Advance online publication
The latest research papers, published online ahead of print. These online versions are definitive and may be cited using the digital object identifier (DOI).
About advance online publicationArticles
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
Published online: 22 November 2009 | doi:10.1038/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.
Abstract - Spontaneous occurrence of telomeric DNA damage response in the absence of chromosome fusions | Full Text - Spontaneous occurrence of telomeric DNA damage response in the absence of chromosome fusions | PDF (1,566 KB) - Spontaneous occurrence of telomeric DNA damage response in the absence of chromosome fusions | Supplementary information
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
Published online: 22 November 2009 | doi:10.1038/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.
Abstract - Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II | Full Text - Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II | PDF (1,015 KB) - Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II | Supplementary information
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
Published online: 22 November 2009 | doi:10.1038/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.
Abstract - Reconstitution of both steps of : Saccharomyces cerevisiae: splicing with purified spliceosomal components | Full Text - Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components | PDF (2,073 KB) - Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components | Supplementary information
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
Published online: 15 November 2009 | doi:10.1038/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.
Abstract - An acetylated form of histone H2A.Z regulates chromosome architecture in : Schizosaccharomyces pombe | Full Text - An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe | PDF (1,678 KB) - An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe | Supplementary information
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
Published online: 15 November 2009 | doi:10.1038/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.
Abstract - A stepwise 2[prime]-hydroxyl activation mechanism for the bacterial transcription termination factor Rho helicase | Full Text - A stepwise 2'-hydroxyl activation mechanism for the bacterial transcription termination factor Rho helicase | PDF (1,228 KB) - A stepwise 2'-hydroxyl activation mechanism for the bacterial transcription termination factor Rho helicase | Supplementary information
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
Published online: 15 November 2009 | doi:10.1038/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.
Abstract - The chromosomal association of condensin II is regulated by a noncatalytic function of PP2A | Full Text - The chromosomal association of condensin II is regulated by a noncatalytic function of PP2A | PDF (1,316 KB) - The chromosomal association of condensin II is regulated by a noncatalytic function of PP2A | Supplementary information
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
Published online: 15 November 2009 | doi:10.1038/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.
Abstract - The chaperonin TRiC blocks a huntingtin sequence element that promotes the conformational switch to aggregation | Full Text - The chaperonin TRiC blocks a huntingtin sequence element that promotes the conformational switch to aggregation | PDF (884 KB) - The chaperonin TRiC blocks a huntingtin sequence element that promotes the conformational switch to aggregation | Supplementary information
Physical determinants of strong voltage sensitivity of K+ channel block
Yanping Xu, Hyeon-Gyu Shin, Szilvia Szép & Zhe Lu
Published online: 15 November 2009 | doi:10.1038/nsmb.1717
PDB code
3D view
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.
Abstract - Physical determinants of strong voltage sensitivity of K: +: channel block | Full Text - Physical determinants of strong voltage sensitivity of K+ channel block | PDF (1,040 KB) - Physical determinants of strong voltage sensitivity of K+ channel block | Supplementary information
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
Published online: 08 November 2009 | doi:10.1038/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.
Abstract - Nonspecifically bound proteins spin while diffusing along DNA | Full Text - Nonspecifically bound proteins spin while diffusing along DNA | PDF (682 KB) - Nonspecifically bound proteins spin while diffusing along DNA | Supplementary information
Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch
Nadia Kulshina, Nathan J Baird & Adrian R Ferré-D'Amaré
Published online: 08 November 2009 | doi:10.1038/nsmb.1701
PDB code
3D view
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.
Abstract - Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch | Full Text - Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch | PDF (1,111 KB) - Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch | Supplementary information
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
Published online: 08 November 2009 | doi:10.1038/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.
Abstract - Basis of substrate binding and conservation of selectivity in the CLC family of channels and transporters | Full Text - Basis of substrate binding and conservation of selectivity in the CLC family of channels and transporters | PDF (1,365 KB) - Basis of substrate binding and conservation of selectivity in the CLC family of channels and transporters | Supplementary information
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
Published online: 08 November 2009 | doi:10.1038/nsmb.1702
PDB code
3D view
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.
Abstract - Structural basis of ligand binding by a c-di-GMP riboswitch | Full Text - Structural basis of ligand binding by a c-di-GMP riboswitch | PDF (770 KB) - Structural basis of ligand binding by a c-di-GMP riboswitch | Supplementary information
Solution structure and functional analysis of the influenza B proton channel
Junfeng Wang, Rafal M Pielak, Mark A McClintock & James J Chou
Published online: 08 November 2009 | doi:10.1038/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.
Abstract - Solution structure and functional analysis of the influenza B proton channel | Full Text - Solution structure and functional analysis of the influenza B proton channel | PDF (781 KB) - Solution structure and functional analysis of the influenza B proton channel | Supplementary information
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
Published online: 05 November 2009 | doi:10.1038/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.
Abstract - Structural insights into the mechanism of abscisic acid signaling by PYL proteins | Full Text - Structural insights into the mechanism of abscisic acid signaling by PYL proteins | PDF (1,336 KB) - Structural insights into the mechanism of abscisic acid signaling by PYL proteins | Supplementary information
Brief Communications
Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain
Yogesh Kulathu, Masato Akutsu, Anja Bremm, Kay Hofmann & David Komander
Published online: 22 November 2009 | doi:10.1038/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.
Abstract - Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain | Full Text - Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain | PDF (585 KB) - Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain | Supplementary information
IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana
Israel Ausin, Todd C Mockler, Joanne Chory & Steven E Jacobsen
Published online: 15 November 2009 | doi:10.1038/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.
Abstract - IDN1 and IDN2 are required for : de novo: DNA methylation in : Arabidopsis thaliana | Full Text - IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana | PDF (423 KB) - IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana | Supplementary information
Until print versions of AOP papers are published, they should be cited in the style "Author(s) Nature Structural & Molecular Biology advance online publication, day month year (doi:10.1038/nsmbXXXXX)". Once the print version (identical to the AOP) is published, it should be cited as follows: "Author(s) Nature Structural & Molecular Biology volume, page (year); advance online publication, (doi:10.1038/nsmbXXXXX)".
Top of page
