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Role of Ion Valence in the Submillisecond Collapse and Folding of a Small RNA Domain

12 Feb 2013 | BioXFEL Publications | Contributor(s): Suzette A. Pabit, Julie L. Sutton, Huimin Chen, Lois Pollack

http://dx.doi.org/10.1021/bi3016636 journal-article Pabit, S.A. et al., 2013. Role of Ion Valence in the Submillisecond Collapse and Folding of a Small RNA Domain. Biochemistry, 52(9), pp.1539–1546. Available at: http://dx.doi.org/10.1021/bi3016636. Suzette A. Pabit and Julie L. Sutton and …

Protein dielectrophoresis: Advances, challenges, and applications

11 Feb 2013 | BioXFEL Publications | Contributor(s): Asuka Nakano, Alexandra Ros

http://dx.doi.org/10.1002/elps.201200482 journal-article Nakano, A. & Ros, A., 2013. Protein dielectrophoresis: Advances, challenges, and applications. ELECTROPHORESIS, 34(7), pp.1085–1096. Available at: http://dx.doi.org/10.1002/elps.201200482. Asuka Nakano and Alexandra Ros

Coordinating the impact of structural genomics on the human α-helical transmembrane proteome

05 Feb 2013 | BioXFEL Publications | Contributor(s): Ursula Pieper, Avner Schlessinger, Edda Kloppmann, Geoffrey A Chang, James J Chou, Mark E Dumont, Brian G Fox, Petra Fromme, Wayne A Hendrickson, Michael G Malkowski, Douglas C Rees, David L Stokes, Michael H B Stowell, Michael C Wiener, Burkhard Rost, Robert Stroud, Raymond C Stevens, Andrej Sali

journal-article http://dx.doi.org/10.1038/nsmb.2508 Pieper, U. et al., 2013. Coordinating the impact of structural genomics on the human α-helical transmembrane proteome. Nature Structural & Molecular Biology, 20(2), pp.135–138. Available at: http://dx.doi.org/10.1038/nsmb.2508. Ursula Pieper …

Volume-conserving trans–cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography

01 Feb 2013 | BioXFEL Publications | Contributor(s): Yang Ouk Jung, Jae Hyuk Lee, Joonghan Kim, Marius Schmidt, Keith Moffat, Vukica Šrajer, Hyotcherl Ihee

http://dx.doi.org/10.1038/nchem.1565 journal-article Jung, Y.O. et al., 2013. Volume-conserving trans–cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography. Nature Chemistry, 5(3), pp.212–220. Available at: …

Purification and SAXS Analysis of the Integrin Linked Kinase, PINCH, Parvin (IPP) Heterotrimeric Complex

31 Jan 2013 | BioXFEL Publications | Contributor(s): Amy L. Stiegler, Thomas D. Grant, Joseph Luft, David A. Calderwood, Edward Snell, Titus J. Boggon

http://dx.doi.org/10.1371/journal.pone.0055591 journal-article Stiegler, A.L. et al., 2013. Purification and SAXS Analysis of the Integrin Linked Kinase, PINCH, Parvin (IPP) Heterotrimeric Complex B. Kobe, ed. PLoS ONE, 8(1), p.e55591. Available at: …

Crystallization of a self-assembled three-dimensional DNA nanostructure

30 Jan 2013 | BioXFEL Publications | Contributor(s): Kimberly N. Rendek, Raimund Fromme, Ingo Grotjohann, Petra Fromme

journal-article http://dx.doi.org/10.1107/s1744309112052128 Rendek, K.N. et al., 2013. Crystallization of a self-assembled three-dimensional DNA nanostructure. Acta Crystallographica Section F Structural Biology and Crystallization Communications, 69(2), pp.141–146. Available at: …

Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane

29 Jan 2013 | BioXFEL Publications | Contributor(s): James D Zook, Trivikram R. Moulgu, Neil Jacobsen, Guangxin Lin, Brian Cherry, Michael F. Brown, Petra Fromme

http://dx.doi.org/10.1016/j.bpj.2012.11.1248 journal-article Zook, J.D. et al., 2013. Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane. Biophysical Journal, 104(2), p.221a. Available at: http://dx.doi.org/10.1016/j.bpj.2012.11.1248. James D. Zook and …

Dielectrophoresis of lambda-DNA using 3D carbon electrodes

24 Jan 2013 | BioXFEL Publications | Contributor(s): Rodrigo Martinez-Duarte, Fernanda Camacho-Alanis, Philippe Renaud, Alexandra Ros

http://dx.doi.org/10.1002/elps.201200447 journal-article Martinez-Duarte, R. et al., 2013. Dielectrophoresis of lambda-DNA using 3D carbon electrodes. ELECTROPHORESIS, 34(7), pp.1113–1122. Available at: http://dx.doi.org/10.1002/elps.201200447. Rodrigo Martinez-Duarte and Fernanda …

Relative Stability of Human Centrins and Its Relationship to Calcium Binding

24 Jan 2013 | BioXFEL Publications | Contributor(s): Belinda Pastrana-Ríos, Myrna Reyes, Jessica De Orbeta, Verónica Meza, Daniel Narváez, Ana María Gómez, Aslin Marie Rodriguez Nassif, Ruth Almodovar, Adalberto Díaz Casas, José Robles, Ana María Ortiz, Lizbeth Irizarry, Melissa Campbell, Mara Colón

journal-article http://dx.doi.org/10.1021/bi301417z Pastrana-Ríos, B. et al., 2013. Relative Stability of Human Centrins and Its Relationship to Calcium Binding. Biochemistry, 52(7), pp.1236–1248. Available at: http://dx.doi.org/10.1021/bi301417z. Belinda Pastrana-Ríos and Myrna Reyes and …

From Systems to Structure: Bridging Networks and Mechanism

24 Jan 2013 | BioXFEL Publications | Contributor(s): James S. Fraser, John D. Gross, Nevan J. Krogan

journal-article http://dx.doi.org/10.1016/j.molcel.2013.01.003 Fraser, J.S., Gross, J.D. & Krogan, N.J., 2013. From Systems to Structure: Bridging Networks and Mechanism. Molecular Cell, 49(2), pp.222–231. Available at: http://dx.doi.org/10.1016/j.molcel.2013.01.003. James S. Fraser and …

Structure of the Bifunctional Acyltransferase/Decarboxylase LnmK from the Leinamycin Biosynthetic Pathway Revealing Novel Activity for a Double-Hot-Dog Fold

15 Jan 2013 | BioXFEL Publications | Contributor(s): Jeremy R. Lohman, Craig A. Bingman, George Phillips, Ben Shen

http://dx.doi.org/10.1021/bi301652y journal-article Lohman, J.R. et al., 2013. Structure of the Bifunctional Acyltransferase/Decarboxylase LnmK from the Leinamycin Biosynthetic Pathway Revealing Novel Activity for a Double-Hot-Dog Fold. Biochemistry, 52(5), pp.902–911. Available at: …

Formation and Fate of a Complete 31-Protein RNA Polymerase II Transcription Preinitiation Complex

10 Jan 2013 | BioXFEL Publications | Contributor(s): Kenji Murakami, Guillermo Calero, Christopher R. Brown, Xin Liu, Ralph E. Davis, Hinrich Boeger, Roger Kornberg

journal-article http://dx.doi.org/10.1074/jbc.m112.433623 Murakami, K. et al., 2013. Formation and Fate of a Complete 31-Protein RNA Polymerase II Transcription Preinitiation Complex. Journal of Biological Chemistry, 288(9), pp.6325–6332. Available at: http://dx.doi.org/10.1074/jbc.m112.433623. …

Breaking the Radiation Damage Limit with Cryo-SAXS

08 Jan 2013 | BioXFEL Publications | Contributor(s): Steve P. Meisburger, Matthew Warkentin, Huimin Chen, Jesse B. Hopkins, Richard E. Gillilan, Lois Pollack, Robert E. Thorne

http://dx.doi.org/10.1016/j.bpj.2012.11.3817 journal-article Meisburger, S.P. et al., 2013. Breaking the Radiation Damage Limit with Cryo-SAXS. Biophysical Journal, 104(1), pp.227–236. Available at: http://dx.doi.org/10.1016/j.bpj.2012.11.3817. Steve P. Meisburger and Matthew Warkentin and …

Phasing coherently illuminated nanocrystals bounded by partial unit cells

31 Dec 2012 | Publications | Contributor(s): R. Kirian, R. Bean, K. Beyerlein, O. Yevanof, T. White, A. Barty, Henry Chapman

With the use of highly coherent femtosecond X-ray pulses from a free-electron laser, it is possible to record protein nanocrystal diffraction patterns with far more information than is present in conventional crystallographic diffraction data. It has been suggested that diffraction phases may be …

Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser

30 Nov 2012 | BioXFEL Publications | Contributor(s): L. Redecke, K. Nass, D. P. DePonte, T. A. White, D. Rehders, A. Barty, F. Stellato, M. Liang, T. R. M. Barends, S. Boutet, G. J. Williams, M. Messerschmidt, M. M. Seibert, A. Aquila, D. Arnlund, S. Bajt, T. Barth, M. J. Bogan, C. Caleman, T.-C. Chao, R. B. Doak, H. Fleckenstein, M. Frank, R. Fromme, L. Galli, I. Grotjohann, M. S. Hunter, L. C. Johansson, S. Kassemeyer, G. Katona, R. A. Kirian, R. Koopmann, C. Kupitz, L. Lomb, A. V. Martin, S. Mogk, R. Neutze, R. L. Shoeman, J. Steinbrener, N. Timneanu, D. Wang, U. Weierstall, N. A. Zatsepin, J. C. H. Spence, P. Fromme, I. Schlichting, M. Duszenko, C. Betzel, H. N. Chapman

http://dx.doi.org/10.1126/science.1229663 journal-article Redecke, L. et al., 2013. Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser. Science, 339(6116), pp.227–230. Available at: http://dx.doi.org/10.1126/science.1229663. L. Redecke and K. Nass …

Subcongenic Analyses Reveal Complex Interactions between Distal Chromosome 4 Genes Controlling Diabetogenic B Cells and CD4 T Cells in Nonobese Diabetic Mice

26 Jun 2012 | BioXFEL Publications | Contributor(s): J. Stolp, Y.-G. Chen, S. L. Cox, V. Henck, W. Zhang, S.-W. Tsaih, H. Chapman, T. Stearns, D. V. Serreze, P. A. Silveira

http://dx.doi.org/10.4049/jimmunol.1200120 journal-article Stolp, J. et al., 2012. Subcongenic Analyses Reveal Complex Interactions between Distal Chromosome 4 Genes Controlling Diabetogenic B Cells and CD4 T Cells in Nonobese Diabetic Mice. The Journal of Immunology, 189(3), pp.1406–1417. …

X-ray crystal structure of the transmembrane beta-domain from intimin from EHEC strain O157:H7

12 Jun 2012 | BioXFEL Publications | Contributor(s): J.W. Fairman, N. Dautin, D. Wojtowicz, L. Wei, N. Noinaj, T.J. Barnard, E. Udho, A. Finkelstein, T.M. Przytycka, V. Cherezov, S.K. Buchanan

http://dx.doi.org/10.2210/pdb4e1s/pdb component Fairman, J.W. et al., 2012. X-ray crystal structure of the transmembrane beta-domain from intimin from EHEC strain O157:H7. Available at: http://dx.doi.org/10.2210/pdb4e1s/pdb. J.W. Fairman and N. Dautin and D. Wojtowicz and L. Wei and N. Noinaj …

X-ray crystal structure of the transmembrane beta-domain from invasin from Yersinia pseudotuberculosis

12 Jun 2012 | BioXFEL Publications | Contributor(s): J.W. Fairman, N. Dautin, D. Wojtowicz, L. Wei, N. Noinaj, T.J. Barnard, E. Udho, A. Finkelstein, T.M. Przytycka, V. Cherezov, S.K. Buchanan

http://dx.doi.org/10.2210/pdb4e1t/pdb component Fairman, J.W. et al., 2012. X-ray crystal structure of the transmembrane beta-domain from invasin from Yersinia pseudotuberculosis. Available at: http://dx.doi.org/10.2210/pdb4e1t/pdb. J.W. Fairman and N. Dautin and D. Wojtowicz and L. Wei and N. …

Bacterial phytochromes: More than meets the light

21 Jan 2011 | BioXFEL Publications | Contributor(s): Michele E. Auldridge, Katrina T. Forest

http://dx.doi.org/10.3109/10409238.2010.546389 journal-article Auldridge, M.E. & Forest, K.T., 2011. Bacterial phytochromes: More than meets the light. Critical Reviews in Biochemistry and Molecular Biology, 46(1), pp.67–88. Available at: http://dx.doi.org/10.3109/10409238.2010.546389. Michele …

The Coherent X-ray Imaging Data Bank

31 Dec 2010 | Publications | Contributor(s): F. R. N. C. Maia

www.cxidb.org The Coherent X-ray Imaging Data Bank (CXIDB) is a database offering scientists access to data from Coherent X-ray Imaging (CXI) experiments, including serial femtosecond crystallography and single particle imaging. www.cxidb.org The Coherent X-ray Imaging Data Bank Filipe R …

Damage threshold of amorphous carbon mirror for 177eV FEL radiation

10 Nov 2010 | BioXFEL Publications | Contributor(s): Sh. Dastjani Farahani, Jaromir Chalupsky, T. Burian, Henry Chapman, A.J. Gleeson, V. Hajkoya, L. Juha, M. Jurek, Dorota Klinger, Harald Sinn, R. Sobierajski, M. Störmer, K. Tiedtke, S. Toleikis, Thomas Tschentscher, H. Wabnitz, Jerome Gaudin

http://dx.doi.org/10.1016/j.nima.2010.10.133 journal-article Dastjani Farahani, S. et al., 2011. Damage threshold of amorphous carbon mirror for 177eV FEL radiation. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, …

Electrophysiology of Viral Envelope Protein Ion Channels in Lipid Membranes Across Apertures in Polystyrene and Silicon

27 Jan 2010 | BioXFEL Publications | Contributor(s): Nipun Chaplot, Latrice Faulkner, Sasha Daskalova, Brenda Hogue, Michael Goryll

http://dx.doi.org/10.1016/j.bpj.2009.12.300 journal-article Chaplot, N. et al., 2010. Electrophysiology of Viral Envelope Protein Ion Channels in Lipid Membranes Across Apertures in Polystyrene and Silicon. Biophysical Journal, 98(3), p.52a. Available at: …

Nonlinear Optical Imaging of Integral Membrane Protein Crystals in Lipidic Mesophases

21 Dec 2009 | BioXFEL Publications | Contributor(s): David J. Kissick, Ellen J. Gualtieri, Garth J. Simpson, Vadim Cherezov

http://dx.doi.org/10.1021/ac902139w journal-article Kissick, D.J. et al., 2010. Nonlinear Optical Imaging of Integral Membrane Protein Crystals in Lipidic Mesophases. Analytical Chemistry, 82(2), pp.491–497. Available at: http://dx.doi.org/10.1021/ac902139w. David J. Kissick and Ellen J. …

Suppression of lipopolysaccharide-induced inflammatory responses in RAW 264.7 murine macrophages by aqueous extract of Clinopodium vulgare L. (Lamiaceae)

20 Sep 2009 | BioXFEL Publications | Contributor(s): David R. Burk, Patti Senechal-Willis, Linda C. Lopez, Brenda Hogue, Sasha M. Daskalova

http://dx.doi.org/10.1016/j.jep.2009.09.026 journal-article Burk, D.R. et al., 2009. Suppression of lipopolysaccharide-induced inflammatory responses in RAW 264.7 murine macrophages by aqueous extract of Clinopodium vulgare L. (Lamiaceae). Journal of Ethnopharmacology, 126(3), pp.397–405. …

ID: 294 Tumor Cell Signaling Through Integrin alpha5beta1 Requires Urokinase Receptor Binding

06 Nov 2006 | BioXFEL Publications | Contributor(s): H. Chapman, C. Tang, L. Robillard, Y. Kim, Y. Wei

http://dx.doi.org/10.1111/j.1538-7836.2006.00294.x journal-article Chapman, H. et al., 2006. ID: 294 Tumor Cell Signaling Through Integrin alpha5beta1 Requires Urokinase Receptor Binding. Journal of Thrombosis and Haemostasis, 4(s1), pp.78–78. Available at: …

Field dependence of cross relaxation in scandium (I=7/2)

03 Sep 2003 | BioXFEL Publications | Contributor(s): L. Pollack, E.N. Smith, R.C. Richardson

https://doi.org/10.1016/0921-4526(94)90501-0 journal-article Pollack, L., Smith, E. N., & Richardson, R. C. (1994). Field dependence of cross relaxation in scandium (I=7/2). Physica B: Condensed Matter, 194–196, 343–344. https://doi.org/10.1016/0921-4526(94)90501-0 L. Pollack and E.N. Smith …

Morphology of GaAs-quantum-well interfaces grown by liquid-phase epitaxy

26 Jul 2002 | BioXFEL Publications | Contributor(s): U. Morlock, J. Christen, D. Bimberg, E. Bauser, H.-J. Queisser, A. Ourmazd

http://dx.doi.org/10.1103/physrevb.44.8792 journal-article Morlock, U. et al., 1991. Morphology of GaAs-quantum-well interfaces grown by liquid-phase epitaxy. Physical Review B, 44(16), pp.8792–8797. Available at: http://dx.doi.org/10.1103/physrevb.44.8792. U. Morlock and J. Christen and D. …

Solution and Crystal Structures of a Sperm Whale Myoglobin Triple Mutant That Mimics the Sulfide-binding Hemoglobin fromLucina pectinata

26 Jul 2002 | BioXFEL Publications | Contributor(s): Bao D. Nguyen, Xuefeng Zhao, Krishnamurthi Vyas, Gerd N. La Mar, R. Ashley Lile, Eric Allen Brucker, George Phillips, John S. Olson, Jonathan B. Wittenberg

http://dx.doi.org/10.1074/jbc.273.16.9517 journal-article Nguyen, B.D. et al., 1998. Solution and Crystal Structures of a Sperm Whale Myoglobin Triple Mutant That Mimics the Sulfide-binding Hemoglobin fromLucina pectinata. Journal of Biological Chemistry, 273(16), pp.9517–9526. Available at: …

Quantitative Analysis of the Electrostatic Potential in Rock-Salt Crystals Using Accurate Electron Diffraction Data

26 Jul 2002 | BioXFEL Publications | Contributor(s): V. G. Tsirelson, A. S. Avilov, G. G. Lepeshov, A. K. Kulygin, J. Stahn, U. Pietsch, J. C. H. Spence

http://dx.doi.org/10.1021/jp0015729 journal-article Tsirelson, V.G. et al., 2001. Quantitative Analysis of the Electrostatic Potential in Rock-Salt Crystals Using Accurate Electron Diffraction Data. The Journal of Physical Chemistry B, 105(21), pp.5068–5074. Available at: …