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Molecular dissection of the signaling and costimulatory functions of CD150 (SLAM): CD150/SAP binding and CD150-mediated costimulation.

CD150 signaling lymphocytic activation molecule (SLAM), a T/B/dendritic cell surface glycoprotein, is a costimulatory receptor involved in T-cell activation and is also a receptor for measles virus. CD150-induced signal transduction is controlled by SAP/SH2D1A, the gene that is aberrant in X-linked lymphoproliferative disease and familial hemophagocytic lymphohistiocytosis. This report shows that CD150 colocalizes with the T-cell receptor (TCR) following CD3 triggering in human peripheral blood T cells and is rapidly and reversibly tyrosine phosphorylated on TCR cross-linking. The Src-like kinases Lck and Fyn phosphorylate tyrosine residues in the cytoplasmic tail of CD150. The results demonstrate that the SAP protein has 2 modes of binding to CD150. Binding to the motif Thr-Ile-Tyr281Ala-Gln-Val occurs in a phosphotyrosine-independent fashion and to the motif Thr-Val-Tyr327Ala-Ser-Val in a phosphotyrosine-dependent manner. Within both SAP binding motifs the threonine residue at position -2 to tyrosine is essential to stabilize the interaction irrespective of tyrosine phosphorylation, a feature unique to the SAP SH2 domain. A leucine residue, Leu278, further stabilizes nonphospho binding of SAP to Tyr281 of CD150. SAP blocking of the tyrosine phosphatase SHP-2 occurs primarily on Tyr281 of CD150 because SHP-2 requires both Tyr281 and Tyr327 for binding to CD150, and SAP binds to nonphosphorylated Tyr281. CD150 exhibits lateral mobility, segregating into intercellular contacts. The lateral mobility and homophilic clustering of CD150 between neighboring cells is not dependent on SAP/CD150 interaction.

Amino Acid Sequence↗

MxiM and MxiJ, base elements of the Mxi-Spa type III secretion system of Shigella, interact with and stabilize the MxiD secretin in the cell envelope.

The type III secretion pathway is broadly distributed across many parasitic bacterial genera and serves as a mechanism for delivering effector proteins to eukaryotic cell surface and cytosolic targets. While the effectors, as well as the host responses elicited, differ among type III systems, they all utilize a conserved set of 9 to 11 proteins that together form a bacterial envelope-associated secretory organelle or needle complex. The general structure of the needle complex consists of a transenvelope base containing at least three ring-forming proteins (MxiD, MxiJ, and MxiG in Shigella) that is connected to a hollow needle-like extension that projects away from the cell surface. Several studies have shown that the initial steps in needle complex assembly require interactions among the base proteins, although specific details of this process remain unknown. Here we identify a role for another base element in Shigella, MxiM, in interactions with the major outer-membrane-associated ring-forming protein, MxiD. MxiM affects several features of MxiD, including its stability, envelope association, and assembly into homomultimeric structures. Interestingly, many of the effects were also elicited by the inner-membrane-associated base element, MxiJ. We confirmed that MxiM-MxiD and MxiJ-MxiD interactions occur in vivo in the cell envelope, and we present evidence that together these base elements can form a transmembrane structure which is likely an important intermediary in the process of needle complex assembly.

Bacterial Outer Membrane Proteins↗

Aromatic stacking as a determinant of the thermal stability of CYP119 from Sulfolobus solfataricus.

Two notable features of the thermophilic CYP119, an Arg154-Glu212 salt bridge between the F-G loop and the I helix and an extended aromatic cluster, were studied to determine their contributions to the thermal stability of the enzyme. Site-specific mutants of the salt bridge (Arg154, Glu212) and aromatic cluster (Tyr2, Trp4, Trp231, Tyr250, Trp281) were expressed and purified. The substrate-binding and kinetic constants for lauric acid hydroxylation are little affected in most mutants, but the E212D mutant is inactive and the R154Q mutant has higher K(s),K(m), and k(cat) values. The salt bridge mutants, like wild-type CYP119, melt at 91+/-1 degrees C, whereas mutation of individual residues in the extended aromatic cluster lowers the T(m) by 10-15 degrees C even though no change is observed on mutation of an unrelated aromatic residue. The extended aromatic cluster, but not the Arg154-Glu212 salt bridge, contributes to the thermal stability of CYP119.

Archaeal Proteins↗

Enzyme hyperactivity in AOT water-in-oil microemulsions is induced by 'lone' sodium counterions in the water-pool.

Water-in-oil microemulsions are thermodynamically stable single-phase dispersions of water and surfactant within a continuous oil phase. The classical ternary system, based on the surfactant sodium bis(2-ethylhexyl)sulfosuccinate ('AOT'), water and an alkane such as n-heptane, is an optically transparent monodispersion of spherical water-droplets coated with a close-packed surfactant monolayer and the droplet radius is, to a good first approximation, directly proportional to the molar water: surfactant ratio, R. Enzymes dissolved in the water droplets retain activity and stability. These systems have attracted interest as media for biotransformations. Principally based upon studies in AOT-stabilized w/o microemulsions, a peculiar feature of the kinetics of enzyme-catalyzed reactions has long been apparent: the reaction rate characteristically increases from around zero at R=3, through a maximum, in the range R= 10-20, and thereafter decreases again, so that plots of rate vs. R are characteristically 'bell-shaped'. Furthermore, at optimal R, enzymes seem to be 'hyperactive', i.e., they are more active, by a modest but significant factor of 2-3-fold, than in aqueous solution. In this paper we propose the hypothesis that this kind of R-dependence arises because of the presence of freely mobile lone surfactant counterions (Na+) within the water-pool. These ions have no charge partners within the water pool and consequently have a high electrochemical potential. According to our model, lone counterions facilitate the hydrolysis of ester or amide substrates, for example, by stabilizing the tetrahedral intermediate formed during the reaction through ion-pairing with the carbonyl oxygen of the substrate, thus facilitating transfer of negative charge from the carbonyl carbon as it is attacked by the incoming nucleophile. An expression for the relationship between the concentration of free counterions in the water-pool and the compositional parameter R leads directly, through Debye-Hückel theory, to an expression for the relationship between the reaction rate and R, log k(R)= log k(o) + C(1/R)1/2 where k(R) is the rate constant at some finite R, k(o) is the rate constant extrapolated to R = infinity and C is an R-independent coefficient. For enzymes that display bell-shaped kinetics, such as bovine alpha-chymotrypsin and Chromobacterium viscosum lipase, the descending part of the plot (i.e. from optimal R to high R) obeys this equation very well. Inspection of the above equation shows that the rate constant, k(R) is greater than k(o). Furthermore it is reasonable to equate k(o) with k(aq), the aqueous solution value of k since the condition R = infinity may be equated with the condition of infinite dilution with respect to counterions, so eliminating their specific effect on the kinetics. It follows from the inequality, k(R) > k(o) approximately equal to k(aq), that the enzyme is 'hyperactive' in the microemulsion compared with aqueous solution. We show that this is indeed the case for the chymotrypsin-catalyzed hydrolysis of N-trans-cinnamoylimidazole and the lipase catalyzed hydrolysis of 4-nitrophenyl acetate. The tailing off of enzyme activity at low R (< 10) is most likely due to conformational immobilization, probably due to partial dehydration in these low-water preparations (water activity, a(w), drops off rapidly below R = 15). We show that the reaction of glycylglycine with 4-nitrophenyl acetate, a 'hyperactive' non-enzymic reaction, does not suffer from this effect and obeys the above equation across the whole range of R.

Arylsulfonates↗

Tau aggregation is driven by a transition from random coil to beta sheet structure.

The abnormal aggregation of the microtubule associated protein tau into paired helical filaments (PHFs) is one the hallmarks of Alzheimer's disease. The soluble protein is one of the longest natively unfolded proteins, lacking significant amounts of secondary structure over a sequence of 441 amino acids in the longest isoform. Furthermore, the unfolded character is consistent with some notable features of the protein like stability towards heat and acid treatment. It is still unclear how these characteristics support the physiological function of binding to and stabilization of microtubules. We review here some recent studies on how an unfolded protein such as tau can adopt beta-structure, which then leads to the highly ordered morphology of the PHFs. The core sequence for both microtubule binding and PHF formation is the microtubule binding domain containing three or four repeats. This region alone is sufficient for PHF formation and mostly unfolded in the soluble state. A search for sequence motifs within this region crucial for PHF building revealed two hexapeptides in the second and the third repeat. Some of the genetically linked cases of FTDP-17 show missense mutations in or adjacent to these hexapeptide motifs. Proteins containing the P301L and the DeltaK280 mutations exhibit accelerated aggregation. The importance of the two hexapeptides stems from their capacity to undergo a conformational change from a random coil to a beta sheet structure. The increase of beta sheet structure is a typical feature of an amyloidogenic protein and is the basis of other characteristics like a decreased sensitivity towards proteolytic degradation and Congo red binding. PHFs aggregated in vitro and in vivo contain beta-sheet structure, as judged by circular dichroism (CD) spectroscopy, Fourier transform infrared (FTIR) spectroscopy and X-ray diffraction.

Alzheimer Disease↗

A high-throughput digital imaging screen for the discovery and directed evolution of oxygenases.

BACKGROUND: Oxygenases catalyze the hydroxylation of a wide variety of organic substrates. An ability to alter oxygenase substrate specificities and improve their activities and stabilities using recombinant DNA techniques would expand their use in processes such as chemical synthesis and bioremediation. Discovery and directed evolution of oxygenases require efficient screens that are sensitive to the activities of interest and can be applied to large numbers of crude enzyme samples. RESULTS: Horseradish peroxidase (HRP) couples the phenolic products of hydroxylation of aromatic substrates to generate colored and/or fluorescent compounds that are easily detected spectroscopically in high-throughput screening. Coexpression of the coupling enzyme with a functional mono- or dioxygenase creates a pathway for the conversion of aromatic substrates into fluorescent compounds in vivo. We used this approach for detecting the products of the toluene-dioxygenase-catalyzed hydroxylation of chlorobenzene and to screen large mutant libraries of Pseudomonas putida cytochrome P450cam by fluorescence digital imaging. Colors generated by the HRP coupling reaction are sensitive to the site of oxygenase-catalyzed hydroxylation, allowing the screen to be used to identify catalysts with new or altered regiospecificities. CONCLUSIONS: The coupled oxygenase-peroxidase reaction system is well suited for screening oxygenase libraries to identify mutants with desired features, including higher activity or stability and altered reaction specificity. This approach should also be useful for screening expressed DNA libraries and combinatorial chemical libraries for hydroxylation catalysts and for optimizing oxygenase reaction conditions.

Camphor 5-Monooxygenase↗

On the Elastic Properties of the Interfaces That Stabilize Gas Cavitation Nuclei

Many important systems feature strongly curved interfaces with low surface tension. Four examples are micelles, emulsions, giant bilayer vesicles, and biological membranes. A fifth is the microbubble nuclei that initiate cavitation in aqueous media. A model describing these nuclei and how they respond to changes in ambient pressure attributes their remarkable resiliency to a surrounding film of surface-active molecules. An independent derivation of this model is obtained in this paper by applying thermodynamic methods formulated recently to describe strongly curved amphiphilic interfaces. This illuminates previous models for microbubble nuclei and provides additional information on the mechanical and thermodynamic properties of interfaces in general. Copyright 1997Academic Press

Journal Article↗

[A replication enhancer of viral origin increases the mitotic stability of yeast transformants].

It is shown in this paper that a DNA fragment of Hepatitis B virus possessing structural features of yeast replication enhancer increases the mitotic stability of yeast transformants containing hybrid plasmids of episomal and replicative types. The mitotic stability of transformants with plasmid of the replicative type and with the replication enhancer increases only in [cir+] cells. Comparison of primary sequences of HBV DNA of different subtypes revealed that only DNA has unique structural features of the yeast enhancer of replication.

Base Sequence↗

The 1.5 A crystal structure of a prokaryote serpin: controlling conformational change in a heated environment.

Serpins utilize conformational change to inhibit target proteinases; the price paid for this conformational flexibility is that many undergo temperature-induced polymerization. Despite this thermolability, serpins are present in the genomes of thermophilic prokaryotes, and here we characterize the first such serpin, thermopin. Thermopin is a proteinase inhibitor and, in comparison with human alpha(1)-antitrypsin, possesses enhanced stability at 60 degrees C. The 1.5 A crystal structure reveals novel structural features in regions implicated in serpin folding and stability. Thermopin possesses a C-terminal "tail" that interacts with the top of the A beta sheet and plays an important role in the folding/unfolding of the molecule. These data provide evidence as to how this unusual serpin has adapted to fold and function in a heated environment.

Actinomycetales↗

Comparison of the human and worm p53 structures suggests a way for enhancing stability.

Maintaining the native conformation is essential for the proper function of tumor suppressor protein p53. However, p53 is a low-stability protein that can easily lose its function upon structural perturbations such as those resulting from missense mutations, leading to the development of cancer. Therefore, it is important to develop strategies to design stable p53 which still maintains its normal function. Here, we compare the stabilities of the human and worm p53 core domains using molecular dynamics simulations. We find that the worm p53 is significantly more stable than the human form. Detailed analysis of the structural fluctuations shows that the stability difference lies in the peripheral structural motifs that contrast in their structural features and flexibility. The most dramatic difference in stability originates from loop L1, from the turn between helix H1 and beta-strand S5, and from the turn that connects beta-strands S7 and S8. Structural analysis shows significant differences for these motifs between the two proteins. Loop L1 lacks secondary structure, and the turns between helix H1 and strand S5 and between strands S7 and S8 are much longer in the human form p53. On the basis of these differences, we designed a mutant by shortening the turn between strands S7 and S8 to enhance the stability. Surprisingly, this mutant was very stable when probed by molecular dynamics simulations. In addition, the stabilization was not localized in the turn region. Loop L1 was also significantly stabilized. Our results show that stabilizing peripheral structural motifs can greatly enhance the stability of the p53 core domain and therefore is likely to be a viable alternative in the development of stable p53. In addition, loop- or turn-related mutants with different stabilities may also be used to probe the relationship between function, a particular structural motif, and its flexibility.

Animals↗

Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: effect on stability, cooperativity and kinetics.

BACKGROUND: The most conspicuous feature of a right-handed alpha helix is the presence of hydrogen bonds between the backbone carbonyl oxygen and NH groups along the chain. A simple off-lattice model that includes hydrogen bond interactions using virtual atoms is used to examine the stability, cooperativity and kinetics of the helix-coil transition. RESULTS: We have studied the thermodynamics (using multiple histogram method) and kinetics (by Brownian dynamics simulations) of 16-mer minimal off-lattice models of four-turn alpha-helix sequences. The carbonyl and NH groups are represented as virtual moieties located between two alpha-carbon atoms along the polypeptide chain. The characteristics of the native conformations of the model helices, such as the helical pitch and angular correlations, coincide with those found in real proteins. The transition from coil to helix is quite broad, which is typical of these finite-sized systems. The cooperativity, as measured by a dimensionless parameter, omegac, that takes into account the width and the slope of the transition curves, is enhanced when hydrogen bonds are taken into account. The value of omegac for our model is consistent with that inferred from experiment for an alanine-based helix-forming peptide. The folding time tauF ranges from 6 to 1000 ns in the temperature range 0.7-1.9 T(F), where T(F) is the helix-coil transition temperature. These values are in excellent agreement with the results from recent fast folding experiments. The temperature dependence of tauF exhibits a nearly Arrhenius behavior. Thermally induced unfolding occurs on a time scale that is less than 40-170 ps depending on the final temperature. Our calculations also predict that, although tauF can be altered by changes in the sequence, the dynamic range over which such changes take place is not as large as that predicted for beta-turn formation. CONCLUSIONS: Hydrogen bonds not only affect the stability of alpha-helix formation but also have profound influence on the kinetics. The excellent agreement between our calculations and experiments suggests that these models can be used to investigate the effects of sequence, temperature and viscosity on the helix-coil transition.

Animals↗

The stability of E. coli gene transcripts is dependent on determinants localized to specific mRNA segments.

To map the structural features responsible for the 5-fold difference in stability of the E. coli ompA and bla gene transcripts, we have constructed gene fusions that encode chimeric ompA/bla transcripts and a deletion that eliminates a large internal segment of bla mRNA. Shortening of bla transcripts by internal deletion or replacement of the 3' end with the corresponding segment of the ompA transcript had little effect on bla mRNA stability. However, fusion of a 5'-terminal 147 nucleotide segment of the ompA message 5' to full-length or truncated bla transcripts increased the half-life of the bla segments 3- to 5-fold. These and other findings indicate that E. coli transcripts contain discrete structural determinants of stability and instability that can influence the decay rate of linked mRNA segments derived from other genes.

Chimera↗

The foldability landscape of model proteins.

Molecular evolution may be considered as a walk in a multidimensional fitness landscape, where the fitness at each point is associated with features such as the function, stability, and survivability of these molecules. We present a simple model for the evolution of protein sequences on a landscape with a precisely defined fitness function. We use simple lattice models to represent protein structures, with the ability of a protein sequence to fold into the structure with lowest energy, quantified as the foldability, representing the fitness of the sequence. The foldability of the sequence is characterized based on the spin glass model of protein folding. We consider evolution as a walk in this foldability landscape and study the nature of the landscape and the resulting dynamics. Selective pressure is explicitly included in this model in the form of a minimum foldability requirement. We find that different native structures are not evenly distributed in interaction space, with similar structures and structures with similar optimal foldabilities clustered together. Evolving proteins marginally fulfill the selective criteria of foldability. As the selective pressure is increased, evolutionary trajectories become increasingly confined to "neutral networks," where the sequence and the interactions can be significantly changed while a constant structure is maintained.

Amino Acid Sequence↗

Interpreting the posture and locomotion of Australopithecus afarensis: where do we stand?

Reconstructing the transition to bipedality is key to understanding early hominin evolution. Because it is the best-known early hominin species, Australopithecus afarensis forms a baseline for interpreting locomotion in all early hominins. While most researchers agree that A. afarensis individuals were habitual bipeds, they disagree over the importance of arboreality for them. There are two main reasons for the disagreement. First, there are divergent perspectives on how to interpret primitive characters. Primitive traits may be retained by stabilizing selection, pleiotropy, or other ontogenetic mechanisms. Alternately, they could be in the process of being reduced, or they simply could be selectively neutral. Second, researchers are asking fundamentally different questions about the fossils. Some are interested in reconstructing the history of selection that shaped A. afarensis, while others are interested in reconstructing A. afarensis behavior. By explicitly outlining whether we are interested in reconstructing selective history or behavior, we can develop testable hypotheses to govern our investigations of the fossils. To infer the selective history that shaped a taxon, we must first consider character polarity. Derived traits that enhance a particular function, are found to be associated with that function in extant homologs, and that epigenetically sensitive data indicate were actually being used for that function, can be interpreted as adaptations. The null hypothesis to explain the retention of primitive traits is that of selective neutrality, or nonaptation. Disproving this requires demonstration of active stabilizing or negative selection (disaptation). Stabilizing selection can be inferred when primitive traits compromise a derived function clearly of adaptive value. Prolonged stasis, continued use of the trait for a particular function, or no change in variability in the trait are evidence that can support a hypothesis of adaptation for primitive traits, but still do not falsify the null hypothesis. Disaptation, or negative selection, should result in a trait being reduced or lost. To infer the behaviors of a fossil species, we must first determine its adaptations, use this to make hypotheses about its behavior, and test these hypotheses using epigenetically sensitive traits that are modified by an individual's activity pattern. When the A. afarensis data are evaluated using this framework, it is clear that these hominins had undergone selection for habitual bipedality, but the null hypothesis of nonaptation to explain the retention of primitive, ape-like characters cannot be falsified at present. The apparent stasis in Australopithecus postcranial form is currently the strongest evidence for stabilizing selection maintaining its primitive features. Evidence from features affected by individual behaviors during ontogeny shows that A. afarensis individuals were habitually traveling bipedally, but evidence presented for arboreal behavior so far is not conclusive. By clearly identifying the questions we are asking about early hominin fossils, refining our knowledge about character polarities, and elucidating the factors influencing morphology, we will be able to progress in our understanding of the posture and locomotion of A. afarensis and all early hominins.

Adaptation, Physiological↗

Comparative analysis of thermoadaptation within the archaeal glyceraldehyde-3-phosphate dehydrogenases from mesophilic Methanobacterium bryantii and thermophilic Methanothermus fervidus.

To gain insight into the molecular determinants of thermoadaptation within the family of archaeal glyceraldehyde-3-phosphate dehydrogenases (GAPDH), a homology-based 3-D model of the mesophilic GAPDH from Methanobacterium bryantii was built and compared with the crystal structure of the thermophilic GAPDH from Methanothermus fervidus. The homotetrameric model of the holoenzyme was initially assembled from identical subunits completed with NADP molecules. The structure was then refined by energy minimization and simulated-annealing procedures. PROCHECK and the 3-D profile method were used to appraise the model reliability. Striking molecular features underlying the difference in stability between the enzymes were deduced from their structural comparison. First, both the increase in hydrophobic contacts and the decrease in accessibility to the protein core were shown to discriminate in favor of the thermophilic enzyme. Besides, but to a lesser degree, the number of ion pairs involved in cooperative clusters appeared to correlate with thermostability. Finally, the decreased stability of the mesophilic enzyme was also predicted to proceed from both the lack of charge-dipole interactions within alpha-helices and the enhanced entropy of unfolding due to an increase in chain flexibility. Thus, archaeal GAPDHs appear to be governed by thermoadaptation rules that differ in some aspects from those previously observed within their eubacterial counterparts.

Adaptation, Physiological↗

Liposomes containing fluorinated steroids: an analysis based on photon correlation and fluorine-19 nuclear magnetic resonance spectroscopy.

Small unilamellar liposomes containing fluorinated steroids (flumethasone and dexamethasone) were obtained. A physicochemical evaluation was conducted based on photon correlation spectroscopy (PCS) and fluorine-19 (19F) nuclear magnetic resonance (NMR) spectroscopy compared with standard biochemical methods (HPLC). The PCS method provides a fast and adequate evaluation of some critical features of liposomes (size, physical stability). In addition, 19F NMR spectroscopy gives substantial information, in a nondestructive manner, on steroid behavior in the membrane upon encapsulation and also when the temperature of liposomes is increased. The combined spectroscopic approach proposed here might prove useful in (1) the management of liposomal formulation, especially in the documentation of physicochemical properties, (2) pharmaceutical control in the industrial production line, and (3) control preceding injection at the clinical site. Spectroscopic techniques might offer a complementary approach to classical biochemical methods in the evaluation of the properties of a liposomal formulation and could be usefully integrated into quality control procedures.

Chemical Phenomena↗

A common structural motif incorporating a cystine knot and a triple-stranded beta-sheet in toxic and inhibitory polypeptides.

A common structural motif consisting of a cystine knot and a small triple-stranded beta-sheet has been defined from comparison of the 3-dimensional structures of the polypeptides omega-conotoxin GVIA (Conus geographus), kalata BI (Oldenlandia affinis DC), and CMTI-I (Curcurbita maxima). These 3 polypeptides have diverse biological activities and negligible amino acid sequence identity, but each contains 3 disulfide bonds that give rise to a cystine knot. This knot consists of a ring formed by the first 2 bonds (1-4 and 2-5) and the intervening polypeptide backbone, through which the third disulfide (3-6) passes. The other component of this motif is a triple-stranded, anti-parallel beta-sheet containing a minimum of 10 residues, XXC2, XC5X, XXC6X (where the numbers on the half-cysteine residues refer to their positions in the disulfide pattern). The presence in these polypeptides of both the cysteine knot and antiparallel beta-sheet suggests that both structural features are required for the stability of the motif. This structural motif is also present in other protease inhibitors and a spider toxin. It appears to be one of the smallest stable globular domains found in proteins and is commonly used in toxins and inhibitors that act by blocking the function of larger protein receptors such as ion channels or proteases.

Amino Acid Sequence↗

Structure of a legume lectin from the bark of Robinia pseudoacacia and its complex with N-acetylgalactosamine.

The structure of the bark lectin RPbAI (isoform A4) from Robinia pseudoacacia has been determined by protein crystallography both in the free form and complexed with N-acetylgalactosamine. The free form is refined at 1.80 A resolution to an R-factor of 18.9% whereas the complexed structure has an R-factor of 19.7% at 2.05 A resolution. Both structures are compared to each other and to other available legume lectin structures. The polypeptide chains of the two structures exhibit the characteristic legume lectin tertiary fold. The quaternary structure resembles that of the Phaseolus vulgaris lectin, the soybean agglutinin, and the Dolichos biflorus lectin, but displays some unique features leading to the extreme stability of this lectin.

Acacia↗