Portal de Periódicos da CAPES

Paper alert

2001; Elsevier BV; Volume: 9; Issue: 9 Linguagem: Inglês

10.1016/s0969-2126(01)00652-9

1878-4186

Chosen by Robert Liddington, Christin Frederick, Stephen D. Fuller, Sophie Jackson,

Epigenetics and DNA Methylation

A selection of interesting papers that were published in the month before our press date in major journals most likely to report significant results in structural biology, protein, and RNA folding. □ Microtubule structure at improved resolution. Patricia Meurer-Grob, Jérôme Kasparian, and Richard H. Wade (2001). Biochemistry 40, 8000–8008. The biological functions of microtubules require that tubulin assembles to form a range of structures with similar energies. Hence the high-resolution structure of the tubulin dimer needs to be placed into the context of these different assemblies to understand the molecular function in vivo. Microtubule architecture and protofilament number vary with eukaryotic species, with different cell types, and with the presence of stabilizing agents. The authors have used cEM and image reconstruction to determine the structures of taxotere-stabilized and GMPCPP microtubules to an unprecedented 14 Å resolution. These improved maps allow unambiguous docking of the tubulin crystal structure and examination of the dimer packing within the microtubule wall. The docked tubulin and simulated images calculated from atomic models of these microtubules show tubulin heterodimers are aligned head to tail along the protofilaments. The β subunit caps the microtubule plus end. The relative positions of the tubulin dimers in neighboring protofilaments are the same for different types of microtubule. This supports their hypothesis that conserved lateral interactions between tubulin subunits are responsible for the surface lattice accommodation observed in different microtubule architectures. The authors conclude that lateral contacts between tubulin subunits in neighboring protofilaments have a decisive role for microtubule stability, rigidity, and architecture. □ Crystal structure of Negative Cofactor 2 recognizing the TBP-DNA transcription complex. Katsuhiko Kamada, Fong Shu, Hua Chen, Sohail Malik, Gertraud Stelzer, Robert G. Roeder, Michael Meisterernst, and Stephen K. Burley (2001). Cell 106, 71–81. The X-ray structure of a ternary complex of Negative Cofactor 2 (NC2), the TATA box binding protein (TBP), and DNA has been determined at 2.6 Å resolution. The N termini of NC2 α and β resemble histones H2A and H2B, respectively, and form a heterodimer that binds to the bent DNA double helix on the underside of the preformed TBP-DNA complex via electrostatic interactions. NC2β contributes to inhibition of TATA-dependent transcription through interactions of its C-terminal α helix with a conserved hydrophobic feature on the upper surface of TBP, which in turn positions the penultimate α helix of NC2β to block recognition of the TBP-DNA complex by transcription factor IIB. □ The path of messenger RNA through the ribosome. Gulnara Zh. Yusupova, Marat M. Yusupov, J.H.D. Cate, and Harry F. Noller (2001). Cell 106, 233–241. Using X-ray crystallography, the authors have directly observed the path of mRNA in the 70S ribosome in Fourier difference maps at 7 Å resolution. About 30 nucleotides of the mRNA are wrapped in a groove that encircles the neck of the 30S subunit. The Shine-Dalgarno helix is bound in a large cleft between the head and the back of the platform. At the interface, only about eight nucleotides (−1 to +7), centered on the junction between the A and P codons, are exposed and bond almost exclusively to 16S rRNA. The mRNA enters the ribosome around position +13 to +15, the location of downstream pseudoknots that stimulate −1 translational frame shifting. □ The three-dimensional structure of α-actinin obtained by cryo-electron microscopy suggests a model for Ca(2+)-dependent actin binding. Jinghua Tang, Dianne W. Taylor, and Kenneth A. Taylor (2001). J. Mol. Biol. 310, 845–858. α-actinin is a bivalent actin-crosslinking protein that controls the organization of actin filaments. The authors formed two-dimensional arrays of rabbit skeletal α-actinin on positively charged lipid monolayers and determined their structure by cEM and electron crystallography. The 15 Å resolution map was interpreted by docking the structures of the actin binding, three-helix motif and the C-terminal calmodulin-like domains which had been determined to high resolution by NMR and X-ray crystallography. The proximity of the C-terminal calmodulin-like domain to the linker between the two calponin-like repeats of the actin binding domain suggest a mechanism for Ca2+ regulation of actin binding . □ Finding and using local symmetry in identifying lower domain movements in hexon subunits of the herpes simplex virus type 1 B capsid. Jing He, Michael F. Schmid, Z. Hong Zhou, Frazer Rixon, and Wah Chiu (2001). J. Mol. Biol. 309, 903–914. The authors have developed a computational procedure for evaluating the quality of local symmetries in intermediate resolution maps from cEM. They apply this method to their 8.5 Å resolution map of herpes simplex virus type I B capsid to examine the variations between the 16 independent copies of VP5 in the asymmetric unit. The copies of VP5 that form the penton are quite distinct from those forming the hexons. The detailed analysis of the VP5 in the hexons reveals more subtle but systematic variations with the lower domain of the molecule. VP5 appears able to adjust itself to different environments by domain movement but does not adapt a different conformation at every quasi-equivalent position. The variation in local symmetry suggests that the scaffold directs the formation of the procapsid shell rather than directing those interactions that lead to the creation of a highly stable and symmetrical particle. □ Complete in vitro assembly of the reovirus outer capsid produces highly infectious particles suitable for genetic studies of the receptor binding protein. Kartik Chandran, Xing Zhang, Norman H. Olson, Stephen B. Walker, James D. Chappell, Terence S. Dermody, Timothy S. Baker, and Max L. Nibert (2001). J. Virol. 75, 5335–5342. One of the fascinating aspects of mammalian, double-stranded RNA viruses such as the reoviruses is their special mode of replication. These studies are inhibited by the lack of a good system for reverse genetics. Introduction of defined mutations into infective virions is more difficult than in other viruses. This paper uses in vitro assembly to overcome this problem by producing genome-containing core particles lacking defined viral proteins and recoating with recombinant versions of the missing proteins. cEM reconstruction of the reassembled particles shows that they match the authentic virion structure. Reconstitution with recombinant σ1 protein from two different reovirus strains confirmed that differences in cell attachment and infectivity are determined by the σ1. The recoated particles containing σ1 proteins with engineered mutations can be used to analyze the effects of such mutations on infection. This powerful reconstitution system will allow the study of defined mutations to probe aspects of the replication pathway. □ Structural analysis of a fiber-pseudotyped adenovirus with ocular tropism suggests differential modes of cell receptor interactions. Charles Y. Chiu, Eugene Wu, Swati L. Brown, Dan J. Von Seggern, Glen R. Nemerow, and Phoebe L. Stewart (2001). J. Virol. 75, 5375–5380. The entry of adenovirus begins with the binding of the knob on the ends of fibers at the vertices of the virion to a receptor on the cell surface. The coxsackie- and adenovirus receptor (CAR) functions for e attachment of many adenovirus serotypes. Subtype D viruses, including type 37, which causes conjunctivitis, does not utilize the CAR, although sequence analysis and direct binding studies of the type 37 knob indicate that it posses CAR binding activity. cEM of an adenovirus type 5 fiber deletion mutant that had been complemented with the type 37 fiber (Ad37f) was used to explore the role of geometry in receptor binding. The Ad37f fiber is visualized along its entire length in the cEM reconstruction. This differs from the situation in previous adenovirus reconstructions, in which only the base of the fiber is seen due to the combined effects of 5-fold averaging and a bend in the fiber. The straight Ad37f fiber would not be able to contact the CAR receptor in the same way as the bent fibers. Hence, the geometry of the receptor/knob interaction does not allow the use of CAR and forces the virus to use another receptor for entry. Fiber flexibility affects receptor usage and hence cellular tropism. □ Structural analysis of a functional DIAP1 fragment bound to Grim and Hid peptides. Jia-Wei Wu, Amy E. Cocina, Jijie Chai, Bruce A. Hay, and Yigong Shi (2001). Mol. Cell 8, 95–104. The inhibitor of apoptosis protein DIAP1 suppresses apoptosis in Drosophila, with the second BIR domain (BIR2) playing an important role. Three proteins, Hid, Grim, and Reaper, promote apoptosis, in part by binding to DIAP1 through their conserved N-terminal sequences. The crystal structures of DIAP1-BIR2 by itself and in complex with the N-terminal peptides from Hid and Grim reveal that these peptides bind a surface groove on DIAP1, with the first four amino acids mimicking the binding of the Smac tetrapeptide to XIAP. The next three residues also contribute to binding through hydrophobic interactions. Peptide binding induces the formation of an additional α helix in DIAP1. □ Structure of the Rho-activating domain of Escherichia coli cytotoxic necrotizing factor 1. Lori Buetow, Gilles Flatau, Katy Chiu, Patrice Boquet, and Partho Ghosh (2001). Nat. Struct. Biol. 8, 584–588. Certain uropathogenic and neonatal meningitis-causing strains of Escherichia coli express a 114 kDa protein toxin called cytotoxic necrotizing factor 1 (CNF1). The toxin causes alteration of the host cell actin cytoskeleton and promotes bacterial invasion of blood-brain barrier endothelial cells. CNF1 belongs to a unique group of large cytotoxins that cause constitutive activation of Rho guanosine triphosphatases (GTPases), which are key regulators of the actin cytoskeleton. The catalytic region of CNF1 exhibits a novel protein fold as determined by its 1.83 Å resolution crystal structure. The structure reveals that CNF1 has a Cys-His-main chain oxygen catalytic triad reminiscent of enzymes belonging to the catalytic triad superfamily. The position of the catalytic Cys residue at the base of a deep pocket restricts access to potential substrates and helps explain the high specificity of this and related toxins. □ Structure of GSK3β reveals a primed phosphorylation mechanism. Ernst ter Haar, Joyce T. Coll, Douglas A. Austen, Hsun-Mei Hsiao, Lora Swenson, and Jugnu Jain (2001). Nat. Struct. Biol. 8, 593–596. GSK3β was identified as the kinase that phosphorylates glycogen synthase but is now known to be involved in multiple signaling pathways. GSK3β prefers prior phosphorylation of its substrates. The authors present the structure of unphosphorylated GSK3β at 2.7 Å. The orientation of the two domains and positioning of the activation loop of GSK3β are similar to those observed in activated kinases. A phosphate ion held by Arg96, Arg180, and Lys205 occupies the same position as the phosphate group of the phosphothreonine in activated p38γ, CDK2, or ERK2. A loop from a neighboring molecule in the crystal occupies a portion of the substrate binding groove. The structure explains the unique primed phosphorylation mechanism of GSK3β and how GSK3β relies on a phosphoserine in the substrate for the alignment of the β- and α-helical domains. □ The SAND domain structure defines a novel DNA binding fold in transcriptional regulation. Matthew J. Bottomley, Michael W. Collard, Jodi I. Huggenvik, Zhihong Liu, Toby J. Gibson, and Michael Sattler (2001). Nat. Struct. Biol. 8, 626–633. The SAND domain is a conserved sequence motif found in a number of nuclear proteins, including the Sp100 family and NUDR. These are thought to play important roles in chromatin-dependent transcriptional regulation and are linked to many diseases. The authors have determined the three-dimensional structure of the SAND domain from Sp100b. The structure represents a novel α/β fold, in which a conserved KDWK sequence motif is found within an α-helical, positively charged surface patch. For NUDR, the SAND domain is shown to be sufficient to mediate DNA binding. The DNA binding surface is mapped to the α-helical region encompassing the KDWK motif. The DNA binding activity of wild-type and mutant proteins in vitro correlates with transcriptional regulation activity of full length NUDR in vivo. The evolutionarily conserved SAND domain defines a new DNA binding fold that is involved in chromatin-associated transcriptional regulation. □ Crystal structure and mutational analysis of a perlecan binding fragment of nidogen-1. Michael Hopf, Walter Göhring, Albert Ries, Rupert Timpl, and Erhard Hohenester (2001). Nat. Struct. Biol. 8, 634–640. Nidogen, an invariant component of basement membranes, is a multifunctional protein that interacts with most other major basement membrane proteins. The authors report the crystal structure of the mouse nidogen-1 G2 fragment, which contains binding sites for collagen IV and perlecan. The structure is composed of an EGF-like domain and an 11-stranded β-barrel with a central helix. The β-barrel domain has unexpected similarity to green fluorescent protein. A large surface patch on the β-barrel is strikingly conserved in all metazoan nidogens and is shown to be involved in perlecan binding. □ Structure of 4-diphosphocytidyl-2-C-methylerythritol synthetase involved in mevalonate-independent isoprenoid biosynthesis. Stéphane B. Richard, Marianne E. Bowman, Witek Kwiatkowski, Ilgu Kang, Cathy Chow, Antonietta M. Lillo, David E. Cane, and Joseph P. Noel (2001). Nat. Struct. Biol. 8, 641–648. The YgbP protein of Escherichia coli encodes the enzyme 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME) synthetase, a member of the cytidyltransferase family of enzymes. CDP-ME is an intermediate in the mevalonate-independent pathway for isoprenoid biosynthesis in a number of prokaryotic organisms, algae, the plant plastids and the malaria parasite. Because vertebrates synthesize isoprenoid precursors using a mevalonate pathway, CDP-ME synthetase and other enzymes of the mevalonate-independent pathway for isoprenoid production represent attractive targets for the structure-based design of selective antibacterial, herbicidal and antimalarial drugs. The high-resolution structures of E. coli CDP-ME synthetase in the apo form and complexed with both CTP–Mg2 and CDP-ME–Mg2+ reveal the stereochemical principles underlying both substrate and product recognition as well as catalysis in CDP-ME synthetase. Moreover, these complexes represent the first experimental structuresfor any cytidyltransferase with both substrates and products bound. □ Deciphering the design of the tropomyosin molecule. Jerry H. Brown, Kyoung-Hee Kim, Gyo Jun, Norma J. Greenfield, Roberto Dominguez, Niels Volkmann, Sarah E. Hitchcock-DeGregori, and Carolyn Cohen (2001). Proc. Natl. Acad. Sci. USA 98, 8496–8501. Published online before print as 10.1073/pnas.131219198. The crystal structure at 2.0 Å resolution of an 81-residue N-terminal fragment of muscle α-tropomyosin reveals a parallel two-stranded α-helical coiled-coil structure with a remarkable core. The high alanine content of the molecule is clustered into short regions where the local 2-fold symmetry is broken by a small (∼1.2 Å) axial staggering of the helices. The joining of these regions with neighboring segments, where the helices are in axial register, gives rise to specific bends in the molecular axis. This asymmetric design in a dimer of identical (or highly similar) sequences allows the tropomyosin molecule to adopt multiple bent conformations. The seven alanine clusters in the core of the complete molecule (which spans seven monomers of the actin helix) promote the semiflexible winding of the tropomyosin filament necessary for its regulatory role in muscle contraction. □ BeF−3 acts as a phosphate analog in proteins phosphorylated on aspartate: Structure of a BeF−3 complex with phosphoserine phosphatase. Ho Cho, Weiru Wang, Rosalind Kim, Hisao Yokota, Steven Damo, Sung-Hou Kim, David Wemmer, Sydney Kustu, and Dalai Yan (2001). Proc. Natl. Acad. Sci. USA 98, 8525–8530. Published online before print as 10.1073/pnas.131213698. Protein phosphoaspartate bonds play a variety of roles. In response regulator proteins of two-component signal transduction systems, phosphorylation of an aspartate residue is coupled to a change from an inactive to an active conformation. In phosphatases and mutases of the haloacid dehalogenase (HAD) superfamily, phosphoaspartate serves as an intermediate in phosphotransfer reactions, and in P-type ATPases, also members of the HAD family, it serves in the conversion of chemical energy to ion gradients. For response regulators, a phosphate analog, BeF−3, yields persistent complexes with the active site aspartate of their receiver domains. The authors have solved at 1.5 Å resolution the X-ray crystal structure of the complex of BeF−3 with a HAD superfamily member, phosphoserine phosphatase (PSP) from Methanococcus jannaschii. The structure is comparable to that of a phosphoenzyme intermediate: BeF−3 is bound to Asp-11 with the tetrahedral geometry of a phosphoryl group, is coordinated to Mg2+, and is bound to residues surrounding the active site that are conserved in the HAD superfamily. □ An autoinhibitory mechanism for nonsyntaxin SNARE proteins revealed by the structure of Ykt6p. Hidehito Tochio, Marco M.K. Tsui, David K. Banfield, and Mingjie Zhang (2001). Science 293, 698–702. Ykt6p is a nonsyntaxin SNARE implicated in multiple intracellular membrane trafficking steps. The NH2-terminal domain plays an important biological role in the function of Ykt6p, which in vitro studies revealed to include influencing the kinetics and proper assembly of SNARE complexes. The authors present the structure of the NH2-terminal domain of Ykt6p (Ykt6pN, residues 1 to 140). The structure of Ykt6pN differed entirely from that of syntaxin and resembled the overall fold of the actin regulatory protein, profilin. Like some syntaxins, Ykt6p adopted a folded back conformation in which Ykt6pN bound to its COOH-terminal core domain. □ The crystal structure of uncomplexed actin in the ADP state. Ludovic R. Otterbein, Philip Graceffa, and Roberto Dominguez (2001). Science 293, 708–711. The dynamics and polarity of actin filaments are controlled by a conformational change coupled to the hydrolysis of adenosine 5′-triphosphate (ATP) by a mechanism that remains to be elucidated. Actin modified to block polymerization was crystallized in the adenosine 5′-diphosphate (ADP) state, and the structure was solved to 1.54 Å resolution. Compared with previous ATP-actin structures from complexes with deoxyribonuclease I, profilin, and gelsolin, monomeric ADP-actin is characterized by a marked conformational change in subdomain 2.