Domain Translation Research Articles

The FEN-1 family of structure-specific nucleases in eukaryotic DNA replication, recombination and repair.

Unlike the most well-characterized prokaryotic polymerase, E. coli DNA pol l, none of the eukaryotic polymerases have their own 5' to 3' exonuclease domain for nick translation and Okazaki fragment processing. In eukaryotes, FEN-1 is an endo- and exonuclease that carries out this function independently of the polymerase molecules. Only seven nucleases have been cloned from multicellular eukaryotic cells. Among these, FEN-1 is intriguing because it has complex structural preferences; specifically, it cleaves at branched DNA structures. The cloning of FEN-1 permitted establishment of the first eukaryotic nuclease family, predicting that S. cerevisiae RAD2 (S. pombe Rad13) and its mammalian homolog, XPG, would have similar structural specificity. The FEN-1 nuclease family includes several similar enzymes encoded by bacteriophages. The crystal structures of two enzymes in the FEN-1 nuclease family have been solved and they provide a structural basis for the interesting steric requirements of FEN-1 substrates. Because of their unique structural specificities, FEN-1 and its family members have important roles in DNA replication, repair and, potentially, recombination. Recently, FEN-1 was found to specifically associate with PCNA, explaining some aspects of FEN-1 function during DNA replication and potentially in DNA repair.

A combined SPALEED and helium-atom diffraction investigation of the structure of oxidized Cu(001)

The structure of the oxidized Cu(001) surface has been investigated at room temperature using spot profile analysis LEED (SPALEED) and helium-atom diffraction. In both measurements the observed 1 4 - order diffraction spots of the (2√2 × √2)R45° structure show a splitting which is attributed to a large number of small translationally displaced domains. Extensive Eikonal simulations of the helium atom results indicate that [ 3 2 , 1 2 ,0] a translational domain displacements are preferred. Evidence for areas with different lattice constants is also presented.

Phase diagram of domain walls in the cubic superstructures of the fcc lattice

The thermodynamical behavior of non-conservative [100] domain walls is investigated in the L12 and L10 binary alloys, close to their respective first order–disorder transition lines. Calculations are made using an inhomogeneous cluster variation method in the tetrahedron approximation, within the framework of antiferromagnetic Ising Hamiltonian formulation. Critical phenomena are discussed close to the L12–disorder and L10–disorder transitions, and in the vicinity of the triple point. Different kinds of wetting are exhibited in relation to the relative orientations of the outer variants. The following features are examined: (i) the translational domain wall in the L12 phase is found to be wetted by the disordered phase on the coexistence line; (ii) the orientational domain wall between two L10 variants undergoes a first-order dewetting transition close to the triple point; and (iii) the translational domain wall in the L10 phase undergoes a prewetting transition followed by a wetting process up to the transition line.

Ribosome-mediated translational pause and protein domain organization.

Because regions on the messenger ribonucleic acid differ in the rate at which they are translated by the ribosome and because proteins can fold cotranslationally on the ribosome, a question arises as to whether the kinetics of translation influence the folding events in the growing nascent polypeptide chain. Translationally slow regions were identified on mRNAs for a set of 37 multidomain proteins from Escherichia coli with known three-dimensional structures. The frequencies of individual codons in mRNAs of highly expressed genes from E. coli were taken as a measure of codon translation speed. Analysis of codon usage in slow regions showed a consistency with the experimentally determined translation rates of codons; abundant codons that are translated with faster speeds compared with their synonymous codons were found to be avoided; rare codons that are translated at an unexpectedly higher rate were also found to be avoided in slow regions. The statistical significance of the occurrence of such slow regions on mRNA spans corresponding to the oligopeptide domain termini and linking regions on the encoded proteins was assessed. The amino acid type and the solvent accessibility of the residues coded by such slow regions were also examined. The results indicated that protein domain boundaries that mark higher-order structural organization are largely coded by translationally slow regions on the RNA and are composed of such amino acids that are stickier to the ribosome channel through which the synthesized polypeptide chain emerges into the cytoplasm. The translationally slow nucleotide regions on mRNA possess the potential to form hairpin secondary structures and such structures could further slow the movement of ribosome. The results point to an intriguing correlation between protein synthesis machinery and in vivo protein folding. Examination of available mutagenic data indicated that the effects of some of the reported mutations were consistent with our hypothesis.

Native 3D structure of eukaryotic 80s ribosome: morphological homology with E. coli 70S ribosome.

A three-dimensional reconstruction of the eukaryotic 80S monosome from a frozen-hydrated electron microscopic preparation reveals the native structure of this macromolecular complex. The new structure, at 38A resolution, shows a marked resemblance to the structure determined for the E. coli 70S ribosome (Frank, J., A. Verschoor, Y. Li, J. Zhu, R.K. Lata, M. Radermacher, P. Penczek, R. Grassucci, R.K. Agrawal, and Srivastava. 1996b. In press; Frank, J., J. Zhu, P. Penczek, Y. Li, S. Srivastava ., A. Verschoor, M. Radermacher, R. Grassucci, R.K. Lata, and R. Agrawal. 1995. Nature (Lond.).376:441-444.) limited to a comparable resolution, but with a number of eukaryotic elaborations superimposed. Although considerably greater size and intricacy of the features is seen in the morphology of the large subunit (60S vs 50S), the most striking differences are in the small subunit morphology (40S vs 30S): the extended beak and crest features of the head, the back lobes, and the feet. However, the structure underlying these extra features appears to be remarkably similar in form to the 30S portion of the 70S structure. The intersubunit space also appears to be strongly conserved, as might be expected from the degree of functional conservation of the ribosome among kingdoms (Eukarya, Eubacteria, and Archaea). The internal organization of the 80S structure appears as an armature or core of high-density material for each subunit, with the two cores linked by a single bridge between the platform region of the 40S subunit and the region below the presumed peptidyltransferase center of the 60S subunit. This may be equated with a close contact of the 18S and 28S rRNAs in the translational domain centered on the upper subunit:subunit interface.

TEM observations of domains in ferroelectric and nonferroelectric perovskites

Abstract In situ transmission electron microscopy has been used to examine the domain structures arising from several types of phase transitions in perovskite-structured materials. Dark field imaging techniques have been used to isolate different types of domains in some technologically important ceramics. The complex domain structures which occur in Pb(SC1/2Ta1/2)O3 have been studied as a function of temperature and the observed changes have been discussed. The orientational and translational (antiphase) domains which arise from octahedral tilt transitions have been illustrated. Finally, the domain structures in bulk and thin film Pb(Zr, Ti)O3 have been compared and contrasted.

Molecular images of [M(phthalocyaninato)O]n, where M = Si and Ge: Microphases and structures of crystal domains

AbstractThis contribution is a study of the crystal structures and crystal domains in the thin epitaxially growing films of [M(Pc)O]n (M = Si and Ge, Pc = phthalocyaninato) revealed by high‐resolution electron microscopy. Microphases detectable only on the microscopic level were observed: (a) γ‐phase for [Si(Pc)O]n, orthorhombic system, a = 1.38 nm, b = 5.52 nm, c = 0.66 nm; and (b) α‐phase for [Ge(Pc)O]n, base‐centered orthorhombic, a = 1.33 nm, b = 2.66 nm, c = 0.35 nm. Translation and rotation crystal domains were visualized on the nanometeric scale. The high‐resolution images are rich in irregularity and provide direct information on the defects and imperfections in the polymer films. © 1995 John Wiley & Sons, Inc.

Phase transformations in the (Ti, Nb) 3 Al section of the TiAlNb system—II. Experimental tem study of microstructures

In Part I of this paper possible transformation paths that involve no long range diffusion and their corresponding microstructural details were predicted for TiAlNb alloys cooled from the high temperature b.c.c./B2 phase field into close-packed orthorhombic or hexagonal phase fields. In the present paper experimental TEM results show that two of the predicted transformation paths are indeed followed for different alloy compositions. For Ti25Al12.5Nb (at.%), the path includes the formation of intermediate hexagonal phases, A3 and D0 19, and subsequent formation of a metastable domain structure of the low-temperature O phase. For alloys close to Ti25Al25Nb (at. %), path involves an intermediate B19 structure and subsequent formation of a translational domain structure of the O phase. The path selection depends on whether B2 order forms in the high temperature cubic phase prior to transformation to the close-packed structure. The paper also analyzes the formation of a two-phase modulated microstructure during long term annealing 700°C. The thermodynamics underlying the path selection and the two-phase formation are also discussed.

Potential secondary structure at the translational start domain of eukaryotic and prokaryotic mRNAs

In order to identify conserved potential secondary wtructures within translational start sites, mRNA sequences derived from different species were studied with programs able to depict such features. The potential secondary structure of 71 bases around the initiator AUG or AUGs in the coding sequences of 290 eukaryotic mRNAs was first examined and compared to 290 similarly analyzed regions derived from prokaryotic mRNA sequences ( Nucleic Acids Res (1987) 15, 345–360). In both sets of sequences the initiator codon was often found to be in an open potential structure whereas a denser region characterized by nearly-periodic spacings defined the coding regions. Randomization of the sequences obliterated the observed patterns suggesting that the structure of the mRNA may determine these differences. Three sets of eukaryotic and prokaryotic mRNAs of approximately equal length were analyzed and found to preservedan open unpaired non-coding region 5′ to the start codon. The start codon was found free of potential secondary structure in over 80% of all the sequences nalyzed. These data, and study of mutants that restrict the accessibility of the start codon to the ribosomal initiation complex, suggest that both the prokaryotic and eukaryotic mRNA start sites must occur free of potential secondary structure for efficient initiation. A striking difference of the eukaryotic mRNA sequences analyzed was the high propensity of the coding region vicinal to the start codon to form secondary structures. Certain translation-defective mutants exhibit impaired formation of these secondary structures suggesting that the structure of the coding regions adjacent to the start codons of eukaryotic mRNAs may be an important, thus far unexamined, determinant of initiation. We propose that, for all genes studied, the transition in secondary structure between the coding and non-coding regions may be an important determinant of initiation.

Microstructure of GdBa 2Cu 3O 7–δ films grown on SrTiO 3 substrate

GdBa 2Cu 3O 7-δ thin films deposited on SrTiO 3 substrate by DC magnetron sputtering were observed by a JEM-200CX HREM, two cross-sectional samples for HREM observation having been prepared by Ar ion thinning. An effective and reliable procedure for preparing a TEM sample by Ar ion thinning is proposed on the basis of the fact that the sample thinned at 6 kV was seriously damaged by ion bombardment, while that thinned at 4 kV was not damaged. The formation of 90° domains, which were frequently observed, is considered to be accompanied by the existence of defects such as dislocations and stacking faults. The steps and other types of unsmoothness of the substrate surface can also lead to different kinds of defects: a c/3 translation domain boundary is shown to originate from a step on the substrate surface.

Transformation of BCC and B2 High Temperature Phases to HCP and Orthorhombic Structures in the Ti-Al-Nb System. Part II: Experimental TEM Study of Microstructures.

Possible transformation paths that involve no long range diffusion and their corresponding microstructural details were predicted by Bendersky, Roytburd, and Boettinger [J. Res. Natl. Inst. Stand. Technol. 98, 561 (1993)] for Ti-Al-Nb alloys cooled from the high temperature BCC/B2 phase field into close-packed orthorhombic or hexagonal phase fields. These predictions were based on structural and symmetry relations between the known phases. In the present paper experimental TEM results show that two of the predicted transformation paths are indeed followed for different alloy compositions. For Ti-25Al-12.5Nb (at%), the path includes the formation of intermediate hexagonal phases, A3 and DO19, and subsequent formation of a metastable domain structure of the low-temperature O phase. For alloys close to Ti-25Al-25Nb (at%), the path involves an intermediate B19 structure and subsequent formation of a translational domain structure of the O phase. The path selection depends on whether B2 order forms in the high temperature cubic phase prior to transformation to the close-packed structure. The paper also analyzes the formation of a two-phase modulated microstructure during long term annealing at 700 °C. The structure forms by congruent ordering of the DO19 phase to the O phase, and then reprecipitation of the DO19 phase, possibly by a spinodal mechanism. The thermodynamics underlying the path selection and the two-phase formation are also discussed.

The 3' untranslated region of satellite tobacco necrosis virus RNA stimulates translation in vitro.

The RNA of satellite tobacco necrosis virus (STNV) is a monocistronic messenger that lacks both a 5' cap structure and a 3' poly(A) tail. We show that in a cell-free translation system derived from wheat germ, STNV RNA lacking the 600-nucleotide trailer is translated an order of magnitude less efficiently than full-size RNA. Deletion analyses positioned the translational enhancer domain (TED) within a conserved hairpin structure immediately downstream from the coat protein cistron. TED enhances translation when fused to a heterologous mRNA, but the level of enhancement depends on the nature of the 5' untranslated sequence and is maximal in combination with the STNV leader. The STNV leader and TED have two regions of complementarity. One of the complementary regions in TED resembles picornavirus box A, which is involved in cap-independent translation but which is located upstream of the coding region.

The 3' Untranslated Region of Satellite Tobacco Necrosis Virus RNA Stimulates Translation in Vitro

The RNA of satellite tobacco necrosis virus (STNV) is a monocistronic messenger that lacks both a 5' cap structure and a 3' poly(A) tail. We show that in a cell-free translation system derived from wheat germ, STNV RNA lacking the 600-nucleotide trailer is translated an order of magnitude less efficiently than full-size RNA. Deletion analyses positioned the translational enhancer domain (TED) within a conserved hairpin structure immediately downstream from the coat protein cistron. TED enhances translation when fused to a heterologous mRNA, but the level of enhancement depends on the nature of the 5' untranslated sequence and is maximal in combination with the STNV leader. The STNV leader and TED have two regions of complementarity. One of the complementary regions in TED resembles picornavirus box A, which is involved in cap-independent translation but which is located upstream of the coding region.

Translational energy dependence of the reactive cross-section of the C + NO ? CN + O reaction studied in pulsed, crossed, supersonic molecular beams

The C(3PJ)+ NO(X 2Πr)→ CN(X 2Σ+)+ O(3PJ) reaction is studied using combined pulsed lasers and pulsed, crossed, supersonic molecular beams. The relative reactive cross-section is found to decrease slowly in the relative translational energy domain sampled, εtr= 0.038 – 0.163 eV (1 eV ≈ 1.602 18 × 10–19 J), with a dependence that can be fitted to a (εtr)–1/3 functionality.

A new proof of the Brouwer plane translation theorem

AbstractLet f be an orientation-preserving homeomorphism of ℝ2 which is fixed point free. The Brouwer ‘plane translation theorem’ asserts that every x0 ∈ ℝ2 is contained in a domain of translation for f i.e. an open connected subset of ℝ2 whose boundary is L ∪ f(L) where L is the image of a proper embedding of ℝ in ℝ2, such that L separates f(L) and f−1(L). In addition to a short new proof of this result we show that there exists a smooth Morse function g: ℝ2 → ℝ such that g(f(x)) < g(x) for all x and the level set of g containing x0 is connected and non-compact (and hence the image of a properly embedded line).

Specific interactions of HeLa cell proteins with proposed translation domains of the poliovirus 5' noncoding region.

To determine which sequences or structures in the poliovirus 5' noncoding region (5'NCR) are involved in binding proteins used for internal ribosome binding and protein synthesis initiation, translation competition assays were performed in rabbit reticulocyte lysates in the presence and absence of HeLa cell extract. The results revealed two functional domains in the poliovirus 5'NCR. One, requiring nucleotides (nts) 457 to 626, binds proteins that are required for translation of all mRNAs and that are present in both reticulocyte lysates and HeLa cell extracts. Another, contained within nts 286 to 456, interacts with proteins that are specific for poliovirus translation and are present in HeLa cells but not in significant amounts in rabbit reticulocyte lysates. In order to detect HeLa cell proteins that interact stably with the 5'NCR of poliovirus, UV cross-linking was used. At least four major protein-RNA complexes were identified, three of which were shown by RNA competition analysis to bind specifically to defined domains within the 5'NCR. Protein A (54 kDa) cross-linked to RNA sequences and/or structures located between nts 457 and 626; proteins B (48 kDa) and C (38 kDa) bound to nts 286 to 456.

Structures of shear planes, intersection areas and translation domains in the Al5CuLi3Frank-Kasper phase

Networks of the {110} shear plane family in the Al5CuLi3 crystal structure have been observed during the phase transformation from AlCuLi icosahedral phase to the crystalline phase, i.e. Al5CuLi3 crystal. HREM images of the shear planes are reported along both [111] and [001] directions which establish the shear vectors uniquely. Structural models for the shear planes, intersection areas and translation domains have been symmetrically proposed and are in good agreement with experiments.

Learning Recursive Distributed Representations for Holistic Computation

A number of connectionist models capable of representing data with compositional structure have recently appeared. These new models suggest the intriguing possibility of performing holistic structure-sensitive computations with distributed representations. Two possible forms of holistic inference, transformational inference and confluent inference, are identified and compared. Transformational inference was successfully demonstrated by Chalmers; however, the pure transformational approach does not consider the eventual inference tasks during the process of learning its representations. Confluent inference is introduced as a method for achieving a tight coupling between the distributed representations of a problem and the solution for the given inference task while the net is still learning its representations. A dual-ported RAAM architecture based on Pollack's Recursive Auto-Associative Memory is implemented and demonstrated in the domain of Natural Language translation.

The subset of mouse B1 (Alu-equivalent) sequences expressed as small processed cytoplasmic transcripts

B1 (Alu-equivalent) is a murine short interspersed element whose amplification probably involved an RNA intermediate. B1-homologous RNA comprise a population of heterogenous transcripts of questionable function. A cloned B1 is expressed in the injected frog oocyte by RNA polymerase III transcription, ribonucleoprotein formation, post-transcriptional 3'-processing, and nucleocytoplasmic transport. The present study characterizes small cytoplasmic B1 transcripts of mouse cells. Analyses of ten cDNA clones revealed a subset of a high degree of sequence identity (98%) from which a novel consensus was developed. Structural analyses of these RNAs demonstrated a conserved Alu domain originally identified as part of the 7SL RNA within the translational control domain of the signal recognition particle, while this structure was not conserved in the majority of B1s in the sequence database. Furthermore, it was demonstrated that 3'-processing occurred in only a subset of B1 transcripts in-vitro using homologous nuclear extracts, and in the injected oocyte. The data demonstrate that a limited set of B1 sequences are expressed as processed RNA polymerase III-transcripts of a high degree of structural conservation. Although this subset is transcriptionally active, the selective expression may be due to regulation at the levels of processing and cytoplasmic accumulation. Their lack of Poly-(A) or 3'-oligo-(U) tracts argue that these RNAs are unlikely to represent transposition intermediates. Rather, their cytosolic compartmentalization and conservation of a biologically recognized structure, suggests potential involvement in other aspects of cellular metabolism.

Three-dimensional structure of the mammalian cytoplasmic ribosome

A three-dimensional reconstruction of the 80 S ribosome from rabbit reticulocytes has been calculated from low-dose electron micrographs of a negatively stained single-particle specimen. At 37 Å resolution, the precise orientations of the 40 S and 60 S subunits within the monosome can be discerned. The translational domain centered on the upper portion of the subunit/subunit interface is quite open, allowing considerable space between the subunits for interactions with the non-ribosomal macromolecules involved in protein synthesis. Further, the cytosolic side of the monosome is strikingly more open than the membrane-attachment side, suggesting a greater ease of communication with the cytoplasm, which would facilitate the inwards and outwards diffusion of a number of ligands. Although the 60 S subunit portion of the 80 S structure shows essentially all of the major morphological features identified for the eubacterial 50 S large subunit, it appears to possess a region of additional mass that evidently accounts for the more ellipsoidal form of the eukaryotic subunit.