Defining the minimum size of a hydrophobic cluster in two-stranded alpha-helical coiled-coils: effects on protein stability

The alpha-helical coiled-coil motif is characterized by a heptad repeat pattern (abcdefg)(n) in which residues a and d form the hydrophobic core. Long coiled-coils (e.g., tropomyosin, 284 residues per polypeptide chain) typically do not have a continuous hydrophobic core of stabilizing residues, but rather one that consists of alternating clusters of stabilizing and destabilizing residues. We have arbitrarily defined a cluster as a minimum of three consecutive stabilizing or destabilizing residues in the hydrophobic core. We report here on a series of two-stranded, disulfide-bridged parallel alpha-helical coiled-coils that contain a central cassette of three consecutive hydrophobic core positions (d, a, and d) with a destabilizing cluster of three consecutive Ala residues in the hydrophobic core on each side of the cassette. The effect of adding one to three stabilizing hydrophobes in these positions (Leu or Ile; denoted as [see text]) was investigated. Alanine residues (denoted as [see text]) are used to represent destabilizing residues. The peptide with three Ala residues in the d a d cassette positions ([see text]) was among the least stable coiled-coil (T(m) = 39.3 degrees C and Urea(1/2) = 1.9 M). Surprisingly, the addition of one stabilizing hydrophobe (Leu) to the cassette or two stabilizing hydrophobes (Leu), still interspersed by an Ala in the cassette ([see text]), also did not lead to any gain in stability. However, peptides with two adjacent hydrophobes in the cassette ([see text])([see text]) did show a gain in stability of 0.9 kcal/mole over the peptide with two interspersed hydrophobes ([see text]). Because the latter three peptides have the same inherent hydrophobicity, the juxtaposition of stabilizing hydrophobes leads to a synergistic effect, and thus a clustering effect. The addition of a third stabilizing hydrophobe to the cassette ([see text]) resulted in a further synergistic gain in stability of 1.7 kcal/mole (T(m) = 54.1 degrees C and Urea(1/2) = 3.3M). Therefore, the role of hydrophobicity in the hydrophobic core of coiled-coils is extremely context dependent and clustering is an important aspect of protein folding and stability.     

Resistance to CD4+CD25+ regulatory T cells and TGF-beta in Cbl-b-/- mice

Cbl-b(-/-) mice have signaling defects that result in CD28-independent T cell activation, increased IL-2 production, hyper-reactive T cells, and increased autoimmunity. Although the increased autoimmunity in these mice is believed to result from the hyper-reactive T cells, the mechanisms leading from T cell hyper-reactivity to autoimmunity remain unclear. Specifically, the function and interaction of CD4(+)CD25(+) regulatory T cells (T(reg)) and CD4(+)CD25(-) effector T cells (T(eff)) in Cbl-b(-/-) mice have not been examined. We now report that Cbl-b(-/-) CD4(+)CD25(+) T(reg) exhibit normal regulatory function in vitro. In contrast, the in vitro response of Cbl-b(-/-) CD4(+)CD25(-) T(eff) is abnormal, in that it is not inhibited by either Cbl-b(-/-) or wild-type T(reg). This resistance of Cbl-b(-/-) T(eff) to in vitro regulation is seen at the levels of both DNA synthesis and cell division. In addition to this resistance to CD4(+)CD25(+) T(reg), Cbl-b(-/-) T(eff) demonstrate in vitro resistance to inhibition by TGF-beta. This second form of resistance in Cbl-b(-/-) T(eff) is seen despite the expression of normal levels of type II TGF-beta receptors and normal levels of phosphorylated Smad3 after TGF-beta stimulation. Coupled with recent reports of resistance to T(reg) in T(eff) exposed to LPS-treated dendritic cells, our present findings suggest that resistance to regulation may be a relevant mechanism in both normal immune function and autoimmunity.     

Ligand binding to symmetrical FeZn hybrids of variants of human HbA with modifications in the alpha1-beta2 interface

The equilibria of oxygen binding to and kinetics of CO combination with the symmetrical iron-zinc hybrids of a series of variants of human adult hemoglobin A have been measured at pH 7 in the presence of inositol hexaphosphate (IHP). In addition, the kinetics of CO combination have also been measured in the absence of IHP. The hybrids have the heme groups of either the alpha or the beta subunits replaced by zinc protoporphyrin IX, which is unable to bind a ligand and is a good model for permanently deoxygenated heme. The variants examined involve residues located in the alpha1beta2 interface of the hemoglobin tetramer. Alterations of residues located in the hinge region of the interface are found to affect the properties of both the alpha and the beta subunits of the protein. In contrast, alterations of residues in the switch region of the interface have substantial effects only on the mutant subunit and are poorly communicated to the normal partner subunit. When the logarithms of the rate constants for the combination of the first CO molecule with a single subunit in the presence of IHP are analyzed as functions of the logarithms of the dissociation equilibrium constants for the binding of the first oxygen under the same conditions, a linear relationship is found. The relationship is somewhat different for the alpha and beta subunits, consistent with the well-known differences in the geometries of their ligand binding sites.     

Crystal structure of a truncated urease accessory protein UreF from Helicobacter pylori

Urease plays a central role in the pathogenesis of Helicobacter pylori in humans. Maturation of this nickel metalloenzyme in bacteria requires the participation of the accessory proteins UreD (termed UreH in H. pylori), UreF, and UreG, which form sequential complexes with the urease apoprotein as well as UreE, a metallochaperone. Here, we describe the crystal structure of C‐terminal truncated UreF from H. pylori (residues 1–233), the first UreF structure to be determined, at 1.55 Å resolution using SAD methods. UreF forms a dimer in vitro and adopts an all‐helical fold congruent with secondary structure prediction. On the basis of evolutionary conservation analysis, the structure reveals a probable binding surface for interaction with other urease components as well as key conserved residues of potential functional relevance. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Concanavalin A-binding glycoproteins in the subcommissural and the pineal organ of the sheep (Ovis aries)

Summary Glycoproteins rich in mannosyl or glucosyl residues were analyzed in the subcommissural organ (SCO) and the pineal organ of the sheep (Ovis aries). By use of concanavalin A labelled with fluorescein isothiocyanate, fluorescent material was found both in ependymal and hypendymal cells of the SCO. In the pineal organ, either isolated or grouped parenchymal cells showed a marked fluorescence. These cells may correspond to ependymal elements also called interstitial cells or supporting cells. In addition, scarce slender, fluorescent processes were observed in the pineal parenchyma. The techniques of electrophoresis and electrotransfer on nitrocellulose paper have been applied to analyze the glycopeptide content of the SCO and the pineal organ in comparison to cerebellar and cerebral fractions solubilized by use of Triton X 100. Approximately 30 different concanavalin A-reactive glycopeptides were revealed in each fraction. In the SCO extract four glycopeptides (30, 54, 72, 100 kd) might correspond to subunits of the glycoprotein(s) characteristically stored in the ependymal cells of the SCO. In addition, two glycopeptides (32/33, 115 kd) are specific to the pineal organ extract. The possible similarity of the concanavalin A-reactive material in both organs is discussed and a putative secretory activity of the pineal ependymal cells is postulated.     

Behavior of Pythium torulosum Zoospores During Their Interaction with Tobacco Roots and Bacillus cereus

Bacillus cereus UW85 suppresses seedling damping-off diseases caused by Oomycetes and produces antibiotics that inhibit development of Oomycetes in culture. The goal of this study was to determine how UW85 and its antibiotics affected the behavior of an Oomycete, Pythium torulosum, in its interaction with plant roots. We studied tobacco seedlings inoculated with zoospores of P. torulosum and UW85 culture, culture filtrate, washed cells, antibiotics (zwittermicin A or kanosamine), purified from cultures of UW85, and UW030, a mutant of UW85 that does not suppress disease and does not produce the antibiotics. Microscopic observation revealed that all of the treatments inhibited zoospore activity around roots and encystment on roots. Treatment with UW85 culture, culture filtrate, zwittermicin A, or kanosamine delayed cyst germination and the elongation rate of germ tubes, whereas treatment with UW030 or washed UW85 cells did not. In an in vitro seedling bioassay of disease suppression, the antibiotics, zwittermicin A and kanosamine, suppressed disease singly or together, although UW85 culture suppressed disease more effectively than did the antibiotics. The results show that B. cereus cultures affect zoospore behavior in the presence of roots, and B. cereus-produced antibiotics, zwittermicin A and kanosamine, contribute to disease suppression and inhibition of germ tube elongation in the presence of the plant root. Received: 9 September 1998 / Accepted: 13 October 1998     

Random field models for fitness landscapes

 In many cases fitness landscapes are obtained as particular instances of random fields by randomly assigning a large number of parameters. Models of this type are often characterized reasonably well by their covariance matrices. We characterize isotropic random fields on finite graphs in terms of their Fourier series expansions and investigate the relation between the covariance matrix of the random field model and the correlation structure of the individual landscapes constructed from this random field. Correlation measures are a good characteristic of “rugged landscapes” models as they are closely related to quantities like the number of local optima or the length of adaptive walks. Our formalism suggests to approximate landscape with known autocorrelation function by a random field model that has the same correlation structure. Received: 10 November 1995 / Revised version: 19 February 1996     

Isotopic tracking of foraging and long-distance migration in northeastern Pacific pinnipeds

We investigated the impact of foraging location (nearshore vs offshore) and foraging latitude (high vs middle) on the carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope compositions of bone collagen of northern fur seals (Callorhinus ursinus), harbor seals (Phoca vitulina), California sea lions (Zalophus californianus), and northern elephant seals (Mirounga angustirostris). Nearshore-foraging harbor seals from California had δ¹³C values 2.0‰ higher than female northern elephant seals foraging offshore at similar latitudes. Likewise, nearshore-foraging harbor seals from Alaska had values 1.7‰ higher than male northern fur seals, which forage offshore at high latitudes. Middle-latitude pinnipeds foraging in either the nearshore or offshore were ¹³C enriched by ∼1.0‰ over similar populations from high latitudes. Male northern elephant seals migrate between middle and high latitudes, but they had δ¹³C values similar to high-latitude, nearshore foragers. Female northern fur seal δ¹³C values were intermediate between those of high- and middle-latitude offshore foragers, reflecting their migration between high- and middle-latitude waters. The δ¹³C values of California sea lions were intermediate between nearshore- and offshore-foraging pinnipeds at middle latitudes, yet there was no observational support for the suggestion that they use offshore food webs. We suggest that their “intermediate” values reflect migration between highly productive and less-productive, nearshore ecosystems on the Pacific coasts of California and Mexico. The relative uniformity among all of these pinnipeds in δ¹⁵N values, which are strongly sensitive to trophic level, reveals that the carbon isotope patterns result from differences in the δ¹³C of organic carbon at the base of the food web, rather than differences in trophic structure, among these regions. Finally, the magnitude and direction of the observed nearshore-offshore and high-to middle-latitude differences in δ¹³C values suggest that these gradients may chiefly reflect differences in rates and magnitudes of phytoplankton production as well as the δ¹³C value of inorganic carbon available for photosynthesis, rather than the input of ¹³C-enriched macroalgal carbon to nearshore food webs. Received: 8 September 1998 / Accepted: 24 February 1999