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- Come together, right now
- Nature structural & molecular biology 16(12):1201 (2009)
Some bacteria have the remarkable ability to switch from a free-swimming, planktonic phase to coexistence in a complex biofilm. In this issue of NSMB, the structures of the ligand-bound c-di-GMP riboswitch give insight into some of the molecular processes linked to lifestyle changes but also suggest a potential avenue for applications that begs exploration. - Warren L. DeLano 21 June 1972–3 November 2009
- Nature structural & molecular biology 16(12):1202-1203 (2009)
Introduction On 3 November our community lost a young, extremely talented scientist under tragic circumstances when Warren DeLano died suddenly. To the readers of Nature Structural & Molecular Biology and to the larger biochemical and computer science communities, Warren is best known for his computer system PyMOL, an Open Source program for visualization of complex macromolecular systems. Chances are that in this issue, most of the illustrations of biomolecules were created with PyMOL. Warren grew up in Palo Alto, California, at a time and with a loving family that greatly valued the development of computer technology and science. Warren's life-long commitment to computational biosciences began when he was an undergraduate research student (majoring in molecular biophysics and biochemistry (MB&B) and computer science at Yale University) and asked one of us (A.T.B.) to supervise his MB&B senior thesis research. At the time, MB&B and the Center of Structural Biology had become a powerhouse of what we now know call "structural biology." Warren was attracted to solving the complexities of macromolecular systems using computational tools. I (A.T.B.) still remember when Warren showed up in my office one day. He was clearly very special, full of energy, and eager to become involved in computational research in my lab. I first suggested that he work on structure prediction of helical bundles. Then, after graduating, he continued in the lab for two years as "Scientific Programmer," working on a second project involving molecular replacement. Two first-author papers quickly resulted. But, in my memory, the most remarkable thing happened after a lab discussion about my general idea of creating a universal computing language for X-ray crystallography (what would eventually become the Crystallography and NMR System, CNS). Warren recognized the importance of implementing powerful scripting capabilities for the new system. Within days he had created very complex code in CNS (see subroutines parser.f and define.f), which implemented hierarchical data structures, scope and subroutines, all written in FORTRAN. It is an ex! ample of what the Stanford University computer scientist Donald E. Knuth has called (in the title of his best-known work) The Art of Computer Programming (D.E. Knuth, vols 1–4, Addison-Wesley, Reading, Massachusetts, USA, 1968–2005). Essentially, it does not matter what programming language one is using—elegant programs can be written in any language. And yes, Warren's code is truly elegant. For Warren, programming was not just a job or a means to another goal—it was like playing a musical instrument. The programs he designed were symphonies in computational space: integrated, complex and elegant at the same time. What's more, these masterpieces can be played by everyone. Before Warren moved on to graduate school at the University of California at San Francisco (UCSF), he had already started to work on what would eventually become PyMOL. Based on a rough idea of "defining objects and displaying them on a graphics terminal" and a rather clumsy and simple implementation that I had written in the mid-1980s to feed molecular information to a noisy refrigerator-sized Evans & Sutherland vector graphics computer, he took the concept and made it truly useful and accessible to everybody. PyMOL was the first intuitive molecular graphics program for the laptop era with the kind of click-and-drag functionality that we are now all accustomed to. And of course the rest is history: PyMOL has developed into one of the most widely used molecular visualization systems around. The first time I (J.A.W.) met Warren was when he showed up at my office at Genentech. His hands were sweating and he was shaking as he announced that he had to work in my lab as a rotation student in the Biophysics Program at UCSF, where I had an adjunct appointment. Frankly, I was a little reluctant, as I knew he had virtually no wet-lab experience. But I couldn't resist his intense passion, incredible smarts and no-fear attitude. One of the most amazing things about protein-protein interfaces is their promiscuity—that is, the fact that the same interface can bind multiple partners whose folds can be completely different. Warren's project was to use peptide-phage display to see whether naive peptides would seek out a well-known promiscuous epitope at the Fc region of antibodies. He selected for peptide binders, optimized them and rigorously characterized them using multiple biophysical methods, including solving the X-ray structure of the peptide bound to the Fc. Remarkably, his peptide, shown by the X-ray structure to be a simple -hairpin, bound exactly over the promiscuous epitope! By comparing the contact properties of four natural Fc-binding ligands to that of his naive peptide, he began to define the minimal binding properties. Importantly, he revealed the highly adaptive nature of these interfaces. To visualize this adaptive property, he began to further develop the software for PyMol in his s! pare time. In particular he developed a special application he called RigiMol—one of the first molecular movie programs that allows one to morph between static structures. For Warren's superb thesis, published as a first-author paper in Science entitled "Convergent solutions to binding at a protein-protein interface" (W.L. DeLano , M.H. Ultsch , A.M. de Vos and J.A. Wells , Science 287, 1279–1283, 2000), he was awarded the annual Julius Krevans Award for the best PhD thesis at UCSF. Not bad for a computational geek. Warren was a driven adventurer. About the time he graduated in 1998, I decided to leave Genentech for a start-up company, Sunesis Pharmaceuticals. Warren said he had to join as one of the first founding scientists, and he flew into the opportunity. He was seemingly doing everything, from working at the bench to evaluating novel fragment-based discovery technologies to setting up our computational group. He even insisted on physically setting up our first IT system, pulling wires to work stations, connecting routers and our company e-mail service and developing our website, all just so he could learn it. As the company grew from 10 to 20 to 50 to 70 employees, Warren was intimately involved in recruiting people, including his sister Jennifer (who has comparable DeLano traits) and others to take over parts of his job. This way he could focus on his true love, molecular graphics and visualization tools. It was a sad but not unexpected day for all of us at Sunesis, and a great d! ay for the computational bioscience community, when in 2002 he decided to leave. This way he could devote his full time to the development and dissemination of PyMOL and embellishments through his own company DeLano Scientific, his ultimate adventure. Warren's impact on crystallographic software spreads beyond PyMOL and CNS, spanning almost two decades. Paul Adams retained him as a consultant in the very early days of the Phenix project. There ensued many lively and passionate discussions about how to develop a new crystallographic software system with the current computational tools. Warren's insight and experience developing PyMOL were major contributors to the decision to use Python as the scripting language in Phenix. This choice also made it easy for the Phenix developers to integrate PyMOL with Phenix. PyMOL is Open Source (http://en.wikipedia.org/wiki/Open_source), part of a movement that produced the popular Netscape and Mozilla browser systems and, of course, the GNU/Linux operating system. Early on, Warren made the decision to make his programs accessible to all, in full, including source code. He felt that for pursuit of academic freedom it is essential to have all information about a scientific program fully accessible, promoting innovation. This is an ideal that we can all aspire to. One must also recognize Warren as a humanist and thinker, perhaps best summarized in a recent posting by UCSF structural biologist Linda Brinen on the CCP4 bulletin board (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0911&L=CCP4BB&T=0&F=&S=&P=36748): I—like so many others—[am] shocked, saddened and shaken by this news. Warren's passing is a great loss to his friends, family and to our scientific community. Nearly exactly one year ago, when an MRI found that I had a brain tumor, Warren wrote me an e-mail, part of which I will share here, because it sums up part of him and his approach to life: "...I am so sorry to read your startling news. Not a one of us is excused from life-altering biology and random accidents, any of which can strike suddenly without warning. For that reason, we must never take anything for granted. Not a single day. Not a single friend. But as you well know, there are only two things we can do in defiance of chance, whether in sickness or in health: 1. Do everything you feel is important in life, today, or as soon as possible. 2. Never give up. Ignore the odds. Always believe you will survive and thrive. ...I am personally counting on you to get through this just fine and be back in action...." Warren will be remembered well... and I wish for him to be at peace. —Linda Warren is survived by his wife Beth Pehrson, mother Margaret DeLano, father James DeLano, Jr., stepmother Cathy Groves DeLano, stepfather Tom Snouse, sister Jennifer DeLano and brother Brendan DeLano, as well as five aunts and eight cousins. He left this world with much undone that he wanted to do. He also left us some magnificent science and the huge challenge of living up to his ideals of Open Scientific Software. Warren was a truly visionary thinker, and to be deprived of his future work is a huge blow to the scientific community. - Chromosome end protection becomes even more complex
- Nature structural & molecular biology 16(12):1205-1206 (2009)
Chromosome end protection is accomplished by telomeres. How cells cope with spontaneously unprotected telomeres while avoiding cell cycle arrest or cell death is a fascinating question. - Flu BM2 structure and function
- Nature structural & molecular biology 16(12):1207-1209 (2009)
Flu viruses package essential functions into a small integral membrane protein known as M2. Such small membrane proteins represent major challenges for structural biology. A new study presented in this issue details the structure and functions of the influenza B M2 protein through the use of functional domain–specific solution NMR spectroscopy. - Ubiquitin linkages make a difference
- Nature structural & molecular biology 16(12):1209-1210 (2009)
Ubiquitin chains have critical roles in activating the NF-B pathway and mediating immune responses. Recent structural work on distinct ubiquitin chains in complexes with selective ubiquitin-binding domains provides an explanation for directionality and specificity in the NF-B pathway. - Research highlights
- Nature structural & molecular biology 16(12):1211 (2009)
- Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch
Kulshina N Baird NJ Ferré-D'Amaré AR - Nature structural & molecular biology 16(12):1212-1217 (2009)
The cyclic diguanylate (bis-(3'-5')-cyclic dimeric guanosine monophosphate, c-di-GMP) riboswitch is the first known example of a gene-regulatory RNA that binds a second messenger. c-di-GMP is widely used by bacteria to regulate processes ranging from biofilm formation to the expression of virulence genes. The cocrystal structure of the c-di-GMP responsive GEMM riboswitch upstream of the tfoX gene of Vibrio cholerae reveals the second messenger binding the RNA at a three-helix junction. The two-fold symmetric second messenger is recognized asymmetrically by the monomeric riboswitch using canonical and noncanonical base-pairing as well as intercalation. These interactions explain how the RNA discriminates against cyclic diadenylate (c-di-AMP), a putative bacterial second messenger. Small-angle X-ray scattering and biochemical analyses indicate that the RNA undergoes compaction and large-scale structural rearrangement in response to ligand binding, consistent with organiz! ation of the core three-helix junction of the riboswitch concomitant with binding of c-di-GMP. - Structural basis of ligand binding by a c-di-GMP riboswitch
Smith KD Lipchock SV Ames TD Wang J Breaker RR Strobel SA - Nature structural & molecular biology 16(12):1218-1223 (2009)
The second messenger signaling molecule bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) regulates many processes in bacteria, including motility, pathogenesis and biofilm formation. c-di-GMP–binding riboswitches are important downstream targets in this signaling pathway. Here we report the crystal structure, at 2.7 Å resolution, of a c-di-GMP riboswitch aptamer from Vibrio cholerae bound to c-di-GMP, showing that the ligand binds within a three-helix junction that involves base-pairing and extensive base-stacking. The symmetric c-di-GMP is recognized asymmetrically with respect to both the bases and the backbone. A mutant aptamer was engineered that preferentially binds the candidate signaling molecule c-di-AMP over c-di-GMP. Kinetic and structural data suggest that genetic regulation by the c-di-GMP riboswitch is kinetically controlled and that gene expression is modulated through the stabilization of a previously unidentified P1 helix, illustrating a! direct mechanism for c-di-GMP signaling. - Nonspecifically bound proteins spin while diffusing along DNA
Blainey PC Luo G Kou SC Mangel WF Verdine GL Bagchi B Xie XS - Nature structural & molecular biology 16(12):1224-1229 (2009)
It is known that DNA-binding proteins can slide along the DNA helix while searching for specific binding sites, but their path of motion remains obscure. Do these proteins undergo simple one-dimensional (1D) translational diffusion, or do they rotate to maintain a specific orientation with respect to the DNA helix? We measured 1D diffusion constants as a function of protein size while maintaining the DNA-protein interface. Using bootstrap analysis of single-molecule diffusion data, we compared the results to theoretical predictions for pure translational motion and rotation-coupled sliding along the DNA. The data indicate that DNA-binding proteins undergo rotation-coupled sliding along the DNA helix and can be described by a model of diffusion along the DNA helix on a rugged free-energy landscape. A similar analysis including the 1D diffusion constants of eight proteins of varying size shows that rotation-coupled sliding is a general phenomenon. The average free-energy! barrier for sliding along the DNA was 1.1 0.2 kBT. Such small barriers facilitate rapid search for binding sites. - Structural insights into the mechanism of abscisic acid signaling by PYL proteins
Yin P Fan H Hao Q Yuan X Wu D Pang Y Yan C Li W Wang J Yan N - Nature structural & molecular biology 16(12):1230-1236 (2009)
Abscisic acid (ABA) is an important phytohormone that regulates plant stress responses. Proteins from the PYR-PYL-RCAR family were recently identified as ABA receptors. Upon binding to ABA, a PYL protein associates with type 2C protein phosphatases (PP2Cs) such as ABI1 and ABI2, inhibiting their activity; the molecular mechanisms by which PYLs mediate ABA signaling remain unknown, however. Here we report three crystal structures: apo-PYL2, (+)-ABA-bound PYL2 and (+)-ABA-bound PYL1 in complex with phosphatase ABI1. Apo-PYL2 contains a pocket surrounded by four highly conserved surface loops. In response to ABA binding, loop CL2 closes onto the pocket, creating a surface that recognizes ABI1. In the ternary complex, the CL2 loop is located near the active site of ABI1, blocking the entry of substrate proteins. Together, our data reveal the mechanisms by which ABA regulates PYL-mediated inhibition of PP2Cs. - Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components
Warkocki Z Odenwälder P Schmitzová J Platzmann F Stark H Urlaub H Ficner R Fabrizio P Lührmann R - Nature structural & molecular biology 16(12):1237-1243 (2009)
The spliceosome is a ribonucleoprotein machine that removes introns from pre-mRNA in a two-step reaction. To investigate the catalytic steps of splicing, we established an in vitro splicing complementation system. Spliceosomes stalled before step 1 of this process were purified to near-homogeneity from a temperature-sensitive mutant of the RNA helicase Prp2, compositionally defined, and shown to catalyze efficient step 1 when supplemented with recombinant Prp2, Spp2 and Cwc25, thereby demonstrating that Cwc25 has a previously unknown role in promoting step 1. Step 2 catalysis additionally required Prp16, Slu7, Prp18 and Prp22. Our data further suggest that Prp2 facilitates catalytic activation by remodeling the spliceosome, including destabilizing the SF3a and SF3b proteins, likely exposing the branch site before step 1. Remodeling by Prp2 was confirmed by negative stain EM and image processing. This system allows future mechanistic analyses of spliceosome activation a! nd catalysis. - Spontaneous occurrence of telomeric DNA damage response in the absence of chromosome fusions
Cesare AJ Kaul Z Cohen SB Napier CE Pickett HA Neumann AA Reddel RR - Nature structural & molecular biology 16(12):1244-1251 (2009)
Telomere dysfunction is typically studied under conditions in which a component of the six-subunit shelterin complex that protects chromosome ends is disrupted. The nature of spontaneous telomere dysfunction is less well understood. Here we report that immortalized human cell lines lacking wild-type p53 function spontaneously show many telomeres with a DNA damage response (DDR), commonly affecting only one sister chromatid and not associated with increased chromosome end-joining. DDR+ telomeres represent an intermediate configuration between the fully capped and uncapped (fusogenic) states. In telomerase activity–positive (TA+) cells, DDR is associated with low TA and short telomeres. In cells using the alternative lengthening of telomeres mechanism (ALT+), DDR is partly independent of telomere length, mostly affects leading strand–replicated telomeres, and can be partly suppressed by TRF2 overexpression. In ALT+ (but not TA+) cells, DDR+ telomeres preferentially a! ssociate with large foci of extrachromosomal telomeric DNA and recombination proteins. DDR+ telomeres therefore arise through different mechanisms in TA+ and ALT+ cells and have different consequences. - Physical determinants of strong voltage sensitivity of K+ channel block
Xu Y Shin HG Szép S Lu Z - Nature structural & molecular biology 16(12):1252-1258 (2009)
Strong voltage sensitivity of inward-rectifier K+ (Kir) channels has been hypothesized to arise primarily from an intracellular blocker displacing up to five K+ ions from the wide, intracellular part of the ion conduction pore outwardly across the narrow ion-selectivity filter. The validity of this hypothesis depends on two assumptions: (i) that five ion sites are located intracellular to the filter and (ii) that the blocker can force essentially unidirectional K+ movement in a pore region generally wider than the combined dimensions of the blocker plus a K+ ion. Here we present a crystal structure of the cytoplasmic portion of a Kir channel with five ions bound and demonstrate that a constriction near the intracellular end of the pore, acting as a gasket, prevents K+ ions from bypassing the blocker. This heretofore unrecognized 'gasket' ensures that the blocker can effectively displace K+ ions across the selectivity filter to generate exceedingly strong voltage sensit! ivity. - Distinct passenger strand and mRNA cleavage activities of human Argonaute proteins
Wang B Li S Qi HH Chowdhury D Shi Y Novina CD - Nature structural & molecular biology 16(12):1259-1266 (2009)
Argonaute (AGO) proteins bind to small RNAs and mediate small RNA-induced silencing in eukaryotes. Using a minimal in vitro system, we show that bacterially expressed human AGO1 and AGO2 but not AGO3 and AGO4 possess strand-dissociating activity of microRNA (miRNA) duplexes. Both AGO1 and AGO2 function as RNA chaperones, capable of performing multiple rounds of strand dissociation. Unexpectedly, both AGO1 and AGO2 demonstrate passenger strand cleavage activity of a small interfering RNA (siRNA) duplex, but only AGO2 has target RNA cleavage activity. These observations indicate that passenger strand and mRNA endonuclease activities are mechanistically distinct. We further validate these observations in mammalian extracts and cultured mammalian cells, in which we demonstrate that AGO1 uses only miRNA duplexes when assembling translational repression-competent complexes, whereas AGO2 can use both miRNA and siRNA duplexes. We show that passenger strand cleavage and RNA cha! perone activities that are intrinsic to both AGO1 and AGO2 are sufficient for RNA-induced silencing complex (RISC) loading. - Solution structure and functional analysis of the influenza B proton channel
Wang J Pielak RM McClintock MA Chou JJ - Nature structural & molecular biology 16(12):1267-1271 (2009)
Influenza B virus contains an integral membrane protein, BM2, that oligomerizes in the viral membrane to form a pH-activated proton channel. Here we report the solution structures of both the membrane-embedded channel domain and the cytoplasmic domain of BM2. The channel domain assumes a left-handed coiled-coil tetramer formation with a helical packing angle of -37° to form a polar pore in the membrane for conducting ions. Mutagenesis and proton flux experiments identified residues involved in proton relay and suggest a mechanism of proton conductance. The cytoplasmic domain of BM2 also forms a coiled-coil tetramer. It has a bipolar charge distribution, in which a negatively charged region interacts specifically with the M1 matrix protein that is involved in packaging the genome in the virion. This interaction suggests BM2 also recruits matrix proteins to the cell surface during virus budding, making BM2 an unusual membrane protein with the dual roles of conducting io! ns and recruiting proteins to the membrane. - Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II
Kulaeva OI Gaykalova DA Pestov NA Golovastov VV Vassylyev DG Artsimovitch I Studitsky VM - Nature structural & molecular biology 16(12):1272-1278 (2009)
Transcription of eukaryotic genes by RNA polymerase II (Pol II) is typically accompanied by nucleosome survival and minimal exchange of histones H3 and H4. The mechanism of nucleosome survival and recovery of chromatin structure remains obscure. Here we show how transcription through chromatin by Pol II is uniquely coupled with nucleosome survival. Structural modeling and functional analysis of the intermediates of transcription through a nucleosome indicated that when Pol II approaches an area of strong DNA-histone interactions, a small intranucleosomal DNA loop (zero-size or Ø-loop) containing transcribing enzyme is formed. During formation of the Ø-loop, the recovery of DNA-histone interactions behind Pol II is tightly coupled with their disruption ahead of the enzyme. This coupling is a distinct feature of the Pol II–type mechanism that allows further transcription through the nucleosome, prevents nucleosome translocation and minimizes displacement of H3 and H4! histones from DNA during enzyme passage. - The chaperonin TRiC blocks a huntingtin sequence element that promotes the conformational switch to aggregation
Tam S Spiess C Auyeung W Joachimiak L Chen B Poirier MA Frydman J - Nature structural & molecular biology 16(12):1279-1285 (2009)
Aggregation of proteins containing polyglutamine (polyQ) expansions characterizes many neurodegenerative disorders, including Huntington's disease. Molecular chaperones modulate the aggregation and toxicity of the huntingtin (Htt) protein by an ill-defined mechanism. Here we determine how the chaperonin TRiC suppresses Htt aggregation. Unexpectedly, TRiC does not physically block the polyQ tract itself, but rather sequesters a short Htt sequence element, N-terminal to the polyQ tract, that promotes the amyloidogenic conformation. The residues of this element essential for rapid Htt aggregation are directly bound by TRiC. Our findings illustrate how molecular chaperones, which recognize hydrophobic determinants, can prevent aggregation of polar polyQ tracts associated with neurodegenerative diseases. The observation that short endogenous sequence elements can accelerate the switch of polyQ tracts to an amyloidogenic conformation provides a novel target for therapeutic s! trategies. - An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe
Kim HS Vanoosthuyse V Fillingham J Roguev A Watt S Kislinger T Treyer A Carpenter LR Bennett CS Emili A Greenblatt JF Hardwick KG Krogan NJ Bähler J Keogh MC - Nature structural & molecular biology 16(12):1286-1293 (2009)
Histone variant H2A.Z has a conserved role in genome stability, although it remains unclear how this is mediated. Here we demonstrate that the fission yeast Swr1 ATPase inserts H2A.Z (Pht1) into chromatin and Kat5 acetyltransferase (Mst1) acetylates it. Deletion or an unacetylatable mutation of Pht1 leads to genome instability, primarily caused by chromosome entanglement and breakage at anaphase. This leads to the loss of telomere-proximal markers, though telomere protection and repeat length are unaffected by the absence of Pht1. Strikingly, the chromosome entanglement in pht1 anaphase cells can be rescued by forcing chromosome condensation before anaphase onset. We show that the condensin complex, required for the maintenance of anaphase chromosome condensation, prematurely dissociates from chromatin in the absence of Pht1. This and other findings suggest an important role for H2A.Z in the architecture of anaphase chromosomes. - Basis of substrate binding and conservation of selectivity in the CLC family of channels and transporters
Picollo A Malvezzi M Houtman JC Accardi A - Nature structural & molecular biology 16(12):1294-1301 (2009)
Ion binding to secondary active transporters triggers a cascade of conformational rearrangements resulting in substrate translocation across cellular membranes. Despite the fundamental role of this step, direct measurements of binding to transporters are rare. We investigated ion binding and selectivity in CLC-ec1, a H+-Cl- exchanger of the CLC family of channels and transporters. Cl- affinity depends on the conformation of the protein: it is highest with the extracellular gate removed and weakens as the transporter adopts the occluded configuration and with the intracellular gate removed. The central ion-binding site determines selectivity in CLC transporters and channels. A serine-to-proline substitution at this site confers NO3- selectivity upon the Cl--specific CLC-ec1 transporter and CLC-0 channel. We propose that CLC-ec1 operates through an affinity-switch mechanism and that the bases of substrate specificity are conserved in the CLC channels and transporters. - The chromosomal association of condensin II is regulated by a noncatalytic function of PP2A
Takemoto A Maeshima K Ikehara T Yamaguchi K Murayama A Imamura S Imamoto N Yokoyama S Hirano T Watanabe Y Hanaoka F Yanagisawa J Kimura K - Nature structural & molecular biology 16(12):1302-1308 (2009)
Mitotic chromosomal assembly in vertebrates is regulated by condensin I and condensin II, which work cooperatively but have different chromosomal localization profiles and make distinct mechanistic contributions to this process. We show here that protein phosphatase 2A (PP2A), which interacts with condensin II but not condensin I, plays an essential role in targeting condensin II to chromosomes. Unexpectedly, our data indicate that PP2A acts as a recruiter protein rather than a catalytic enzyme to target condensin II to chromosomes. This recruiting activity of PP2A was inhibited by okadaic acid, but not by fostriecin, even though both molecules strongly inhibited the catalytic activity of PP2A. Additionally, we found that the chromokinesin KIF4a is also targeted to chromosomes via the noncatalytic activity of PP2A. Thus, our studies reveal a previously unknown contribution of PP2A to chromosome assembly. - A stepwise 2'-hydroxyl activation mechanism for the bacterial transcription termination factor Rho helicase
Schwartz A Rabhi M Jacquinot F Margeat E Rahmouni AR Boudvillain M - Nature structural & molecular biology 16(12):1309-1316 (2009)
The bacterial Rho factor is a ring-shaped ATP-dependent helicase that tracks along RNA transcripts and disrupts RNA-DNA duplexes and transcription complexes in its path. Using combinatorial nucleotide analog interference mapping (NAIM), we explore the topology and dynamics of functional Rho–RNA complexes and reveal the RNA-dependent stepping mechanism of Rho helicase. Periodic Gaussian distributions of NAIM signals show that Rho forms uneven productive interactions with the track nucleotides and disrupts RNA-DNA duplexes in a succession of large (7-nucleotide-long) discrete steps triggered by 2'-hydroxyl activation events. This periodic 2'-OH–dependent activation does not depend on the RNA-DNA pairing energy but is finely tuned by sequence-dependent interactions with the RNA track. These features explain the strict RNA specificity and contextual efficiency of the enzyme and provide a new paradigm for conditional tracking by a helicase ring. - Mechanism of potassium-channel selectivity revealed by Na+ and Li+ binding sites within the KcsA pore
Thompson AN Kim I Panosian TD Iverson TM Allen TW Nimigean CM - Nature structural & molecular biology 16(12):1317-1324 (2009)
Potassium channels allow K+ ions to diffuse through their pores while preventing smaller Na+ ions from permeating. Discrimination between these similar, abundant ions enables these proteins to control electrical and chemical activity in all organisms. Selection occurs at the narrow selectivity filter containing structurally identified K+ binding sites. Selectivity is thought to arise because smaller ions such as Na+ do not bind to these K+ sites in a thermodynamically favorable way. Using the model K+ channel KcsA, we examined how intracellular Na+ and Li+ interact with the pore and the permeant ions using electrophysiology, molecular dynamics simulations and X-ray crystallography. Our results suggest that these small cations have a separate binding site within the K+ selectivity filter. We propose that selective permeation from the intracellular side primarily results from a large energy barrier blocking filter entry for Na+ and Li+ in the presence of K+, not from a d! ifference of binding affinity between ions. - IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana
Ausin I Mockler TC Chory J Jacobsen SE - Nature structural & molecular biology 16(12):1325-1327 (2009)
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. - Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain
Kulathu Y Akutsu M Bremm A Hofmann K Komander D - Nature structural & molecular biology 16(12):1328-1330 (2009)
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. - Structural and functional studies of the Ras-associating and pleckstrin-homology domains of Grb10 and Grb14
- Nature structural & molecular biology 16(12):1331 (2009)
Introduction Nat. Struct. Mol. Biol. 16, 833–839 (2009); published online 2 August 2009; corrected after print 22 September 2009 In the version of this article initially published, the Grp1 structure described in Figure 3c was incorrectly labeled Grb1. The corrected figure panel is shown below. The error has been corrected in the HTML and PDF versions of the article. - Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy
- Nature structural & molecular biology 16(12):1331 (2009)
Introduction Nat. Struct. Mol. Biol. 16, 890–896 (2009); published online 13 July 2009; corrected after print 18 November 2009 In the version of this article initially published, Eric A. Gaucher's middle initial was omitted. The error has been corrected in the HTML and PDF versions of the article.
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