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  • 1
    Publication Date: 2013-09-28
    Description: The protein density and arrangement of subunits of a complete, 32-protein, RNA polymerase II (pol II) transcription pre-initiation complex (PIC) were determined by means of cryogenic electron microscopy and a combination of chemical cross-linking and mass spectrometry. The PIC showed a marked division in two parts, one containing all the general transcription factors (GTFs) and the other pol II. Promoter DNA was associated only with the GTFs, suspended above the pol II cleft and not in contact with pol II. This structural principle of the PIC underlies its conversion to a transcriptionally active state; the PIC is poised for the formation of a transcription bubble and descent of the DNA into the pol II cleft.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4039082/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4039082/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murakami, Kenji -- Elmlund, Hans -- Kalisman, Nir -- Bushnell, David A -- Adams, Christopher M -- Azubel, Maia -- Elmlund, Dominika -- Levi-Kalisman, Yael -- Liu, Xin -- Gibbons, Brian J -- Levitt, Michael -- Kornberg, Roger D -- AI21144/AI/NIAID NIH HHS/ -- GM063817/GM/NIGMS NIH HHS/ -- GM49885/GM/NIGMS NIH HHS/ -- R01 AI021144/AI/NIAID NIH HHS/ -- R01 GM036659/GM/NIGMS NIH HHS/ -- R01 GM063817/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Nov 8;342(6159):1238724. doi: 10.1126/science.1238724. Epub 2013 Sep 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24072820" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; DNA, Fungal/chemistry/genetics ; *Gene Expression Regulation, Fungal ; Multiprotein Complexes/*chemistry ; Nucleic Acid Conformation ; Protein Conformation ; RNA Polymerase II/*chemistry ; Saccharomyces cerevisiae/*enzymology/genetics ; Saccharomyces cerevisiae Proteins/*chemistry ; Transcription Factors, General/*chemistry ; *Transcription Initiation, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2014-08-26
    Description: An understanding of how facets of a nanocrystal develop is critical for controlling nanocrystal shape and designing novel functional materials. However, the atomic pathways of nanocrystal facet development are mostly unknown because of the lack of direct observation. We report the imaging of platinum nanocube growth in a liquid cell using transmission electron microscopy with high spatial and temporal resolution. The growth rates of all low index facets are similar until the {100} facets stop growth. The continuous growth of the rest facets leads to a nanocube. Our calculation shows that the much lower ligand mobility on the {100} facets is responsible for the arresting of {100} growing facets. These findings shed light on nanocrystal shape-control mechanisms and future design of nanomaterials.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liao, Hong-Gang -- Zherebetskyy, Danylo -- Xin, Huolin -- Czarnik, Cory -- Ercius, Peter -- Elmlund, Hans -- Pan, Ming -- Wang, Lin-Wang -- Zheng, Haimei -- New York, N.Y. -- Science. 2014 Aug 22;345(6199):916-9. doi: 10.1126/science.1253149.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. ; Gatan, Incorporated, 5794 West Las Positas Boulevard, Pleasanton, CA 94588, USA. ; National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. ; Department of Structural Biology, Medical School, Stanford University, Stanford, CA 94305, USA. ; Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Department of Material Science and Engineering, University of California, Berkeley, CA 94720, USA. hmzheng@lbl.gov.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25146287" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2015-07-18
    Description: Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, Jungwon -- Elmlund, Hans -- Ercius, Peter -- Yuk, Jong Min -- Limmer, David T -- Chen, Qian -- Kim, Kwanpyo -- Han, Sang Hoon -- Weitz, David A -- Zettl, A -- Alivisatos, A Paul -- New York, N.Y. -- Science. 2015 Jul 17;349(6245):290-5. doi: 10.1126/science.aab1343. Epub 2015 Jul 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley, CA 94720, USA. Department of Applied Physics, Harvard University, Cambridge, MA 02138, USA. School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA. ; Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia. ARC Centre of Excellence for Advanced Molecular Imaging, Clayton, VIC 3800, Australia. ; Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. ; Department of Physics, University of California, Berkeley, CA 94720, USA. Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Kavli Energy NanoScience Institute, Berkeley, CA 94720, USA. ; Princeton Center for Theoretical Science, Princeton University, Princeton, NJ 08540, USA. ; Department of Chemistry, University of California, Berkeley, CA 94720, USA. Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Miller Institute for Basic Research in Science, University of California, Berkeley, CA 93720, USA. ; Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 689-798, South Korea. ; Amore-Pacific Co. R&D Center, Yongin 446-829, South Korea. ; Department of Applied Physics, Harvard University, Cambridge, MA 02138, USA. School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA. ; Department of Chemistry, University of California, Berkeley, CA 94720, USA. Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Kavli Energy NanoScience Institute, Berkeley, CA 94720, USA. alivis@berkeley.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26185247" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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