Katharine M. Mullen

Hydrogen Bond Switching among Flavin and Amino Acid Side Chains in the BLUF Photoreceptor Observed by Ultrafast Infrared Spectroscopy

BLUF domains constitute a recently discovered class of photoreceptor proteins found in bacteria and eukaryotic algae. BLUF domains are blue-light sensitive through a FAD cofactor that is involved in an extensive hydrogen-bond network with nearby amino acid side chains, including a highly conserved tyrosine and glutamine. The participation of particular amino acid side chains in the ultrafast hydrogen-bond switching reaction with FAD that underlies photoactivation of BLUF domains is assessed by means of ultrafast infrared spectroscopy. Blue-light absorption by FAD results in formation of FAD(*-) and a bleach of the tyrosine ring vibrational mode on a picosecond timescale, showing that electron transfer from tyrosine to FAD constitutes the primary photochemistry. This interpretation is supported by the absence of a kinetic isotope effect on the fluorescence decay on H/D exchange. Subsequent protonation of FAD(*-) to result in FADH(*) on a picosecond timescale is evidenced by the appearance of a N-H bending mode at the FAD N5 protonation site and of a FADH(*) C=N stretch marker mode, with tyrosine as the likely proton donor. FADH(*) is reoxidized in 67 ps (180 ps in D(2)O) to result in a long-lived hydrogen-bond switched network around FAD. This hydrogen-bond switch shows infrared signatures from the C-OH stretch of tyrosine and the FAD C4=O and C=N stretches, which indicate increased hydrogen-bond strength at all these sites. The results support a previously hypothesized rotation of glutamine by approximately 180 degrees through a light-driven radical-pair mechanism as the determinant of the hydrogen-bond switch.

The Role of Key Amino Acids in the Photoactivation Pathway of the Synechocystis Slr1694 BLUF Domain

BLUF (blue light sensing using FAD) domains belong to a novel group of blue light sensing receptor proteins found in microorganisms. We have assessed the role of specific aromatic and polar residues in the Synechocystis Slr1694 BLUF protein by investigating site-directed mutants with substitutions Y8W, W91F, and S28A. The W91F and S28A mutants formed the red-shifted signaling state upon blue light illumination, whereas in the Y8W mutant, signaling state formation was abolished. The W91F mutant shows photoactivation dynamics that involve the successive formation of FAD anionic and neutral semiquinone radicals on a picosecond time scale, followed by radical pair recombination to result in the long-lived signaling state in less than 100 ps. The photoactivation dynamics and quantum yield of signaling state formation were essentially identical to those of wild type, which indicates that only one significant light-driven electron transfer pathway is available in Slr1694, involving electron transfer from Y8 to FAD without notable contribution of W91. In the S28A mutant, the photoactivation dynamics and quantum yield of signaling state formation as well as dark recovery were essentially the same as in wild type. Thus, S28 does not play an essential role in the initial hydrogen bond switching reaction in Slr1694 beyond an influence on the absorption spectrum. In the Y8W mutant, two deactivation branches upon excitation were identified: the first involves a neutral semiquinone FADH(*) that was formed in approximately 1 ps and recombines in 10 ps and is tentatively assigned to a FADH(*)-W8(*) radical pair. The second deactivation branch forms FADH(*) in 8 ps and evolves to FAD(*-) in 200 ps, which recombines to the ground state in about 4 ns. In the latter branch, W8 is tentatively assigned as the FAD redox partner as well. Overall, the results are consistent with a photoactivation mechanism for BLUF domains where signaling state formation proceeds via light-driven electron and proton transfer from Y8 to FAD, followed by a hydrogen bond rearrangement and radical pair recombination.

Exponential Data Fitting and its Applications

Type Ia supernova light curves are characterized by a rapid rise from zero luminosity to a peak value, followed by a slower quasi-exponential decline. The rise and peak last for a few days, while the decline persists for many months. It is widely believed that the decline is powered by the radioactive decay chain 56Ni → 56Co → 56Fe, but the rates of decline in luminosity do not exactly match the decay rates of Ni and Co. In 1976, Rust, Leventhal, and McCall [19] presented evidence that the declining part of the light curve is well modelled by a linear combination of two exponentials whose decay rates were proportional to, but not exactly equal to, the decay rates for Ni and Co. The proposed reason for the lack of agreement between the rates was that the radioactive decays take place in the interior of a white dwarf star, at densities much higher than any encountered in a terrestrial environment, and that these higher densities accelerate the two decays by the same factor. This paper revisits this model, demonstrating that a variant of it provides excellent fits to observed luminosity data from 6 supernovae.

The variable projection algorithm in time-resolved spectroscopy, microscopy and mass spectrometry applications

Nonlinear least squares optimization problems in which the parameters can be partitioned into two sets such that optimal estimates of parameters in one set are easy to solve for given fixed values of the parameters in the other set are common in practice. Particularly ubiquitous are data fitting problems in which the model function is a linear combination of nonlinear functions, which may be addressed with the variable projection algorithm due to Golub and Pereyra. In this paper we review variable projection, with special emphasis on its application to matrix data. The generalization of the algorithm to separable problems in which the linear coefficients of the nonlinear functions are subject to constraints is also discussed. Variable projection has been instrumental for model-based data analysis in multi-way spectroscopy, time-resolved microscopy and gas or liquid chromatography mass spectrometry, and we give an overview of applications in these domains, illustrated by brief case studies.

Algorithms for separable nonlinear least squares with application to modelling time-resolved spectra

The multiexponential analysis problem of fitting kinetic models to time-resolved spectra is often solved using gradient-based algorithms that treat the spectral parameters as conditionally linear. We make a comparison of the two most-applied such algorithms, alternating least squares and variable projection. A numerical study examines computational efficiency and linear approximation standard error estimates. A new derivation of the Fisher information matrix under the full Golub-Pereyra gradient allows a numerical comparison of parameter precision under variable projection variants. Under the criteria of efficiency, quality of standard error estimates and parameter precision, we conclude that the Kaufman variable projection technique performs well, while techniques based on alternating least squares have significant disadvantages for application in the problem domain.

Mitigation of errors in pair distribution function analysis of nanoparticles

Information on the size and structure of nanoparticles can be obtained via analysis of the atomic pair distribution function (PDF), which is calculated as the Fourier transform of X-ray/neutron total scattering. The structural parameters are commonly extracted by fitting a model PDF calculated from atomic coordinates to the experimental data. This paper discusses procedures for minimizing systematic errors in PDF calculations for nanoparticles and also considers the effects of noise due to counting statistics in total scattering data used to obtain the PDF. The results presented here demonstrate that smoothing of statistical noise in reciprocal-space data can improve the precision of parameter estimates obtained from PDF analysis, facilitating identification of the correct model (from multiple plausible choices) from real-space PDF fits.

Atomic structure analysis at the nanoscale using the pair distribution function: simulation studies of simple elemental nanoparticles

The pair distribution function (PDF), as determined from total X-ray or neutron scattering, is a valuable probe of atomic arrangements in nanoparticles. Structural information in the experimental PDF is modified by the effects of particle shape, particle size, extended defects and internal substructure. This study uses synthetic PDF data, generated for simple elemental nanoparticles having different degrees of displacive atomic disorder in the particle surface compared with the interior, to explore the feasibility of reliably extracting key features (i.e. a lattice constant, particle diameter, atomic displacement parameters for the interior and the surface, and thickness of the surface layer) from experimental data in the absence of systematic errors using a statistical modeling approach. This approach determines a model PDF via simulation of an ensemble of nanoparticles. Several methods for model optimization were tested and a differential evolution algorithm was selected as the most reliable and accurate. Fitting synthetic PDF data using this algorithm was demonstrated to estimate all features well with small standard uncertainties. Identification of larger displacive atomic disorder in the particle surface compared with the interior was shown to be possible via model selection. Software for nanoparticle simulation and model optimization is provided in open-source form, to allow reproduction and extension of the results presented here.

Honoring the Lion: A Festschrift for Jan de Leeuw

This special volume celebrates the 20th anniversary of the Journal of Statistical Software (JSS) and is a Festschrift for its founding editor Jan de Leeuw. Jan recently retired from his long-held position as founding chair of the Department of Statistics at the University of California, Los Angeles. The contributions to this special volume look back at some of his research interests and accomplishments during the half-century that he has been active in psychometrics and statistics. In this introduction, the guest editors also reminisce on their own first encounters with Jan, ten years ago. Since that time JSS has solidified its place as a leading journal of computational statistics, a fact that has a lot to do with Jans stewardship. We include a brief history of JSS.