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475 results on '"Pollack, Lois"'

101. Enzyme Intermediates Captured “on-the-fly” by Mix-and-Inject Serial Crystallography

Author

Olmos, Jose, primary, Pandey, Suraj, additional, Martin-Garcia, Jose M., additional, Calvey, George, additional, Katz, Andrea, additional, Knoska, Juraj, additional, Kupitz, Christopher, additional, Hunter, Mark S., additional, Liang, Mengning, additional, Oberthuer, Dominik, additional, Yefanov, Oleksandr, additional, Wiedorn, Max, additional, Heyman, Michael, additional, Holl, Mark, additional, Pande, Kanupriya, additional, Barty, Anton, additional, Miller, Mitchell D., additional, Stern, Stephan, additional, Roy-Chowdhury, Shatabdi, additional, Coe, Jesse, additional, Nagaratnam, Nirupa, additional, Zook, James, additional, Verburgt, Jacob, additional, Norwood, Tyler, additional, Poudyal, Ishwor, additional, Xu, David, additional, Koglin, Jason, additional, Seaberg, Matt, additional, Zhao, Yun, additional, Bajt, Saša, additional, Grant, Thomas, additional, Mariani, Valerio, additional, Nelson, Garrett, additional, Subramanian, Ganesh, additional, Bae, Euiyoung, additional, Fromme, Raimund, additional, Fung, Russel, additional, Schwander, Peter, additional, Frank, Matthias, additional, White, Thomas, additional, Weierstall, Uwe, additional, Zatsepin, Nadia, additional, Spence, John, additional, Fromme, Petra, additional, Chapman, Henry N., additional, Pollack, Lois, additional, Tremblay, Lee, additional, Ourmazd, Abbas, additional, Phillips, George N., additional, and Schmidt, Marius, additional

Published
2017
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102. 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update

Author

Trewhella, Jill, primary, Duff, Anthony P., additional, Durand, Dominique, additional, Gabel, Frank, additional, Guss, J. Mitchell, additional, Hendrickson, Wayne A., additional, Hura, Greg L., additional, Jacques, David A., additional, Kirby, Nigel M., additional, Kwan, Ann H., additional, Pérez, Javier, additional, Pollack, Lois, additional, Ryan, Timothy M., additional, Sali, Andrej, additional, Schneidman-Duhovny, Dina, additional, Schwede, Torsten, additional, Svergun, Dmitri I., additional, Sugiyama, Masaaki, additional, Tainer, John A., additional, Vachette, Patrice, additional, Westbrook, John, additional, and Whitten, Andrew E., additional

Published
2017
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103. Correction: Corrigendum: Double-flow focused liquid injector for efficient serial femtosecond crystallography

Author

Oberthuer, Dominik, primary, Knoška, Juraj, additional, Wiedorn, Max O., additional, Beyerlein, Kenneth R., additional, Bushnell, David A., additional, Kovaleva, Elena G., additional, Heymann, Michael, additional, Gumprecht, Lars, additional, Kirian, Richard A., additional, Barty, Anton, additional, Mariani, Valerio, additional, Tolstikova, Aleksandra, additional, Adriano, Luigi, additional, Awel, Salah, additional, Barthelmess, Miriam, additional, Dörner, Katerina, additional, Xavier, P. Lourdu, additional, Yefanov, Oleksandr, additional, James, Daniel R., additional, Nelson, Garrett, additional, Wang, Dingjie, additional, Calvey, George, additional, Chen, Yujie, additional, Schmidt, Andrea, additional, Szczepek, Michael, additional, Frielingsdorf, Stefan, additional, Lenz, Oliver, additional, Snell, Edward, additional, Robinson, Philip J., additional, Šarler, Božidar, additional, Belšak, Grega, additional, Maček, Marjan, additional, Wilde, Fabian, additional, Aquila, Andrew, additional, Boutet, Sébastien, additional, Liang, Mengning, additional, Hunter, Mark S., additional, Scheerer, Patrick, additional, Lipscomb, John D., additional, Weierstall, Uwe, additional, Kornberg, Roger D., additional, Spence, John C. H., additional, Pollack, Lois, additional, Chapman, Henry N., additional, and Bajt, Saša, additional

Published
2017
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114. Structural enzymology using X-ray free electron lasers

Author

Kupitz, Christopher, primary, Olmos, Jose L., additional, Holl, Mark, additional, Tremblay, Lee, additional, Pande, Kanupriya, additional, Pandey, Suraj, additional, Oberthür, Dominik, additional, Hunter, Mark, additional, Liang, Mengning, additional, Aquila, Andrew, additional, Tenboer, Jason, additional, Calvey, George, additional, Katz, Andrea, additional, Chen, Yujie, additional, Wiedorn, Max O., additional, Knoska, Juraj, additional, Meents, Alke, additional, Majriani, Valerio, additional, Norwood, Tyler, additional, Poudyal, Ishwor, additional, Grant, Thomas, additional, Miller, Mitchell D., additional, Xu, Weijun, additional, Tolstikova, Aleksandra, additional, Morgan, Andrew, additional, Metz, Markus, additional, Martin-Garcia, Jose M., additional, Zook, James D., additional, Roy-Chowdhury, Shatabdi, additional, Coe, Jesse, additional, Nagaratnam, Nirupa, additional, Meza, Domingo, additional, Fromme, Raimund, additional, Basu, Shibom, additional, Frank, Matthias, additional, White, Thomas, additional, Barty, Anton, additional, Bajt, Sasa, additional, Yefanov, Oleksandr, additional, Chapman, Henry N., additional, Zatsepin, Nadia, additional, Nelson, Garrett, additional, Weierstall, Uwe, additional, Spence, John, additional, Schwander, Peter, additional, Pollack, Lois, additional, Fromme, Petra, additional, Ourmazd, Abbas, additional, Phillips, George N., additional, and Schmidt, Marius, additional

Published
2016
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115. Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics

Author

Plumridge, Alex, Andresen, Kurt, and Pollack, Lois

Abstract

Disordered homopolymeric regions of single-stranded RNA, such as U or A tracts, are found within functional RNAs where they play distinct roles in defining molecular structure and facilitating recognition by partners. Despite this prominence, details of conformational and biophysical properties of these regions have not yet been resolved. We apply a number of experimental techniques to investigate the conformations of these biologically important motifs and provide quantitative measurements of their ion atmospheres. Single strands of RNA display pronounced sequence-dependent conformations that relate to the unique ion atmospheres each attracts. Chains of rU bases are relatively unstructured under all conditions, while chains of rA bases display distinct ordering through stacking or clustering motifs, depending on the composition of the surrounding solution. These dramatic structural differences are consistent with the measured disparity in ion composition and atmospheres around each homopolymer, revealing a complex interplay of base, ion, and single-strand ordering. The unique structural and ionic signatures of homopolymer ssRNAs explains their role(s) in folding structured RNAs and may explain their distinct recognition by protein partners.

Published
2020
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124. Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls.

Author

Yingyuan Sun, Klose, Thomas, Rossmann, Michael G., Roznowski, Aaron P., Fane, Bentley A., Tokuda, Joshua M., Mauney, Alexander, and Pollack, Lois

Subjects
BACTERIOPHAGES, BACTERIAL cell walls, LIPOPOLYSACCHARIDES, DNA, SALMONELLA typhimurium, PHYSIOLOGY
Abstract

Unlike tailed bacteriophages, which use a preformed tail for transporting their genomes into a host bacterium, the ssDNA bacteriophage ΦX174 is tailless. Using cryo-electron microscopy and time-resolved small-angle X-ray scattering, we show that lipopolysaccharides (LPS) form bilayers that interact with ΦX174 at an icosahedral fivefold vertex and induce single-stranded (ss) DNA genome ejection. The structures of ΦX174 complexed with LPS have been determined for the pre- and post-ssDNA ejection states. The ejection is initiated by the loss of the G protein spike that encounters the LPS, followed by conformational changes of two polypeptide loops on the major capsid F proteins. One of these loops mediates viral attachment, and the other participates in making the fivefold channel at the vertex contacting the LPS. [ABSTRACT FROM AUTHOR]

Published
2017
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133. Why double-stranded RNA resists condensation

Author

Computer Science, Physics, Tolokh, Igor S., Pabit, Suzette A., Katz, Andrea M., Chen, Yujie, Drozdetski, Aleksander V., Baker, Nathan, Pollack, Lois, Onufriev, Alexey V., Computer Science, Physics, Tolokh, Igor S., Pabit, Suzette A., Katz, Andrea M., Chen, Yujie, Drozdetski, Aleksander V., Baker, Nathan, Pollack, Lois, and Onufriev, Alexey V.

Abstract

The addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to inter-DNA attraction and eventual condensation. Surprisingly, the condensation is suppressed in double-stranded RNA, which carries the same negative charge as DNA, but assumes a different double helical form. Here, we combine experiment and atomistic simulations to propose a mechanism that explains the variations in condensation of short (25 base-pairs) nucleic acid (NA) duplexes, from B-like form of homopolymeric DNA, to mixed sequence DNA, to DNA: RNA hybrid, to A-like RNA. Circular dichroism measurements suggest that duplex helical geometry is not the fundamental property that ultimately determines the observed differences in condensation. Instead, these differences are governed by the spatial variation of cobalt hexammine (CoHex) binding to NA. There are two major NA-CoHex binding modes-internal and external-distinguished by the proximity of bound CoHex to the helical axis. We find a significant difference, up to 5-fold, in the fraction of ions bound to the external surfaces of the different NA constructs studied. NA condensation propensity is determined by the fraction of CoHex ions in the external binding mode.

Published
2014

135. Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core.

Author

Yujie Chen, Tokuda, Joshua M., Pabit, Suzette A., Pollack, Lois, Meisburger, Steve P., Topping, Traci, and Gloss, Lisa M.

Subjects
GENOMES, EUKARYOTIC cells, HISTONES, DNA analysis, CHROMOSOMES
Abstract

The nucleosome core particle (NCP) is the basic structural unit for genome packaging in eukaryotic cells and consists of DNA wound around a core of eight histone proteins. DNA access is modulated through dynamic processes of NCP disassembly. Partly disassembled structures, such as the hexasome (containing six histones) and the tetrasome (four histones), are important for transcription regulation in vivo. However, the pathways for their formation have been difficult to characterize. We combine time-resolved (TR) small-angle X-ray scattering and TR-FRET to correlate changes in the DNA conformations with composition of the histone core during saltinduced disassembly of canonical NCPs. We find that H2A–H2B histone dimers are released sequentially, with the first dimer being released after the DNA has formed an asymmetrically unwrapped, teardrop-shape DNA structure. This finding suggests that the octasome- to-hexasome transition is guided by the asymmetric unwrapping of the DNA. The link between DNA structure and histone composition suggests a potential mechanism for the action of proteins that alter nucleosome configurations such as histone chaperones and chromatin remodeling complexes. [ABSTRACT FROM AUTHOR]

Published
2017
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