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Oxidation state dependence of the geometry, electronic structure, and magnetic coupling in mixed oxo- and carboxylato-bridged manganese dimers.

Approximate density functional theory has been used to investigate changes in the geometry and electronic structure of the mixed oxo- and carboxylato-bridged dimers [Mn(2)(mu-O)(2)(O(2)CH)(NH(3))(6)](n+)and [Mn(2)(mu-O)(O(2)CH)(2)(NH(3))(6)](n+)in the Mn(IV)Mn(IV), Mn(III)Mn(IV), and Mn(III)Mn(III) oxidation states. The magnetic coupling in the dimer is profoundly affected by changes in both the bridging ligands and Mn oxidation state. In particular, change in the bridging structure has a dramatic effect on the nature of the Jahn-Teller distortion observed for the Mn(III) centers in the III/III and III/IV dimers. The principal magnetic interactions in [Mn(2)(mu-O)(2)(O(2)CH)(NH(3))(6)](n+)() involve the J(xz/xz)and J(yz/yz) pathways but due to the tilt of the Mn(2)O(2) core, they are less efficient than in the planar di-mu-oxo structure and, consequently, the calculated exchange coupling constants are generally smaller. In both the III/III and III/IV dimers, the Mn(III) centers are high-spin, and the Jahn-Teller effect gives rise to axially elongated Mn(III) geometries with the distortion axis along the Mn-O(c) bonds. In the III/IV dimer, the tilt of the Mn(2)O(2) core enhances the crossed exchange J(x)()()2(-)(y)()()2(/)(z)()()2 pathway relative to the planar di-mu-oxo counterpart, leading to significant delocalization of the odd electron. Since this delocalization pathway partially converts the Mn(IV) ion into low-spin Mn(III), the magnetic exchange in the ground state can be considered to arise from two interacting spin ladders, one is the result of coupling between Mn(IV) (S = 3/2) and high-spin Mn(III) (S = 2), the other is the result of coupling between Mn(IV) (S = 3/2) and low-spin Mn(III) (S = 1). In [Mn(2)(mu-O)(O(2)CH)(2)(NH(3))(6)](n+)(), both the III/III dimer and the lowest energy structure for the III/IV dimer involve high-spin Mn(III), but the Jahn-Teller axis is now orientated along the Mn-oxo bond, giving rise to axially compressed Mn(III) geometries with long Mn-O(c) equatorial bonds. In the IV/IV dimer, the ferromagnetic crossed exchange J(yz)()(/)(z)()()2 pathway partially cancels J(yz/yz) and, as a consequence, the antiferromagnetic J(xz/xz) pathway dominates the magnetic coupling. In the III/III dimer, the J(yz/yz) pathway is minimized due to the smaller Mn-O-Mn angle, and since the ferromagnetic J(yz)()(/)(z)()()2 pathway largely negates J(xz/xz), relatively weak overall antiferromagnetic coupling results. In the III/IV dimer, the structures involving high-spin and low-spin Mn(III) are almost degenerate. In the high-spin case, the odd electron is localized on the Mn(III) center, and the resulting antiferromagnetic coupling is similar to that found for the IV/IV dimer. In the alternative low-spin structure, the odd electron is significantly delocalized due to the crossed J(yz)()(/)(z)()()2 pathway, and cancellation between ferromagnetic and antiferromagnetic pathways leads to overall weak magnetic coupling. The delocalization partially converts the Mn(IV) ion into high-spin Mn(III), and consequently, the spin ladders arising from coupling of Mn(IV) (S = 3/2) with high-spin (S = 2) and low-spin (S = 1) Mn(III) are configurationally mixed. Thus, in principle, the ground-state magnetic coupling in the mixed-valence dimer will involve contributions from three spin-ladders, two associated with the delocalized low-spin structure and the third arising from the localized high-spin structure.

Journal Article↗

A new class of bradykinin antagonists: synthesis and in vitro activity of bissuccinimidoalkane peptide dimers.

A systematic study on the dimerization of the bradykinin (BK) antagonist D-Arg0-Arg1-Pro2-Hyp3-Gly4-Phe5-Ser6-D-Phe 7-Leu8-Arg9 has been performed. The first part of this study involved compounds wherein dimerization was carried out by sequentially replacing each amino acid with cysteine and cross-linking with bismaleimidohexane. The second part of this study utilized a series of bissuccinimidoalkane dimers wherein the intervening methylene chain was varied systematically from n = 2 to n = 12 while the point of dimerization was held constant at position 6. The biological activities of these dimers were then evaluated on BK-induced smooth muscle contraction in two different isolated tissue preparations: guinea pig ileum (GPI) and rat uterus (RU). Several of the dimeric BK antagonists displayed remarkable activities and long durations of action. In addition, dimerization at position 4, 7, 8, or 9 produced dimeric analogues with markedly reduced potency. Rank order of antagonist potency as a function of dimerization position is as follows: rat uterus, 6 greater than 5 greater than 0 greater than 2 greater than 1 greater than 3 much greater than 4, 7, 8, 9; guinea pig ileum, 6 greater than 5 greater than 3 greater than 2 greater than 1 greater than 0 much greater than 4, 7, 8, 9. Evaluation of the linker length as represented by the number of methylene units indicated an optimal distance between the two monomeric peptides of six to eight methylene moieties. These studies also revealed that the carbon-chain length significantly affected the duration of action in vitro and resulted in partial agonism effects when n greater than 8. The optimum activity in vitro was achieved with dimerization at position 6 and n = 6 (designated herein as compound 25; alternatively, CP-0127). Similar effects in potency were also seen when the monomeric antagonist D-Arg0-Arg1-Pro2-Hyp3-Gly4-Phe5-Ser6-D-Phe 7-Phe8-Arg9 (NPC-567) was dimerized using similar chemistry. These results suggest that the development of BK antagonists of significant therapeutic potential may be possible using a dimerization strategy that can overcome the heretofore limiting problems of potency and in vivo duration of action found with many of the BK antagonists in the literature.

Amino Acid Sequence↗

Functional differences between dimeric and octameric mitochondrial creatine kinase.

Mitochondrial creatine kinase (Mi-CK) consists of octameric and dimeric molecules that are interconvertible. In the present study, the kinetic properties of purified chicken heart Mi-CK (Mib-CK) dimers and octamers were investigated separately under highly controlled conditions. Gel-permeation chromatography was performed before and after kinetic measurements in order to clearly define the proportions of octamers and dimers. 'Dimeric' Mi-CK solutions consisted of > or = 90% dimers throughout the experiment whereas 'octameric' Mi-CK solutions consisted in the beginning of 90% octamers, but upon measuring with the highest concentrations of creatine (Cr) and ATP approximately one-third of the octamers dissociated into dimers. These proper controls enabled us to pinpoint the observed kinetic differences between dimers and octamers solely to the oligomeric state of Mib-CK. Both dimeric and octameric Mi-CK displayed synergism in substrate binding (Kd values are higher than Km values), meaning that binding of the first substrate facilities subsequent binding of the second substrate. Most interestingly, Km(Cr) and Kd(Cr) values are both 2-3 times higher for octameric than for dimeric Mi-CK. Thus, at low Cr concentrations, the dimer is kinetically favoured for the forward direction of the reaction (phosphorylcreatine synthesis) compared with the octamer. The possible physiological significance of the lower Kd(Cr) value of dimeric versus octameric Mib-CK, as well as the apparent negative cooperativity of ATP binding at higher [Cr], are discussed within the context of a possible functional role for dimeric Mib-CK in vivo.

Animals↗

Validity of D-dimer tests in the diagnosis of deep vein thrombosis: a prospective comparative study of three quantitative assays.

OBJECTIVES: To assess the diagnostic reliability of a new quantitative D-dimer assay (VIDAS New) and an established quick test (Nycocard D-dimer assay) in the diagnosis of deep vein thrombosis (DVT) compared with ultrasonography. A third assay (Auto Dimer) became available during sample collection and has been included in the final assessment. The diagnostic performance of the Auto Dimer assay was evaluated on three different coagulation analysers. DESIGN: A clinical prospective study of patients admitted to hospital for evaluation of DVT. Setting. The admission ward at Aalborg Hospital. Subjects. A total of 113 outpatients with suspected DVT. Main outcome measures. Compression ultrasonography was used as the reference method for a diagnosis of DVT and compared with different D-dimer assays. The results were expressed as sensitivity, specificity, positive predictive value and negative predictive value (NPV). RESULTS: Deep vein thrombosis was established in 49 patients (43%). Two D-dimer assays (VIDAS New and Auto Dimer) showed sensitivities of 90 and 88%, specificities of 42 and 44%, and NPV's of 85 and 83%, respectively. The Nycocard D-dimer assay showed a sensitivity of 63%, specificity of 67% and NPV of 71%. CONCLUSIONS: The diagnostic performance of VIDAS New and the Auto Dimer D-dimer assays is almost identical, but this study suggests that neither of the D-dimer assays is suitable as the only screening method for DVT, in a situation with a high pretest probability of DVT. This call for a differential strategy that distinguishes between cases of low and high clinical probability using either a D-dimer test or ultrasonography. Abbreviations DVT, deep venous thrombosis, NPV, negative predictive value, PPV, positive predictive value

Adult↗

The use of a D-dimer assay in patients undergoing CT pulmonary angiography for suspected pulmonary embolus.

PURPOSE: To assess the ability of a semi-quantitative latex agglutination D-dimer test Accuclot with bedside measurements of arterial oxygen saturation, respiratory and cardiac rates to exclude pulmonary embolism (PE) on computed tomographic pulmonary angiography (CTPA). MATERIALS AND METHODS: All patients referred to our CT unit for investigation of suspected acute pulmonary embolism were enrolled. Pulse oximetery, respiratory rate, heart rate and blood sampling for D-dimer testing were carried out just before CT. A high resolution CT (HRCT) of the chest was followed by a CT pulmonary angiogram (CTPA). The images were independently interpreted at a workstation with cine-paging and 2D reformation facilities by three consultant radiologists blinded to the clinical and laboratory data. If positive, the level of the most proximal embolus was recorded. Discordant imaging results were re-read collectively and consensus achieved. RESULTS: A total of 101 patients were enrolled. The CTPA was positive for PE in 28/101 (28%). The D-dimer was positive in 65/101 (65%). Twenty-six patients had a positive CT and positive D-dimer, two a positive CT but negative D-dimer, 39 a negative CT and positive D-dimer, and 34 a negative CT and negative D-dimer. The negative predictive value of the Accuclot D-dimer test for excluding a pulmonary embolus on spiral CT was 0.94. Combining the D-dimer result with pulse oximetry (normal SaO2 > or = 90%) improved the negative predictive value to 0.97. CONCLUSION: A negative Accuclot D-dimer assay proved highly predictive for a negative CT pulmonary angiogram in suspected acute pulmonary embolus. If this D-dimer assay were included in the diagnostic algorithm of these patients a negative D-dimer would have unnecessary CTPA rendered in 36% of patients.

Acute Disease↗

Measurement of plasma fibrin D-dimer levels with the use of a monoclonal antibody coupled to latex beads.

Recently, monoclonal antibody (DD-3B6) to fibrin D-dimer was prepared and coupled to latex beads to provide a specific test (Dimertest) for fibrinolysis. The purpose of this study was to evaluate the Dimertest assay as a clinical laboratory test for the measurement of plasma fibrin D-dimer derivatives. The Dimer-test assay specifically detected 2 micrograms/mL of purified fibrin D-dimer or fibrin D-dimer/fragment E complex added to afibrinogenemic plasma but did not detect 500 micrograms/mL of either fibrinogen fragments X, D, E, or 160 micrograms/mL cross-linked fibrinogen. The fibrin(ogen) degradation product (FDP) assays of American Dade or Wellcome Diagnostics detected 5.0 micrograms/mL of fibrin D-dimer and from 1 to 10 micrograms/mL of the other FDPs. Twenty-eight percent of 150 random plasma samples assayed from hospitalized patients were positive for fibrin D-dimer derivatives. Plasma samples from 152 patients suspected of having disseminated intravascular coagulation (DIC) were assayed for serum FDP (Wellcome Diagnostics) and plasma fibrin D-dimer derivatives. Samples from 69% of patients with serum FDP levels less than 10 micrograms/mL, and more than 90% of those with serum FDP levels greater than 10 micrograms/mL, were positive for fibrin D-dimer derivatives. Dimertest results were not modified by heparin, streptokinase, freeze-thawing, or clotting plasma. Serum fibrinogen-related antigens were immunoadsorbed from Dimer-test positive sera by anti-fibrinogen antibody and formalin-fixed Cowan I strain Staphylococcus aureus. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and protein blotting with the use of monoclonal antibody DD-3B6 demonstrated a protein band with similar mobility to purified D-dimer. The measurement of plasma fibrin D-dimer derivatives by the Dimertest assay is a rapid, sensitive, and specific laboratory test for fibrinolysis. The Dimertest assay has proven to be a useful addition to the clinical laboratory and should be helpful in the diagnosis and management of patients with diseases associated with fibrinolysis.

Antibodies, Monoclonal↗

Age, functional status, and racial differences in plasma D-dimer levels in community-dwelling elderly persons.

BACKGROUND: Dysregulation of immunologic and coagulation systems is common in elderly persons and is associated with many diseases of aging. Thrombotic events are a major cause of morbidity and mortality in the elderly population. This study assesses whether D-dimer, a marker of fibrinolytic activity, varies systematically by demographic, health, and functional measures, and derives a prediction model for factors related to D-dimer in a sample of community-dwelling elderly persons. METHODS: D-dimer levels were assessed in a random sample of 1,727 community-dwelling elderly persons from five rural and urban counties in North Carolina in 1992, as part of the Established Populations for the Epidemiologic Studies of the Elderly (Duke University). All subjects were 72 years or older at the time of the blood draw. In addition, all subjects were surveyed yearly by telephone or in person each year from 1986 to 1992 for a variety of health, functional, and social factors. Levels of D-dimer in 1992 were related cross-sectionally to demographics (age, race, education, income, gender, smoking), function (Nagi, Rosow-Breslau, Katz, Older Americans Resources and Services procedures instrumental activities of daily living), life satisfaction and self-rated health, self-reported diseases (heart attack, cancer, stroke, diabetes, and hypertension), and weight change from 1986 to 1992. RESULTS: D-dimer levels increased with increasing age and functional disability. Among the health variables, only high blood pressure was predictive of D-dimer level. D-dimer levels were dramatically higher in blacks. Blacks were nearly four times more likely to have an extreme value of D-dimer (>600 microg/l) than whites when high D-dimer (yes/no) was analyzed, and blacks had an average level that was nearly 40% higher than whites in analyses of the continuous version of the outcome. This racial effect was not substantively affected in multivariable analyses with demographic and socioeconomic variables controlled. Race, age, functional status, current smoking, high blood pressure, and weight loss were related to level of D-dimer, and race, age, and functional status were related to the presence of a high D-dimer level (in the top 10% of the sample). CONCLUSIONS: Black, older, and functionally impaired persons had significantly higher levels of D-dimer in this sample of community-dwelling elderly persons. The findings for race were particularly striking and persisted even after controlling for smoking and other factors known to be related to thrombosis and were not mediated by social factors. This result may contribute to our understanding of the increased levels of thrombotic events found in these groups.

Aged↗

High preoperative plasma D-dimer level is associated with advanced tumor stage and short survival after curative resection in patients with colorectal cancer.

BACKGROUND: An elevated plasma D-dimer level indicates activation of coagulation and fibrinolysis. Previous studies demonstrated that the preoperative plasma D-dimer level correlates with tumor stage in patients with colorectal cancer. This study examined the relationship between preoperative plasma D-dimer level and both pathological findings and TNM classification and examined the prognostic significance of preoperative plasma D-dimer level. METHODS: Preoperative plasma D-dimer levels were measured in 93 patients who underwent curative resection of colorectal cancer and 40 patients with benign colorectal diseases other than inflammatory bowel disease. The results were analyzed for correlations between preoperative plasma D-dimer levels in patients with colorectal cancer and pathological findings, TNM classification and postoperative survival. RESULTS: Preoperative plasma D-dimer levels were significantly higher in patients with colorectal cancer than in patients with benign colorectal diseases. Plasma D-dimer levels were higher in patients with tumors that were relatively large, had relatively deep wall penetration and were at a relatively advanced TNM stage. Higher preoperative plasma D-dimer levels were significantly associated with shorter postoperative overall survival. Results of analysis with a multivariate proportional hazard model suggested that preoperative plasma D-dimer level was the third strongest prognostic factor; exceeded in importance only by lymph node status and preoperative carcinoembryonic antigen level. CONCLUSIONS: Elevated plasma D-dimer levels in patients with colorectal cancer are associated with relatively advanced tumor stage and short postoperative survival after curative resection. It appears that measurement of preoperative D-dimer level would be useful in the preoperative diagnosis of tumor stage and prediction of postoperative survival.

Colectomy↗

Dimerization of human immunodeficiency virus (type 1) RNA: stimulation by cations and possible mechanism.

The retroviral genome consists of two identical RNA molecules joined close to their 5' ends by the dimer linkage structure. Recent findings indicated that retroviral RNA dimerization and encapsidation are probably related events during virion assembly. We studied the cation-induced dimerization of HIV-1 RNA and results indicate that all in vitro generated HIV-1 RNAs containing a 100 nucleotide domain downstream from the 5' splice site are able to dimerize. RNA dimerization depends on the concentration of RNA, mono- and multivalent cations, the size of the monovalent cation, temperature, and pH. Up to 75% of HIV-1 RNA is dimeric in the presence of spermidine. HIV-1 RNA dimer is fairly resistant to denaturing agents and unaffected by intercalating drugs. Antisense HIV-1 RNA does not dimerize but heterodimers can be formed between HIV-1 RNA and either MoMuLV or RSV RNA. Therefore retroviral RNA dimerization probably does not simply proceed through mechanisms involving Watson-Crick base-pairing. Neither adenine and cytosine protonation, nor quartets containing only guanines appear to determine the stability of the HIV-1 RNA dimer, while quartets involving both adenine(s) and guanine(s) could account for our results. A consensus sequence PuGGAPuA found in the putative dimerization-encapsidation region of all retroviral genomes examined may participate in the dimerization process.

Avian Sarcoma Viruses↗

Nucleocapsid protein 10 activates dimerization of the RNA of Moloney murine leukaemia virus in vitro.

Short RNA species that encompass the psi domain of the retroviral genome spontaneously form dimers in vitro, and the retroviral nucleocapsid protein activates this dimerization in vitro. Addition of gag RNA sequences downstream of the 3' end of the psi domain decreases the level of spontaneous dimerization. Here, we report the effects of RNA length on dimerization in vitro, studied with RNA fragments from Moloney murine leukaemia virus that contain the psi domain and all or part of the gag sequence. Extension of the RNA leads to progressive inhibition of the in vitro dimerization process. Sequences located downstream of the 3' end of the psi domain seem to stabilize the monomeric structures. This stabilization participates in dimerization of the RNA sequences involved in the recognition of two RNA molecules. We studied the ability of nucleocapsid protein 10 to promote dimerization of such long RNA fragments, and found that the protein greatly enhances their dimerization in vitro. We propose that nucleocapsid protein 10 stimulates the overall dimerization process by reduction of the energy barrier that must be overcome to allow dimer formation. Our results show that dimerization of RNA form Moloney murine leukaemia virus in vitro is enhanced by nucleocapsid protein 10. This finding is in agreement with the involvement of the nucleocapsid protein in RNA dimerization in vivo.

Base Sequence↗

Beta gamma dimers of G proteins inhibit atrial muscarinic K+ channels.

It has been proposed that beta gamma dimers of signal-transducing G proteins mediate muscarinic activation of atrial K+ channels. We examined this hypothesis by testing the effects of beta gamma dimers from four sources (human erythrocytes, human placenta, bovine brain, and bovine retina) on single channel muscarinic K+ (K+[acetylcholine (ACh)]) currents in inside-out membrane patches of adult guinea pig atria. None of the four beta gamma dimer preparations stimulated K+[ACh] currents; on the contrary, each inhibited the currents whether the currents were activated with GTP alone (agonist-independent activity) or with GTP plus a muscarinic agonist (agonist-dependent activity). Detergents at concentrations used to suspend erythrocyte, brain, and placental beta gamma dimers had no effect by themselves, and detergents were not used with the retinal beta gamma dimers. We conclude that beta gamma dimers do not mediate stimulatory effects of the endogenous G protein that regulates the K+ channels. In fact beta gamma dimers appear to inhibit activation by the endogenous G alpha subunits. Further insight into the role of beta gamma dimers came from the observation that agonist-independent GTP-activated K+[ACh] currents were inhibited by beta gamma dimers at about one-tenth the concentration required to inhibit agonist-dependent activation. One possibility is that dimeric beta gamma may have a higher affinity for free alpha subunits than for alpha subunits associated with agonist-occupied receptors. Thus, in addition to the known requirement of beta gamma dimers for the interaction of alpha subunits with receptors, beta gamma dimers may also improve the signal-to-noise ratio for agonists by reducing agonist-independent background activities.

Acetylcholine↗

A view of the human idiotypic repertoire. Electron microscopic and immunologic analyses of spontaneous idiotype-anti-idiotype dimers in pooled human IgG.

It has previously been reported that up to 40% of the molecules of human IgG from pooled plasma (100,000 donations) spontaneously dimerize, whereas IgG prepared from a single donor contains only trace quantities of dimer. We have conducted immunoelectron microscopic analyses on such samples and have verified that the majority of dimers are composed of complexes in which two arms of each molecule are bound in a reciprocal fashion at or near the distal tips of their respective arms as previously seen in bona fide Id-anti-Id complexes. A significant role for Fc was ruled out by showing the formation of dimeric ring structures in purified F(ab')2 samples. Spontaneous dimerization was also observed in pooled bovine or mouse IgG, but not in that from single animals. Radiolabeled monomeric, single donor human IgG was used as a probe to investigate dimer formation; this material readily codimerized with IgG from other donors or from pooled plasma (either human or bovine), but did not dimerize with IgG from the same donor. Subclass analysis of multiple donor human IgG revealed that the most flexible subclass (IgG3) was overrepresented in the dimer fraction, whereas one of the less flexible subclasses (IgG2) was underrepresented. Although IgG2 could dimerize to some extent with IgG of other subclasses, it could not self-dimerize. These data suggest that structural constraints (hinge flexibility) may play a role in limiting dimerization. This suspicion was confirmed by showing that an additional 15.5% of the monomeric IgG fraction from a multidonor sample could dimerize after a chemically induced increase in hinge flexibility. Our results are interpreted to show that, although the number of functionally distinct Id produced by a species is immense, it is nontheless finite. Moreover, the Id repertoire of an individual is much smaller than that of the species. Pooling the IgG from a number of individuals increases the Id diversity, which increases the chance that any given Id-bearing molecular will encounter a complementary partner.

Alkylation↗

Enhanced pyrimidine dimer removal in repair-proficient murine fibroblasts transformed with the denV gene of bacteriophage T4.

The denV gene of bacteriophage T4, which encodes the pyrimidine dimer-specific repair enzyme endonuclease V, was introduced into murine fibroblasts with normal rodent pyrimidine dimer repair capabilities. Endonuclease V recognizes ultraviolet radiation (UVR)-induced pyrimidine dimers and produces single-strand breaks adjacent to the dimers. These nicks may serve as substrates to initiate excision repair of pyrimidine dimers by endogenous enzymes. In the present study, murine fibroblasts stably transfected with denV were able to remove 50-80% of UVR-induced pyrimidine dimers, while control cells removed only about 20% of dimers under the same conditions of pyrimidine dimer induction and repair. For both control and denV-transfected cells, repair continued for at least 24 h after exposure. When removal of UVR-induced photoproducts was initiated by endogenous excision repair mechanisms, an average of 38 nucleotides were replaced per dimer removed, as determined by bromouracil photolysis; denV-initiated excision repair, on the other hand, resulted in removal of an average of 6 nucleotides per dimer repaired. The enhanced pyrimidine dimer repair capabilities conferred by denV gene expression did not appear to improve post-UVR survival.

Animals↗

Effects of dimerization on protein electron transfer.

In order to investigate the relationship between the rate of protein-protein electron transfer and the structure of the association complex, a dimer of the blue copper protein azurin was constructed and its electron exchange properties were determined. For this purpose, a site for covalent cross-linking was engineered by replacing the surface-exposed asparagine 42 with a cysteine. This mutation enabled the formation of disulfide-linked homo-dimers of azurin. Based on NMR line-broadening experiments, the electron self-exchange (e.s.e.) rate constant for this dimer was determined to be 4.2(+/-0.7) x 10(5)M(-1)s(-1), which is a seven-fold decrease relative to wild-type azurin. This difference is ascribed to a less accessible hydrophobic patch in the dimer. To discriminate between intramolecular electron transfer within a dimer and intermolecular electron transfer between two dimers, the e.s.e. rate constant of (Cu-Cu)-N42C dimers was compared with that of (Zn-Cu)- and (Ag-Cu)-N42C dimers. As Zn and Ag are redox inactive, the intramolecular electron transfer reaction in these latter dimers can be eliminated. The e.s.e. rate constants of the three dimers are the same and an upper limit for the intramolecular electron transfer rate of 10 s(-1) could be determined. This rate is compatible with a Cu-Cu distance of 18 A or more, which is larger than the Cu - Cu distance of 15 A observed in the wild-type crystal structure that shows two monomers that face each other with opposing hydrophobic patches. Modelling of the dimer shows that the Cu-Cu distance should be in the range of 17 A < rCu-Cu < 28 A, which is in agreement with the experimental findings. For efficient electron transfer, it appears crucial that the two molecules interact in the proper orientation. Direct cross-linking may disturb the formation of such an optimal electron transfer complex.

Algorithms↗

Active dimer of Epratuzumab provides insight into the complex nature of an antibody aggregate.

Understanding the intermolecular products of antibodies as a consequence of host-cell expression, aging, and heat-stress can be insightful especially when it involves the development of a stable biopharmaceutical product. The dimerized form of Epratuzumab (an IgG(1) antibody) with a molecular mass of approximately 300 kDa (twice the monomer antibody molecular weight of approximately 150 kDa) was examined to gain a better perspective of its properties pertaining to structure and activity. The nascent dimer was shown to partially dissociate upon incubation at 30 degrees C and 37 degrees C, exhibit no discernable alteration of structure (i.e., secondary or tertiary structure based on CD and 2nd derivative UV spectroscopy), have approximately 70% covalent forms (based upon CE-SDS results) and manifest twofold higher activity relative to the active monomer form (on a weight basis the dimer and monomer have equal activity). Interestingly, these properties were not attributed to a single dimer species, but rather to a more complex dimer assembly. The Epratuzumab dimer was digested with papain to reveal three uniquely dimerized aggregates. The relative molar distribution of Fab:Fab, Fc:Fc, and Fab:Fc was found to be 4:3:8, respectively. The data suggest that all three predominantly covalent dimer adducts are capable of full activity, shedding light on their complex nature and showing that their target specificity was unaltered. ESI-MS data indicated the presence of remnant levels of noncovalent dimers for all three dimerized forms. Material aged at 37 degrees C exhibited a similar papain digest molar distribution of the three dimerized forms, except with enhanced chemical heterogeneity and an increase in covalent forms to approximately 84%.

Antibodies, Monoclonal↗

Characterization of dimeric ATP synthase and cristae membrane ultrastructure from Saccharomyces and Polytomella mitochondria.

There is increasing evidence now that F(1)F(0) ATP synthase is arranged in dimers in the inner mitochondrial membrane of several organisms. The dimers are also considered to be the building blocks of oligomers. It was recently found that the monomers in beef and the alga Polytomella ATP synthase dimer make an angle of approximately 40 degrees and approximately 70 degrees, respectively. This arrangement is considered to induce a strong local bending of the membrane. To further understand the packing of dimers into oligomers we performed an electron microscopy analysis of ATP synthase dimers purified from Saccharomyces cerevisiae. Two types of dimers were found in which the angle between the monomers is either approximately 90 degrees or approximately 35 degrees. According to our interpretation, the wide-angle dimers (70-90 degrees) are "true-dimers" whereas the small-angle dimers (35-40 degrees) rather are "pseudo-dimers", which represent breakdown products of two adjacent true dimers in the oligomer. Ultrathin sectioning of intact Polytomella mitochondria indicates that the inner mitochondrial or cristae membrane is folded into lamellae and tubuli. Oligomers of ATP synthase can arrange in a helical fashion in tubular-shaped cristae membranes. These results strongly support the hypothesized role of ATP synthase oligomers in structural determination of the mitochondrial inner membrane.

Dimerization↗

An algebra of dimerization and its implications for G-protein coupled receptor signaling.

Many species of receptors form dimers, but how can we use this information to make predictions about signal transduction? This problem is particularly difficult when receptors dimerize with many different species, leading to a combinatoric increase in the possible number of dimer pairs. As an example system, we focus on receptors in the G-protein coupled receptor (GPCR) family. GPCRs have been shown to reversibly form dimers, but this dimerization does not directly affect signal transduction. Here we present a new theoretical framework called a dimerization algebra. This algebra provides a systematic and rational way to represent, manipulate, and in some cases simplify large and often complicated networks of dimerization interactions. To compliment this algebra, Monte Carlo simulations are used to predict dimerization's effect on receptor organization on the membrane, signal transduction, and internalization. These simulation results are directly comparable to various experimental measures such as fluorescence resonance energy transfer (FRET), and as such provide a link between the dimerization algebra and experimental data. As an example, we show how the algebra and computational results can be used to predict the effects of dimerization on the dopamine D2 and somatastatin SSTR1 receptors. When these predictions were compared to experimental findings from the literature, good agreement was found, demonstrating the utility of our approach. Applications of this work to the development of a novel class of dimerization-modulating drugs are also discussed.

Animals↗

Evidence of a thermal unfolding dimeric intermediate for the Escherichia coli histone-like HU proteins: thermodynamics and structure.

The Escherichia coli histone-like HU protein pool is composed of three dimeric forms: two homodimers, EcHUalpha(2) and EcHUbeta(2), and a heterodimer, EcHUalphabeta. The relative abundance of these dimeric forms varies during cell growth and in response to environmental changes, suggesting that each dimer plays different physiological roles. Here, differential scanning calorimetry and circular dichroism (CD) were used to study the thermal stability of the three E.coli HU dimers and show that each of them has its own thermodynamic signature. Unlike the other HU proteins studied so far, which melt through a single step (N(2)<-->2D), this present thermodynamic study shows that the three E.coli dimers melt according to a two-step mechanism (N(2)<-->I(2)<-->2D). The native dimer, N(2), melts partially into a dimeric intermediate, I(2), which in turn yields the unfolded monomers, D. In addition, the crystal structure of the EcHUalpha(2) dimer has been solved. Comparative thermodynamic and structural analysis between EcHUalpha(2) and the HU homodimer from Bacillus stearothermophilus suggests that the E.coli dimer is constituted by two subdomains of different energetic properties. The CD study indicates that the intermediate, I(2), corresponds to an HU dimer having partly lost its alpha-helices. The partially unfolded dimer I(2) is unable to complex with high-affinity, single-stranded break-containing DNA. These structural, thermodynamic and functional results suggest that the N(2)<-->I(2) equilibrium plays a central role in the physiology of E.coli HU. The I(2) molecular species seems to be the EcHUbeta(2) preferential conformation, possibly related to its role in the E.coli cold-shock adaptation. Besides, I(2) might be required in E.coli for the HU chain exchange, which allows the heterodimer formation from homodimers.

Amino Acid Sequence↗