Self-assembly of human MxA GTPase into highly ordered dynamin-like oligomers

Human MxA protein is a member of the interferon-induced Mx protein family and an important component of the innate host defense against RNA viruses. The Mx family belongs to a superfamily of large GTPases that also includes the dynamins and the interferon-regulated guanylate-binding proteins. A common feature of these large GTPases is their ability to form high molecular weight oligomers. Here we determined the capacity of MxA to self-assemble into homo-oligomers in vitro. We show that recombinant MxA protein assembles into long filamentous structures with a diameter of about 20 nm at physiological salt concentration as demonstrated by sedimentation assays and electron microscopy. In the presence of guanosine nucleotides the filaments rearranged into rings and more compact helical arrays. Our data indicate that binding and hydrolysis of GTP induce conformational changes in MxA that may be essential for viral target recognition and antiviral activity.     

Folding of peptides characterized by c3Val,a highly constrained analogue of valine

Using a combined chemical/chiral chromatographic approach we synthesized an N-protected derivative of (R)-c(3)Val, a severely conformationally restricted C(alpha)-tetrasubstituted alpha-amino acid characterized by a C(beta,beta)-dimethylated cyclopropane system. A set of terminally protected derivatives and model peptides (to the heptamer level), containing one or two (R)-c(3)Val residues in combination with either Aib or Gly residues, was prepared by solution methods. A detailed solution and crystal-state conformational investigation, based on Fourier transform infrared (FTIR) absorption, (1)H-NMR, and x-ray diffraction techniques, performed in comparison with a similar study on related derivatives and peptides rich in (alphaMe)Val, the prototype of C(alpha)-tetrasubstituted alpha-amino acids of this subfamily, allowed us to conclude the following: (a) c(3)Val is a good beta-bend and helix former, although less efficient than (alphaMe)Val. (b) The relationship between alpha-carbon chirality and screw sense of the folded structure formed is the same as that of (alphaMe)Val, i.e., the (R)-enantiomer has a strong left-handed bias. (c) c(3)Val seems more prone than (alphaMe)Val to fold into a gamma-bend conformation. The conformational propensities of C(beta,beta)-disubstituted Ac(3)c residues are also discussed in comparison with those of the parent cyclopropane residue.     

Folding transition of large DNA completely inhibits the action of a restriction endonuclease as revealed by single-chain observation

The biochemical characteristics of lambda DNA chains in folded/unfolded states upon cleavage by the restriction enzyme ApaLI were investigated in the presence of spermine. These characteristics of DNA chains depending on their higher-order structure were studied at the single-molecule level using fluorescence microscopy. With a low concentration of spermine, lambda DNA takes a random coiled conformation and allows digestion by the enzyme, while under a high concentration of spermine, lambda DNA takes a compact folded structure and inhibits such attack. Together with comparative experiments on short oligomeric DNA, our results suggest that the transition in the higher-order structure causes on/off-type switching of sensitivity to the enzyme.     

Folding into a beta-hairpin can prevent amyloid fibril formation

The tetrapeptide KFFE is one of the shortest amyloid fibril-forming peptides described. Herein, we have investigated how the structural environment of this motif affects polymerization. Using a turn motif (YNGK) or a less rigid sequence (AAAK) to fuse two KFFE tetrapeptides, we show by several biophysical methods that the amyloidogenic properties are strongly dependent on the structural environment. The dodecapeptide KFFEAAAKKFFE forms abundant thick fibril bundles. Freshly dissolved KFFEAAAKKFFE is monomeric and shows mainly disordered secondary structure, as evidenced by circular dichroism, NMR spectroscopy, hydrogen/deuterium exchange measurements, and molecular modeling studies. In sharp contrast, the dodecapeptide KFFEYNGKKFFE does not form fibrils but folds into a stable beta-hairpin. This structure can oligomerize into a stable 12-mer and multiples thereof, as shown by size exclusion chromatography, sedimentation analysis, and electrospray mass spectrometry. These data indicate that the structural context in which a potential fibril forming sequence is present can prevent fibril formation by favoring self-limiting oligomerization over polymerization.     

The existence of a highly ordered phase in fully hydrated dilauroylphosphatidylethanolamine

Dilauroylphosphatidylethanolamine dispersion forms a crystalline phase at physiological pH and temperature and in the presence of excess water. This phenomenon was observed and studied by differential scanning calorimetry, scanning densitometry and X-ray diffraction. The crystalline phase is stable at pH 5.5-9.5 and below 40 degrees C. The crystalline phase formed at pH 5.5 and pH 9.5 index according to orthorhombic cells with a = 9.41, b = 8.15, c = 46.0 and a = 9.33, b = 8.05, c = 45.8 (A), respectively. Around 43 degrees C, the crystalline phase is transformed into a multilayer liquid crystal phase. Cooling from 44 degrees C results in the disappearance of the original transition at 43 degrees C and the appearance of a second transition at around 30 degrees C. Below 30 degrees C the lipid forms a gel phase. This gel phase is metastable at pH 5.5 and a crystalline phase may be recovered from it by dispersing or aging methods. Suspensions of dilauroylphosphatidylethanolamine show similar phase transition behaviour at pH 5.5 and pH 9.5, although the transitions are somewhat broader at the higher pH. The thermotropic phase behaviour of dilauroylphosphatidylethanolamine dispersions may be governed by changes in hydration.     

Folding and stability of sweet protein single-chain monellin. An insight to protein engineering

Engineered single-chain monellin (SCM) proteins were constructed by recombinant technology without disrupting the topology and sweet activity of native protein. Data from 8-anilinonaphthalene-1-sulfonic acid fluorescence, size-exclusion chromatography, and heteronuclear NMR strongly suggest the presence of a folding intermediate at 1.5 m GdnHCl for SCM protein. The structural feature of the folding intermediate from NMR data reveals that the secondary structures became mostly unstable, and protein experiences a dynamic equilibrium between native and unfolded state. All backbone amide protons exchange within 10 min, which imply that no stable hydrogen bonds exist in the secondary structural regions in the folding intermediate. From equilibrium unfolding and mutagenesis studies, the unfolding transition midpoints of mutant proteins gradually shifted toward lower denaturant concentration, indicating stability reductions of mutant proteins. Our results suggest that stability and folding pathways of SCM proteins could be regulated by a combined study of spectroscopy and mutagenesis, and these studies will provide useful information for understanding the folding kinetics of novel engineered proteins.     

Folding of a highly conserved diverging turn motif from the SH3 domain

Recent NMR structural characterization studies showed that a seven-residue segment (FKKGERL) from the src SH3 domain adopts the nativelike diverging type II beta-turn in aqueous solution in support of the prediction based on the I-sites library of sequence structural motifs. We study the conformational variability and folding/unfolding thermodynamics of this peptide in explicit solvent using replica-exchange molecular dynamics simulations, which greatly enhances the sampling of the conformational space. This peptide samples three main free energy basins (nativelike, intermediate, and unfolded) separated by small barriers. The nativelike basin is fractionally populated (DeltaG(300K) = 0.4 kcal/mol) with structures that satisfy a subset of the NMR-derived constraints. The intrinsic stability of the diverging turn is examined in relationship to the nature of three specific contacts: a turn-hydrogen bond, a mainchain-to-sidechain hydrogen bond, and an end-to-end hydrophobic contact. We have carried out simulations of mutants at the highly conserved GE positions in the sequence. The mutation E5D destabilizes the isolated diverging turn motif, contrary to the observation that this mutation stabilizes the fyn SH3 domain. The G4T mutation also destabilizes the isolated diverging turn; however, the extent of destabilization is smaller than that of the reverse mutation in the drk SH3.     

Direct in vivo screening of intrabody libraries constructed on a highly stable single-chain framework

Single-chain Fv antibody fragments (scFv) represent a convenient antibody format for intracellular expression in eukaryotic or prokaryotic cells. These so-called intrabodies have great potential in functional genomics as a tool to study the function of newly identified proteins in vivo, for example by binding-induced modulation of their activity or by blocking interactions with other proteins. However, the intracellular expression and activity of many single-chain Fvs are limited by their instability and folding efficiency in the reducing intracellular environment, where the highly conserved intrachain disulfide bonds do not form. In the present work, we used an in vivo selection system to isolate novel antigen-binding intrabodies. We screened two intrabody libraries carrying a randomized third hypervariable loop onto the heavy chain of a stable framework, which had been further optimized by random mutagenesis for better behavior in the selection system, and we biophysically characterized the selected variants to interpret the outcome of the selection. Our results show that single-framework intrabody libraries can be directly screened in vivo to rapidly select antigen-specific intrabodies.     

Suppressor mutations identify box9 as a central nucleotide sequence in the highly ordered structure of intron RNA in yeast mitochondria.

Data presented here lend support to the notion that RNA splicing in yeast mitochondria depends on the formation of hybrid structures involving the well-conserved intron sequences box9 and box2. Starting with the cis-dominant splicing-defective box2 mutant G2590, a G----A transition, we isolated a revertant having a mitochondrial second site suppressor mutation, which restores splicing competence in the presence of the original mutation. Sequence analysis reveals that the suppressor mutation is a C----T transition in box9(5' part). This second mutation compensates for the first one in box2 and restores a box2/box9(5') hybrid. Combined with previous data demonstrating an interaction of the adjacent sequence box9(3' part) with the upstream box9c sequence in intron 4, the central role of box9 in the formation of the intron 4, the central role of box9 in the formation of the intron 4 RNA high order structure becomes evident.     

Effect of a laminin amphiphatic sequence on DPPC ordered bilayers.

A peptide sequence, stearoyl-GESIKVAVS(NH2), related to a laminin fragment, has been synthesized. Formation of aggregates was controlled by titrating a sodium anilinonaphthalene sulphonate (ANS) solution with peptide and recording fluorescence intensity increases. The results show that this system experiences a sudden increase in fluorescence at peptide concentrations around 2.5 x 10(-4) mol/L. The interaction of this hydrophobic peptide with DPPC vesicles has been studied using fluorescence techniques. Its influence on the microviscosity of bilayers was determined by studying polarization/temperature dependence for ANS and diphenyl hexatriene (DPH) fluorescent probes. With both markers the presence of peptide promotes a clear increase in anisotropy values. This indicates a rigidifying effect. Leakage studies carried out with liposomes loaded with carboxyfluorescein (CF) indicate a stabilizing effect of the peptide on bilayers, in agreement with results obtained with fluorescent probes.     

Folding of the nascent peptide chain into a biologically active protein

The refolding of denatured proteins with complete sequences may not be fast enough to account for the in vivo folding of growing peptide chains during biosynthesis. As some peptide fragments have secondary structures not unlike those of the corresponding segments in the intact molecules and native disulfide bonds of some proteins can form cotranslationally, it is suggested that the folding of the nascent chain begins early during synthesis. However, further adjustments may be necessary during chain elongation and after posttranslational modifications of the completed peptide chain to generate the native conformation of a biologically active protein.     

Structural insights into highly similar spatial organization of zinc-finger associated domains with a very low sequence similarity

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A test for a threshold in an ordered sequence of correlated proportions

A test procedure using chi-square statistics is proposed for determining a threshold in an ordered sequence of correlated proportions. The procedure is based on the multivariate Bernoulli model. It is applied to the problem of ascertaining when visual acuity has stabilized in a group of patients with regular follow-up after a vision-reducing acute abnormality.     

Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins

Full-consensus designed ankyrin repeat proteins were designed with one to six identical repeats flanked by capping repeats. These proteins express well in Escherichia coli as soluble monomers. Compared to our previously described designed ankyrin repeat protein library, randomized positions have now been fixed according to sequence statistics and structural considerations. Their stability increases with length and is even higher than that of library members, and those with more than three internal repeats are resistant to denaturation by boiling or guanidine hydrochloride. Full denaturation requires their heating in 5 M guanidine hydrochloride. The folding and unfolding kinetics of the proteins with up to three internal repeats were analyzed, as the other proteins could not be denatured. Folding is monophasic, with a rate that is nearly identical for all proteins (∼ 400-800 s^− 1), indicating that essentially the same transition state must be crossed, possibly the folding of a single repeat. In contrast, the unfolding rate decreases by a factor of about 10⁴ with increasing repeat number, directly reflecting thermodynamic stability in these extraordinarily slow denaturation rates. The number of unfolding phases also increases with repeat number. We analyzed the folding thermodynamics and kinetics both by classical two-state and three-state cooperative models and by an Ising-like model, where repeats are considered as two-state folding units that can be stabilized by interacting with their folded nearest neighbors. This Ising model globally describes both equilibrium and kinetic data very well and allows for a detailed explanation of the ankyrin repeat protein folding mechanism.     

Genome sequence of the polyhydroxybutyrate producer Pseudomonas extremaustralis, a highly stress-resistant Antarctic bacterium

Pseudomonas extremaustralis 14-3b presents genes involved in the synthesis of different polyhydroxyalkanoates, in tolerance and degradation of pollutants, and in microaerobic metabolism. Several genomic islands were detected. Genetic machinery could contribute to the adaptability to stressful conditions. This is the first genome sequence reported from a Pseudomonas isolated from cold environments.     

Murine macrophage cell lines can be ordered in a linear differentiation sequence

Abstract. The present study investigated whether transformed macrophage cell lines represent certain stages in macrophage differentiation. Cell surface markers linked to macrophage differentiation were characterized in 11 murine macrophage cell lines and compared with markers on isolated resident and exudate peritoneal macrophages. Furthermore, the capacity of the cell lines to phagocytose latex microspheres was analyzed. This analysis indicated that cell lines arrested at an early differentiation stage were characterized by the expression of the 'immature' markers Thy-1 and MIV 113, and the lack of expression of 'mature' macrophage markers such as Mac-1, Mac-2, and F4/80. More mature cell lines, which do not express 'immature' markers, show an increase in the expression of 'mature' macrophage markers. Furthermore, the expression of the 'mature' markers was found to be correlated with the phagocytic capacity of the cells. We have ordered the cell lines in a linear differentiation sequence based on these data. We propose that this sequence represents various stages in the differentiation of macrophages. This panel of cell lines provides a new model of early macrophage differentiation.     

Cloning and characterization of a highly repetitive fish nucleotide sequence

We have cloned and sequenced a highly repetitive HindIII fragment of DNA from the common carp Cyprinus carpio. It represents a tandemly repeated sequence with a monomeric unit of 245 bp and comprises 8% of the fish genome. Higher units of this monomer appear as a ladder in Southern blots. The monomeric unit has been sequenced; it is A + T-rich with some direct and some inverse-repeat nucleotide clusters.     

Characterisation of a highly repeated DNA sequence from Mycobacterium bovis

Abstract We report characterisation of a novel repeat sequence from a Mycobacterium bovis genomic library. The highly repeated sequence belongs to a family consisting of a 24 base pair (bp) direct repeat (DR), that appears to be organized into clusters on the chromosome. We classify the 24-bp DR into the group of prokaryotic DNA repeats known as the interspersed repetitive sequence elements. The 24-bp DR will be of potential use as a DNA fingerprinting tool in epidemiological studies of M. bovis .