Lisa Joss

Crystal Structure of the Flagellar Rotor Protein FliN from Thermotoga maritima

FliN is a component of the bacterial flagellum that is present at levels of more than 100 copies and forms the bulk of the C ring, a drum-shaped structure at the inner end of the basal body. FliN interacts with FliG and FliM to form the rotor-mounted switch complex that controls clockwise-counterclockwise switching of the motor. In addition to its functions in motor rotation and switching, FliN is thought to have a role in the export of proteins that form the exterior structures of the flagellum (the rod, hook, and filament). Here, we describe the crystal structure of most of the FliN protein of Thermotoga maritima. FliN is a tightly intertwined dimer composed mostly of beta sheet. Several well-conserved hydrophobic residues form a nonpolar patch on the surface of the molecule. A mutation in the hydrophobic patch affected both flagellar assembly and switching, showing that this surface feature is important for FliN function. The association state of FliN in solution was studied by analytical ultracentrifugation, which provided clues to the higher-level organization of the protein. T. maritima FliN is primarily a dimer in solution, and T. maritima FliN and FliM together form a stable FliM(1)-FliN(4) complex. Escherichia coli FliN forms a stable tetramer in solution. The arrangement of FliN subunits in the tetramer was modeled by reference to the crystal structure of tetrameric HrcQB(C), a related protein that functions in virulence factor secretion in Pseudomonas syringae. The modeled tetramer is elongated, with approximate dimensions of 110 by 40 by 35 Angstroms, and it has a large hydrophobic cleft formed from the hydrophobic patches on the dimers. On the basis of the present data and available electron microscopic images, we propose a model for the organization of FliN subunits in the C ring.

Evidence that feedback inhibition of NAD kinase controls responses to oxidative stress

Formation of NADP+ from NAD+ is catalyzed by NAD kinase (NadK; EC 2.7.1.23). Evidence is presented that NadK is the only NAD kinase of Salmonella enterica and is essential for growth. NadK is inhibited allosterically by NADPH and NADH. Without effectors, NadK exists as an equilibrium mixture of dimers and tetramers (KD = 1.0 ± 0.8 mM) but is converted entirely to tetramers in the presence of the inhibitor NADPH. Comparison of NadK kinetic parameters with pool sizes of NADH and NADPH suggests that NadK is substantially inhibited during normal growth and, thus, can increase its activity greatly in response to temporary drops in the pools of inhibitory NADH and NADPH. The primary inhibitor is NADPH during aerobic growth and NADH during anaerobic growth. A model is proposed in which variation of NadK activity is central to the adjustment of pyridine nucleotide pools in response to changes in aeration, oxidative stress, and UV irradiation. It is suggested that each of these environmental factors causes a decrease in the level of reduced pyridine nucleotides, activates NadK, and increases production of NADP(H) at the expense of NAD(H). Activation of NadK may constitute a defensive response that resists loss of protective NADPH.

Associative diblock copolymers of poly(ethylene glycol) and coiled-coil peptides

A series of peptides of general primary structure (VSSLESK) n (n=2, 3, 4, 5 and 6) were designed and synthesized by fluorenylmethyloxycarbonyl solid-phase synthesis using a convergent approach. Peptides containing 21, 28, 35 and 42 residues were modified with α-methoxy poly-(ethylene glycol) (mPEG; mol. wt. 2000) by reaction of mPEG-succinimidyl carbonate with the α-amino group of the resin-attached protected peptides. The conformation and thermal stability of the peptides and of their AB block copolymers (A is the mPEG block, B the (VSSLESK) n block) in aqueous medium were investigated by circular dichroism, size-exclusion chromotography and by analytical ultracentrifugation. The helicity of peptides increased with increasing length in a cooperative manner. The peptides and mPEG-peptides with 35 and 42 amino acid residues (block copolymers) adopted a two-stranded α-helical coiled-coil conformation in aqueous solution. The presence of the polymer chain in the diblock hybrid copolymers had no disturbing effect with respect to the stability of the α-helical peptide part in these constructs. Moreover, the thermal stability of mPEG-modified 42-peptide was substantially higher than that of the native 42-peptide. Analytical ultracentrifugation data revealed that in phosphate-buffered saline solution (25-200 μM) the block copolymer mPEG-block-(VSSLESK) 6 (PEG42) associated into stable intermolecular coiled-coil dimers.

Lysine 188 substitutions convert the pattern of proteasome activation by REGγ to that of REGs α and β

11S REGs (PA28s) are multimeric rings that bind proteasomes and stimulate peptide hydrolysis. Whereas REGα activates proteasomal hydrolysis of peptides with hydrophobic, acidic or basic residues in the P1 position, REGγ only activates cleavage after basic residues. We have isolated REGγ mutants capable of activating the hydrolysis of fluorogenic peptides diagnostic for all three active proteasome β subunits. The most robust REGγ specificity mutants involve substitution of Glu or Asp for Lys188. REGγ(K188E/D) variants are virtually identical to REGα in proteasome activation but assemble into less stable heptamers/hexamers. Based on the REGα crystal structure, Lys188 of REGγ faces the aqueous channel through the heptamer, raising the possibility that REG channels function as substrate‐selective gates. However, covalent modification of proteasome chymotrypsin‐like subunits by 125I‐YL3‐VS demonstrates that REGγ(K188E)s activation of all three proteasome active sites is not due to relaxed gating. We propose that decreased stability of REGγ(K188E) heptamers allows them to change conformation upon proteasome binding, thus relieving inhibition of the CT and PGPH sites normally imposed by the wild‐type REGγ molecule.

Nucleotide Sequence of the Head Assembly Gene Cluster of Bacteriophage L and Decoration Protein Characterization

The temperate Salmonella enterica bacteriophage L is a close relative of the very well studied bacteriophage P22. In this study we show that the L procapsid assembly and DNA packaging genes, which encode terminase, portal, scaffold, and coat proteins, are extremely close relatives of the homologous P22 genes (96.3 to 99.1% identity in encoded amino acid sequence). However, we also identify an L gene, dec, which is not present in the P22 genome and which encodes a protein (Dec) that is present on the surface of L virions in about 150 to 180 molecules/virion. We also show that the Dec protein is a trimer in solution and that it binds to P22 virions in numbers similar to those for L virions. Its binding dramatically stabilizes P22 virions against disruption by a magnesium ion chelating agent. Dec protein binds to P22 coat protein shells that have expanded naturally in vivo or by sodium dodecyl sulfate treatment in vitro but does not bind to unexpanded procapsid shells. Finally, analysis of phage L restriction site locations and a number of patches of nucleotide sequence suggest that phages ST64T and L are extremely close relatives, perhaps the two closest relatives that have been independently isolated to date among the lambdoid phages.

The influence of fusion sequences on the thermal stabilities of coiled-coil proteins

Full Paper: Five coiled-coil-containing proteins were synthesized to evaluate the influence of fusion sequences on their thermal stability. All proteins contained the same coiled-coil domain (VSSLESK) 6 , but differed in the fusion sequence attached. Circular dichroism spectroscopy was used to characterize their secondary structure and thermal stability. The proteins formed a coiled-coil structure, but their melting temperatures were different. The diffetence in the melting temperatures was not caused by either protein concentration or trace nickel ions. Sedimentation equilibrium experiments suggested an effect of the fusion sequence on the oligomerization state, but did not show a direct telationship between the oligomerization state and the melting temperature.