SciCombinator

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Concept: Dimer

178

Activated RAS promotes dimerization of members of the RAF kinase family. ATP-competitive RAF inhibitors activate ERK signalling by transactivating RAF dimers. In melanomas with mutant BRAF(V600E), levels of RAS activation are low and these drugs bind to BRAF(V600E) monomers and inhibit their activity. This tumour-specific inhibition of ERK signalling results in a broad therapeutic index and RAF inhibitors have remarkable clinical activity in patients with melanomas that harbour mutant BRAF(V600E). However, resistance invariably develops. Here, we identify a new resistance mechanism. We find that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kDa variant form of BRAF(V600E), p61BRAF(V600E), which lacks exons 4-8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) shows enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) is expressed endogenously or ectopically, ERK signalling is resistant to the RAF inhibitor. Moreover, a mutation that abolishes the dimerization of p61BRAF(V600E) restores its sensitivity to vemurafenib. Finally, we identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumours of six of nineteen patients with acquired resistance to vemurafenib. These data support the model that inhibition of ERK signalling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identify a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.

Concepts: Gene expression, Transcription factor, Enzyme inhibitor, Dimer, Monomer, Inhibitor, Xanthine oxidase inhibitor, Alternative splicing

170

Cullin E3 ligases are the largest family of ubiquitin ligases with diverse cellular functions. One of seven cullin proteins serves as a scaffold protein for the assembly of the multisubunit ubiquitin ligase complex. Cullin binds the RING domain protein Rbx1/Rbx2 via its C-terminus and a cullin-specific substrate adaptor protein via its N-terminus. In the Cul3 ubiquitin ligase complex, Cul3 substrate receptors contain a BTB/POZ domain. Several studies have established that Cul3-based E3 ubiquitin ligases exist in a dimeric state which is required for binding of a number of substrates and has been suggested to promote ubiquitin transfer. In two different models, Cul3 has been proposed to dimerize either via BTB/POZ domain dependent substrate receptor homodimerization or via direct interaction between two Cul3 proteins that is mediated by Nedd8 modification of one of the dimerization partners. In this study, we show that the majority of the Cul3 proteins in cells exist as dimers or multimers and that Cul3 self-association is mediated via the Cul3 N-terminus while the Cul3 C-terminus is not required. Furthermore, we show that Cul3 self-association is independent of its modification with Nedd8. Our results provide evidence for BTB substrate receptor dependent Cul3 dimerization which is likely to play an important role in promoting substrate ubiquitination.

Concepts: Proteins, Protein, Enzyme, Dimer, Ubiquitin, Ubiquitin ligase, SCF complex, RING finger domain

163

Much physiological and behavioral evidence has been provided suggesting that insect Odorant Binding Proteins (OBPs) are indispensable for odorant recognition and thus appealing targets for structure-based discovery and design of novel host-seeking disruptors. Despite the fact that more than 60 putative OBP-encoding genes have been identified in the malaria vector Anopheles gambiae, the crystal structures of only six of them are known. It is therefore clear that OBP structure determination constitutes the bottle-neck for structure-based approaches to mosquito repellent/attractant discovery. Here, we describe the three dimensional structure of an Anopheles gambiae “Plus-C” group OBP, AgamOBP48, which exhibits the second highest expression levels in female antennae. This structure represents the first example of a 3D domain-swapped dimer in dipteran species. A combined binding site is formed at the dimer interface by equal contribution of each monomer. Structural comparisons with the monomeric AgamOBP47 revealed that the major structural difference between the two “Plus-C” proteins localizes in their N- and C-terminal regions and their concerted conformational change may account for monomer-swapped dimer conversion and, furthermore, the formation of novel binding pockets. Using a combination of gel filtration chromatography, differential scanning calorimetry and analytical ultracentrifugation, we demonstrate the AgamOBP48 dimerization in solution. Eventually, molecular modelling calculations were used to predict the binding mode of the most potent synthetic ligand of AgamOBP48 known so far, discovered by ligand- and structure-based virtual screening. The structure-aided identification of multiple OBP-binders represents a powerful tool to be employed in the effort to control the vector-borne diseases transmission.

Concepts: Protein, Molecular biology, Malaria, Polymer, Chromatography, Dimer, Monomer, Differential scanning calorimetry

158

Amyloid-reactive IgGs isolated from pooled blood of normal individuals (pAbs) have demonstrated clinical utility for amyloid diseases by in vivo targeting and clearing amyloidogenic proteins and peptides. We now report the following three novel findings on pAb conformer’s binding to amyloidogenic aggregates: 1) pAb aggregates have greater activity than monomers (HMW species > dimers > monomers), 2) pAbs interactions with amyloidogenic aggregates at least partially involves unconventional (non-CDR) interactions of F(ab) regions, and 3) pAb’s activity can be easily modulated by trace aggregates generated during sample processing. Specifically, we show that HMW aggregates and dimeric pAbs present in commercial preparations of pAbs, intravenous immunoglobulin (IVIg), had up to ~200- and ~7-fold stronger binding to aggregates of Aβ and transthyretin (TTR) than the monomeric antibody. Notably, HMW aggregates were primarily responsible for the enhanced anti-amyloid activities of Aβ- and Cibacron blue-isolated IVIg IgGs. Human pAb conformer’s binding to amyloidogenic aggregates was retained in normal human sera, and mimicked by murine pAbs isolated from normal pooled plasmas. An unconventional (non-CDR) component to pAb’s activity was indicated from control human mAbs, generated against non-amyloid targets, binding to aggregated Aβ and TTR. Similar to pAbs, HMW and dimeric mAb conformers bound stronger than their monomeric forms to amyloidogenic aggregates. However, mAbs had lower maximum binding signals, indicating that pAbs were required to saturate a diverse collection of binding sites. Taken together, our findings strongly support further investigations on the physiological function and clinical utility of the inherent anti-amyloid activities of monomeric but not aggregated IgGs.

Concepts: Immune system, Antibody, Protein, Glycoproteins, Amyloid, Dimer, Monomer, Intravenous immunoglobulin

29

A novel phenanthrenoid symmetrical dimer 8,8'-bidehydrojuncusol [1,1',6,6'-tetramethyl-5,5'-divinyl-8,8'-biphenanthrene-2,2',7,7'-tetraol], a related phenanthrenoid monomer, a phenolic chromone, and five flavonoids derivatives have been isolated from the halophyte Juncus acutus L., Juncaceae. The structure of the dimeric phenanthrenoid was determined on the basis of spectroscopic analyses, including 2D NMR spectroscopy, and by spectral correlations. The new dimer and the other isolated compounds bearing four phenolic hydroxy groups showed the significant in vitro antioxidant activity comparable with that of ascorbic acid using 2,2'-azino-bis[3-ethylbenzothiazoline-6-sulphonate] (ABTS) radical cation decolourisation assay. On the basis of the results from an in vitro anti-inflammatory assay using lipopolysaccharide-stimulated RAW264.7 macrophage cells linked with immunoblot analysis, it was found that dimerisation of dehydrojuncusol [1,6-dimethyl-5-vinyl-8-phenanthrene-2,7-diol] molecule nearly nullified its inhibitory effect on the expression of the pro-inflammatory inducible nitric oxide synthase (iNOS) protein.

Concepts: Antioxidant, Radical, Dimer, Monomer, Vitamin C, Nitric oxide, Nitric oxide synthase, Juncus acutus

28

The use of single domain antibodies (sdAbs) in place of conventional antibodies for both therapeutic and diagnostic applications continues to grow. SdAbs offer a number of advantages when compared to conventional antibodies such as their small size and low structural complexity which allows them to readily be produced as fusions in a variety formats. In this work we compared the utility of various C-terminal fusions and immobilization strategies for two sdAbs; one which recognizes ricin and the other EA1, an S-layer protein, of Bacillus anthracis. Comparisons were made between direct covalent attachment and affinity immobilization using a biotin-streptavidin interaction for the standard sdAb monomers, randomly and site-specifically biotinylated monomers, and fusion constructs of alkaline phosphatase dimers and streptavidin core tetramers. The sdAb binding and regeneration was evaluated by surface plasmon resonance in a multiplexed format. The construct that provided the highest density of active molecules by at least a factor of two was the sdAb -streptavidin core tetramer, followed by the sdAb-alkaline phosphatase and then the site-specifically biotinylated monomer. The poorest performing immobilization methods were the two most common, direct covalent attachment and the randomly biotinylated sdAb attached via NeutrAvidin. These improvements directly correlated to antigen capture in SPR assays. Similarly, the oriented immobilization method also translated to improvements in limit of detection assays using a bead-based system. The sdAb -streptavidin core provided more than a 100-fold improvement in the limit of detection of EA1, from~200ng/mL to to 1.6ng/mL, while improvement for ricin detection was less but still a significant 5-fold decrease, going from 1.6ng/mL down to 0.32ng/mL. This demonstrated improvement in limits of detection is an advantage that should be transferable to most assay formats.

Concepts: Antibody, Bacteria, ELISA, Dimer, Monomer, Surface plasmon resonance, Single domain antibody, Tetramer

28

The bioavailability of flavanols, anthocyanins and anthocyanin-derived pigments like flavanol-anthocyanin dimers already reported to occur in food products is a major unsolved issue. The absorption of the flavanol-anthocyanin dimer (+)-catechin-(4,8)-malvidin-3-O-glucoside (Cat-Mv3glc) through Caco-2 cells was assessed by performing transepithelial transport assays. The ability of Cat-Mv3glc to cross Caco-2 cells was compared with that of malvidin-3-glucoside (Mv3glc), (+)-catechin (Cat) and procyanidin B3 (Cat-Cat), in order to evaluate the influence of some structural features on the transport efficiency. The flavanol-anthocyanin dimer was absorbed in this intestinal model although with a lower efficiency than the monomers Cat and Mv3glc. On the other hand, Cat-Mv3glc was found to cross the intestinal barrier model more significantly than Cat-Cat. This feature may be related to the presence of the glucose moiety in its structure. Overall, this study brings more insights into the bioavailability of anthocyanins and flavanols and represents the first report on the bioavailability of flavanol-anthocyanins.

Concepts: Protein, Nutrition, Structure, Dimer, Monomer, Acetic acid, Proanthocyanidins, Proanthocyanidin B3

27

Re126W122CuI Pseudomonas aeruginosa azurin incorporates three redox sites, ReI(CO)3(4,7-dimethyl-1,10-phenanthroline) covalently bound at H126, the W122 indole side chain, and CuI, which are well separated in the protein fold: Re-W122(indole) = 13.1 Å; dmp-W122(indole) = 10.0 Å, Re-Cu = 25.6 Å. In view of the long intramolecular Re-Cu distance, it is surprising that CuI is oxidized in less than 50 ns after near-UV excitation of the Re chromophore. Back electron transfer (BET) regenerating CuI and ground-state ReI takes much longer (220 ns and 6 us). We show that these ET reactions occur in protein dimers, (Re126W122CuI)2, which are in equilibrium with unreactive monomers. In support of this interpretation, ET yields and kinetics are concentration-dependent and solution mass spectrometry (LILBID-MS) confirms the presence of a broad oligomer distribution with prevalent monomers and dimers; in the crystal structure, two Re126W122CuII molecules are oriented in such a way that the redox cofactors Re(dmp) and W122-indole belonging to different monomers are located at a protein-protein interface (//), where the intermolecular ET-relevant distances (Re-W122(indole) = 6.9 Å, dmp-W122(indole) = 3.5 Å, and Re-Cu = 14.0 Å) are much shorter than intramolecular ones. We propose that forward ET is accelerated by intermolecular electron hopping through a surface tryptophan: *Re//<-W122<-CuI; our kinetics analysis indicates that an equilibrium (K = 0.8-0.9) between *Re and charge-separated Re(dmp•-)(W122•+), which is established in a few ns, stores part of the excitation energy. The second ET step, intramolecular CuI oxidation, CuI->W122•+, occurs in 30 ns. The system is well coupled for forward ET but not for ReI(dmp•-)->CuII BET. Our work on interfacial electron hopping in (Re126W122CuI)2 sheds new light on redox-unit placements required for functional long-range charge separation in protein complexes.

Concepts: Electron, Redox, Chemical bond, Pseudomonas aeruginosa, Nitrogen, Dimer, Monomer, Electron transfer

27

Doubling up: The direct bio-inspired dimerization of commercially available amine-free tryptophan derivatives in aqueous acidic media provides C2 -symmetrical and nonsymmetrical dimeric compounds. Further processing completes the concise syntheses of naturally occurring dimeric diketopiperazine alkaloids such as (+)-WIN 64821 in overall yields of up to 20 %.

Concepts: Dimer

25

The K-, N-, and HRas small GTPases are key regulators of cell physiology and are frequently mutated in human cancers. Despite intensive research, previous efforts to target hyperactive Ras based on known mechanisms of Ras signaling have been met with little success. Several studies have provided compelling evidence for the existence and biological relevance of Ras dimers, establishing a new mechanism for regulating Ras activity in cells additionally to GTP-loading and membrane localization. Existing data also start to reveal how Ras proteins dimerize on the membrane. We propose a dimer model to describe Ras-mediated effector activation, which contrasts existing models of Ras signaling as a monomer or as a 5-8 membered multimer. We also discuss potential implications of this model in both basic and translational Ras biology.

Concepts: DNA, Protein, Biology, Cell biology, Avicenna, Dimer, Monomer, Small GTPase