Assessment of blind predictions of protein-protein interactions: current status of docking methods

The current status of docking procedures for predicting protein-protein interactions starting from their three-dimensional structure is assessed from a first major evaluation of blind predictions. This evaluation was performed as part of a communitywide experiment on Critical Assessment of PRedicted Interactions (CAPRI). Seven newly determined structures of protein-protein complexes were available as targets for this experiment. These were the complexes between a kinase and its protein substrate, between a T-cell receptor beta-chain and a superantigen, and five antigen-antibody complexes. For each target, the predictors were given the experimental structures of the free components, or of one free and one bound component in a random orientation. The structure of the complex was revealed only at the time of the evaluation. A total of 465 predictions submitted by 19 groups were evaluated. These groups used a wide range of algorithms and scoring functions, some of which were completely novel. The quality of the predicted interactions was evaluated by comparing residue-residue contacts and interface residues to those in the X-ray structures and by analyzing the fit of the ligand molecules (the smaller of the two proteins in the complex) or of interface residues only, in the predicted versus target complexes. A total of 14 groups produced predictions, ranking from acceptable to highly accurate for five of the seven targets. The use of available biochemical and biological information, and in one instance structural information, played a key role in achieving this result. It was essential for identifying the native binding modes for the five correctly predicted targets, including the kinase-substrate complex where the enzyme changes conformation on association. But it was also the cause for missing the correct solution for the two remaining unpredicted targets, which involve unexpected antigen-antibody binding modes. Overall, this analysis reveals genuine progress in docking procedures but also illustrates the remaining serious limitations and points out the need for better scoring functions and more effective ways for handling conformational flexibility.     

CAPRI: a Critical Assessment of PRedicted Interactions

CAPRI is a communitywide experiment to assess the capacity of protein-docking methods to predict protein-protein interactions. Nineteen groups participated in rounds 1 and 2 of CAPRI and submitted blind structure predictions for seven protein-protein complexes based on the known structure of the component proteins. The predictions were compared to the unpublished X-ray structures of the complexes. We describe here the motivations for launching CAPRI, the rules that we applied to select targets and run the experiment, and some conclusions that can already be drawn. The results stress the need for new scoring functions and for methods handling the conformation changes that were observed in some of the target systems. CAPRI has already been a powerful drive for the community of computational biologists who development docking algorithms. We hope that this issue of Proteins will also be of interest to the community of structural biologists, which we call upon to provide new targets for future rounds of CAPRI, and to all molecular biologists who view protein-protein recognition as an essential process.     

Shift in nucleotide conformational equilibrium contributes to increased rate of catalysis of GpAp versus GpA in barnase

The microbial ribonuclease barnase exhibits low catalytic activity toward GpN dinucleotides, where G is guanosine, p is phosphate and N represents any nucleoside. When a phosphate is added to the 3'-end, as in GpNp, substrate affinity is enhanced by one order of magnitude, and the catalytic rate by two. In order to gain insight into this phenomenon, we analyzed the nucleotide conformations and protein-nucleotide interactions of 4 ns molecular dynamics (MD) trajectories of complexes of barnase with guanylyl(3'-5') adenosine (GpA) and guanylyl(3'-5') adenosine 3'-monophosphate (GpAp), respectively, in the presence of solvent and counter ions. We found that, in a majority of the bound GpA conformations, the guanine base was firmly bound to the recognition site. The phosphate and adenosine moieties pointed into the solvent, and interactions with key catalytic residues were absent. In contrast, the bound GpAp adopted conformations in which all of the nucleotide portions remained tightly bound to the enzyme and interactions with key catalytic residues were maintained. These observations indicate that, for GpA, a significant proportion of the bound nucleotide adopts non-productive conformations and that adding the terminal phosphate as in GpAp shifts the equilibrium of the bound conformations towards structures capable of undergoing catalysis. Incorporating this property into the kinetic equations yields an increase in both the apparent rate constant (kcat) and the apparent dissociation constant (K(M)) for GpAp versus GpA. The increase in K(M), caused by the presence of additional non-productive binding modes for GpA, should however be counterbalanced by the propensity of free GpA to adopt folded conformations in solution, which are unable to bind the enzyme and by the tighter binding of GpAp (Giraldo J, Wodak SJ, Van Belle D. Conformational analysis of GpA and GpAp in aqueous solution by molecular dynamics and statistical methods. J Mol Biol 1998; 283:863-882). Addition of the terminal phosphate is shown to significantly influence the collective motion of the enzyme in a manner that fosters interactions with key catalytic residues, representing a further likely contribution to the catalytic rate enhancement.     

The tetraspanin CD81 regulates the expression of CD19 during B cell development in a postendoplasmic reticulum compartment

CD81 is a widely expressed tetraspanin that associates in B cells with CD19 in the CD19-CD21-CD81 signaling complex. CD81 is necessary for normal CD19 expression; cd81(-/-) B cells express lower levels of CD19, especially cd81(-/-) small pre-BII cells, which are almost devoid of surface CD19. The dependence of CD19 expression on CD81 is specific to this particular tetraspanin since cd9(-/-) B cells express normal levels of CD19. Furthermore, expression of human CD81 in mouse cd81(-/-) B cells restored surface CD19 to normal levels. Quantitative analysis of CD19 mRNA demonstrated normal levels, even in cd81(-/-) pre-BII cells. Analysis of CD19 at the protein level identified two CD19 glycoforms in both wild-type and cd81(-/-) B cells. The higher M(r) glycoform is significantly reduced in cd81(-/-) B cells and is endoglycosidase H (endo-H) resistant. In contrast, the low M(r) glycoform is comparably expressed in cd81(-/-) and in wild-type B cells and is endo-H sensitive. Because endo-H sensitivity is tightly correlated with endoplasmic reticulum localization, we suggest that the dependency of CD19 expression on CD81 occurs in a postendoplasmic reticulum compartment where CD81 is necessary for normal trafficking or for surface membrane stability of CD19.     

Mouse methionine sulfoxide reductase B: effect of selenocysteine incorporation on its activity and expression of the seleno-containing enzyme in bacterial and mammalian cells

The mammalian methionine sulfoxide reductase B (MsrB) has been found to be a selenoprotein which can reduce R form of both free and protein-incorporated methionine sulfoxide to methionine. Together with MsrA, which reduces specifically the S form of methionine sulfoxide, the living cell can repair methionine-damaged proteins and salvage free methionine under oxidative stress conditions. Here, we report about the pivotal role of the selenocysteine residue in the protein putative active site by site-directed mutagenesis directed to the selenocysteine codon. Using the Escherichia coli SECIS (selenocysteine insertion sequence) element, needed for the recognition of the UGA codon as a selenocysteine codon in E. coli, we expressed the seleno-MsrB as a recombinant selenoprotein in E. coli. The recombinant seleno-MsrB has been shown to be much more active than the cysteine mutant, whereas the mutations to alanine and serine rendered the protein inactive. Although the yields of expression of the full-length N-terminus and C-terminus His-tagged seleno-MsrB were only 3% (of the total MsrB expressed), the C-terminus His-tagged protein enabled us to get a pure preparation of the seleno-MsrB. Using both recombinant selenoproteins, the N-terminus His-tagged and the C-terminus His-tagged proteins, we were able to determine the specific activities of the recombinant seleno-MsrB, which were found to be much higher than the cysteine mutant homologue. This finding confirmed our suggestion that the selenocysteine is essential for maintaining high reducing activity of MsrB. In addition, using radioactive selenium we were able to determine the in vivo presence of MsrB as a selenoprotein in mammalian cell cultures.     

CELL-WALL FORMATION DURING THE CELL CYCLE OF PORPHYRIDIUM SP. (RHODOPHYTA)

The cell wall of the red microalgae Porphyridium sp. (UTEX 637) comprises a complex amorphous polysaccharide (6–7 × 10⁶ Da). The polysaccharide is made up of xylose, glucose, and galactose as the main sugars, as well as some minor sugars, protein, sulfate, and glucuronic acid, the latter two conferring a negative charge on the polysaccharide. In this study, we used synchronized cultures as one of the ways of unraveling the mechanism of biosynthesis of this complex polysaccharide by following cell-wall formation during the cell cycle. Synchronization of Porphyridium sp. was achieved with an alternating light:dark regime of 12:12 h LD and dilution of the culture at the end of the cycle. Under these conditions, cell duplication occurred between the 12th and 14th hours of the cycle. The following order of building toward formation of the final polysaccharide appeared to take place: Intermediate polysaccharides with molecular masses ranging from 0.5 × 10⁶ to 2 × 10⁶ Da appeared in succession during hours 2–6 of the cycle, and the full-sized polysaccharide was detected by the 8th hour. At the beginning of the cycle, xylose was the predominant sugar. Sulfur peaked at hours 2–4; glucose, galactose, and glucuronic acid at hours 8–12; and the minor sugars at hours 12–14. Upon incubation of low molecular mass polymer (0.5 × 10⁶ Da) collected from the 4th hour with cellular crude extract from cells of the 6th hour of the cycle, two intermediates were formed (0.8 × 10⁶ Da and 2 × 10⁶ Da). We suggest that the 0.5 × 10⁶ Da polymer intermediate, which is composed mainly of xylose, is the first polymer secreted into the medium, where it is further polymerized enzymatically to produce the 2 × 10⁶ Da polymer via an intermediate 0.8 × 10⁶ Da polymer. Later, the full-size polysaccharide is produced.     

NOTE MOLECULAR ANALYSIS OF THE AHAS GENE OF PORPHYRIDIUM SP. (RHODOPHYTA) AND OF A MUTANT RESISTANT TO SULFOMETURON METHYL

Acetohydroxyacid synthase (AHAS) is the target enzyme of the sulfonylurea herbicides, and here we report the sequence of the gene from wild-type and herbicide-resistant Porphyridium sp. (Rhodophyta). The resistant mutant has a single residue substitution at a position known to confer herbicide resistance in E. coli and in plants. The rhodophyte gene is of cyanobacterial origin and distinct from the nuclear-encoded chlorophyte gene, which may be of mitochondrial origin.     

A GLYCOPROTEIN NONCOVALENTLY ASSOCIATED WITH CELL‐WALL POLYSACCHARIDE OF THE RED MICROALGA PORPHYRIDIUM SP. (RHODOPHYTA)1

The cells of the red microalga Porphyridium sp. (UTEX 637) are encapsulated in a cell wall of a negatively charged mucilaginous polysaccharide complex composed of 10 different sugars, sulfate, and proteins. In this work, we studied the proteins associated with the cell‐wall polysaccharide. A number of noncovalently associated proteins were resolved by SDS‐PAGE, but no covalently bound proteins were detected. The most prominent protein detected was a 66‐kDa glycoprotein consisting of a polypeptide of approximately 58 kDa and a glycan moiety of approximately 8 kDa containing N‐linked terminal mannose. In size‐exclusion chromatography, the 66‐kDa protein was coeluted with the polysaccharide and could be separated from the polysaccharide only after denaturation of the protein, indicating that the 66‐kDa protein was tightly bound to the polysaccharide. Western blot analysis revealed that the 66‐kDa protein was specific to Porphyridium sp. and P. cruentum, because it was not detected in the other species of red microalgae examined. Indirect immunofluorescence assay confirmed the location of the protein in the algal cell wall. The sequence of cDNA clone encoding the 66‐kDa glycoprotein, detected in our in‐house expressed sequence tag database of Porphyridium sp., revealed that this is a novel protein with no similarity to any protein in the public domain databases and our in‐house expressed sequence tag database of the red microalga Rhodella reticulata. The 66‐kDa protein bound polysaccharides from red algae but not from those of other origins tested. Possible roles of the 66‐kDa protein in the biosynthesis of the polysaccharide are discussed.     

BIOSYNTHESIS OF EICOSAPENTAENOIC ACID (EPA) IN THE FRESHWATER EUSTIGMATOPHYTE MONODUS SUBTERRANEUS (EUSTIGMATOPHYCEAE)1

In an attempt to elucidate the biosynthesis of the polyunsaturated fatty acid eicosapentaenoic acid (20:5ω3, EPA), we treated cultures of the eustigmatophyte Monodus subterraneus Peterson with either salicylhydroxamic acid or the herbicide SAN 9785. Labeled linoleic acid was incorporated into the cultures in the presence and absence of the latter inhibitor, and the redistribution of label was followed. Our results suggest that the major biosynthetic pathway leading to EPA involves fatty acids of the ω6 family. In the early stages of the biosynthesis, 18:1 is predominantly incorporated to the sn‐2 position of phosphatidylcholine, where it is stepwise desaturated by the Δ12 and Δ6 desaturases to 18:3ω6. The latter is released from the lipid, elongated to 20:3ω6 and reincorporated to both positions of phosphatidylethanolamine (PE) where it is further desaturated by the Δ5 and ω3 desaturases to EPA. We suggest that PE is the donor of the 20:5/20:5 diacylglycerol that is imported to the chloroplast to form the eukaryotic‐like molecular species of monogalactosyldiacylglycerol. Likewise, 20:3ω6 can be also incorporated into diacylglyceryltrimethylhomoserine, mostly to the sn‐2 position and similarly desaturated to 20:4ω6 and 20:5ω3. These fatty acids can be exported and incorporated into the sn‐1 position of the prokaryotic‐like molecular species of the chloroplastic lipids. We thus suggest that both the eukaryotic‐like and the prokaryotic‐like molecular species are biosynthesized by different extraplastidial lipids.     

FIXED CARBON PARTITIONING IN THE RED MICROALGA PORPHYRIDIUM SP. (RHODOPHYTA)

The main products of carbon fixation in the red algae are sulfated cell-wall polysaccharides, floridean starch, and low molecular weight (LMW) carbohydrates, mainly floridoside. In the red microalga Porphyridium sp., sulfated polysaccharide—cell bound and soluble—comprises up to 70% of the algal biomass. The purpose of this study was to elucidate the partitioning of fixed carbon in Porphyridium sp. toward the different products of carbon fixation. Using pulse-chase technique with [¹⁴C]bicarbonate, we followed ¹⁴C flow into the major compounds, namely, cell-wall polysaccharide, floridoside, starch, and protein, under various environmental conditions (i.e. carbon dioxide enrichment and nitrate starvation). ¹³C-NMR and gas chromatography analysis showed the main LMW product in Porphyridium sp. to be floridoside. After the short [¹⁴C]bicarbonate pulse (20 min), 42%–53% of total ¹⁴C uptake was initially found in floridoside. The appearance of ¹⁴C in the soluble polysaccharide was evident immediately at the end of the 20-min [¹⁴C]bicarbonate pulse. The specific radioactivity in the floridoside fraction declined by 80% after the 48-h chase, this decline being accompanied by increased labeling of starch and the soluble polysaccharide. In cells exposed to high CO₂ concentration, larger amounts of ¹⁴C (about twice as much) were channeled into starch and soluble polysaccharide than in cells under low CO₂ concentration. The most significant increase (1500%) in labeling during chase was found in the soluble polysaccharide of the nitrate-deprived cultures. It therefore seems likely that the large amounts of carbon incorporated by Porphyridium sp. cells into floridoside were subsequently used for the synthesis of macromolecular components. The data thus support the premise that floridoside serves as a dynamic carbon pool, which channels the fixed carbon toward polysaccharides and other end products according to the ambient conditions.