and unfolded single proteins by measuring their excluded volumes. The DNA-calibrated translocation signals of beta-lactoglobulin and histidine-containing phosphocarrier protein match quantitatively with that predicted by a simple sum of the partial volumes of the amino acids in the polypeptide segment inside the pore when translocation stalls due to the primary charge sequence. Our analysis suggests that the majority of the protein molecules were linear or looped during translocation and that the electrical forces present under physiologically relevant potentials can unfold proteins. Our results show that the nanopore translocation signals are sensitive enough to distinguish the folding state of a protein and distinguish between proteins based on the excluded volume of a local segment of the polypeptide chain that transiently stalls in the nanopore due to the primary sequence of charges.
Abstract: We introduce a new approach to global data fitting based on a regularization condition that invokes continuity in the global data coordinate. Stabilization of the data fitting procedure comes from probabilistic constraint of the global solution to physically reasonable behavior rather than to specific models of the system behavior. This method is applicable to the fitting of many types of spectroscopic data including dynamic light scattering, time-correlated single-photon counting (TCSPC), and circular dichroism. We compare our method to traditional approaches to fitting an inverse Laplace transform by examining the evolution of multiple lifetime components in synthetic TCSPC data. The global regularizer recovers features in the data that are not apparent from traditional fitting. We show how our approach allows one to start from an essentially model-free fit and progress to a specific model by moving from probabilistic to deterministic constraints in both Laplace transformed and nontransformed coordinates.
Abstract: We have investigated the aggregation and amyloid fibril formation of bovine beta-lactoglobulin variant A, with a focus on the early stages of aggregation. We used noncovalent labeling with thioflavin T and 1-anilino-8-naphthalenesulfonate to follow the conformational changes occurring in beta-lactoglobulin during aggregation using time resolved luminescence. 1-Anilino-8-naphthalenesulfonate monitored the involvement of the hydrophobic core/calyx of beta-lactoglobulin in the aggregation process. Thioflavin T luminescence monitored the formation of amyloid. The luminescence lifetime distributions of both probes showed changes that could be attributed to conformational changes occurring during and following aggregation. To correlate the luminescence measurements with the degree of aggregation and the morphology of the aggregates, we also measured dynamic light scattering and atomic force microscopy images. We evaluated the relative stability of the intermediates with an assay that is sensitive to aggregation reversibility. Our results suggest that initial aggregation during the first 5 days occurred with partial disruption of the characteristic calyx in beta-lactoglobulin. As the globular aggregates grew from days 5 to 16, the calyx was completely disrupted and the globular aggregates became more stable. After this second phase of aggregation, conversion into a fibrillar form occurred, marking the growth phase, and still more changes in the luminescence signals were observed. Based on these observations, we propose a three-step process by which monomer is converted first into weakly associated aggregates, which rearrange into stable aggregates, which eventually convert into protofibrils that elongate in the growth phase.
Abstract: We use time-dependent fluorescence Stokes shift (TDFSS) information to study the fluctuation rates of the lipocalin, beta-lactoglobulin A in the vicinity of an encapsulated coumarin 153 molecule. The system has three unique dielectric environments in which the fluorophore binds. We develop a method to decompose the static and dynamic contributions to the spectral heterogeneity. This method is applied to temperature-dependent steady-state fluorescence spectra providing us with site-specific information about thermodynamic transitions in beta-lactoglobulin. We confirm previously reported transitions and discuss the presence of an unreported transition of the central calyx at 18 degrees C. Our method also resolves the contributions to the TDFSS from the coumarin 153 centrally located in the calyx of beta-lactoglobulin despite overlapping signals from solvent exposed dyes. Our experiments show dynamics ranging from 3-12,00 ps. The analysis shows a decrease in the encapsulated dye's heterogeneity during the relaxation, which is taken as evidence of the breakdown of linear response.
Abstract: Glucose/galactose binding protein (GGBP) functions in two different larger systems of proteins used by enteric bacteria for molecular recognition and signaling. Here we report on the thermodynamics of conformational equilibrium distributions of GGBP. Three fluorescence components appear at zero glucose concentration and systematically transition to three components at high glucose concentration. Fluorescence anisotropy correlations, fluorescent lifetimes, thermodynamics, computational structure minimization, and literature work were used to assign the three components as open, closed, and twisted conformations of the protein. The existence of three states at all glucose concentrations indicates that the protein continuously fluctuates about its conformational state space via thermally driven state transitions; glucose biases the populations by reorganizing the free energy profile. These results and their implications are discussed in terms of the two types of specific and nonspecific interactions GGBP has with cytoplasmic membrane proteins.
Abstract: This article examines the current status of Markov processes in single molecule fluorescence. For molecular dynamics to be described by a Markov process, the Markov process must include all states involved in the dynamics and the FPT distributions out of those states must be describable by a simple exponential law. The observation of non-exponential first-passage time distributions or other evidence of non-Markovian dynamics is common in single molecule studies and offers an opportunity to expand the Markov model to include new dynamics or states that improve understanding of the system.
Abstract: The interpretation of single-molecule measurements is greatly complicated by the presence of multiple fluorescent labels. However, many molecular systems of interest consist of multiple interacting components. We investigate this issue using multiply labeled dextran polymers that we intentionally photobleach to the background on a single-molecule basis. Hidden Markov models allow for unsupervised analysis of the data to determine the number of fluorescent subunits involved in the fluorescence intermittency of the 6-carboxy-tetramethylrhodamine labels by counting the discrete steps in fluorescence intensity. The Bayes information criterion allows us to distinguish between hidden Markov models that differ by the number of states, that is, the number of fluorescent molecules. We determine information-theoretical limits and show via Monte Carlo simulations that the hidden Markov model analysis approaches these theoretical limits. This technique has resolving power of one fluorescing unit up to as many as 30 fluorescent dyes with the appropriate choice of dye and adequate detection capability. We discuss the general utility of this method for determining aggregation-state distributions as could appear in many biologically important systems and its adaptability to general photometric experiments.
Abstract: We use Shannonâs definition of information to develop a theory to predict a photon-counting-based single-molecule experimentâs ability to measure the desired property. We treat three phenomena that are commonly measured on single molecules: spectral fluctuations of a solvatochromic dye; assignment of the azimuthal dipole angle; determination of a distance by fluorescence resonant energy transfer using Forsterâs theory. We consider the effect of background and other âimperfectionsâ on the measurement through the decrease in information.
Abstract: The interpretation of single-molecule measurements is greatly complicated by the presence of multiple fluorescent labels. However, many molecular systems of interest consist of multiple interacting components. We investigate this issue using multiply labeled dextran polymers that we intentionally photobleach to the background on a single-molecule basis. Hidden Markov models allow for unsupervised analysis of the data to determine the number of fluorescent subunits involved in the fluorescence intermittency of the 6-carboxy-tetramethylrhodamine labels by counting the discrete steps in fluorescence intensity. The Bayes information criterion allows us to distinguish between hidden Markov models that differ by the number of states, that is, the number of fluorescent molecules. We determine information-theoretical limits and show via Monte Carlo simulations that the hidden Markov model analysis approaches these theoretical limits. This technique has resolving power of one fluorescing unit up to as many as 30 fluorescent dyes with the appropriate choice of dye and adequate detection capability. We discuss the general utility of this method for determining aggregation-state distributions as could appear in many biologically important systems and its adaptability to general photometric experiments.
Abstract: We use Shannon's definition of information to develop a theory to predict a photon-counting-based single-molecule experiment's ability to measure the desired property. We treat three phenomena that are commonly measured on single molecules: spectral fluctuations of a solvatochromic dye; assignment of the azimuthal dipole angle; determination of a distance by fluorescence resonant energy transfer using Förster's theory. We consider the effect of background and other "imperfections" on the measurement through the decrease in information.
Abstract: The measurement of fluorescence from single protein molecules has become an important new tool in the study of dynamic processes, allowing for the direct visualization of the motions experienced by individual proteins and macromolecular complexes. The data from such single-molecule experiments are in the form of photon trajectories, consisting of arrival times and wavelength information on individual photons. The analysis of photon trajectories can be difficult, particularly if the motions are occurring at rates comparable to the photon arrival rate or in the presence of noise. In this paper, we introduce the use of hidden Markov models (HMMs) for the analysis of photon trajectory data that operate using the photon data directly, without the need for ensemble averaging of the data as implied by correlation function analysis. Using a simple kinetic model, we examine the relationship between the uncertainty in the estimates of the motional rate and the photon detection rate. Remarkably, we obtain relative uncertainties in the rate constants of as little as 3% even when the interconversion rate is equal to the photon detection rate, and the uncertainty increases to only 10% when the interconversion rate is 10 times the photon detection rate. This suggests that useful information can be obtained for much faster kinetic regimes than have typically been studied. We also examine the impact of background photons on the determination of the rate and demonstrate that the HMM-based approach is robust, displaying small uncertainties for background photon arrival rates approaching that of the signal. These results not only are relevant in establishing the theoretical limits on precision, but are also useful in the context of experimental design. Finally, to demonstrate how the methodology can be extended to more complex kinetic models and how it can allow one to make use of the full power of statistics for purposes of model evaluation and selection, we consider a four-state kinetic model for protein conformational transitions previously studied by Schenter et al. (J. Phys. Chem. A1999, 103, 10477). We show how an HMM can be used as an alternative to higher-order correlation function analysis for the detection of "conformational memory" and apparent non-Markovian dynamics arising from such temporally inhomogeneous kinetic schemes.
Abstract: Intervalence electron transfer spectra in mixed-valence molecules are frequently modeled by an interacting pair of adiabatic potential energy surfaces. The presence or absence of a double minimum in the lower surface is correlated with trapped or delocalized charges, respectively. The coordinate involved in this interpretation is the asymmetric normal coordinate representing the nuclear motions taking the molecule from one extreme to the other. In this paper, a model is developed involving both a symmetric and an asymmetric coordinate on an equal footing. The time dependent theory of electronic spectroscopy is used to calculate both absorption and resonance Raman spectra. The model uses physically meaningful interactions in the mixed-valence molecule including the electronic coupling, vibrational coupling, vibrational force constants, and bond length changes as a result of the electron transfer. The effect of these interactions on the relative intensities of symmetric and asymmetric modes in both the absorption and resonance Raman spectra are examined. The quantitative calculations are discussed in parallel with the physical meaning. The calculations show how the spectra can smoothly go from domination by one type of mode to the other. The most important effects are caused by the bond length changes, the electronic coupling, and the force constant changes.
Abstract: We report single-molecule measurements on the folding and unfolding conformational equilibrium distributions and dynamics of a disulfide crosslinked version of the two-stranded coiled coil from GCN4. The peptide has a fluorescent donor and acceptor at the N termini of its two chains and a Cys disulfide near its C terminus. Thus, folding brings the two N termini of the two chains close together, resulting in an enhancement of fluorescent resonant energy transfer. End-to-end distance distributions have thus been characterized under conditions where the peptide is nearly fully folded (0 M urea), unfolded (7.4 M urea), and in dynamic exchange between folded and unfolded states (3.0 M urea). The distributions have been compared for the peptide freely diffusing in solution and deposited onto aminopropyl silanized glass. As the urea concentration is increased, the mean end-to-end distance shifts to longer distances both in free solution and on the modified surface. The widths of these distributions indicate that the molecules are undergoing millisecond conformational fluctuations. Under all three conditions, these fluctuations gave nonexponential correlations on 1- to 100-ms time scale. A component of the correlation decay that was sensitive to the concentration of urea corresponded to that measured by bulk relaxation kinetics. The trajectories provided effective intramolecular diffusion coefficients as a function of the end-to-end distances for the folded and unfolded states. Single-molecule folding studies provide information concerning the distributions of conformational states in the folded, unfolded, and dynamically interconverting states.
Abstract: We have prepared a bichromophoric crosslinked variant of GCN4-P1 for single-molecule fluorescence energy transfer experiments (GCN4-Pf). The folding and unfolding fluctuations of single GCN4-Pf molecules are measured in a two-channel confocal microscope with which donor and acceptor fluorescence trajectories are measured simultaneously. The energy transfer efficiency is thereby determined and its probability distributions as a function of added denaturant [urea] are calculated The distributions indicate that single molecule GCN4-Pf is in dynamic folding equilibrium with the position of the equilibrium being altered by the concentration of urea. (C) 1999 Elsevier Science B.V. All rights reserved.
Abstract: The luminescence that is observed under gas phase photolytic deposition conditions is studied for Cr(hfac)(3), Ni(hfac)(2), and Pt(hfac)(2). This luminescence is analyzed under a variety of conditions, including the relatively high pressures of an evacuated gas cell and the collision-free conditions of a molecular beam. The effects of inert buffer gas are also studied. Features in these spectra indicate that, in general, multiple photolysis processes occur. Some simple fragments that are produced from these compounds are identified, including bare metal atoms (Ni, Cr), metal monofluorides (NiF, CrF), CH (in the case of Ni(hfac)(2)), and metal carbide from Pt(hfac)(2). It is postulated that the difference in the observed photofragmentation pathway in the case of platinum is due to sigma bonding to the beta carbon of the hfac moiety as opposed to the bidentate bonding of the other two metals. Possible mechanisms are presented. Detailed analysis of the spectra allows characterization of the internal energy of the platinum carbide photofragment.
Abstract: NiS and PdS thin films are prepared at 10(-2) Torr from the single-source precursors M(S2COCHMe2)(2), M = Ni and Pd. Two different vapor deposition processes, photochemical and thermal, are employed. Gas-phase emission spectroscopy is used during the photochemical deposition to identify the two elemental components of the final materials, the metal atom and sulfur, in the gas phase. NiS and PdS thin films are grown by the thermal process at 300 and 350 degrees C, respectively, on Si and quartz substrates. The NiS films are highly oriented rhombohedral (gamma) phase, and the PdS films are tetragonal-phase polycrystalline. The metal sulfide films are grown photolytically by 308 nn laser irradiation of the gas-phase precursors at lower temperatures (near the sublimation temperature). The NiS films show no X-ray diffraction patterns, but the PdS films are polycrystalline tetragonal phase. The films are analyzed by various surface analytical tools including scanning electron microscopy, X-ray photoelectron, and Rutherford backscattering techniques.
Abstract: ZnS thin films are made by laser driven chemical vapor deposition (CVD) from a single-source precursor, Zn(S(2)COCHMe(2))(2) under vacuum conditions. Photofragments in the gas phase are identified simultaneously by luminescence spectroscopy. The laser selectively activates the initial decomposition of the precursor and drives its conversion to the desired materials under mild conditions. These photolytically produced films are compared to films made by thermal deposition from the same precursor. The deposits from both techniques, characterized by X-ray diffraction, Rutherford backscattering, and X-ray photoelectron spectroscopy, are pure stoichiometric ZnS in the hexagonal phase. Surface morphology differs in shape and granule size. During the laser-driven CVD process, gas-phase photochemical intermediates are identified by luminescence spectroscopy. The luminescent photoproducts are Zn and S-2, the two elemental components of the final material. Photofragmentation mechanisms leading to ZnS, the luminescent species Zn and S-2, and the gaseous organic byproducts are discussed. Further characterization of the photofragmentation pathways is provided by the trapping of the photoreaction products and by mass spectroscopy.
Abstract: Gas phase 308 and 350-370 nm photolysis of bis(1,1,1,5,5,5-hexafluoro-2,4-pentanedionato)copper(II), Cu(hfac)(2), produces CuF as well as copper atoms and dimers. These metal-containing fragments, identified by luminescence spectroscopy, are studied under a variety of gas phase conditions ranging from 1 bar in a static chamber to 10(-4) mbar in a collision-free molecular beam. Copper atom and dimer luminescence is observed at the higher pressures, whereas at low pressures (total pressure no greater than the vapor pressure of the sample) exclusively CuF emission is observed. The a, A (omega = 0, 1, 2), B, and C excited states at 681.0, 567.6, and 505.1, and 491.7 nm are observed. The (3)Pi(0)(-) component of the A state is observed for the first time. The CuF luminescence obeys a quadratic power law with 308 nm excitation. The partitioning of excess energy into fragment degrees of freedom is determined from the intensities of the emission lines. The vibrational and rotational temperatures of the CuF fragment are in excess of 1700 K. Mechanisms of CuF formation, comparisons with the free ligand and with other volatile copper complexes, and the implications for laser-assisted chemical vapor deposition are discussed.
Abstract: Intervalence electron transfer spectra in mixed-valence molecules are frequently modeled by an interacting pair of adiabatic potential energy surfaces. The presence or absence of a double minimum in the lower surface is correlated with trapped or delocalized charges, respectively. In the time-dependent picture of the spectroscopy, calculations an conveniently carried out in a diabatic basis. The choice of a diabatic basis for a given adiabatic potential surface is not unique. The appropriateness of a given representation depends on the physical model that is chosen to represent the system. We present three diabatic models that give the same adiabatic potential surface. The first model represents charge transfer between two sites, the second represents a transition between bonding and antibonding molecular orbitals, and the third represents a nonbonding to nonbonding transition. Each of these models gives rise to a different calculated absorption spectrum even though they arise from the same adiabatic picture. A very important consideration after a modal is chosen is the selection of the transition dipole moment. We derive and discuss the symmetry of the transition dipole moment for each of the models for the different polarization directions of the incident light and show how the symmetry depends on the choice of the model. Surprisingly, the Condon approximation corresponds to different polarization directions in the different models. We derive the explicit relationships and interconnections between the three models and the adiabatic model.
Abstract: Intervalence absorption spectra are calculated and interpreted by using the time-dependent theory of spectroscopy and the Feit and Fleck method of numerically integrating the time-dependent Schrodinger equation. These methods give exact eigenvalues and eigenfunctions (within the constraints of the model and the numerical accuracy of the computer implementation). The results provide a new physical picture of the absorption spectrum and emphasize that Born-Oppenheimer separation of electronic and vibrational wave functions does not apply to the problem. The details of the calculation are discussed and interpreted. The exact calculation is compared to results obtained in the adiabatic limit. The effect of the temperature on intervalence absorption spectra is discussed. Localization and delocalization are interpreted in terms of the eigenfunctions.
