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Peptide aptamers: specific inhibitors of protein function.

In recent years, peptide aptamers have emerged as novel molecular tools that are useful for both basic and applied aspects of molecular medicine. Due to their ability to specifically bind to and inactivate a given target protein at the intracellular level, they provide a new experimental strategy for functional protein analyses, both in vitro and in vivo. In addition, by using peptide aptamers as "pertubagens", they can be employed for genetic analyses, in order to identify biochemical pathways, and their components, that are associated with the induction of distinct cellular phenotypes. Furthermore, peptide aptamers may be developed into diagnostic tools for the detection of a given target protein or for the generation of high-throughput protein arrays. Finally, the peptide aptamer technology has direct therapeutic implications. Peptide aptamers can be used in order to validate therapeutic targets at the intracellular level. Moreover, the peptide aptamer molecules themselves should possess therapeutic potential, both as lead structures for drug design and as a basis for the development of protein drugs.

Animals↗

Xenopus Zic4: conservation and diversification of expression profiles and protein function among the Xenopus Zic family.

We compared the expression and function of Xenopus Zic4 with those of the other four Xenopus laevis Zic family members (Zic1, Zic2, Zic3, and Zic5). Zic4 expression was detected mainly in the neural plate border, dorsal neural tube, and somites, and was similar to that of Zic1, which is adjacent to Zic4 on the same chromosome. Injection of wild-type or mutant Zic4 RNA caused the induction of neural crest marker gene expression, hyperplastic neural tissue, and ectopic pigment cell formation, indicating that Zic4 can induce neural and neural crest tissue, as can other Xenopus Zic genes. Deletion analysis showed that the zinc-finger domain is critical for many Zic4 functions, but the C-terminal region is differently involved in induction of two neural crest markers, Slug and Sox10. The protein function as determined by the animal cap explant assay was similar to that of Zic5, but different from those of Zic1, Zic2, and Zic3, suggesting that Xenopus Zic genes can be divided into two groups based on function. These results indicate that the five Xenopus Zic genes cooperatively regulate both neural and neural crest development, despite significantly diverged expression profiles and functions.

Amino Acid Sequence↗

Predicting protein functional sites with phylogenetic motifs.

In this report, we demonstrate that phylogenetic motifs, sequence regions conserving the overall familial phylogeny, represent a promising approach to protein functional site prediction. Across our structurally and functionally heterogeneous data set, phylogenetic motifs consistently correspond to functional sites defined by both surface loops and active site clefts. Additionally, the partially buried prosthetic group regions of cytochrome P450 and succinate dehydrogenase are identified as phylogenetic motifs. In nearly all instances, phylogenetic motifs are structurally clustered, despite little overall sequence proximity, around key functional site features. Based on calculated false-positive expectations and standard motif identification methods, we show that phylogenetic motifs are generally conserved in sequence. This result implies that they can be considered motifs in the traditional sense as well. However, there are instances where phylogenetic motifs are not (overall) well conserved in sequence. This point is enticing, because it implies that phylogenetic motifs are able to identify key sequence regions that traditional motif-based approaches would not. Further, phylogenetic motif results are also shown to be consistent with evolutionary trace results, and bootstrapping is used to demonstrate tree significance.

Amino Acid Motifs↗

Superoxide release and NADPH oxidase components in mature human phagocytes: correlation between functional capacity and amount of functional proteins.

We evaluated the interrelationship between the respiratory activity and amount of proteins responsible for this function in normal and subnormal human phagocytes, neutrophils, eosinophils, monocytes, and macrophages. The superoxide-producing capacity was eosinophils > neutrophils > monocytes = macrophages when the cells were stimulated with chemotactic peptide or phorbol ester. Consonant with this finding, the protein content of three essential components of phagocyte oxidase (p22-phox, p67-phox, and p47-phox) was also eosinophils > neutrophils > monocytes = macrophages. On the other hand, the amount of another essential component, gp91-phox, was macrophage > neutrophils > eosinophils > monocytes. These findings together indicate an overall positive interrelationship between protein content and its responsible function, though only gp91-phox was not associated with the functional capacity and low amounts of this component supported the increased respiratory burst activity of eosinophils.

Adult↗

Automated discovery of 3D motifs for protein function annotation.

MOTIVATION: Function inference from structure is facilitated by the use of patterns of residues (3D motifs), normally identified by expert knowledge, that correlate with function. As an alternative to often limited expert knowledge, we use machine-learning techniques to identify patterns of 3-10 residues that maximize function prediction. This approach allows us to test the assumption that residues that provide function are the most informative for predicting function. RESULTS: We apply our method, GASPS, to the haloacid dehalogenase, enolase, amidohydrolase and crotonase superfamilies and to the serine proteases. The motifs found by GASPS are as good at function prediction as 3D motifs based on expert knowledge. The GASPS motifs with the greatest ability to predict protein function consist mainly of known functional residues. However, several residues with no known functional role are equally predictive. For four groups, we show that the predictive power of our 3D motifs is comparable with or better than approaches that use the entire fold (Combinatorial-Extension) or sequence profiles (PSI-BLAST). AVAILABILITY: Source code is freely available for academic use by contacting the authors. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Algorithms↗

Antiferritin single-chain antibody: a functional protein with incomplete folding?

The pET(scF11) plasmid was constructed comprising the gene of a single-chain antibody against human ferritin. This plasmid encodes the leader peptide pelB followed by the heavy chain variable V(H) domain, (Gly4Ser)3 linker peptide, and light chain variable V(L) domain. The correctly processed scF11 antibody was expressed in Escherichia coli as an insoluble protein without the leader peptide. Purified soluble scF11 was obtained after solubilization in 6 M GdnHCl followed by a sequential dialysis against decreasing urea concentrations and ion-exchange chromatography. ScF11 demonstrated only a approximately 8-fold decrease in the affinity (Ka = 5.1 x 10(8) M(-1) in RIA and 1.8 x 10(8) M(-1) in ELISA) vs. the parent IgG2a/kappa monoclonal antibody F11. The emission maximum of intrinsic fluorescence strongly suggests a compact conformation with tryptophanyl fluorophores buried in the protein interior, consistent with the functionality of the protein. However, scF11 demonstrated (i) the lack of denaturant-induced fluorescence 'dequenching' effect characteristic of the completely folded parent antibody, and (ii) prominent binding, under physiological conditions, of a hydrophobic probe 8-anilino-1-naphthalenesulfonate (ANS) recognizing partially structured states of a protein. These findings are indicative of an incomplete tertiary fold that gives ANS access to the protein hydrophobic core. This work provides the first indication that the functional single-chain antibody scF11 displays some properties of a partially structured state and therefore may possess incomplete folding.

Amino Acid Sequence↗

Effect of site-directed mutagenesis of conserved lysine residues upon Pas1 protein function in peroxisome biogenesis.

The Pas1 protein (Pas1p) is required for peroxisome biogenesis in Saccharomyces cerevisiae and contains two putative ATP-binding sites, each within a domain which is conserved among members of the recently characterized AAA-family. To elucidate whether both putative ATP-binding sites are essential for Pas1p function, lysine 467 of the first and lysine 744 of the second putative ATP-binding site were each changed to glutamate by site-directed mutagenesis. While replacement of lysine 744 abolished the function of the Pas1 protein in peroxisome biogenesis, replacement of lysine 467 had no obvious effect.

ATPases Associated with Diverse Cellular Activitie↗

Fine tuning of intracellular protein concentrations, a collective protein function involved in aneuploid lethality, sex-determination and speciation?

The assertion that sex chromosome dosage compensation arose because aneuploidy for an entire chromosome is lethal, begs the question of why aneuploidy is lethal. It has been proposed that aneuploid lethality results from impairment of a collective protein function (Forsdyke, 1994, J. theor. Biol. 167, 7-12). Cytosolic proteins, by virtue of their concentrations, exert a pressure tending to drive members of individual protein species into self-aggregates. Other evolutionary time, each gene has fine-tuned the concentration of its product to a maximum consistent with avoiding self-aggregation in the crowded cytosol. Because of this aggregation pressure and the imprecision of their own fine-tuning, the proteins of members of other species, the corresponding genes of which may have been transported to a cell as viruses (or gametes), are specifically aggregated. The death of the cell and its enclosed virus results. Aneuploidy impairs this process, with lethal consequences for the organism. The hypothesis leads to explanations for a variety of phenomena. On the assumption that the concentration of autosomal products determines cell volume, the observed dependence of sex-determination on the ratio of X chromosomes to autosomes is shown merely to be a dependence on the concentration of the products of one X chromosome. The inviability of the heterogametic sex among the offspring of an interspecies cross (Haldane's rule), follows from the species-specific fine-tuning of the concentrations of X chromosome-encoded products relative to the concentration of autosomally-encoded products. Species may initially have evolved as a barrier behind which fine-tuning could occur to protect cells against intracellular pathogens.

Aneuploidy↗

Strategies for the in vitro evolution of protein function: enzyme evolution by random recombination of improved sequences.

Sets of genes improved by directed evolution can be recombined in vitro to produce further improvements in protein function. Recombination is particularly useful when improved sequences are available; costs of generating such sequences, however, must be weighed against the costs of further evolution by sequential random mutagenesis. Four genes encoding para-nitrobenzyl (pNB) esterase variants exhibiting enhanced activity were recombined in two cycles of high-fidelity DNA shuffling and screening. Genes encoding enzymes exhibiting further improvements in activity were analyzed in order to elucidate evolutionary processes at the DNA level and begin to provide an experimental basis for choosing in vitro evolution strategies and setting key parameters for recombination. DNA sequencing of improved variants from the two rounds of DNA shuffling confirmed important features of the recombination process: rapid fixation and accumulation of beneficial mutations from multiple parent sequences as well as removal of silent and deleterious mutations. The five to sixfold further enhancement of total activity towards the para-nitrophenyl (pNP) ester of loracarbef was obtained through recombination of mutations from several parent sequences as well as new point mutations. Computer simulations of recombination and screening illustrate the trade-offs between recombining fewer parent sequences (in order to reduce screening requirements) and lowering the potential for further evolution. Search strategies which may substantially reduce screening requirements in certain situations are described.

Carboxylic Ester Hydrolases↗

The Salmonella SpiC protein targets the mammalian Hook3 protein function to alter cellular trafficking.

The Salmonella SpiC protein is secreted into the cytosol of macrophages via a unique type III secretion system that functions intracellularly to translocate proteins across the phagosomal membrane. The SpiC protein is required for survival within macrophages and inhibition of phagosome-lysosome fusion in vivo, and it is sufficient to inhibit endosome-endosome fusion in vitro. Here, we establish that SpiC targets the function of Hook3, a mammalian protein implicated in cellular trafficking. Purified GST-SpiC pulled down Hook3 from murine macrophages, and anti-Hook3 antibodies precipitated SpiC from the cytosol of Salmonella-infected macrophages. Expression of the spiC gene disrupted Golgi morphology in Vero cells and altered the distribution of lysosomes in macrophages, mimicking the phenotype of cells expressing a hook3 dominant-negative mutant. By inactivating Hook3 function, the SpiC protein may alter the lysosome network and prevent phagosome-lysosome fusion.

Amino Acid Sequence↗

Ribosome-display technology: applications for directed evolution of functional proteins.

In vitro display technologies, especially ribosome display, are valuable tools for many applications. In this paper, ribosome display technology and its applications for directed evolution of functional proteins will be reviewed. Ribosome display has great potential for directed evolution of protein stability and affinity, the generation of high-quality libraries by in vitro preselection, the selection of enzymatic activities, and the display of cDNA and random-peptide libraries. Ribosome display is carried out fully in vitro, which overcomes some of the limitations of cell-based display systems. We anticipate that ribosome display will have a great impact on applications in biotechnology, medicine and proteomics.

Animals↗

Alternative splicing mechanisms for the modulation of protein function: conservation between human and other species.

Alternative splicing (AS) is an important process in eukaryotic organisms by which a given gene may express a set of different protein isoforms depending on the tissue, or the developmental stage of the individual. In the present work, we have compared AS among species, focusing on the conservation of AS mechanisms for the modulation of protein function. For this purpose, we first analysed the frequency with which different species, human, mouse, rat and fruitfly, utilise them. Second, we focused more directly on the conservation among species of the mechanisms themselves. To this end, we compared biologically equivalent AS events between human and mouse, or rat. Our results indicate only minor differences in the frequency of use of these mechanisms, as well as a high degree of conservation among the species studied.

Alternative Splicing↗

Chironomus tentans-repressor splicing factor represses SR protein function locally on pre-mRNA exons and is displaced at correct splice sites.

Chironomus tentans-repressor splicing factor (Ct-RSF) represses the activation of splicing by SR proteins in vitro. Ct-RSF colocalizes with the Ser-Arg-rich (SR) protein hrp45 in interchromatin granule clusters and coimmunoprecipitates with hrp45 in nuclear extracts. Ct-RSF and hrp45 can also interact directly in vitro. Ct-RSF and hrp45 are recruited together to transcribing genes and associate with growing pre-mRNAs. Ct-RSF and hrp45 colocalize at a large number of gene loci. Injection of anti-Ct-RSF antibodies into nuclei of living cells blocks association of both Ct-RSF and hrp45 with the growing pre-mRNA, whereas binding of U2 small nuclear ribonucleoprotein particle (snRNP) to the pre-mRNA is unaffected. On the intron-rich Balbiani ring (BR) 3 pre-mRNA, hrp45 as well as U1 and U2 snRNPs bind extensively, whereas relatively little Ct-RSF is present. In contrast, the BR1 and BR2 pre-mRNAs, dominated by exon sequences, bind relatively much Ct-RSF compared with hrp45 and snRNPs. Our data suggest that Ct-RSF represses SR protein function at exons and that the assembly of spliceosomes at authentic splice sites displaces Ct-RSF locally.

Animals↗

Functional protein microarrays: ripe for discovery.

The manufacture and use of protein microarrays with correctly folded and functional content presents significant challenges. Despite this, the feasibility and utility of such undertakings are now clear, and exciting progress has recently been demonstrated in the areas of content generation, printing strategies and protein immobilization. More importantly, we are now beginning to enjoy the fruits of these efforts as functional protein microarrays are being increasingly employed for biological discovery purposes. Recent examples of this include the characterization of autoantibody responses, antibody specificity profiling, protein-protein domain interaction profiling and a comprehensive characterization of coiled-coil interactions. The best, however, is yet to come.

Animals↗

Neuralization of the Xenopus embryo by inhibition of p300/ CREB-binding protein function.

p300/ CREB-binding protein (CBP) is a transcriptional coactivator for a plethora of transcription factors and plays critical roles in signal transduction pathways. We report that the inhibition of p300/CBP function in the Xenopus embryo abolishes non-neural tissue formation and, strikingly, initiates neural induction and primary neurogenesis in the entire embryo. The observed neuralization is achieved in the absence of anterior or posterior gene expression, suggesting that neural fate activation and anterior patterning may represent distinct molecular events. We further demonstrate that the neuralizing and anteriorizing activities of chordin and noggin are separable properties of these neural inducers. This study reveals that all embryonic cells possess intrinsic neuralizing capability and that p300/CBP function is essential for embryonic germ layer formation and neural fate suppression during vertebrate embryogenesis.

Animals↗

A lysine-rich protein functions as an H1 histone in Dictyostelium discoideum chromatin.

Mononucleosomes released from Dictyostelium discoideum chromatin by micrococcal nuclease contained two distinctive DNA sizes (166-180 and 146 bp). Two dimensional gel electrophoresis suggested a lysine-rich protein protected the larger mononucleosomes from nuclease digestion. This was confirmed by stripping the protein from chromatin with Dowex resin. Subsequently, only the 146 bp mononucleosome was produced by nuclease digestion. Reconstitution of the stripped chromatin with the purified lysine-rich protein resulted in the reappearance of the larger mononucleosomes. Two-dimensional gel electrophoresis showed the protein was associated with mononucleosomes. Hence, the protein functions as an H1 histone in bringing the two DNA strands together at their exit point from the nucleosome. Trypsin digestion of the lysine-rich protein in nuclei resulted in a limiting peptide of approx. 10 kilodaltons. Trypsin concentrations which degraded the protein to peptides of 12-14 kilodaltons and partially degraded the core histones did not change the DNA digestion patterns obtained with micrococcal nuclease. Thus, the trypsin-resistant domain of the lysine-rich protein is able to maintain chromatosome structure.

Animals↗

A novel role for testicular descent; temperature-dependent induction of pertussis toxin-sensitive Gi protein function in postnatal rat Leydig cells.

The role of temperature and testicular descent in postnatal appearance of inhibitory guanine nucleotide-binding regulatory protein (G(i)) function was studied in the rat testis. Dispersed testicular cells of 5-day-old rats were incubated for 24 h at 32 or 37 C, then for another 24 h at the same temperatures in the presence and absence of pertussis toxin (PT; 100 micrograms/liter), and finally for a third 24-h period with cholera toxin (CT; 500 ng/liter) with or without PT. At both temperatures, PT treatment significantly (P < 0.05) increased the CT-stimulated cAMP output, but had no effect on basal cAMP production. When testosterone (T) production, as an indicator of Leydig cell function, was measured in the same incubation, CT-stimulated T production was greater at 32 C, but PT had no effect at either temperature. A similar finding was made when hCG (10 micrograms/liter), instead of CT, was used as the stimulus of T production. Hence, a functional G(i) protein is present in seminiferous tubules of 5-day-old testes cultured for 3 days at 32 and 37 C, but not in Leydig cells. We then examined the effects of longer exposure of 5-day-old testes to the two temperatures. After culture for 7 days with 0.1 microgram/liter ovine LH, the presence of PT at 32 C significantly (P < 0.01) enhanced CT-stimulated T production during the last 24 h of culture, but the PT effect was not observed when the culture was carried out at 37 C. Hence, G(i)-mediated modulation of Leydig cell function appears to require several days of induction at the lower temperature of 32 C. As the postnatal descent also changes the ambient testicular temperature, we next studied whether this event alters the G(i) protein function of Leydig cells. Five-day-old rats were rendered bilaterally cryptorchid or sham operated, and studied after 12 days. Testis weights did not differ between the abdominal and scrotal testes. In contrast, the basal and hCG-stimulated rates of T production were significantly (P < 0.01-0.05) higher in the scrotal testes. When dispersed cells of the scrotal and abdominal testes were incubated for 24 h at 37 C in the presence of CT with or without PT, enhancement of T production by PT was only observed in cells of the scrotal testes.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

Three-dimensional chemical structures by protein functionalized micron-sized beads bound to polylysine-coated silicone surfaces.

A novel method is described here that allows three-dimensional (3D) control of both chemistry and morphology by a series of wet chemical steps: the attachment of protein functionalized micron-sized beads onto a flat silicone surface that has been functionalized with a distinct chemical modification. Bovine serum albumin (BSA), laminin, or polylysine is covalently bound to 6.5-microm-diameter spherical beads. A chemical method is then used to bind these beads to a flat silicone surface that is subsequently functionalized with polylysine. This process leads to a nonspecific cell adhesive background on the flat surface (polylysine) with the option of differing chemistry on the third-dimension due to the protein BSA or laminin on the bead protruding from the surface. The beads do not detach during cyclic stretching in vitro. Neo-natal rat cardiac fibroblasts are cultured on the beaded surfaces and compared with fibroblasts cultured on nonbeaded, flat polylysine surfaces. Fibroblast plating density, integrin, and physical responses are examined as a function of varying the ligands on the beads.

Animals↗