Capturing protein dynamics with time-resolved luminescence spectroscopy

The presented doctoral research utilizes time-resolved spectroscopy to characterize protein dynamics and folding mechanisms. We resolve millisecond-timescale folding by coupling time-resolved fluorescence energy transfer (trFRET) to a continuous flow microfluidic mixer to obtain intramolecular distance distributions throughout the folding process. We have elucidated the folding mechanisms of two cytochromes---one that exhibits two-state folding (cytochrome cb₅₆₂) and one that has both a kinetic refolding intermediate ensemble and a distinct equilibrium unfolding intermediate (cytochrome c₅₅₂). Our data reveal that the distinct structural features of cytochrome c₅₅₂ contribute to its thermostability.

We have also investigated intrachain contact dynamics in unfolded cytochrome cb₅₆₂ by monitoring electron transfer, which occurs as the heme collides with a ruthenium photosensitizer, covalently bound to residues along the polypeptide. Intrachain diffusion for chemically denatured proteins proceeds on the microsecond timescale with an upper limit of 0.1 microseconds. The power-law dependence (slope = -1.5) of the rate constants on the number of peptide bonds between the heme and Ru complex indicate that cytochrome cb₅₆₂ is minimally frustrated.

In addition, we have explored the pathway dependence of electron tunneling rates between metal sites in proteins. Our research group has converted cytochrome b₅₆₂ to a c-type cytochrome with the porphyrin covalently bound to cysteine sidechains. We have investigated the effects of the changes to the protein structure (i.e., increased rigidity and potential new equatorial tunneling pathways) on the electron transfer rates, measured by transient absorption, in a series of ruthenium photosensitizer-modified proteins.

Cooperative properties of lipid bilayers : collective director fluctuations and the effects of hydrophobic mismatch in protein/lipid membrane systems

Cooperative director fluctuations in lipid bilayers have been postulated for many years. ^2H-NMR T_1^(-1), T_(1P)^(-1) , and T_2^(-1); measurements have been used identify these motions and to determine the origin of increased slow bilayer motion upon addition of unlike lipids or proteins to a pure lipid bilayer.

The contribution of cooperative director fluctuations to NMR relaxation in lipid bilayers has been expressed mathematically using the approach of Doane et al.^1 and Pace and Chan.^2 The T_2^(-1)’s of pure dimyristoyllecithin (DML) bilayers deuterated at the 2, 9 and 10, and all positions on both lipid hydrocarbon chains have been measured. Several characteristics of these measurements indicate the presence of cooperative director fluctuations. First of all, T_2^(-1) exhibits a linear dependence on S2/CD. Secondly, T_2^(-1) varies across the ^2H-NMR powder pattern as sin^2 (2, β), where , β is the angle between the average bilayer director and the external magnetic field. Furthermore, these fluctuations are restricted near the lecithin head group suggesting that the head group does not participate in these motions but, rather, anchors the hydrocarbon chains in the bilayer.

T_2^(-1)has been measured for selectively deuterated liquid crystalline DML hilayers to which a host of other lipids and proteins have been added. The T_2^(-1) of the DML bilayer is found to increase drastically when chlorophyll a (chl a) and Gramicidin A' (GA') are added to the bilayer. Both these molecules interfere with the lecithin head group spacing in the bilayer. Molecules such as myristic acid, distearoyllecithin (DSL), phytol, and cholesterol, whose hydrocarbon regions are quite different from DML but which have small,neutral polar head groups, leave cooperative fluctuations in the DML bilayer unchanged.

The effect of chl a on cooperative fluctuations in the DML bilayer has been examined in detail using ^2H-NMR T_1^(-1), T_(1P)^(-1) , and T_2^(-1); measurements. Cooperative fluctuations have been modelled using the continuum theory of the nematic state of liquid crystals. Chl a is found to decrease both the correlation length and the elastic constants in the DML bilayer.

A mismatch between the hydrophobic length of a lipid bilayer and that of an added protein has also been found to change the cooperative properties of the lecithin bilayer. Hydrophobic mismatch has been studied in a series GA' / lecithin bilayers. The dependence of 2H-NMR order parameters and relaxation rates on GA' concentration has been measured in selectively deuterated DML, dipalmitoyllecithin (DPL), and DSL systems. Order parameters, cooperative lengths, and elastic constants of the DML bilayer are most disrupted by GA', while the DSL bilayer is the least perturbed by GA'. Thus, it is concluded that the hydrophobic length of GA' best matches that of the DSL bilayer. Preliminary Raman spectroscopy and Differential Scanning Calorimetry experiments of GA' /lecithin systems support this conclusion. Accommodation of hydrophobic mismatch is used to rationalize the absence of H_(II) phase formation in GA' /DML systems and the observation of H_(II) phase in GA' /DPL and GA' /DSL systems.

1. J. W. Doane and D. L. Johnson, Chem. Phy3. Lett., 6, 291-295 (1970). 2. R. J. Pace and S. I. Chan, J. Chem. Phy3., 16, 4217-4227 (1982).

Cooperative and market-based solutions to pollution abatement problems

This work concerns itself with the possibility of solutions, both cooperative and market based, to pollution abatement problems. In particular, we are interested in pollutant emissions in Southern California and possible solutions to the abatement problems enumerated in the 1990 Clean Air Act. A tradable pollution permit program has been implemented to reduce emissions, creating property rights associated with various pollutants.

Before we discuss the performance of market-based solutions to LA's pollution woes, we consider the existence of cooperative solutions. In Chapter 2, we examine pollutant emissions as a trans boundary public bad. We show that for a class of environments in which pollution moves in a bi-directional, acyclic manner, there exists a sustainable coalition structure and associated levels of emissions. We do so via a new core concept, one more appropriate to modeling cooperative emissions agreements (and potential defection from them) than the standard definitions.

However, this leaves the question of implementing pollution abatement programs unanswered. While the existence of a cost-effective permit market equilibrium has long been understood, the implementation of such programs has been difficult. The design of Los Angeles' REgional CLean Air Incentives Market (RECLAIM) alleviated some of the implementation problems, and in part exacerbated them. For example, it created two overlapping cycles of permits and two zones of permits for different geographic regions. While these design features create a market that allows some measure of regulatory control, they establish a very difficult trading environment with the potential for inefficiency arising from the transactions costs enumerated above and the illiquidity induced by the myriad assets and relatively few participants in this market.

It was with these concerns in mind that the ACE market (Automated Credit Exchange) was designed. The ACE market utilizes an iterated combined-value call market (CV Market). Before discussing the performance of the RECLAIM program in general and the ACE mechanism in particular, we test experimentally whether a portfolio trading mechanism can overcome market illiquidity. Chapter 3 experimentally demonstrates the ability of a portfolio trading mechanism to overcome portfolio rebalancing problems, thereby inducing sufficient liquidity for markets to fully equilibrate.

With experimental evidence in hand, we consider the CV Market's performance in the real world. We find that as the allocation of permits reduces to the level of historical emissions, prices are increasing. As of April of this year, prices are roughly equal to the cost of the Best Available Control Technology (BACT). This took longer than expected, due both to tendencies to mis-report emissions under the old regime, and abatement technology advances encouraged by the program. Vve also find that the ACE market provides liquidity where needed to encourage long-term planning on behalf of polluting facilities.

Luminescence properties of electron-hole-droplets in pure and doped germanium

This work contains 4 topics dealing with the properties of the luminescence from Ge.

The temperature, pump-power and time dependences of the photoluminescence spectra of Li-, As-, Ga-, and Sb-doped Ge crystals were studied. For impurity concentrations less than about 10¹⁵cm^-3, emissions due to electron-hole droplets can clearly be identified. For impurity concentrations on the order of 10¹⁶cm^-3, the broad lines in the spectra, which have previously been attributed to the emission from the electron-hole-droplet, were found to possess pump-power and time dependent line shape. These properties show that these broad lines cannot be due to emission of electron-hole-droplets alone. We interpret these lines to be due to a combination of emissions from (1) electron-hole- droplets, (2) broadened multiexciton complexes, (3) broadened bound-exciton, and (4) plasma of electrons and holes. The properties of the electron-hole-droplet in As-doped Ge were shown to agree with theoretical predictions.

The time dependences of the luminescence intensities of the electron-hole-droplet in pure and doped Ge were investigated at 2 and 4.2°K. The decay of the electron-hole-droplet in pure Ge at 4.2°K was found to be pump-power dependent and too slow to be explained by the widely accepted model due to Pokrovskii and Hensel et al. Detailed study of the decay of the electron-hole-droplets in doped Ge were carried out for the first time, and we find no evidence of evaporation of excitons by electron-hole-droplets at 4.2°K. This doped Ge result is unexplained by the model of Pokrovskii and Hensel et al. It is shown that a model based on a cloud of electron-hole-droplets generated in the crystal and incorporating (1) exciton flow among electron-hole-droplets in the cloud and (2) exciton diffusion away from the cloud is capable of explaining the observed results.

It is shown that impurities, introduced during device fabrication, can lead to the previously reported differences of the spectra of laser-excited high-purity Ge and electrically excited Ge double injection devices. By properly choosing the device geometry so as to minimize this Li contamination, it is shown that the Li concentration in double injection devices may be reduced to less than about 10¹⁵cm^-3 and electrically excited luminescence spectra similar to the photoluminescence spectra of pure Ge may be produced. This proves conclusively that electron-hole-droplets may be created in double injection devices by electrical excitation.

The ratio of the LA- to TO-phonon-assisted luminescence intensities of the electron-hole-droplet is demonstrated to be equal to the high temperature limit of the same ratio of the exciton for Ge. This result gives one confidence to determine similar ratios for the electron-hole-droplet from the corresponding exciton ratio in semiconductors in which the ratio for the electron-hole-droplet cannot be determined (e.g., Si and GaP). Knowing the value of this ratio for the electron-hole-droplet, one can obtain accurate values of many parameters of the electron-hole-droplet in these semiconductors spectroscopically.