Biomedical subjects

D G Steel

Publications and source records attributed to D G Steel.

At least 19 recordsLinked to original sources

PubMed2006

Density matrix tomography through sequential coherent optical rotations of an exciton qubit in a single quantum dot.

We demonstrate single qubit density matrix tomography in a single semiconductor quantum dot system through consecutive phase sensitive rotations of the qubit via ultrafast coherent optical excitations. The result is important for quantifying gate operations in quantum information processing in the quantum dot systems as well as demonstrating consecutive arbitrary qubit rotations.

Journal Article↗

PubMed2005

Stimulated and spontaneous optical generation of electron spin coherence in charged GaAs quantum dots.

We report on the coherent optical excitation of electron spin polarization in the ground state of charged GaAs quantum dots via an intermediate charged exciton (trion) state. Coherent optical fields are used for the creation and detection of the Raman spin coherence between the spin ground states of the charged quantum dot. The measured spin decoherence time, which is likely limited by the nature of the spin ensemble, approaches 10 ns at zero field. We also show that the Raman spin coherence in the quantum beats is caused not only by the usual stimulated Raman interaction but also by simultaneous spontaneous radiative decay of either excited trion state to a coherent combination of the two spin states.

Journal Article↗

PubMed2002

Optical RKKY interaction between charged semiconductor quantum dots.

We show how a spin interaction between electrons localized in neighboring quantum dots can be induced and controlled optically. The coupling is generated via virtual excitation of delocalized excitons and provides an efficient coherent control of the spins. This quantum manipulation can be realized in the adiabatic limit and is robust against decoherence by spontaneous emission. Applications to the realization of quantum gates, scalable quantum computers, and to the control of magnetization in an array of charged dots are proposed.

Journal Article↗

PubMed2002

Raman coherence beats from entangled polarization eigenstates in InAs quantum dots.

The homodyne-detected transient four-wave-mixing response of InAs/GaAs self-assembled quantum dots shows temporal oscillations of the optically induced Raman coherence arising from two entangled polarization eigenstates of the exciton. The phase sensitive nature of the homodyne detection enables us to follow the time evolution of the nonradiative quantum coherence between the polarization states, providing a measurement of the fine-structure splitting in the dots, which is much less than the inhomogeneous broadening, and the corresponding decoherence rate of the entangled state.

Journal Article↗

PubMed2002

Biexciton quantum coherence in a single quantum dot.

Nondegenerate (two-wavelength) two-photon absorption using coherent optical fields is used to show that there are two different quantum mechanical pathways leading to formation of the biexciton in a single quantum dot. Of specific importance to quantum information applications is the resulting coherent dynamics between the ground state and the biexciton from the pathway involving only optically induced exciton/biexciton quantum coherence. The data provide a direct measure of the biexciton decoherence rate which is equivalent to the decoherence of the Bell state in this system, as well as other critical optical parameters.

Journal Article↗

PubMed2001

Near-field coherent spectroscopy and microscopy of a quantum dot system.

We combined coherent nonlinear optical spectroscopy with nano-electron volt energy resolution and low-temperature near-field microscopy with subwavelength resolution (<lambda/2) to provide direct and local access to the excitonic dipole in a semiconductor nanostructure quantum system. Our technique allows the ability to address, excite, and probe single eigenstates of solid-state quantum systems with spectral and spatial selectivity while simultaneously providing a measurement of all the various time scales of the excitation including state relaxation and decoherence rates. In analogy to scanning tunneling microscopy measurements, we can now map the optical local density of states of a disordered nanostructure. These measurements lay the groundwork for studying and exploiting spatial and temporal coherence in the nanoscopic regime of solid-state systems.

Journal Article↗

PubMed2001

Mg2+ binding to alkaline phosphatase correlates with slow changes in protein lability.

The in vitro reactivation of unfolded Escherichia coli alkaline phosphatase (AP) in the presence of the two natively bound metals Zn2+ and Mg2+ produces two protein species, characterized by different guanidine hydrochloride denaturation kinetics. The high-lability AP form slowly converts to the low-lability form in a first-order reaction with a characteristic lifetime (inverse rate constant) of approximately 300 h at pH 8.0 and 25 degrees C. Addition of Zn2+ and Mg2+ ligands to (folded) apo-AP also produces two protein species, with denaturation kinetics and a long conversion lifetime similar to those found in refolding AP. In contrast, adding Zn2+ alone to apo-AP produces only the high-lability species with no subsequent structural change, suggesting that Mg2+ binding is the event which is responsible for the production of the low-lability AP. The rate of conversion from high- to low-lability AP was found to be linearly dependent on Mg2+ concentration, indicating that Mg2+ binding is rate limiting for this reaction. Experiments where either Zn2+ or Mg2+ was added first, with the second metal added later, show that Mg2+ binding is slowed by the prior presence of bound Zn2+. Mg2+ binding to Zn-AP also slightly increases the enzymatic activity; however, the extent of formation of the low-lability species is related to the square of the Mg2+-induced activity increase. Thus the binding of two Mg2+ to AP produces the dramatic reduction in the rate of denaturation that characterizes the low-lability species. The data suggest the possibility of long distance intersubunit interactions and a role for Mg2+ in providing "kinetic stability" for AP.

Alkaline Phosphatase↗

PubMed2001

Rabi oscillations of excitons in single quantum dots.

Transient nonlinear optical spectroscopy, performed on excitons confined to single GaAs quantum dots, shows oscillations that are analogous to Rabi oscillations in two-level atomic systems. This demonstration corresponds to a one-qubit rotation in a single quantum dot which is important for proposals using quantum dot excitons for quantum computing. The dipole moment inferred from the data is consistent with that directly obtained from linear absorption studies. The measurement extends the artificial atom model of quantum dot excitonic transitions into the strong-field limit, and makes possible full coherent optical control of the quantum state of single excitons using optical pi pulses.

Journal Article↗

PubMed2001

Differences in the pathways for unfolding and hydrogen exchange among mutants of Escherichia coli alkaline phosphatase.

Our initial studies of hydrogen-deuterium (H-D) exchange of tryptophan 109 in Escherichia coli alkaline phosphatase (AP) suggested that significant local unfolding of the protein might occur to allow for the exchange reaction, which is very slow at room temperature (Fischer et al., Biochemistry 39 (2000) 1455-1461). In order to investigate whether the partial unfolding and/or 'breathing' motions leading to H-D exchange were part of the unfolding pathway of the protein we prepared a series of mutants, designed to produce cavities around the exchanging residue, and compared their rates of H-D exchange to their lability (rate of inactivation) in guanidine hydrochloride (Gd:HCl). The complex unfolding kinetics of the mutants in the presence of Gd:HCl showed several components with rates that differed substantially among these proteins, but none of the rates of denaturation induced with Gd:HCl was consistently correlated with the H-D exchange rates. We conclude that the partial opening of the AP structure during the H-D exchange of tryptophan 109, although very slow, is not a rate determining step in the unfolding of this protein.

Alkaline Phosphatase↗

PubMed2000

Hydrogen exchange at the core of Escherichia coli alkaline phosphatase studied by room-temperature tryptophan phosphorescence.

The room-temperature tryptophan (Trp) phosphorescence lifetime is sensitive to details of the local environment and has been shown to increase significantly in some proteins following H-D exchange. Careful analysis of the phosphorescence lifetime distribution of Trp 109 in Escherichia coli alkaline phosphatase (AP) in solution as a function of time during the H-D exchange shows that this process corresponds to a two-state reaction resulting from the deuteration of a single, specific hydrogen in the core of the protein. The absence of a pH dependence of the exchange rate suggests that the exchange is not an EX2 process, and therefore, a certain degree of unfolding is required for exchange to occur. This discovery opens up the use of phosphorescence-detected hydrogen exchange as a sensitive tool for monitoring the local susceptibility and activation energy for exchange in proteins having a phosphorescent Trp and, for example, for studying the effects of local mutations upon that susceptibility.

Alkaline Phosphatase↗

PubMed1999

Proline isomerization is unlikely to be the cause of slow annealing and reactivation during the folding of alkaline phosphatase.

The in vitro folding of Escherichia coli alkaline phosphatase (AP) from the guanidine hydrochloride (GdnHCl) denatured state is characterized by a significant slow phase in the post activational recovery of native protein lability (probed by the susceptibility to GdnHCl denaturation and occurring on the time scale of days) as well as a slow phase in the recovery of activity (on the time scale of minutes). Slow folding events have often been attributed to cis-trans isomerizations of X-Pro peptide bonds, a plausible explanation for AP, which contains 21 prolines per subunit. To investigate the role of proline isomerization in the two measures of refolding mentioned above, we have performed "double-jump" GdnHCl denaturation/renaturation experiments, with a third jump, where the rate of unfolding of refolded protein upon exposure to denaturant was added to assess the rate of change of lability. Our measurements of the time evolution of both the lability and the reactivation of refolded AP as a function of denaturation time show that proline isomerization is unlikely to be the cause of either of these slow events in the refolding of AP. The conclusions are further confirmed by the absence of proline isomerization effects when AP is refolded in the presence of human and periplasmic E. coli peptidyl-prolyl isomerase.

Alkaline Phosphatase↗

PubMed1998

Using census data to investigate the causes of the ecological fallacy.

"The authors show how data from the 2% Sample of Anonymised Records (SAR) can be combined with data from the Small Area Statistics (SAS) database to investigate the causes of the ecological fallacy in an Enumeration District (ED) level analysis. A range of census variables are examined in three ¿SAR districts'...in England. Results of comparable analyses from the 1986 Australian census are also given. The ecological fallacy arises when results from an analysis based on area-level aggregate statistics are incorrectly assumed to apply at the individual level.... A methodology is introduced which allows aggregate-level statistics to be adjusted by using individual-level information on those variables that explain much of the within-area homogeneity."

Australia↗

PubMed1997

Time-resolved room temperature tryptophan phosphorescence in proteins.

The application of luminescence, primarily fluorescence, to the study of protein structure and dynamics has been extensively exploited to facilitate the understanding of complex biological problems. The interest in the application of phosphorescence, however, shows that new and complementary information can be had by careful optical studies of the phosphorescence lifetime. As in the early days of fluorescence spectroscopy in proteins, a complete and rigorous interpretation of the room temperature phosphorescence remains to be developed; nevertheless, it is clear that time-resolved phosphorescence yields new information on proteins in solution, for example, the detection of subtle conformational changes during protein folding, which is outside the sensitivity of earlier techniques. In addition, the great sensitivity of the phosphorescence lifetime to structural changes associated with rigidity and of nearby quenchers suggests that detailed structural information can be obtained when this approach is combined with the power of site-directed mutagenesis or other more biophysical techniques such as energy transfer to attached acceptors. We have presented basic aspects of time-resolved room temperature phosphorescence spectroscopy and demonstrated some useful features of the spectroscopic signals as well as the general approach to data analysis. However, it should be understood that extensions of this approach will easily allow faster and improved time resolution with greater sensitivity to highly quenched phosphorescing states. In addition, many extensions of this approach that are common to fluorescence spectroscopy have yet to be developed. For example, combining time-resolved phosphorescence with anaerobic stopped-flow techniques and more rapid data acquisition electronics will enable studies of conformational dynamics with considerably shortened dead times. Other possibilities include extending the preliminary studies of in vivo-based spectroscopy, such as to microscopy. In conclusion, time-resolved phosphorescence presents a new dimension to biophysical methodologies for the study of proteins, and it is likely that this area will continue to grow in capability as the fundamental understanding improves.

Animals↗

PubMed1996

Long time-scale probing of the protein globular core using hydrogen-exchange and room temperature phosphorescence.

Preliminary room temperature phosphorescence measurements of the highly buried Trp109 in E. coli alkaline phosphatase have been used to report on the kinetics of protein hydrogen-deuterium exchange. Upon dilution in D2O the phosphorescence lifetime increases (at 20 degrees C) in a biphasic manner with an immediate change (< 30 seconds) followed by a slow change occurring on an extremely long timescale (days). The immediate D2O-induced lifetime increase is similar to that observed upon dilution into glycerol, a known protein hydrating agent. On the other hand, the slow D2O-induced first order growth in Trp109 lifetime is due to exchange at highly protected protein groups. As the phosphorescence lifetime of Trp109 is dependent on local rigidity, this increase in lifetime reflects changes in alkaline phosphatase structure. This first use of room temperature phosphorescence to monitor proton exchange shows promise as a sensitive and selective probe of protein core dynamics.

Alkaline Phosphatase↗

PubMed1996

In vitro renaturation of bovine beta-lactoglobulin A leads to a biologically active but incompletely refolded state.

When bovine beta-lactoglobulin (beta-LG) was refolded after extensive denaturation in 4.8 M guanidine hydrochloride (GuHCl), the functional activity of the protein, retinol binding, as measured by the enhancement of this ligand's fluorescence, was completely recovered. In contrast, the room-temperature tryptophan phosphorescence lifetime of the refolded protein, a local measure of the residue environment, was approximately 10 ms, significantly shorter than the phosphorescence lifetime of the untreated native protein (approximately 20 ms). The lability of the freshly refolded protein, as monitored by following the time course of its unfolding when incubated in 2.5 M GuHCl through the change in fluorescence intensity at 385 nm, was also determined and found to be increased significantly relative to untreated native protein. In contrast to the long term postactivation conformational changes detected previously in Escherichia coli alkaline phosphatase (Subramaniam V, Bergenhem NCH, Gafni A, Steel DG, 1995, Biochemistry 34:1133-1136), we found no changes in either the lability or phosphorescence decays of beta-LG during a period of 24 h. Our results are in agreement with the report by Hattori et al. (1993, J Biol Chem 268:22414-22419), using conformation-specific monoclonal antibodies to recognize native-like structure, that long-term changes occur in the protein conformation, compared with the native structure, on refolding.

Animals↗

PubMed1996

Detection of a pH-dependent conformational change in azurin by time-resolved phosphorescence.

Azurin, a blue copper protein from the bacterial species Pseudomonas aeruginosa, contains a single tryptophan residue. Previous fluorescence measurements indicate that this residue is highly constrained and unusually inaccessible to water. In the apoprotein this residue also possesses a long-lived room-temperature phosphorescence (RTP), the nonexponential decay of which can be resolved into two major components associated with lifetimes of 417 and 592 ms, which likely originate from at least two conformations of the protein. The relative weights of these two decay components change with pH in good correlation with a change in protonation of His-35, which has been studied in Cu(II) azurin. Interestingly, the structural changes characterized in earlier work have little effect on the fluorescence decay and appear to occur away from the tryptophan residue. However, in the present work, the two RTP lifetimes suggest conformations with different structural rigidities in the vicinity of the tryptophan residue. The active conformation that predominates below a pH of 5.6 has the shorter lifetime and is less rigid. Phosphorescence decays of several metal derivatives of azurin were also measured and revealed strong similarities to that of apoazurin, indicating that the structural constraints upon the metal-binding site are imposed predominately by the protein.

Apoproteins↗

PubMed1996

Improved differentiation between luminescence decay components by use of time-resolved optical activity measurements and selective lifetime modulation.

The analysis of luminescence decay experiments from proteins is typically modeled as a combination of independent first-order decay functions. However, Poisson noise in the photon counting experiment limits the ability of this approach to resolve decay components from separate lumiphores with similar lifetimes. To provide further differentiation, we incorporate time-resolved circular polarization of luminescence, an additional independent observable, into the analysis. In the simplest case, for example, each lumiphore's chirality is assumed to be time independent and is determined by the position of the lumiphore with respect to the surrounding chiral environment within the protein. In this paper, we describe the analysis of simultaneously recorded time-resolved luminescence and circularly polarized luminescence data to obtain improved temporal resolution. When combined with selective dynamic luminescence quenching, in a model system comprising a mixture of Tb/transferrin and Tb/conalbumin, we demonstrate resolution between two decay components with a lifetime difference of 7% and a difference in emission anisotropy of 5 X 10(-2). Evidence for the improved discrimination is further demonstrated by the increase in curvature of the chi 2 surface that results from the additional information.

Animals↗

PubMed1995

Direct kinetic evidence for triplet state energy transfer from Escherichia coli alkaline phosphatase tryptophan 109 to bound terbium.

The addition of excess Tb3+ to metal-depleted Escherichia coli alkaline phosphatase results in enhanced luminescence from enzyme-bound terbium, which increases with sample deoxygenation and exhibits a tryptophan-like excitation spectrum. Following pulsed excitation at 280 nm, the time-resolved terbium emission shows a negative prefactor associated with a submillisecond rise time, which is independent of the concentration of dissolved oxygen. The absence of a build-up phase and similarity in lifetime in the decay kinetics of directly excited (488 nm) terbium allows for the assignment of the submillisecond component in the 280 nm excited sample to bound terbium. The results of the steady state and time-resolved experiments suggest that the time evolution of alkaline phosphatase-bound terbium emission is determined by energy transfer (kET approximately 360 and 120 s-1) from the triplet state of tryptophan to terbium followed by terbium decay. This model is based on the observations that 1) the tryptophan phosphorescence lifetime (previously assigned to Trp109) corresponds to the longer component of the terbium emission and 2) the long-lived emission is enhanced, as is the Trp109 phosphorescence, by deoxygenation. An energy transfer mechanism involving the Trp109 triplet state is shown to be inconsistent with a dipole-dipole process and is best understood as a through-space electron exchange over a donor-acceptor distance of 9-10 A.

Alkaline Phosphatase↗