S. P. Mielke

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Acaryochloris marina is the only species known to utilize chlorophyll (Chl) d as a principal photopigment. The peak absorption wavelength of Chl d is redshifted ≈40nm in vivo relative to Chl a, enabling this cyanobacterium to perform oxygenic phototrophy in niche environments enhanced in far-red light. We present measurements of the in vivo energy-storage(More)
Knowledge of the three-dimensional structure of proteins is integral to understanding their functions, and a necessity in the era of proteomics. A wide range of computational methods is employed to estimate the secondary, tertiary, and quaternary structures of proteins. Comprehensive experimental methods, on the other hand, are limited to nuclear magnetic(More)
The cyanobacterium Acaryochloris marina uses chlorophyll d to carry out oxygenic photosynthesis in environments depleted in visible and enhanced in lower-energy, far-red light. However, the extent to which low photon energies limit the efficiency of oxygenic photochemistry in A. marina is not known. Here, we report the first direct measurements of the(More)
Random coil chemical shifts are commonly used to detect protein secondary structural elements in chemical shift index (CSI) calculations. Though this technique is widely used and seems reliable for folded proteins, the choice of reference random coil chemical shift values can significantly alter the outcome of secondary structure estimation. In order to(More)
The topological state of DNA in vivo is dynamically regulated by a number of processes that involve interactions with bound proteins. In one such process, the tracking of RNA polymerase along the double helix during transcription, restriction of rotational motion of the polymerase and associated structures, generates waves of overtwist downstream and(More)
We review the history of DNA mechanics and its analysis. We evaluate several methods to analyze the structures of superhelical DNA molecules, each predicated on the assumption that DNA can be modeled with reasonable accuracy as an extended, linearly elastic polymer. Three main approaches are considered: mechanical equilibrium methods, which seek to compute(More)
The torque generated by RNA polymerase as it tracks along double-stranded DNA can potentially induce long-range structural deformations integral to mechanisms of biological significance in both prokaryotes and eukaryotes. In this paper, we introduce a dynamic computer model for investigating this phenomenon. Duplex DNA is represented as a chain of(More)
Numerical models of mesoscale DNA dynamics relevant to in vivo scenarios require methods that incorporate important features of the intracellular environment, while maintaining computational tractability. Because the explicit inclusion of ions leads to electrostatic calculations that scale as the square of the number of charged particles, such models(More)
We report results from scanning tunneling microscopy experiments in which supercoiling of the plasmid, pTNT, leads to localized duplex denaturation at a single location. Measurements of the imaged strand-separated region suggest an extent of approximately 60 base pairs (bp's), in excellent agreement with the prediction of a statistical mechanical analysis(More)