Evolutionary information for specifying a protein fold.

Classical studies show that for many proteins, the information required for specifying the tertiary structure is contained in the amino acid sequence. Here, we attempt to define the sequence rules for specifying a protein fold by computationally creating artificial protein sequences using only statistical information encoded in a multiple sequence alignment and no tertiary structure information. Experimental testing of libraries of artificial WW domain sequences shows that a simple statistical energy function capturing coevolution between amino acid residues is necessary and sufficient to specify sequences that fold into native structures.

The nutritional impact of dairy product consumption on dietary intakes of adults (1995-1996): the Bogalusa Heart Study.

Objective: To examine the nutritional impact of dairy product consumption on the dietary intakes of adults.

Design: Dietary intakes of adults who participated in a cross-sectional survey (1995-1996) in Bogalusa, LA.

Subjects: Dietary intake data were collected on 1,266 adults (61% women, 39% men; 74% white, 26% African American) in Bogalusa, LA.

A small-angle neutron scattering study of biologically relevant mixed surfactant micelles comprising 1,2-diheptanoyl-sn-phosphatidylcholine and sodium dodecyl sulfate or dodecyltrimethylammonium bromide.

Small-angle neutron scattering (SANS) has been employed to characterize mixed micelles comprising the surfactants 1,2-diheptanoyl--phosphatidylcholine (DHPC)/sodium dodecyl sulfate (SDS) and 1,2-diheptanoyl--phosphatidylcholine (DHPC)/dodecyltrimethylammonium bromide (DTAB) using the classical model of a micelle consisting of a hydrocarbon core surrounded by a polar shell. Various constraints are applied to the data fitting, specifically the volume of the hydrocarbon core using the aggregation number determined from time-resolved fluorescence quenching (TRFQ) and the degree of micelle hydration as determined from an electron paramagnetic resonance (EPR) experiment. The morphologies of the DHPC/SDS and DHPC/DTAB mixed micelles are largely invariant with composition-as might be expected given the similarity in the tail volumes of the respective surfactants, and the observed behaviour of the aggregation number-with a radius comparable to the fully extended length of a dodecyl chain, the longer of the two hydrophobic moieties.

Phospholipid containing mixed micelles. Characterization of diheptanoyl phosphatidylcholine (DHPC) and sodium dodecyl sulfate and DHPC and dodecyl trimethylammonium bromide.

Mixed micelles of l,2-diheptanoyl-sn-grycero-3-phosphocholine (DHPC) with ionic detergents were prepared to develop well characterized substrates for the study of lipolytic enzymes. The aggregates that formed on mixing DHPC with the anionic surfactant sodium dodecyl sulfate (SDS) and with the positively charged dodecyl trimethylammonium bromide (DTAB) were investigated using time-resolved fluorescence quenching (TRFQ) to determine the aggregation numbers and bimolecular collision rates, and electron spin resonance (ESR) to measure the hydration index and microviscosity of the micelles at the micelle-water interface. Mixed micelles between the phospholipid and each of the detergents formed in all compositions, yielding interfaces with varying charge, hydration, and microviscosity.

Effects of interactions on the formation of mixed micelles of 1,2-diheptanoyl-sn-glycero-3-phosphocholine with sodium dodecyl sulfate and dodecyltrimethylammonium bromide.

Mixed micelles of the phospholipid 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC) with sodium dodecyl sulfate (SDS) or dodecyltrimethylammonium bromide (DTAB) in aqueous solutions and the effects of interactions between the components were studied by fluorescence and NMR measurements. The regular solution theory (RST) was applied to analyze the experimental critical micelle concentration values determined from the fluorescence spectra of pyrene in the mixed micelles. Negative values for the interaction parameter (beta12) were obtained for both DHPC + SDS and DHPC + DTAB mixtures, with the value being more negative in the former case.

Effect of N-glycinylmaleamic acid on microstructural characteristics and solubilization properties of sodium dodecyl sulfate micellar assemblies.

The cosurfactant activity of N-glycinylmaleamic acid (NGMA) in sodium dodecyl sulfate (SDS) micelles has been demonstrated. The complementary techniques of electron spin resonance (ESR) and fluorescence spectroscopy have been used to draw information on hydration index (H), microviscosity (eta), and aggregation number (N) of micellar assemblies. The estimate of the critical micelle concentration of SDS in the presence of NGMA suggests a synergistic effect of NGMA.

Structural determinants of allosteric ligand activation in RXR heterodimers.

Allosteric communication underlies ligand-dependent transcriptional responses mediated by nuclear receptors. While studies have elucidated many of the components involved in this process, the energetic architecture within the receptor protein that mediates allostery remains unknown. Using a sequence-based method designed to detect coevolution of amino acids in a protein, termed the statistical coupling analysis (SCA), we identify a network of energetically coupled residues that link the functional surfaces of nuclear receptor ligand binding domains.

Local complexity of amino acid interactions in a protein core.

Atomic resolution structures of proteins indicate that the core is typically well packed, suggesting a densely connected network of interactions between amino acid residues. The combinatorial complexity of energetic interactions in such a network could be enormous, a problem that limits our ability to relate structure and function. Here, we report a case study of the complexity of amino acid interactions in a localized region within the core of the GFP, a particularly stable and tightly packed molecule.

Allosteric determinants in guanine nucleotide-binding proteins.

Members of the G protein superfamily contain nucleotide-dependent switches that dictate the specificity of their interactions with binding partners. Using a sequence-based method termed statistical coupling analysis (SCA), we have attempted to identify the allosteric core of these proteins, the network of amino acid residues that couples the domains responsible for nucleotide binding and protein-protein interactions. One-third of the 38 residues identified by SCA were mutated in the G protein Gs alpha, and the interactions of guanosine 5'-3-O-(thio)triphosphate- and GDP-bound mutant proteins were tested with both adenylyl cyclase (preferential binding to GTP-Gs alpha) and the G protein beta gamma subunit complex (preferential binding to GDP-Gs alpha).

Evolutionarily conserved networks of residues mediate allosteric communication in proteins.

A fundamental goal in cellular signaling is to understand allosteric communication, the process by which signals originating at one site in a protein propagate reliably to affect distant functional sites. The general principles of protein structure that underlie this process remain unknown. Here, we describe a sequence-based statistical method for quantitatively mapping the global network of amino acid interactions in a protein.

Overview of the Alliance for Cellular Signaling.

The Alliance for Cellular Signaling is a large-scale collaboration designed to answer global questions about signalling networks. Pathways will be studied intensively in two cells--B lymphocytes (the cells of the immune system) and cardiac myocytes--to facilitate quantitative modelling. One goal is to catalyse complementary research in individual laboratories; to facilitate this, all alliance data are freely available for use by the entire research community.

Polymethylated DOTA ligands. 2. Synthesis of rigidified lanthanide chelates and studies on the effect of alkyl substitution on conformational mobility and relaxivity.

M4DOTA, [(2S,5S,8S,11S)-4,7,10-tris-carboxymethyl-2,5,8,11-tetramethyl-1,4,7,10-tetraazacyclododecan-1-yl]acetic acid (2e), and M4DOTMA, (R)-2-[(2S,5S,8S,11S)-4,7,10-tris-((R)-1-carboxyethyl)-2,5,8,11-tetramethyl-1,4,7,10-tetraazacyclododecan-1-yl]propionic acid (3e), are derivatives of ligand DOTA (1e) that form sterically crowded lanthanide chelates. M4DOTMA forms highly symmetric and totally rigid single Y(3+) and Yb(3+) species in which the ring substituents occupy corner positions in a square antiprismatic arrangement as shown by molecular mechanics calculations and by a quantitative interpretation of the relative magnitudes of the paramagnetic (1)H NMR shifts of dipolar origin. The NMR spectrum of YbM4DOTMA(-) displays two intense methyl peaks outside the 0-10 ppm range whose shift difference is strongly temperature dependent.

Polymethylated DOTA ligands. 1. Synthesis of rigidified ligands and studies on the effects of alkyl substitution on acid-base properties and conformational mobility.

This work describes the synthesis and the conformational properties of new polymethylated macrocyclic ligands of potential interest for magnetic resonance imaging. M4cyclen, (2S,5S,8S,11S)-2,5,8,11-tetramethyl-1,4,7,10-tetraazacyclododecane, was obtained by cyclotetramerization of (2S)-1-benzyl-2-methylaziridine followed by catalytic hydrogenation. The ligands M4DOTA, [(2S,5S,8S,11S)-4,7,10-tris-carboxymethyl-2,5,8,11-tetramethyl- 1,4,7,10-tetraazacyclododecan-1-yl]acetic acid, and M4DOTMA, (R)-2-[(2S,5S,8S,11S)-4,7,10-tris-((R)-1-carboxyethyl)-2,5,8,11-tetramethyl-1,4,7,10-tetraazacyclododecan-1-yl]propionic acid, were prepared by carboxyalkylation of M4cyclen in the presence of Na(2)CO(3).

Olfactory axon pathfinding: who is the pied piper?

Mammalian olfactory sensory neurons that express a particular odorant receptor (OR) project axons to the same few glomeruli in the olfactory bulb. In this issue of Neuron, Vassalli et al. use OR minigenes that coexpress histochemical markers and show that the determinants in the sensory neurons required to generate the stereotyped olfactory bulb map are the same as those needed for appropriate expression of the OR.

Knowledge-based potential functions in protein design.

Predicting protein sequences that fold into specific native three-dimensional structures is a problem of great potential complexity. Although the complete solution is ultimately rooted in understanding the physical chemistry underlying the complex interactions between amino acid residues that determine protein stability, recent work shows that empirical information about these first principles is embedded in the statistics of protein sequence and structure databases. This review focuses on the use of 'knowledge-based' potentials derived from these databases in designing proteins.

Mutations in the Caenorhabditis elegans serotonin reuptake transporter MOD-5 reveal serotonin-dependent and -independent activities of fluoxetine.

We isolated two mutants defective in the uptake of exogenous serotonin (5-HT) into the neurosecretory motor neurons of Caenorhabditis elegans. These mutants were hypersensitive to exogenous 5-HT and hyper-responsive in the experience-dependent enhanced slowing response to food modulated by 5-HT. The two allelic mutations defined the gene mod-5 (modulation of locomotion defective), which encodes the only serotonin reuptake transporter (SERT) in C.

Effect of interferon-alpha on CD20 antigen expression of B-cell chronic lymphocytic leukemia.

Chimeric CD20 monoclonal antibody as alternative therapy in relapsed low-grade non-Hodgkin's lymphoma (NHL) has produced responses in nearly 50% of patients. Augmenting CD20 expression on tumor cells and/or inducing its expression may increase the cell kill and effectiveness of antibody therapy. Peripheral blood lymphocytes from 19 patients with B-cell chronic lymphocytic leukemia (B-CLL) were incubated in vitro in the presence of interferon-alpha (IFN-alpha) (500 U/ml and 1,000 U/ml) for 24 and 72 hours.

The structural basis for red fluorescence in the tetrameric GFP homolog DsRed.

Green fluorescent protein (GFP) has rapidly become a standard tool for investigating a variety of cellular activities, and has served as a model system for understanding spectral tuning in chromophoric proteins. Distant homologs of GFP in reef coral and anemone display two new properties of the fluorescent protein family: dramatically red-shifted spectra, and oligomerization to form tetramers. We now report the 1.

MOD-1 is a serotonin-gated chloride channel that modulates locomotory behaviour in C. elegans.

The neurotransmitter and neuromodulator serotonin (5-HT) functions by binding either to metabotropic G-protein-coupled receptors (for example, 5-HT1, 5-HT2, 5-HT4 to 5-HT7), which mediate 'slow' modulatory responses through numerous second messenger pathways, or to the ionotropic 5-HT3 receptor, a non-selective cation channel that mediates 'fast' membrane depolarizations. Here we report that the gene mod-1 (for modulation of locomotion defective) from the nematode Caenorhabditis elegans encodes a new type of ionotropic 5-HT receptor, a 5-HT-gated chloride channel. The predicted MOD-1 protein is similar to members of the nicotinic acetylcholine receptor family of ligand-gated ion channels, in particular to GABA (gamma-aminobutyric acid)- and glycine-gated chloride channels.

A molecular pathway for light-dependent photoreceptor apoptosis in Drosophila.

Light-induced photoreceptor apoptosis occurs in many forms of inherited retinal degeneration resulting in blindness in both vertebrates and invertebrates. Though mutations in several photoreceptor signaling proteins have been implicated in triggering this process, the molecular events relating light activation of rhodopsin to photoreceptor death are yet unclear. Here, we uncover a pathway by which activation of rhodopsin in Drosophila mediates apoptosis through a G protein-independent mechanism.

C. elegans locomotory rate is modulated by the environment through a dopaminergic pathway and by experience through a serotonergic pathway.

Caenorhabditis elegans modulates its locomotory rate in response to its food, bacteria, in two ways. First, well-fed wild-type animals move more slowly in the presence of bacteria than in the absence of bacteria. This basal slowing response is mediated by a dopamine-containing neural circuit that senses a mechanical attribute of bacteria and may be an adaptive mechanism that increases the amount of time animals spend in the presence of food.

Tumor necrosis factor modulates CD 20 expression on cells from chronic lymphocytic leukemia: a new role for TNF alpha?

Tumor necrosis factor alpha (TNF alpha) is a pleiotropic cytokine that is constitutively produced by leukemic cells in B Chronic Lymphocytic Leukemia (B-CLL). It has been shown to have autocrine and paracrine functions in normal B cells and in B lymphoproliferative diseases. This study was conducted to determine the effect of TNF alpha (in vitro) on CD20 expression on cells from patients with B-CLL.

Selective removal of nitrogen from quinoline and petroleum by Pseudomonas ayucida IGTN9m.

Enrichment culture experiments employing soil and water samples obtained from petroleum-contaminated environments succeeded in the isolation of a pure culture possessing the ability to utilize quinoline as a sole nitrogen source but did not utilize quinoline as a carbon source. This culture was identified as Pseudomonas ayucida based on a partial 16S rRNA gene sequence, and the strain was given the designation IGTN9m. Examination of metabolites using thin-layer chromatography and gas chromatography-mass spectrometry suggests that P.