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PubMed2006

Benchmarking of dimeric threading and structure refinement.

The understanding of protein-protein interactions is a major goal in the postgenomic era. The prediction of interaction from sequence and the subsequent generation of full-length dimeric models is therefore of great interest especially because the number of structurally characterized protein-protein complexes is sparse. A quality assessment of a benchmark comprised of 170 weakly homologous dimeric target-template pairs is presented. They are predicted in a two-step method, similar to the previously described MULTIPROSPECTOR algorithm: each target sequence is assigned to a monomeric template structure by threading; then, those templates that belong to the same physically interacting dimer template are selected. Additionally we use structural alignments as the "gold standard" to assess the percentage of correctly assigned monomer and dimer templates and to evaluate the threading results with a focus on the quality of the alignments in the interfacial region. This work aims to give a quantitative picture of the quality of dimeric threading. Except for one, all monomer templates are identified correctly, but approximately 40% of the dimer templates are still problematic or incorrect. Preliminary results for three full-length dimeric models generated with the TASSER method show on average a significant improvement of the final model over the initial template.

Algorithms↗
PubMed2007

A novel cross-linked RNase A dimer with enhanced enzymatic properties.

A new cross-linked ribonuclease A (RNase A) dimer composed of monomeric units covalently linked by a single amide bond between the side-chains of Lys(66) and Glu(9) is described. The dimer was prepared in the absence of water by incubating a lyophilized preparation of RNase, sealed under vacuum, in an oven at 85 degrees C. It was determined that the in vacuo procedure does not induce any significant conformational changes to the overall structure of RNase A, yet the amide cross-link has an increased acid lability, indicating that it is exposed and conformationally strained. Examination of X-ray crystallographic structures indicates that Lys(66) and Glu(9) are not close enough for the in vacuo dimer to adopt any of the known domain-swapped conformations. Therefore, the in vacuo RNase A dimer appears to be a novel dimeric structure. The in vacuo RNase A dimer also exhibits a twofold increase in activity over monomeric RNase A on a per monomer basis. This doubling of enzymatic activity was shown using dsRNA and ssRNA as substrates. In addition to this enhanced ability to degrade RNA, the dimer is not inhibited by the cellular ribonuclease inhibitor protein (cRI).

Animals↗
PubMed2002

Parallel and antiparallel dimers of magainin 2: their interaction with phospholipid membrane and antibacterial activity.

Magainin 2 (M2) forms pores by associating with several other M2 molecules in lipid membranes and shows antibacterial activity. To examine the effect of M2 dimerization on biological activity and membrane interaction, parallel and antiparallel M2 dimers were prepared from two monomeric precursors. Antibacterial and haemolytic activities were enhanced by dimerization. CD measurements showed that both dimers and monomers have an alpha-helical structure in the presence of lipid vesicles. Tryptophan fluorescence shift and KI quenching studies showed that all the peptides were more deeply embedded in acidic liposomes than in neutral liposomes. Experiments on dye-leakage activity and membrane translocation of peptides suggest that dimers and monomers form pores through lipid membranes, although the pore formation may be accompanied by membrane disturbance. Although dimerization of M2 increased the interaction activity with lipid membranes, no appreciable difference between the activities of parallel and antiparallel M2 dimers was observed.

Amino Acid Sequence↗
PubMed1998

Reactions of pyridine coenzyme dimers and monomers with viologens.

DCMV++ (1,1'-dimethyl-2,2'-dicyano-4,4'-bipyridinium, bis-methylsulfate) promotes the aerobic oxidation of the NAD(P) dimers (NADP)2 and (NAD)2 with the formation of 2 mol of NADP+ or NAD+ per mole of dimers. The reaction appears to follow a pseudo-first-order kinetics with respect to the dimer concentration. One mole of oxygen was consumed in the reaction per mole of NAD(P) dimer oxidized and hydrogen peroxide was produced. The monomers NADPH and NADH under the same reaction conditions were not oxidized by DCMV++. In anaerobiosis NAD(P) dimers but not NAD(P)H rapidly reduced DCMV++ to its radical cation DCMV++, which was rapidly back-oxidized by air to its parent dication. Paraquat (MV++) was also able to catalyze the aerobic oxidation of NAD(P) dimers and, at a much lower extent, NADPH and NADH, but only under light irradiation. In anaerobiosis and upon light irradiation all the above nucleotides were able to convert paraquat to its radical cation MV++, reoxidized to MV++ by air admission. This study shows the different ability of NAD(P) dimers and NAD(P)H to undergo one-electron and two-electron oxidation reactions, with different viologens.

Aerobiosis↗
PubMed2000

Copper-dependent formation of disulfide-linked dimer of S100B protein.

Previous cell biological studies demonstrated that S100B protein enhances neurite extension of cortical neurons and stimulates proliferation of glial cells. Although these activities of the protein are ascribed to its disulfide-linked dimeric form, there have been no indications as to how the dimer is formed in vivo. We have found by an in vitro study that it is produced by copper-dependent oxidation of noncovalent S100B dimer. The disulfide-linked dimer markedly stimulated nitric oxide production in a microglial cell line, BV2. Interestingly, the disulfide-linked dimer formation was found to be prevented by ascorbic acid. The copper-dependent formation of the dimer may not happen in vivo under normal conditions; however, under pathological conditions where copper is likely to be released from tissues and catalyze autoxidation of ascorbic acid, the dimer formation may proceed, resulting in the stimulated production of nitric oxide that would induce toxic signaling pathways.

Animals↗
PubMed1996

The carboxyl-terminal region is essential for Sec-A dimerization.

SecA, comprising 901 amino acid residues, exists as a dimer. By means of size exclusion chromatography and chemical cross-linking analysis, five truncated SecA derivatives were examined to identify the region of SecA essential for dimer formation. Among them, only N95 (delta 832-901) retained SecA activity. N95 existed as a dimer, indicating that the carboxyl-terminal three cysteine residues are dispensable for physiological dimerization. Both N76 (delta 675-901) and N66 (delta 583-901) existed as monomers. Monomeric N76 was able to bind to ATP, indicating that the dimerization of SecA is not a prerequisite for ATP binding. However, the rate of ATP hydrolysis by N76 was 25% of that by SecA. C53 (delta 1-437) and C28 (delta 1-661) formed dimers irrespective of the presence or absence of 2-mercaptoethanol. C28, but not C53, also existed as an oligomer in the absence of 2-mercaptoethanol, suggesting that the 438-661 region present in C53 prevents intermolecular disulfide bond formation at the carboxyl-terminal cysteine residue. From these results, the region essential for the physiological dimer formation was concluded to be located in the 662-831 region of SecA.

Adenosine Triphosphatases↗
PubMed2000

Duality monomer-dimer of the pheromone-binding protein from Bombyx mori.

The analysis of a recombinant pheromone-binding protein from the silkworm moth, Bombyx mori, by native gel electrophoresis with Coomassie staining showed one single band with a molecular mass consistent with a monomer. A slow migrating band, detected in the recombinant and native samples by a polyclonal antibody, was indistinguishable from the monomer in the mass spectrum fragmentation pattern and chromatographic behavior. Flow injection analyses of the protein by mass spectrometry in the negative mode showed fragments of a dimer. The dimeric form was also supported by estimation of the molecular mass by gel filtration at basic pH. A cross-linked dimer coeluted with the noncovalent dimer on a gel filtration column. The molecular mass of the protein changed in a pH-dependent way with a dramatic transition from dimer to monomer between pH 6 and 4.5. A low pH induced not only dissociation of the dimer, but also a conformational change in the protein. In marked contrast to denaturation with guanidinium chloride, the emission maxima of tryptophan was not significantly changed at low pH. BmPBP is thus a dimer at slightly acid, neutral, and basic pH, which dissociates and then undergoes conformational change at low pH.

Animals↗
PubMed1997

The central region of RepE initiator protein of mini-F plasmid plays a crucial role in dimerization required for negative replication control.

The RepE protein (251 residues, 29 kDa) of mini-F plasmid, mostly found as dimers, plays a key role in mini-F replication. Whereas monomers bind to the origin to initiate replication, dimers bind to the repE operator to repress its own transcription. Among the host factors required for mini-F replication, a set of molecular chaperones (DnaK, DnaJ and GrpE) is thought to facilitate monomerization of RepE dimers. To further understand the structural basis of functional differentiation between the two forms of RepE, we examined the region(s) critical for dimerization by isolation and characterization of RepE mutants that were defective in autogenous repressor function. Such mutations were isolated from two separate regions of RepE, the central region (residues 111 to 161) and the C-terminal region (residues 195 to 208). The central region overlapped the region where the chaperone-independent copy-up mutations were previously isolated (residues 93 to 135). Likewise the mini-F mutant plasmids, carrying the mutations in the central region, could replicate in a dnaK null mutant host. One of them, S111P (111th serine changed to proline), showed a very high origin-binding activity vis-à-vis a severely reduced operator-binding activity, much like the RepE54 (R118P) mutant previously shown to form only monomers. Gel filtration and chemical crosslinking studies with purified RepE revealed that S111P primarily formed monomers, whereas other mutant proteins formed mostly dimers. On the other hand, analysis of deletion mutants revealed that the N-terminal 42 and the C-terminal 57 residues were dispensable for dimerization. Thus, the region spanning residues 93 to 161 of RepE (including Ser111 and Arg118) appeared to be primarily involved in dimerization, contributing to the negative regulation of plasmid replication.

Bacterial Proteins↗
PubMed1998

Plasmid pIP501 encoded transcriptional repressor CopR binds to its target DNA as a dimer.

The CopR protein is one of the two regulators of pIP501 copy number. It acts as transcriptional repressor at the essential repR promoter pII. Previously, we found that CopR contacts two consecutive major grooves (site I and site II) on the same face of the DNA. In spite of identical sequence motifs in these sites, neighboring bases were contacted differently. Furthermore, we showed that CopR can dimerize in solution. We demonstrate by two independent methods that CopR binds the DNA as a dimer. We present data that suggest that the sigmoidal CopR-DNA binding curve published previously is the result of two coupled equilibria: dimerization of CopR monomers and CopR dimer-DNA binding. A KD-value of 1.44(+/-0.49)x10(-6) M for CopR dimers was determined by analytical ultracentrifugation. Based on this value and the binding curve, the equilibrium dissociation constant K2 for the CopR-DNA complex was calculated to be 4(+/-1. 3)x10(-10) M. Quantitative Western blot analysis was used to determine the intracellular concentration of CopR in Bacillus subtilis. This value, 20x10(-6) to 30x10(-6) M, is 10 to 20-fold higher than the equilibrium constant for dimer dissociation, suggesting that CopR binds in vivo as a preformed dimer.

Bacillus subtilis↗
PubMed1999

A dimeric form of Escherichia coli succinyl-CoA synthetase produced by site-directed mutagenesis.

Succinyl-CoA synthetase (SCS) catalyzes the substrate-level phosphorylation step of the citric acid cycle. The enzyme from Escherichia coli is an (alphabeta)2-heterotetramer with two active sites, one in each alphabeta-dimer. To determine whether the two active sites could function independently, mutations were made to split the tetramer into alphabeta-dimers. Because two choices for the tetramer (I and II) were possible from the X-ray crystallographic analyses, mutations were made at two different interfaces. All mutations based on tetramer I resulted in an intact tetramer. Of the two mutants based on tetramer II, one was insoluble and the other, where M156beta, Y158beta, R161beta and E162beta were changed to D, D, E and R, respectively, was a dimer. This quaternary structure was confirmed by fast protein liquid chromatography, blue native PAGE and ultracentrifugation. The DDER mutant has kinetic parameters similar to the tetrameric E. coli enzyme. Like the tetrameric enzyme, it shows ATP-facilitated dethiophosphorylation, proving that this property is a single-site effect. The ATP-facilitated dethiophosphorylation is inhibited by phosphate. It is concluded that dimerization of alphabeta-dimers is not a prerequisite for catalytic competency nor for alternating sites cooperativity in the tetramer. The rationale behind the dimer-of-dimers in E. coli SCS is still not known, but increased solubility, increased stability and in vivo interactions of the tetramer with other proteins are still possibilities.

Amino Acid Sequence↗
PubMed1999

MAD structure of Pseudomonas nautica dimeric cytochrome c552 mimicks the c4 Dihemic cytochrome domain association.

The monohemic cytochrome c552from Pseudomonas nautica (c552-Pn) is thought to be the electron donor to cytochrome cd1, the so-called nitrite reductase (NiR). It shows as high levels of activity and affinity for the P. nautica NiR (NiR-Pn), as the Pseudomonas aeruginosa enzyme (NiR-Pa). Since cytochrome c552is by far the most abundant electron carrier in the periplasm, it is probably involved in numerous other reactions. Its sequence is related to that of the c type cytochromes, but resembles that of the dihemic c4cytochromes even more closely. The three-dimensional structure of P. nautica cytochrome c552has been solved to 2.2 A resolution using the multiple wavelength anomalous dispersion (MAD) technique, taking advantage of the presence of the eight Fe heme ions in the asymmetric unit. Density modification procedures involving 4-fold non-crystallographic averaging yielded a model with an R -factor value of 17.8 % (Rfree=20.8 %). Cytochrome c552forms a tight dimer in the crystal, and the dimer interface area amounts to 19% of the total cytochrome surface area. Four tighly packed dimers form the eight molecules of the asymmetric unit. The c552dimer is superimposable on each domain of the monomeric cytochrome c4from Pseudomomas stutzeri (c4-Ps), a dihemic cytochrome, and on the dihemic c domain of flavocytochrome c of Chromatium vinosum (Fcd-Cv). The interacting residues which form the dimer are both similar in character and position, which is also true for the propionates. The dimer observed in the crystal also exists in solution. It has been hypothesised that the dihemic c4-Ps may have evolved via monohemic cytochrome c gene duplication followed by evolutionary divergence and the adjunction of a connecting linker. In this process, our dimeric c552structure might be said to constitute a "living fossile" occurring in the course of evolution between the formation of the dimer and the gene duplication and fusion. The availability of the structure of the cytochrome c552-Pn and that of NiR from P. aeruginosa made it possible to identify putative surface patches at which the docking of c552to NiR-Pn may occur.

Amino Acid Sequence↗
PubMed1996

A murine host cell factor required for nicking of the dimer bridge of MVM recognizes two CG nucleotides displaced by 10 basepairs.

During replication of the minute virus of mice (MVM) genome, a dimer replicative form (RF) intermediate is resolved into two monomer RF molecules in such a way as to retain a unique sequence within the left hand hairpin terminus of the viral genome. Although the proposed mechanism for resolution of the dimer RF remains uncertain, it likely involves site-specific nicking of the dimer bridge. The RF contains two double-stranded copies of the viral genome joined by the extended 3' hairpin. Minor sequence asymmetries within the 3' hairpin allow the two halves of the dimer bridge to be distinguished. The A half contains the sequence [sequence: see text], whereas the B half contains the sequence [sequence: see text]. Using an in vitro assay, we show that only the B half of the MVM dimer bridge is nicked site-specifically when incubated with crude NS-1 protein (expressed in insect cells) and mouse LA9 cellular extract. When highly purified NS-1, the major nonstructural protein of MVM, is used in this nicking reaction, there is an absolute requirement for the LA9 cellular extract, suggesting a cellular factor (or factors) is (are) required. A series of mutations were created in the putative host factor binding region (HFBR) on the B half of the MVM dimer bridge adjacent to the NS-1 binding site. Nicking assays of these B half mutants showed that two CG motifs displaced by 10 nucleotides are important for nicking. Gel mobility shift assays demonstrated that a host factor(s) can bind to the HFBR of the B half of the dimer bridge and efficient binding depends on the presence of both CG motifs. Competitor DNA containing the wild-type HFBR sequence is able to specifically inhibit nicking of the B half, indicating that the host factor(s) bound to the HFBR is(are) essential for site-specific nicking to occur.

Animals↗
PubMed2002

Deficient dimerization of human immunodeficiency virus type 1 RNA caused by mutations of the u5 RNA sequences.

The human immunodeficiency virus type 1 (HIV-1) virion contains two copies of genomic RNA that are noncovalently attached along a region at their 5' ends, in which two contact sites have been observed by electron microscopy. One of these sites is believed to be the stem-loop 1 (SL1) sequence which serves as the dimerization initiation site (DIS), and the other site, closer to the 5' end of the viral RNA, may involve the R or U5 RNA sequences. In this study, we present biochemical evidence showing that alteration of the U5 RNA sequence in the context of full-length viral RNA leads to diminished dimerization of virion RNA. In particular, two stretches of GU-rich sequences, which are located at nucleotides (nt) 99 to 108 and nt 112 to 123 within U5, were either deleted or substituted with exogenous sequences. The mutated viruses thus generated all exhibited deficient RNA dimerization. This dimerization deficit was not corrected by second-site mutations that preserved local RNA structures, such as the poly(A) hairpin, and was overcome to only a limited extent by compensatory mutations within Gag; these mutations were identified after long-term culture of the relevant mutant viruses in permissive cell lines and were able to restore viral infectiousness and RNA packaging to wild-type levels. Therefore, these GU sequences do not regulate RNA dimerization by the formation of local secondary structures nor by the maintenance of efficient viral RNA packaging; instead, they may mediate direct RNA-RNA interactions in the dimer structure. In contrast, mutation of palindrome 5'-AAGCUU-3', which resides within R and crowns the poly(A) hairpin, did not affect either RNA dimerization or RNA packaging.

5' Untranslated Regions↗
PubMed2005

Agonist and antagonist dual effect of the cross-linked S19 ribosomal protein dimer in the C5a receptor-mediated respiratory burst reaction of phagocytic leukocytes.

OBJECTIVE: To examine the behavior of the crosslinked dimer of S19 ribosomal protein (RP S19), a natural C5a receptor ligand, in the C5a receptor-mediated respiratory burst reaction of monocytes and neutrophils. METHODS: The respiratory burst reaction of leukocytes was quantitatively observed by continuous spectrophotometric measurement of the reduction of a water-soluble tetrazolium salt, WST-1. RESULTS: The RP S19 dimer induced the respiratory burst of monocytes, but not of neutrophils. Furthermore, in neutrophils, the RP S19 dimer inhibited the reaction induced by C5a, but did not affect the formyl-Met-Leu-Phe-induced reaction. The dimer of a deletion mutant at the C-terminal portion of the RP S19 induced a respiratory burst reaction similar to the one induced by C5a, both in monocytes and neutrophils. Inversely, a chimeric fusion protein between C5a and RPS19, consisting of the addition of the 12 C-terminal amino acid residues of RP S19 after the C-terminal Arg74 of the C5a molecule, behaved similarly to the RP S19 dimer. CONCLUSIONS: The RP S19 dimer works as an agonist and antagonist of the C5a receptor in the monocyte and the neutrophil respiratory burst reactions, respectively. The switch moiety between the antagonist and agonist of the RP S19 dimer for the C5a receptor in the induction of respiratory burst of phagocytes localizes at the C-terminal region of RP S19.

Cross-Linking Reagents↗
PubMed2024

Early Events in β2AR Dimer Dynamics Mediated by Activation-Related Microswitches.

G-Protein-Coupled Receptors (GPCRs) make up around 3-4% of the human genome and are the targets of one-third of FDA-approved drugs. GPCRs typically exist as monomers but also aggregate to form higher-order oligomers, including dimers. β2AR, a pharmacologically relevant GPCR, is known to be targeted for the treatment of asthma and cardiovascular diseases. The activation of β2AR at the dimer level remains under-explored. In the current study, molecular dynamics (MD) simulations have been performed to understand activation-related structural changes in β2AR at the dimer level. The transition from inactive to active and vice versa has been studied by starting the simulations in the apo, agonist-bound, and inverse agonist-bound β2AR dimers for PDB ID: 2RH1 and PDB ID: 3P0G, respectively. A cumulative total of around 21-μs simulations were performed. Residue-based distances, RMSD, and PCA calculations suggested that either of the one monomer attained activation-related features for the apo and agonist-bound β2AR dimers. The TM5 and TM6 helices within the two monomers were observed to be in significant variation in all the simulations. TM5 bulge and proximity of TM2 and TM7 helices may be contributing to one of the early events in activation. The dimeric interface between TM1 and helix 8 were observed to be well maintained in the apo and agonist-bound simulations. The presence of inverse agonists favored inactive features in both the monomers. These key features of activation known for monomers were observed to have an impact on β2AR dimers, thereby providing an insight into the oligomerization mechanism of GPCRs.

Receptors, Adrenergic, beta-2↗
PubMed2000

Gating and permeation in ion channels formed by gramicidin A and its dioxolane-linked dimer in Na(+) and Cs(+) solutions.

The association of two gramicidin A (gA) peptides via H-bonds in lipid bilayers causes the formation of an ion channel that is selective for monovalent cations only. In this study, two gAs were covalently linked with a dioxolane group (SS dimer). Some functional properties of natural gA channels were compared to that synthetic dimer in Na(+)- or Cs(+)-containing solutions. The SS dimer remained in the open configuration most of the time, while natural gA channels had a relatively brief mean open time. Single channel conductances to Na(+) (g(Na)) or Cs(+) (g(Cs)) in the SS dimer were smaller than in natural gA. However, g(Na) was considerably more attenuated than g(Cs). This probably results from a tight solvation of Na(+) by the dioxolane linker in the SS channel. In Cs(+) solutions, the SS had frequent closures. By contrast, in Na(+) solutions the synthetic dimer remained essentially in the open state. The mean open times of SS channels in different solutions (T(open, Na) > T(open,Cs) > T(open,H)) were inversely proportional to the single channel conductances (g(H) > g(Cs) > g(Na)). This suggests that ion occupancy inside the pore stabilizes the open configuration of the gA dimer. The mean closed time of the SS dimer was longer in Cs(+) than in H(+) solutions. Possible mechanisms for these effects are discussed.

Cesium↗
PubMed2005

Humanization of a recombinant monoclonal antibody to produce a therapeutic HER dimerization inhibitor, pertuzumab.

Dimerization is essential for activity of human epidermal growth factor receptors (HER1/EGFR, HER2/ErbB2, HER3/ErbB3, and ErbB4) and mediates intracellular signaling events leading to cancer cell proliferation, survival, and resistance to therapy. HER2 is the preferred dimerization partner. Activation of HER signaling pathways may be blocked by inhibition of dimer formation using a monoclonal antibody (MAb) directed against the dimerization domain of HER2. The murine MAb 2C4 that specifically binds the HER2 dimerization domain was cloned as a chimeric antibody, humanized using a computer-generated model to guide framework substitutions, and variants were tested as Fabs. Pharmacokinetics and toxicology were evaluated in rodents and cynomolgus monkeys. Cloning the variable domains of MAb 2C4 into a vector containing human kappa and CH1 domains allowed construction of a mouse-human chimeric Fab. DNA sequencing of the chimeric clone permitted identification of CDR residues. The full-length IgG1 of variant F-10 was equivalent in binding to chimeric IgG1 and was designated pertuzumab (rhuMAb 2C4; Omnitarg). Pertuzumab pharmacokinetics was best described by a two-compartment model with a distribution phase of <1 day, terminal half-life of approximately 10 days, and volume of distribution of approximately 40 mL/kg that approximates serum volume. With the exception of diarrhea, pertuzumab was generally well tolerated in cynomolgus monkeys. Pertuzumab, a recombinant humanized IgG1 MAb, is the first of a new class of agents known as HER dimerization inhibitors. Inhibition of HER dimerization may be an effective anticancer strategy in tumors with either normal or elevated expression of HER2.

Animals↗
PubMed2006

Molecular-dynamics simulations of pyronine 6G and rhodamine 6G dimers in aqueous solution.

We have carried out molecular-dynamics (MD) simulations on dimers of the positively charged laser dyes pyronine 6G (P6G) and rhodamine 6G (R6G) in aqueous solution, generating trajectories of 2.5 ns for various computational protocols. We discuss how the choice of atomic partial charges and the length of the trajectories affect the predicted structures of the dimers and compare our results to those of earlier MD-simulations, which were restricted to only 0.7 ns. Our results confirm that monomers of P6G easily undergo relative rotations within the dimer, but we found new conformations of the R6G dimer at longer simulation times. In addition, we analyzed in detail the energy change during the formation of dimers. With suitable corrections, the electrostatic energy from an Ewald treatment agrees with the results from an approach relying on a residue-based cutoff. For P6G, we show that the strong solvent-mediated electrostatic attraction between the monomers is counteracted by an almost equally large solvent-induced entropy contribution to yield a small driving force to dimer formation, in very good agreement with the free-energy change from a thermodynamic-integration procedure. Thus, earlier rationalizations of the dimer formation, based only on energy arguments, yield a qualitatively wrong picture.

Computer Simulation↗