Refined crystal structure of methylamine dehydrogenase from Paracoccus denitrificans at 1.75 A resolution

We extend the random intercept logistic model to accommodate negative intracluster correlations for bivariate binary response data. This approach assumes a single random effect per cluster, but entails separate affine transformations of this random effect for the two responses of the pair. We show this approach works for two data sets and a simulation, whereas other mixed effects approaches fail. The two data sets are from a crossover trial and a developmental toxicity study of the effects of chemical exposure on malformation risk among rat pups. Comparisons are made with the conditional likelihood approach and with generalized estimating equations estimation of the population-averaged logit model. Simulations show the conditional likelihood approach does not perform well for moderate to strong negative correlations, as a positive intracluster correlation is assumed. The proposed mixed effects approach appears to be slightly more conservative than the population-averaged approach with respect to coverage of confidence intervals. Nonetheless, the statistical literature suggests that mixed effects models provide information in addition to that provided by population-averaged models under scientific contexts such as crossover trials. Extensions to trivariate and higher-dimensional responses also are addressed. However, such extensions require certain constraints on the correlation structure.     

Streptomyces griseus aminopeptidase: X-ray crystallographic structure at 1.75 A resolution

The X-ray crystal structure of the enzyme Streptomyces griseus aminopeptidase (SGAP) has been determined in its double zinc form to 1.75 A resolution, in its apo-enzyme from (zinc removed) to 2.1 A resolution, and as a mercury replaced derivative to 2.1 A resolution. The structure solution was achieved by single isomorphous replacement with phasing from anomalous scattering (SIRAS), followed by density modification with histogram matching. The protein consists of a central beta-sheet made up of eight parallel and antiparallel strands, surrounded by helices on either side. The active site is located at the carbonyl ends of two middle strands of the beta-sheet region. Two sections of the chain that could not be traced were Glu196 to Arg202, which borders the active site, and the final seven C-terminal residues starting with Gly278. The active site contains two zinc cations, each with similar ligands, at a distance of 3.6 A from each other. An unknown molecule appears to be bound to both zinc ions in the active site at partial occupancy and has been modelled as a phosphate ion. A calcium binding site has also been identified, consistent with the observations that calcium modulates the activity of the enzyme, and increases its heat stability. The mechanism by which the calcium cation modulates enzyme activity is not apparent, since the location of the calcium binding site is approximately 25 A distant from the active site zinc ions. Comparison of the structure of SGAP to other known aminopeptidases shows that the enzyme is most similar to Aeromonas proteolytica aminopeptidase (AAP). Both enzymes share a similar topology, although the overall sequence identity is very low (24% in aligned regions). The coordination of the two active site zinc cations in SGAP resembles that of AAP. These two microbial enzymes differ from bovine lens leucine aminopeptidase (LAP) in both overall structure and in coordination of the two zinc ions.     

A fosmid-based genomic map and identification of 474 genes of the hyperthermophilic archaeon Pyrobaculum aerophilum

Polydimethylsiloxane (PEP) is widely used in medical prostheses and therefore is in contact with plasma and secretory proteins. Two pair of globular proteins, lactoferrin (Lf) and transferrin (Trf), and bovine IgG1 and IgG2a, which differ substantially between pair members in their pl, were used to study the interaction of a PEP widely used in breast implants and soluble protein. Studies were done using iodinated proteins over a concentration range that resulted in an apparent protein monolayer. Secondary incubations with dilute protein solutions were needed to form the monolayer on PEP, possibly as a consequence of micro air bubbles trapped on its highly textured surface as shown by atomic force microscopy. Immunoassay quality polystyrene microtiter wells were used as controls. Adsorption studies were routinely performed at pH 4, 7 and 10 and at ionic strengths corresponding to 0.95, 9.5 and 90.0 mS. The protein capture capacity (PCC) of PEP for Lf and Trf was optimal at physiological pH and ionic strength and comparable under these conditions to that of Immulon 2 (Imm 2) microtiter wells. While increasing the ionic strength and pH further increases the PCC of Imm 2 for Lf and Trf, this markedly lowered the PCC of PEP for these proteins suggesting that initial polar interactions may precede subsequent hydrophobic bonding to PEP. This was tested using a hydrophilic variant of PEP, which when tested in a 90.0 mS buffer, showed a > five-fold lower PCC at neutral and alkaline pH. The greatly reduced PCC of the hydrophilic variant might also suggest that hydrophilic variants of silicone would be more biocompatible than those currently used. The PCC of PEP for the IgGs was less than that of Imm 2 but still optimal at physiological conditions. Consistent with the data on Lf/Trf, PCC progressively decreased with increasing ionic strength at alkaline pH. Differences in pl between the protein pairs had only a marginal effect on the PCC of PEP. Monolayer adsorption on both PEP and Imm 2 was slowly reversible and greater in the presence of free ligand (< 2% in 16 h) suggesting that the process follows Mass Law principles. However, even in the presence of non-ionic detergent and free ligand, 85-90% remained bound on either surface. Thus, desorption of proteins in the monolayer should not complicate subsequent immunochemical studies conducted on adsorbed monolayers.     

A novel functional human eukaryotic translation initiation factor 4G

Mammalian eukaryotic translation initiation factor 4F (eIF4F) is a cap-binding protein complex consisting of three subunits: eIF4E, eIF4A, and eIF4G. In yeast and plants, two related eIF4G species are encoded by two different genes. To date, however, only one functional eIF4G polypeptide, referred to here as eIF4GI, has been identified in mammals. Here we describe the discovery and functional characterization of a closely related homolog, referred to as eIF4GII. eIF4GI and eIF4GII share 46% identity at the amino acid level and possess an overall similarity of 56%. The homology is particularly high in certain regions of the central and carboxy portions, while the amino-terminal regions are more divergent. Far-Western analysis and coimmunoprecipitation experiments were used to demonstrate that eIF4GII directly interacts with eIF4E, eIF4A, and eIF3. eIF4GII, like eIF4GI, is also cleaved upon picornavirus infection. eIF4GII restores cap-dependent translation in a reticulocyte lysate which had been pretreated with rhinovirus 2A to cleave endogenous eIF4G. Finally, eIF4GII exists as a complex with eIF4E in HeLa cells, because eIF4GII and eIF4E can be purified together by cap affinity chromatography. Taken together, our findings indicate that eIF4GII is a functional homolog of eIF4GI. These results may have important implications for the understanding of the mechanism of shutoff of host protein synthesis following picornavirus infection.     

Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families

As the amount of available sequence data increases, it becomes apparent that our understanding of translation initiation is far from comprehensive and that prior conclusions concerning the origin of the process are wrong. Contrary to earlier conclusions, key elements of translation initiation originated at the Universal Ancestor stage, for homologous counterparts exist in all three primary taxa. Herein, we explore the evolutionary relationships among the components of bacterial initiation factor 2 (IF-2) and eukaryotic IF-2 (eIF-2)/eIF-2B, i.e., the initiation factors involved in introducing the initiator tRNA into the translation mechanism and performing the first step in the peptide chain elongation cycle. All Archaea appear to posses a fully functional eIF-2 molecule, but they lack the associated GTP recycling function, eIF-2B (a five-subunit molecule). Yet, the Archaea do posses members of the gene family defined by the (related) eIF-2B subunits alpha, beta, and delta, although these are not specifically related to any of the three eukaryotic subunits. Additional members of this family also occur in some (but by no means all) Bacteria and even in some eukaryotes. The functional significance of the other members of this family is unclear and requires experimental resolution. Similarly, the occurrence of bacterial IF-2-like molecules in all Archaea and in some eukaryotes further complicates the picture of translation initiation. Overall, these data lend further support to the suggestion that the rudiments of translation initiation were present at the Universal Ancestor stage.     

Phosphorylation of tobacco eukaryotic translation initiation factor 4A upon pollen tube germination

Eukaryotic translation initiation factor eIF-4A is a member of the DEAD box family of RNA helicases and RNA-dependent ATPases. In tobacco, eIF-4A is encoded by a gene family with one isoform, eIF-4A8, being exclusively expressed in pollen. This pollen-specific isoform is a candidate for mediating translational control in the developing gametophyte. Here we show that eIF-4A is barely phosphorylated in mature pollen, but during pollen tube germination, two isoforms of eIF-4A become phosphorylated. Phosphoamino acid analysis indicated phosphorylation of threonine. In order to determine whether pollen-specific eIF-4A8 is among the phosphorylated isoforms, we raised transgenic tobacco plants overexpressing eIF-4A8 containing a histidine tag. Hereby, we could show that indeed eIF-4A8 is modified through phosphorylation. The biological relevance of the phosphorylation of eIF-4A is discussed.     

The sequence of a subtilisin-type protease (aerolysin) from the hyperthermophilic archaeum Pyrobaculum aerophilum reveals sites important to thermostability

The hyperthermophilic archaeum Pyrobaculum aerophilum grows optimally at 100 degrees C and pH 7.0. Cell homogenates exhibit strong proteolytic activity within a temperature range of 80-130 degrees C. During an analysis of cDNA and genomic sequence tags, a genomic clone was recovered showing strong sequence homology to alkaline subtilisins of Bacillus sp. The total DNA sequence of the gene encoding the protease (named "aerolysin") was determined. Multiple sequence alignment with 15 different serine-type proteases showed greatest homology with subtilisins from gram-positive bacteria rather than archaeal or eukaryal serine proteases. Models of secondary and tertiary structure based on sequence alignments and the tertiary structures of subtilisin Carlsberg, BPN', thermitase, and protease K were generated for P. aerophilum subtilisin. This allowed identification of sites potentially contributing to the thermostability of the protein. One common transition put alanines at the beginning and end of surface alpha-helices. Aspartic acids were found at the N-terminus of several surface helices, possibly increasing stability by interacting with the helix dipole. Several of the substitutions in regions expected to form surface loops were adjacent to each other in the tertiary structure model.     

Conservation and diversity of eukaryotic translation initiation factor eIF3

The largest of the mammalian translation initiation factors, eIF3, consists of at least eight subunits ranging in mass from 35 to 170 kDa. eIF3 binds to the 40 S ribosome in an early step of translation initiation and promotes the binding of methionyl-tRNAi and mRNA. We report the cloning and characterization of human cDNAs encoding two of its subunits, p110 and p36. It was found that the second slowest band during polyacrylamide gel electrophresis of eIF3 subunits in sodium dodecyl sulfate contains two proteins: p110 and p116. Analysis of the cloned cDNA encoding p110 indicates that its amino acid sequence is 31% identical to that of the yeast protein, Nip1. The p116 cDNA was cloned and characterized as a human homolog of yeast Prt1, as described elsewhere (Methot, N., Rom, E., Olsen, H., and Sonenberg, N. (1997) J. Biol. Chem. 272, 1110-1116). p36 is a WD40 repeat protein, which is 46% identical to the p39 subunit of yeast eIF3 and is identical to TRIP-1, a phosphorylation substrate of the TGF-beta type II receptor. The p116, p110, and p36 subunits localize on 40 S ribosomes in cells active in translation and co-immunoprecipitate with affinity-purified antibodies against the p170 subunit, showing that these proteins are integral components of eIF3. Although p36 and p116 have homologous protein subunits in yeast eIF3, the p110 homolog, Nip1, is not detected in yeast eIF3 preparations. The results indicate both conservation and diversity in eIF3 between yeast and humans.     

Structure of human des(1-45) factor Xa at 2.2 A resolution

The structure of a large molecular fragment of factor Xa that lacks only a Gla (gamma-carboxyglutamic acid) domain (N-terminal 45 residues) has been solved by X-ray crystallography and refined at 2.2 A resolution to a crystallographic R-value of 0.168. The fragment identity was clearly established by automated Edman degradation. X-ray structure analysis confirmed the biochemical characterization and also revealed that the N-terminal epidermal growth factor (EGF)-like domain is flexibly disordered in crystals. The second EGF module, however, is positionally ordered making contacts with the catalytic domain. The overall folding of the catalytic domain is similar to that of alpha-thrombin, excluding the insertion loops of the latter with respect to simpler serine proteinases. The C-terminal arginine of the A-chain interacts in a substrate-like manner with the S1 specificity site of the active site of a crystallographically neighboring molecule. Based on this interaction and the structure of D-PheProArg methylene-thrombin, a model of the commonly used dansylGluGlyArg methylene inhibitor-factor Xa interaction is proposed. The region of factor Xa corresponding to the fibrinogen recognition site of thrombin has a reversed electrical polarity to the anion binding fibrinogen recognition site of thrombin but possesses a site similar to the Ca2+ binding site of trypsin and other serine proteinases. The structure of the C-terminal EGF domain of factor Xa is the first to be determined crystallographically. Its folding has been comprehensively compared with similar domains determined by NMR. Although the A-chain makes 44 contacts at less than 3.5 A with the catalytic domain, only 16 involve the EGF module. In addition, the A-chain makes 30 intermolecular contacts with a neighboring catalytic domain.     

Structure of a sarcoplasmic calcium-binding protein from amphioxus refined at 2.4 A resolution

The three-dimensional structure of a sarcoplasmic Ca(2+)-binding protein from the protochordate amphioxus has been determined at 2.4 A resolution using multiple-isomorphous-replacement techniques. The refined model includes all 185 residues, three calcium ions, and one water molecule. The final crystallographic R-factor is 0.199. Bond lengths and bond angles in the molecules have root-mean-square deviations from ideal values of 0.015 A and 2.8 degrees, respectively. The overall structure is highly compact and globular with a predominantly hydrophobic core, unlike the extended dumbbell-shaped structures of calmodulin or troponin C. There are four distinct domains with the typical helix-loop-helix Ca(2+)-binding motif (EF hand). The conformation of the pair of EF hands in the N-terminal half of the protein is unusual due to the presence of an aspartate residue in the twelfth position of the first Ca(2+)-binding loop, rather than the usual glutamate. The C-terminal half of the molecule contains one Ca(2+)-binding domain with a novel helix-loop-helix conformation and one Ca(2+)-binding domain that is no longer functional because of amino acid changes. The overall structure is quite similar to a sarcoplasmic Ca(2+)-binding protein from sandworm, although there is only about 12% amino acid sequence identity between them. The similarity of the structures of these two proteins suggests that all sarcoplasmic Ca(2+)-binding proteins will have the same general conformation, even though there is very little conservation of primary structure among the proteins from various species.     

Malignant transformation by overproduction of translation initiation factor eIF4G

N4G3, a cell line that overexpresses translation initiation factor eIF4G, one of the components of eIF4F, was made by stable transfection of the human eIF4G cDNA into NIH3T3 cells. The cells expressed 80-100 times greater levels of eIF4G mRNA than did NIH3T3 cells. N4G3 cells formed transformed foci on a monolayer of cells, showed anchorage-independent growth, and formed tumors in nude mice. These results indicate that overexpression of eIF4G caused malignant transformation of NIH3T3 cells. It is also known that overexpression of eIF4E, another component of eIF4F, causes transformation of NIH3T3 cells. However, there was no difference in the amount of eIF4E protein between N4G3 and NIH3T3 cells, indicating that cell transformation does not involve a change in eIF4E levels. The results may be due to an effect of eIF4G on translational control of protein synthesis directed by mRNAs having long 5'-untranslated region.     

Importance of initiation factor preparations in the translation of reovirus and globin mRNAs lacking a 5'-terminal 7-methylguanosine

Reovirus and globin mRNAs which lack a 5'-terminal 7-methylguanosine are translated in a fractionated cell-free protein-synthesizing system. Efficient translation occurs only at optimal concentrations of reticulocyte initiation factor preparations and does not occur at optimal concentrations of ascites initiation factor preparations or at suboptimal concentrations of reticulocyte initiation factor preparations. The translation of "uncapped" mRNA in vitro, therefore, appears to be related to the efficiency of initiation of protein synthesis. At optimal concentrations of reticulocyte initiation factors, mRNA containing a 5'-terminal 7-methylguanosine is preferentially translated in the presence of mRNA which lacks a "cap." These results indicate that the 5'-terminal 7-methylguanosine on mRNA has a facilitatory rather than obligatory role in translation.     

Cloning, expression, and crystallization of a hyperthermophilic protein that is homologous to the eukaryotic translation initiation factor, eIF5A

A gene coding for a protein homologous to a translation initiation factor of eukaryotes, eIF5A, was cloned from Methanococcus jannaschii, a hyperthermophile with an optimum growth temperature of 85 degrees C. The protein was overexpressed, purified and crystallized. The crystals were obtained by vapor diffusion method with 8% PEG 4000 as precipitant and belong to space group P4(1)22 with unit cell dimensions a = b = 45.52 A and c = 155.59 A. These crystals diffract to at least 2.2 A resolution.     

Complex formation by all five homologues of mammalian translation initiation factor 3 subunits from yeast Saccharomyces cerevisiae

The PRT1, TIF34, GCD10, and SUI1 proteins of Saccharomyces cerevisiae were found previously to copurify with eukaryotic translation initiation factor 3 (eIF3) activity. Although TIF32, NIP1, and TIF35 are homologous to subunits of human eIF3, they were not known to be components of the yeast factor. We detected interactions between PRT1, TIF34, and TIF35 by the yeast two-hybrid assay and in vitro binding assays. Discrete segments (70-150 amino acids) of PRT1 and TIF35 were found to be responsible for their binding to TIF34. Temperature-sensitive mutations mapping in WD-repeat domains of TIF34 were isolated that decreased binding between TIF34 and TIF35 in vitro. The lethal effect of these mutations was suppressed by increasing TIF35 gene dosage, suggesting that the TIF34-TIF35 interaction is important for TIF34 function in translation. Pairwise in vitro interactions were also detected between PRT1 and TIF32, TIF32 and NIP1, and NIP1 and SUI1. Furthermore, PRT1, NIP1, TIF34, TIF35, and a polypeptide with the size of TIF32 were specifically coimmunoprecipitated from the ribosomal salt wash fraction. We propose that all five yeast proteins homologous to human eIF3 subunits are components of a stable heteromeric complex in vivo and may comprise the conserved core of yeast eIF3.     

Ligand interactions with eukaryotic translation initiation factor 2: role of the gamma-subunit

Eukaryotic translation initiation factor 2 (eIF-2) comprises three non-identical subunits alpha, beta and gamma. In vitro, eIF-2 binds the initiator methionyl-tRNA in a GTP-dependent fashion. Based on similarities between eukaryotic eIF-2gamma proteins and eubacterial EF-Tu proteins, we previously proposed a major role for the gamma-subunit in binding guanine nucleotide and tRNA. We have tested this hypothesis by examining the biochemical activities of yeast eIF-2 purified from wild-type strains and strains harboring mutations in the eIF-2gamma structural gene (GCD11) predicted to alter ligand binding by eIF-2. The alteration of tyrosine 142 in yeast eIF-2gamma, corresponding to histidine 66 in Escherichia coli EF-Tu, dramatically reduced the affinity of eIF-2 for Met-tRNAi(Met) without affecting the k(off) value for guanine nucleotides. In contrast, non-lethal substitutions at a conserved lysine residue (K250) in the putative guanine ring-binding loop increased the off-rate for GDP, thereby mimicking the function of the guanine nucleotide exchange factor eIF-2B, without altering the apparent dissociation constant for Met-tRNAi(Met). For eIF-2[gamma-K250R], the increased off-rate also seen for GTP was masked by the presence of Met-tRNAi(Met) in vitro. In vivo, increasing the dose of the yeast initiator tRNA gene suppressed the slow-growth phenotype and reduced GCN4 expression in gcd11-K250R and gcd11-Y142H strains. These studies indicate that the gamma-subunit of eIF-2 does indeed provide EF-Tu-like function to the eIF-2 complex, and further suggest that the level of Met-tRNAi(Met) is critical for maintaining wild-type rates of initiation in vivo.     

Magnetic Transition and Magnetic Entropy Change of Gd5Si1.75Ge1.75Sn0.5

Gd5Si2Ge2.2 alloy was synthesized by arcmelting and its phase components, microstructure, and especially the line features were investigated by X- ray diffraction （XRD）, scanning-electron microscope （SEM）, energy-dispersive spectroscopy （EDS）, and transmission-electron microscope （TEM）. Gd5Si2Ge2.2 consists of Gd5Si2Ge2-type and GdGe-type phases and presents eutectic characteristics. There are many regular line features on the Gd5Si2Ge2-type phase according to SEM. EDS shows that the line feature is not the Gd5 （Si,Ge）3-type phase because Gd content decreases at the line features. Two types of line features are found in the fine microstructure of Gd5Si2Ge2-type phase by TEM. Selected area diffraction （SAD） confirms that both line features are not the secondary phase or twins. There is no changes observed in the microstructure of Gd5Si2Ge2 2 from room temperature to 1400 ℃ with in situ high temperature optical microscope, therefore, it is deduced that the line features observed by SEM are formed during the solidification.     

Structure at 0.85 A resolution of an early protein photocycle intermediate

Protein photosensors from all kingdoms of life use bound organic molecules, known as chromophores, to detect light. A specific double bond within each chromophore is isomerized by light, triggering slower changes in the protein as a whole. The initial movements of the chromophore, which can occur in femtoseconds, are tightly constrained by the surrounding protein, making it difficult to see how isomerization can occur, be recognized, and be appropriately converted into a protein-wide structural change and biological signal. Here we report how this dilemma is resolved in the photoactive yellow protein (PYP). We trapped a key early intermediate in the light cycle of PYP at temperatures below -100 degrees C, and determined its structure at better than 1 A resolution. The 4-hydroxycinnamoyl chromophore isomerizes by flipping its thioester linkage with the protein, thus avoiding collisions resulting from large-scale movement of its aromatic ring during the initial light reaction. A protein-to-chromophore hydrogen bond that is present in both the preceding dark state and the subsequent signalling state of the photosensor breaks, forcing one of the hydrogen-bonding partners into a hydrophobic pocket. The isomerized bond is distorted into a conformation resembling that in the transition state. The resultant stored energy is used to drive the PYP light cycle. These results suggest a model for phototransduction, with implications for bacteriorhodopsin, photoactive proteins, PAS domains, and signalling proteins.     

Structure of Peptococcus aerogenes ferredoxin. Refinement at 2 A resolution

The model for ferredoxin from Peptococcus aerogenes, derived from a 2.8-A resolution map, has been refined with a 2-A resolution data set. The conventional index, R, decreased from 0.449 for the initial model to 0.188 for the unconstrained one and 0.206 for the constrained one. The standard deviations of the iron and sulfur atoms are 0.04 to 0.05 A and for the oxygen, nitrogen, and carbon atoms they range from 0.14 to 0.26 A. One hundred forty-six water oxygen atoms were included in the solvent part of the model and were checked by a highly selective criterion, suggesting that most of them represented water molecules.     

Molecular cloning and functional expression of a human cDNA encoding translation initiation factor 6

Eukaryotic translation initiation factor 6 (eIF6) binds to the 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit. In this paper, we devised a procedure for purifying eIF6 from rabbit reticulocyte lysates and immunochemically characterized the protein by using antibodies isolated from egg yolks of laying hens immunized with rabbit eIF6. By using these monospecific antibodies, a 1.096-kb human cDNA that encodes an eIF6 of 245 amino acids (calculated Mr 26,558) has been cloned and expressed in Escherichia coli. The purified recombinant human protein exhibits biochemical properties that are similar to eIF6 isolated from mammalian cell extracts. Database searches identified amino acid sequences from Saccharomyces cerevisiae, Drosophila, and the nematode Caenorhabditis elegans with significant identity to the deduced amino acid sequence of human eIF6, suggesting the presence of homologues of human eIF6 in these organisms.     

A six-domain structural model for Escherichia coli translation initiation factor IF2. Characterisation of twelve surface epitopes

The Escherichia coli translation initiation factor IF2 is a 97 kDa protein which interacts with the initiator fMet-tRNAfMet, GTP and the ribosomal subunits during initiation of protein biosynthesis. For structural and functional investigations of the factor, we have raised and characterised monoclonal antibodies against E. coli IF2. Twelve epitopes have been localised at the surface of the protein molecule by three different methods: Interactions of the monoclonal antibodies with nested deletion mutants of IF2, comparison of the relative location of the epitopes in a competition immunoassay and cross-reactivity analyses of the monoclonal antibodies towards IF2 from Salmonella typhimurium, Klebsiella oxytoca, Enterobacter cloacae, Proteus vulgaris, and Bacillus stearothermophilus. These data are combined with predicted secondary structure and discussed in relation to a six-domain structural model for IF2. The model describes IF2 as a slightly elongated molecule with a structurally compact C-terminal domain, a well-conserved central GTP-binding domain, and a highly charged, solvent exposed N-terminal with protruding alpha-helical structures.