Nature Structural & Molecular Biology - AOP - nature.com science feeds Nature Structural & Molecular Biology is an integrated forum for structural and molecular studies. The journal places a strong emphasis on functional and mechanistic understanding of how molecular components in a biological process work together. Structural data may provide such insights, but they are not a pre-requisite for publication in the journal. http://www.nature.com/nsmb/current_issue/ Nature Publishing Group en © Nature Publishing Group Nature Structural & Molecular Biology 1545-9993 1545-9985 © Nature Publishing Group permissions@nature.com Nature Structural & Molecular Biology http://www.nature.com/includes/rj_globnavimages/nsmb_logo.gif http://www.nature.com/nsmb/ Spontaneous occurrence of telomeric DNA damage response in the absence of chromosome fusions http://feeds.nature.com/~r/nsmb/rss/aop/~3/fkBFARED7Ps/nsmb.1725 Telomeric DNA is protected by the shelterin complex, whose disruption triggers DNA-damage responses, checkpoint activation and chromosomal fusions. Now analysis of human cell lines reveals a spontaneously occurring intermediate state in which the DNA-damage response is activated at the telomeres without cell cycle arrest or chromosomal fusions, and with TRF2 playing a central role in determining such a state. Spontaneous occurrence of telomeric DNA damage response in the absence of chromosome fusions

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1725

Authors: Anthony J Cesare, Zeenia Kaul, Scott B Cohen, Christine E Napier, Hilda A Pickett, Axel A Neumann & Roger R Reddel

]]> Spontaneous occurrence of telomeric DNA damage response in the absence of chromosome fusions Anthony J Cesare Zeenia Kaul Scott B Cohen Christine E Napier Hilda A Pickett Axel A Neumann Roger R Reddel doi:10.1038/nsmb.1725 Nature Structural & Molecular Biology 2009-11-22 Nature Structural & Molecular Biology 2009-11-22 10.1038/nsmb.1725 http://dx.doi.org/10.1038/nsmb.1725 Article http://dx.doi.org/10.1038/nsmb.1725 Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II http://feeds.nature.com/~r/nsmb/rss/aop/~3/mmuVSa-QXjM/nsmb.1689 On specific DNA sequences in vitro, a nucleosome is a polar barrier to RNA polymerase II (Pol II). Further analyses of the sequences underlying this barrier effect now indicate the formation of a loop that would preserve the position of the nucleosome on the DNA, while allowing passage of Pol II. Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1689

Authors: Olga I Kulaeva, Daria A Gaykalova, Nikolai A Pestov, Viktor V Golovastov, Dmitry G Vassylyev, Irina Artsimovitch & Vasily M Studitsky

]]> Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II Olga I Kulaeva Daria A Gaykalova Nikolai A Pestov Viktor V Golovastov Dmitry G Vassylyev Irina Artsimovitch Vasily M Studitsky doi:10.1038/nsmb.1689 Nature Structural & Molecular Biology 2009-11-22 Nature Structural & Molecular Biology 2009-11-22 10.1038/nsmb.1689 http://dx.doi.org/10.1038/nsmb.1689 Article http://dx.doi.org/10.1038/nsmb.1689 Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components http://feeds.nature.com/~r/nsmb/rss/aop/~3/ksOUMUEICzE/nsmb.1729 Pre-mRNA splicing is catalyzed by the spliceosome in a two-step reaction. Both catalytic steps have now been reconstituted using purified, defined components. This system identifies a role for Cwc25 in the first step of splicing and allows future detailed mechanistic analyses of splicing. Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1729

Authors: Zbigniew Warkocki, Peter Odenwälder, Jana Schmitzová, Florian Platzmann, Holger Stark, Henning Urlaub, Ralf Ficner, Patrizia Fabrizio & Reinhard Lührmann

]]> Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components Zbigniew Warkocki Peter Odenwälder Jana Schmitzová Florian Platzmann Holger Stark Henning Urlaub Ralf Ficner Patrizia Fabrizio Reinhard Lührmann doi:10.1038/nsmb.1729 Nature Structural & Molecular Biology 2009-11-22 Nature Structural & Molecular Biology 2009-11-22 10.1038/nsmb.1729 http://dx.doi.org/10.1038/nsmb.1729 Article http://dx.doi.org/10.1038/nsmb.1729 An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe http://feeds.nature.com/~r/nsmb/rss/aop/~3/0rd8gbhbPkw/nsmb.1688 H2A.Z is implicated in genome stability across species. Acetylation of this histone variant in S. pombe is now found to be involved in maintaining condensed chromosomes during mitosis, with premature dissociation of condensin occurring in its absence. An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1688

Authors: Hyun-Soo Kim, Vincent Vanoosthuyse, Jeffrey Fillingham, Assen Roguev, Stephen Watt, Thomas Kislinger, Alex Treyer, Laura Rocco Carpenter, Christopher S Bennett, Andrew Emili, Jack F Greenblatt, Kevin G Hardwick, Nevan J Krogan, Jürg Bähler & Michael-Christopher Keogh

]]> An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe Hyun-Soo Kim Vincent Vanoosthuyse Jeffrey Fillingham Assen Roguev Stephen Watt Thomas Kislinger Alex Treyer Laura Rocco Carpenter Christopher S Bennett Andrew Emili Jack F Greenblatt Kevin G Hardwick Nevan J Krogan Jürg Bähler Michael-Christopher Keogh doi:10.1038/nsmb.1688 Nature Structural & Molecular Biology 2009-11-15 Nature Structural & Molecular Biology 2009-11-15 10.1038/nsmb.1688 http://dx.doi.org/10.1038/nsmb.1688 Article http://dx.doi.org/10.1038/nsmb.1688 A stepwise 2′-hydroxyl activation mechanism for the bacterial transcription termination factor Rho helicase http://feeds.nature.com/~r/nsmb/rss/aop/~3/LfrSk6N_w6I/nsmb.1711 The bacterial transcriptional termination factor Rho is a hexameric helicase that tracks along RNA and dissociates DNA-RNA hybrids. Here the activity of Rho is examined using nucleotide analog interference mapping, revealing that the helicase takes large, 7-nt steps, triggered by contacts with 2′OH in the tracked RNA substrate. A stepwise 2′-hydroxyl activation mechanism for the bacterial transcription termination factor Rho helicase

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1711

Authors: Annie Schwartz, Makhlouf Rabhi, Frédérique Jacquinot, Emmanuel Margeat, A Rachid Rahmouni & Marc Boudvillain

]]> A stepwise 2′-hydroxyl activation mechanism for the bacterial transcription termination factor Rho helicase Annie Schwartz Makhlouf Rabhi Frédérique Jacquinot Emmanuel Margeat A Rachid Rahmouni Marc Boudvillain doi:10.1038/nsmb.1711 Nature Structural & Molecular Biology 2009-11-15 Nature Structural & Molecular Biology 2009-11-15 10.1038/nsmb.1711 http://dx.doi.org/10.1038/nsmb.1711 Article http://dx.doi.org/10.1038/nsmb.1711 The chromosomal association of condensin II is regulated by a noncatalytic function of PP2A http://feeds.nature.com/~r/nsmb/rss/aop/~3/hBZvbtLPEP0/nsmb.1708 Condensins are protein complexes essential for eukaryotic mitosis and whose chromosome association is regulated by phosphorylation and dephosphorylation events. Now protein phosphatase PP2A is important for association of condensin II to mitotic chromosomes, but its catalytic activity is not required. The chromosomal association of condensin II is regulated by a noncatalytic function of PP2A

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1708

Authors: Ai Takemoto, Kazuhiro Maeshima, Tsuyoshi Ikehara, Kazumitsu Yamaguchi, Akiko Murayama, Shihoko Imamura, Naoko Imamoto, Shigeyuki Yokoyama, Tatsuya Hirano, Yoshinori Watanabe, Fumio Hanaoka, Junn Yanagisawa & Keiji Kimura

]]> The chromosomal association of condensin II is regulated by a noncatalytic function of PP2A Ai Takemoto Kazuhiro Maeshima Tsuyoshi Ikehara Kazumitsu Yamaguchi Akiko Murayama Shihoko Imamura Naoko Imamoto Shigeyuki Yokoyama Tatsuya Hirano Yoshinori Watanabe Fumio Hanaoka Junn Yanagisawa Keiji Kimura doi:10.1038/nsmb.1708 Nature Structural & Molecular Biology 2009-11-15 Nature Structural & Molecular Biology 2009-11-15 10.1038/nsmb.1708 http://dx.doi.org/10.1038/nsmb.1708 Article http://dx.doi.org/10.1038/nsmb.1708 The chaperonin TRiC blocks a huntingtin sequence element that promotes the conformational switch to aggregation http://feeds.nature.com/~r/nsmb/rss/aop/~3/HPxLSvxkQgs/nsmb.1700 The eukaryotic group II chaperonin TRiC can block polyQ tract aggregation, present in proteins such as Htt. Here the TRiC-Htt interaction is examined using in vitro and in vivo experiments, revealing that TRiC does not physically block the polyQ tract, but rather sequesters a short N-terminal sequence that promotes the amyloidogenic conformation. The chaperonin TRiC blocks a huntingtin sequence element that promotes the conformational switch to aggregation

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1700

Authors: Stephen Tam, Christoph Spiess, William Auyeung, Lukasz Joachimiak, Bryan Chen, Michelle A Poirier & Judith Frydman

]]> The chaperonin TRiC blocks a huntingtin sequence element that promotes the conformational switch to aggregation Stephen Tam Christoph Spiess William Auyeung Lukasz Joachimiak Bryan Chen Michelle A Poirier Judith Frydman doi:10.1038/nsmb.1700 Nature Structural & Molecular Biology 2009-11-15 Nature Structural & Molecular Biology 2009-11-15 10.1038/nsmb.1700 http://dx.doi.org/10.1038/nsmb.1700 Article http://dx.doi.org/10.1038/nsmb.1700 Physical determinants of strong voltage sensitivity of K+ channel block http://feeds.nature.com/~r/nsmb/rss/aop/~3/U37y9clbK9M/nsmb.1717 Inward-rectifier K+ channels respond to voltage via blockage by intracellular polyamines. How these blockers work is not entirely clear. Now a crystal structure of the cytoplasmic portion of Kir3.1 reveals five ion sites, and functional analyses indicate these ions are displaced by spermine binding. Physical determinants of strong voltage sensitivity of K+ channel block

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1717

Authors: Yanping Xu, Hyeon-Gyu Shin, Szilvia Szép & Zhe Lu

]]> Physical determinants of strong voltage sensitivity of K+ channel block Yanping Xu Hyeon-Gyu Shin Szilvia Szép Zhe Lu doi:10.1038/nsmb.1717 Nature Structural & Molecular Biology 2009-11-15 Nature Structural & Molecular Biology 2009-11-15 10.1038/nsmb.1717 http://dx.doi.org/10.1038/nsmb.1717 Article http://dx.doi.org/10.1038/nsmb.1717 Nonspecifically bound proteins spin while diffusing along DNA http://feeds.nature.com/~r/nsmb/rss/aop/~3/P6s4_o4Fdxc/nsmb.1716 Some proteins move along DNA, searching for a specific target. Now these proteins are shown to follow a helical path, i.e., they rotate while sliding, hence maintaining a specific orientation to the DNA helix. This is accomplished by tracking single molecules of labeled human oxoguanine DNA glycosylase 1, alone or bound to a bulky streptavidin moiety, and calculating their diffusion constants. Nonspecifically bound proteins spin while diffusing along DNA

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1716

Authors: Paul C Blainey, Guobin Luo, S C Kou, Walter F Mangel, Gregory L Verdine, Biman Bagchi & X Sunney Xie

]]> Nonspecifically bound proteins spin while diffusing along DNA Paul C Blainey Guobin Luo S C Kou Walter F Mangel Gregory L Verdine Biman Bagchi X Sunney Xie doi:10.1038/nsmb.1716 Nature Structural & Molecular Biology 2009-11-08 Nature Structural & Molecular Biology 2009-11-08 10.1038/nsmb.1716 http://dx.doi.org/10.1038/nsmb.1716 Article http://dx.doi.org/10.1038/nsmb.1716 Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch http://feeds.nature.com/~r/nsmb/rss/aop/~3/yEaaSM5xmoQ/nsmb.1701 c-di-GMP is a bacterial second messenger implicated in processes such as biofilm formation and switches between motile and sedentary lifestyles. The structure of the c-di-GMP–binding GEMM riboswitch is now presented with ligand and the large conformational changes between ligand-bound and unbound forms analyzed by small-angle X-ray scattering. Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1701

Authors: Nadia Kulshina, Nathan J Baird & Adrian R Ferré-D'Amaré

]]> Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch Nadia Kulshina Nathan J Baird Adrian R Ferré-D'Amaré doi:10.1038/nsmb.1701 Nature Structural & Molecular Biology 2009-11-08 Nature Structural & Molecular Biology 2009-11-08 10.1038/nsmb.1701 http://dx.doi.org/10.1038/nsmb.1701 Article http://dx.doi.org/10.1038/nsmb.1701 Basis of substrate binding and conservation of selectivity in the CLC family of channels and transporters http://feeds.nature.com/~r/nsmb/rss/aop/~3/4EB8YaKkXZw/nsmb.1704 The crucial ion-binding events that drive H+/Cl− exchange in the bacterial transporter CLC-ec1 are now probed by isothermal calorimetry and detergent-solubilized proteins. The results indicate that transport via CLC channels have an inherent directionality, rather than being driven by an electrochemical gradient. Basis of substrate binding and conservation of selectivity in the CLC family of channels and transporters

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1704

Authors: Alessandra Picollo, Mattia Malvezzi, Jon C D Houtman & Alessio Accardi

]]> Basis of substrate binding and conservation of selectivity in the CLC family of channels and transporters Alessandra Picollo Mattia Malvezzi Jon C D Houtman Alessio Accardi doi:10.1038/nsmb.1704 Nature Structural & Molecular Biology 2009-11-08 Nature Structural & Molecular Biology 2009-11-08 10.1038/nsmb.1704 http://dx.doi.org/10.1038/nsmb.1704 Article http://dx.doi.org/10.1038/nsmb.1704 Structural basis of ligand binding by a c-di-GMP riboswitch http://feeds.nature.com/~r/nsmb/rss/aop/~3/7Iq7iSWJ8T0/nsmb.1702 The GEMM riboswitch is conserved in diverse bacteria and recognizes the second messenger c-di-GMP which mediates many processes, such as the transition between sedentary and motile behavior. The structure of the GEMM riboswitch with ligand now elucidates ligand recognition and specificity. Structural basis of ligand binding by a c-di-GMP riboswitch

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1702

Authors: Kathryn D Smith, Sarah V Lipchock, Tyler D Ames, Jimin Wang, Ronald R Breaker & Scott A Strobel

]]> Structural basis of ligand binding by a c-di-GMP riboswitch Kathryn D Smith Sarah V Lipchock Tyler D Ames Jimin Wang Ronald R Breaker Scott A Strobel doi:10.1038/nsmb.1702 Nature Structural & Molecular Biology 2009-11-08 Nature Structural & Molecular Biology 2009-11-08 10.1038/nsmb.1702 http://dx.doi.org/10.1038/nsmb.1702 Article http://dx.doi.org/10.1038/nsmb.1702 Solution structure and functional analysis of the influenza B proton channel http://feeds.nature.com/~r/nsmb/rss/aop/~3/Mk903hBBG0k/nsmb.1707 Influenza B virus is responsible for about half of all the seasonal flu cases. The integral protein BM2 oligomerizes and forms a pH-activated proton channel that is essential for viral entry into host cells. The solution structures of the membrane-embedded chain domain and the C-terminal cytoplasmic domain reveal significant differences from the AM2 protein of influenza A virus and explain antiviral drug resistance. Solution structure and functional analysis of the influenza B proton channel

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1707

Authors: Junfeng Wang, Rafal M Pielak, Mark A McClintock & James J Chou

]]> Solution structure and functional analysis of the influenza B proton channel Junfeng Wang Rafal M Pielak Mark A McClintock James J Chou doi:10.1038/nsmb.1707 Nature Structural & Molecular Biology 2009-11-08 Nature Structural & Molecular Biology 2009-11-08 10.1038/nsmb.1707 http://dx.doi.org/10.1038/nsmb.1707 Article http://dx.doi.org/10.1038/nsmb.1707 Structural insights into the mechanism of abscisic acid signaling by PYL proteins http://feeds.nature.com/~r/nsmb/rss/aop/~3/jJDzZ8cb0gw/nsmb.1730 PYL-PYR proteins were recently described as receptors for the plant hormone abscisic acid (ABA) and as inhibitors of the phosphatases ABI1 and ABI2 in the presence of ABA. The crystal structures of PYL2 in its apo and ABA-bound forms and of the ternary complex PYL1–ABA–ABI1 have now been solved, providing insight into ABA sensing and signaling. Structural insights into the mechanism of abscisic acid signaling by PYL proteins

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1730

Authors: Ping Yin, He Fan, Qi Hao, Xiaoqiu Yuan, Di Wu, Yuxuan Pang, Chuangye Yan, Wenqi Li, Jiawei Wang & Nieng Yan

]]> Structural insights into the mechanism of abscisic acid signaling by PYL proteins Ping Yin He Fan Qi Hao Xiaoqiu Yuan Di Wu Yuxuan Pang Chuangye Yan Wenqi Li Jiawei Wang Nieng Yan doi:10.1038/nsmb.1730 Nature Structural & Molecular Biology 2009-11-05 Nature Structural & Molecular Biology 2009-11-05 10.1038/nsmb.1730 http://dx.doi.org/10.1038/nsmb.1730 Article http://dx.doi.org/10.1038/nsmb.1730 Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain http://feeds.nature.com/~r/nsmb/rss/aop/~3/jAnaRpQHCmQ/nsmb.1731 The TAK1 kinase binds K63-linked ubiquitin specifically via its TAB2 subunit. The structure of the TAB2 NZF domain in complex with K63-linked ubiquitins now indicates that this domain interacts with neighboring ubiquitins through distinct sites, explaining the basis of specific recognition. Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1731

Authors: Yogesh Kulathu, Masato Akutsu, Anja Bremm, Kay Hofmann & David Komander

The protein kinase TAK1 is activated by binding to Lys63 (K63)-linked ubiquitin chains through its subunit TAB2. Here we analyze crystal structures of the TAB2 NZF domain bound to Lys63-linked di- and triubiquitin, revealing that TAB2 binds adjacent ubiquitin moieties via two distinct binding sites. The conformational constraints imposed by TAB2 on a Lys63 dimer cannot be adopted by linear chains, explaining why TAK1 cannot be activated by linear ubiquitination events.

]]> Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain Yogesh Kulathu Masato Akutsu Anja Bremm Kay Hofmann David Komander doi:10.1038/nsmb.1731 Nature Structural & Molecular Biology 2009-11-22 Nature Structural & Molecular Biology 2009-11-22 10.1038/nsmb.1731 http://dx.doi.org/10.1038/nsmb.1731 Brief Communication http://dx.doi.org/10.1038/nsmb.1731 IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana http://feeds.nature.com/~r/nsmb/rss/aop/~3/NHc-rSOoLF0/nsmb.1690 De novo methylation of DNA can affect the function of underlying genes and transposons in plants. Using a genetic screen, two factors required for de novo demethylation in Arabidopsis thaliana are identified and analyzed. IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana

Nature Structural & Molecular Biology. doi:10.1038/nsmb.1690

Authors: Israel Ausin, Todd C Mockler, Joanne Chory & Steven E Jacobsen

DNA methylation is an epigenetic mark affecting genes and transposons. Screening for mutants that fail to establish DNA methylation yielded two we termed “involved in de novo” (idn) 1 and 2. IDN1 encodes DMS3, an SMC-related protein, and IDN2 encodes a previously unknown double-stranded RNA–binding protein with homology to SGS3. IDN1 and IDN2 control de novo methylation and small interfering RNA (siRNA)-mediated maintenance methylation and are components of the RNA-directed DNA methylation pathway.

]]> IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana Israel Ausin Todd C Mockler Joanne Chory Steven E Jacobsen doi:10.1038/nsmb.1690 Nature Structural & Molecular Biology 2009-11-15 Nature Structural & Molecular Biology 2009-11-15 10.1038/nsmb.1690 http://dx.doi.org/10.1038/nsmb.1690 Brief Communication http://dx.doi.org/10.1038/nsmb.1690