Biomedical subjects

Haw Yang

Publications and source records attributed to Haw Yang.

10 recordsLinked to original sources

PubMed2006

Quantitative single-molecule conformational distributions: a case study with poly-(L-proline).

Precise measurement of the potential of mean force is necessary for a fundamental understanding of the dynamics and chemical reactivity of a biological macromolecule. The unique advantage provided by the recently developed constant-information approach to analyzing time-dependent single-molecule fluorescence measurements was used with maximum entropy deconvolution to create a procedure for the accurate determination of molecular conformational distributions, and analytical expressions for the errors in these distributions were derived. This new method was applied to a derivatized poly(L-proline) series, P(n)CG3K(biotin) (n = 8, 12, 15, 18, and 24), using a modular, server-based single-molecule spectrometer that is capable of registering photon arrival times with a continuous-wave excitation source. To account for potential influence from the microscopic environment, factors that were calibrated and corrected molecule by molecule include background, cross-talk, and detection efficiency. For each single poly(L-proline) molecule, sharply peaked Förster type resonance energy transfer (FRET) efficiency and distance distributions were recovered, indicating a static end-to-end distance on the time scale of measurement. The experimental distances were compared with models of varying rigidity. The results suggest that the 23 angstroms persistence length wormlike chain model derived from experiments with high molecular weight poly(L-proline) is applicable to short chains as well.

Algorithms↗

PubMed2006

Three-dimensional chiral imaging by sum-frequency generation.

A sum-frequency generation (SFG) microscope that is sensitive toward molecular chirality was demonstrated for the first time. Optically active images of chiral 1,1'-bi-2-naphthol solutions were obtained with submicron spatial resolution. Three-dimensional sectioning capability of our microscope was also demonstrated. This optically active SFG microscopy can potentially become a powerful imaging technique for biological samples.

Image Processing, Computer-Assisted↗

PubMed2006

Continuous distribution of emission states from single CdSe/ZnS quantum dots.

The photoluminescence dynamics of colloidal CdSe/ZnS/streptavidin quantum dots were studied using time-resolved single-molecule spectroscopy. Statistical tests of the photon-counting data suggested that the simple "on/off" discrete state model is inconsistent with experimental results. Instead, a continuous emission state distribution model was found to be more appropriate. Autocorrelation analysis of lifetime and intensity fluctuations showed a nonlinear correlation between them. These results were consistent with the model that charged quantum dots were also emissive, and that time-dependent charge migration gave rise to the observed photoluminescence dynamics.

Cadmium Compounds↗

PubMed2005

Photon-by-photon determination of emission bursts from diffusing single chromophores.

One of the difficulties in diffusion-type single-molecule experiments is the determination of signal amid photon-counting noise. A commonly used approach is to further average the noisy time trace by binning, followed by placing a threshold to discriminate signal from background. The choice of smoothing parameters and the placement of the threshold may impact on the efficiency with which the information-rich region can be harvested, among other potential complications. Here we introduce a procedure that operates on the data sequence photon by photon, thereby relieving the incertitude in choosing binning-thresholding parameters. We characterize this procedure by detecting the two-photon emission bursts from diffusing single gold nanoparticles. The results support our burst-finding procedure as a reliable and efficient way of detecting and harvesting photon bursts from diffusing experiments.

Diffusion↗

PubMed2005

Detection of intensity change points in time-resolved single-molecule measurements.

We present a method for the analysis of optical single molecule emission data that exhibit discrete intensity jumps. This new method uses a generalized likelihood ratio test that determines the location of an intensity change point based on individual photon arrival times. This test is applied recursively to an entire single molecule intensity trajectory, thus finding each change points. Expectation-maximization clustering and the Bayesian information criterion is then used for accurate determination of the true number of states accessible to the system. This procedure allows rigorous and quantitative determination of intensity change points without the artificial time resolution limitations that arise from binning and thresholding.

Journal Article↗

PubMed2004

Discrete nanostructures of quantum dots/Au with DNA.

Nanostructures of colloidal CdSe/ZnS core/shell quantum dots (QDs) surrounded by a discrete number of Au nanoparticles were generated via DNA hybridization and purified by gel electrophoresis. Statistics from TEM analysis showed a high yield of designed structures. The distance between Au particles and QD, the number of Au around the central QD, and the size of Au and QD can be adjusted. Rationally designed structures such as these hold great promise for researching the physical interactions between semiconductor and Au nanoparticles and for developing more efficient nanoprobes.

DNA↗

PubMed2004

Information bounds and optimal analysis of dynamic single molecule measurements.

Time-resolved single molecule fluorescence measurements may be used to probe the conformational dynamics of biological macromolecules. The best time resolution in such techniques will only be achieved by measuring the arrival times of individual photons at the detector. A general approach to the estimation of molecular parameters based on individual photon arrival times is presented. The amount of information present in a data set is quantified by the Fisher information, thereby providing a guide to deriving the basic equations relating measurement uncertainties and time resolution. Based on these information-theoretical considerations, a data analysis algorithm is presented that details the optimal analysis of single-molecule data. This method natively accounts and corrects for background photons and cross talk, and can scale to an arbitrary number of channels. By construction, and with corroboration from computer simulations, we show that this algorithm reaches the theoretical limit, extracting the maximal information out of the data. The bias inherent in the algorithm is considered and its implications for experimental design are discussed. The ideas underlying this approach are general and are expected to be applicable to any information-limited measurement.

Algorithms↗

PubMed2003

Protein conformational dynamics probed by single-molecule electron transfer.

Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over time. We could then determine the potential of mean force between the flavin and the tyrosine, and a correlation analysis revealed conformational fluctuation at multiple time scales spanning from hundreds of microseconds to seconds. This phenomenon suggests the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.

Amino Acid Substitution↗

PubMed2002

Ultrafast UV pump/IR probe studies of C-H activation in linear, cyclic, and aryl hydrocarbons.

The photochemical C-H activation reactions of eta(3)-TpRh(CO)(2) (Tp = HB-Pz(3), Pz = 3,5-dimethylpyrazolyl) and CpRh(CO)(2) (Cp = C(5)H(5)) have been studied in a series of linear, cyclic, and aromatic hydrocarbon solvents on a femtosecond to microsecond time scale. These results have revealed that the structure of the hydrocarbon substrate affects the final C-H bond activation step, which is in accordance with the known preference of bond activation toward primary C-H sites. In the case of aromatic C-H activation, the reaction is divided into parallel channels involving sigma- and pi-solvated intermediates. Results for the analogous CpRh(CO)(2) molecule have shown that the coordination of the cyclopentadienyl ligand does not play a direct role in the dynamics of the reaction, in contrast to the C-H activation mechanism observed in eta(3)-TpRh(CO)(2) studies.

Journal Article↗

PubMed2002

FAD is a preferred substrate and an inhibitor of Escherichia coli general NAD(P)H:flavin oxidoreductase.

Escherichia coli general NAD(P)H:flavin oxidoreductase (Fre) does not have a bound flavin cofactor; its flavin substrates (riboflavin, FMN, and FAD) are believed to bind to it mainly through the isoalloxazine ring. This interaction was real for riboflavin and FMN, but not for FAD, which bound to Fre much tighter than FMN or riboflavin. Computer simulations of Fre.FAD and Fre.FMN complexes showed that FAD adopted an unusual bent conformation, allowing its ribityl side chain and ADP moiety to form an additional 3.28 H-bonds on average with amino acid residues located in the loop connecting Fbeta5 and Falpha1 of the flavin-binding domain and at the proposed NAD(P)H-binding site. Experimental data supported the overlapping binding sites of FAD and NAD(P)H. AMP, a known competitive inhibitor with respect to NAD(P)H, decreased the affinity of Fre for FAD. FAD behaved as a mixed-type inhibitor with respect to NADPH. The overlapped binding offers a plausible explanation for the large K(m) values of Fre for NADH and NADPH when FAD is the electron acceptor. Although Fre reduces FMN faster than it reduces FAD, it preferentially reduces FAD when both FMN and FAD are present. Our data suggest that FAD is a preferred substrate and an inhibitor, suppressing the activities of Fre at low NADH concentrations.

Binding Sites↗