Domain structure and antiparallel dimers of microtubule-associated protein 2 (MAP2).

We have studied the microtubule-associated protein MAP2 from porcine brain and its subfragments by limited proteolysis, antibody labeling, and electron microscopy. Two major chymotryptic fragments start at lys 1528 and arg 1664, generating microtubule-binding fragments of Mr 36 kDa (303 residues, analogous to the "assembly domain" of Vallee, 1980) and 18 kDa (167 residues). These fragments can be labeled with the antibody 2-4 which recognizes the last internal repeat of MAP2 (Dingus et al., 1991). The epitope of another monoclonal antibody, AP18 (Binder et al., 1986), was mapped to the first 151 residues of MAP2. The interaction with AP18 is phosphorylation dependent; dephosphorylated MAP2 is not recognized. Intact MAP2 forms rod-like particles of 97 nm mean length, similar to Gottlieb and Murphy's (1985) observations. Both antibodies bind near an end of the rod, suggesting that the sequence and the structure are approximately colinear. There is a pronounced tendency for MAP2 to form dimers whose components are nearly in register but of opposite polarity. MAP2 can also fold in a hairpin-like fashion, generating 50-nm rods, and it can self-associate into oligomers and fibers. The 36-kDa microtubule-binding fragment also has a rod-like shape; its mean length is 49 nm, half of the intact molecule, even though the fragment contains only one-sixth of the mass. The antibody 2-4 decorates one end of the rod, similar to the intact protein. The fragment also forms antiparallel dimers, but its tendency for higher self-assembly forms is much lower than with intact MAP2.     

The single source preparation of rod-like mercury sulfide nanostructures via hydrothermal method

High-quality and high-yield rod-like HgS dendrites with cubic structure was synthesized by a wet chemical route, without using any surfactant and organic solvents at 180 °C for 5 h, by using Hg(NO₃)₂·H₂O and thioglycolic acid (TGA) as starting reagents. The obtained HgS with different morphologies and sized were characterized by Fourier transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive X-ray analysis (EDX), and X-ray diffraction (XRD). The effects of reaction parameters, such as temperature, precursor concentration and reaction time on the morphology and particle size of products were investigated. Our experimental results showed that temperature reaction played key role in the final morphology of HgS. The morphology of HgS nanostructures could be changed from rod-like dendrites to nanoparticles by only decreased temperature reaction to 110 °C. In the present study the possible mechanism of HgS nanoparticles growth to dendrites in the aqueous solution was also discussed and the optical properties rod-like HgS dendrites were investigated by ultraviolet-visible (UV-Vis) spectroscopy.     

Solution scattering studies of dimeric and tetrameric spectrin

The structure of spectrin dimers and tetramers in solution has been examined by light, low-angle X-ray and neutron scattering. The results show a good correspondence between the solution dimensions of these molecules and their appearance in the electron microscope after shadowing. The scattering profiles are not compatible with an extended rod-like character, but reflect the presence of a considerable degree of bending. The radii of gyration of the dimer and tetramer were determined to be 170 and 375 Å and the cross-section radii of gyration 14 and 12.3 Å. respectively. Both are thus long. thin. rather bent molecules, and the tetramer is twice the length of the dimer.     

Effect of 1-n-Decylimidazole on Gibberellin Biosynthesis in Tan-ginbozu,a Dwarf Variety of Rice

Previous structural studies of less-polar dimers in autoxidized methyl linoleate (ML) have been extended to polar dimers. After isolation by successive silicic acid and gel permeation chromatography, the dimeric fraction of linoleate was separated into two major fractions, A₁ and A₂, according to their polarities. The polar dimers (A₁) were further fractionated by HPLC either directly or after reduction with triphenyl phosphine on a micro silica column. Isolated subfractions were characterized by UV, IR, GC-MS and FD-MS after suitable derivatizations. FD-MS of all these dimers showed a molecular ion peak which corresponds to 2 × ML + 6 × O and the reduction of each subfraction with stannous chloride gave equimolar amounts of 9 and 13-hydroxy octadecadienoate, and 9, 10, 13 and/or 9, 12, 13-trihydroxy octadecenoate. These results combined with others show that the A₁ dimers are composed of isomeric mixtures containing a peroxide bridge linking a methyl octadecadienoate and a 9, 12 and/or 10, 13-dihydroperoxy octadecenoate across C-9 and/or 13 on each of them.     

Molecular organization and dynamics of the melatonin MT1 receptor/RGS20/Gi protein complex reveal asymmetry of receptor dimers for RGS and Gi coupling

Functional asymmetry of G‐protein‐coupled receptor (GPCR) dimers has been reported for an increasing number of cases, but the molecular architecture of signalling units associated to these dimers remains unclear. Here, we characterized the molecular complex of the melatonin MT₁ receptor, which directly and constitutively couples to G_i proteins and the regulator of G‐protein signalling (RGS) 20. The molecular organization of the ternary MT₁/G_i/RGS20 complex was monitored in its basal and activated state by bioluminescence resonance energy transfer between probes inserted at multiple sites of the complex. On the basis of the reported crystal structures of G_i and the RGS domain, we propose a model wherein one G_i and one RGS20 protein bind to separate protomers of MT₁ dimers in a pre‐associated complex that rearranges upon agonist activation. This model was further validated with MT₁/MT₂ heterodimers. Collectively, our data extend the concept of asymmetry within GPCR dimers, reinforce the notion of receptor specificity for RGS proteins and highlight the advantage of GPCRs organized as dimers in which each protomer fulfils its specific task by binding to different GPCR‐interacting proteins.     

Molecular architecture of intermediate filaments

Together with microtubules and actin microfilaments, approximately 11 nm wide intermediate filaments (IFs) constitute the integrated, dynamic filament network present in the cytoplasm of metazoan cells. This network is critically involved in division, motility and other cellular processes. While the structures of microtubules and microfilaments are known in atomic detail, IF architecture is presently much less understood. The elementary 'building block' of IFs is a highly elongated, rod-like dimer based on an alpha-helical coiled-coil structure. Assembly of cytoplasmic IF proteins, such as vimentin, begins with a lateral association of dimers into tetramers and gradually into the so-called unit-length filaments (ULFs). Subsequently ULFs start to anneal longitudinally, ultimately yielding mature IFs after a compaction step. For nuclear lamins, however, assembly starts with a head-to-tail association of dimers. Recently, X-ray crystallographic data were obtained for several fragments of the vimentin dimer. Based on the dimer structure, molecular models of the tetramer and the entire filament are now a possibility.     

Three-dimensional structure of Na,K-ATPase determined from membrane crystals induced by cobalt-tetrammine-ATP.

The three-dimensional structure of Na,K-ATPase has been analyzed with electron microscopy and image processing. The enzyme, purified from pig kidney outer medulla, was arranged in a new form of tetragonal two-dimensional membrane crystals after incubation with cobalt-tetrammine-ATP, a stable MgATP complex analogue. Each continuous protein domain, as delineated by negative stain, consists of two alpha beta-protomers related by a dyad axis. The two rod-like regions are connected by a bridge displaced about 20 A away from the center of the structure toward the lipid bilayer. The domain connecting the two promoters is more constricted and closer to the center of the structure in the Co(NH3)4ATP-induced crystals than in the vanadate-induced p21 crystals. These observations suggest that the difference between previously analyzed dimers of two-dimensional p21 crystals induced with vanadate/magnesium and dimers of p4 crystals induced with Co(NH3)4ATP reflects two different conformational states of the enzyme.     

Packing interactions of aib-containing helices: Molecular modeling of parallel dimers of simple hydrophobic helices and of alamethicin

α-Aminoisobutyric acid (Aib) is a helicogenic α,α-dimethyl amino acid found in channel-forming peptaibols such as alamethicin. Possible effects of Aib on helix–helix packing are analyzed. Simulated annealing via restrained molecular dynamics is used to generate ensembles of approximately parallel helix dimers. Analysis of variations in geometrical and energetic parameters within ensembles defines how tightly a pair of helices interact. Simple hydrophobic helix dimers are compared: Ala₂₀, Leu₂₀, Aib₂₀, and P20, the latter a simple channel-forming peptide [G. Menestrina, K. P. Voges, G, Jung, and G. Boheim (1986) Journal of Membrane Biology, Vol. 93, pp. 111–132]. Ala₂₀ and Leu₂₀ dimers exhibit well-defined ridges-in-grooves packing with helix crossing angles (Ω) of the order of +20°. Aib₂₀ α-helix dimers are much more loosely packed, as evidenced by a wide range of Ω values and small helix-helix interaction energies. However, when in a 3₁₀ conformation Aib₂₀ helices pack in three well-defined parallel modes, with Ω ca. ?15°, +5°, and 10°. Comparison of helix–helix interaction energies suggests that dimerization may favor the 3₁₀ conformation. P20, with 8 Aib residues, also shows looser packing of α-helices. The results of these studies of hydrophobic helix dimers are analyzed in the context of the ridges-in-grooves packing model. Simulations are extended to dimers of alamethicin, and of an alamethicin derivative in which all Aib residues are replaced by Leu. This substitution has little effect on helix–helix packing. Rather, such interactions appear to be sensitive to interactions between polar side chains. Overall, the results suggest that Aib may modulate the packing of simple hydrophobic helices, in favor of looser interactions. For more complex amphipathic helices, interactions between polar side chains may be more critical. © 1995 John Wiley & Sons, Inc.     

Analysis of differential sensitivities of synchronized HeLa S3 cells to radiations and chemical carcinogen during the cell cycle. II. Ultraviolet light

UV-induction of thymine dimers in cellular DNA and their excision during different phases of the cell cycle of HeLa S3 cells were studied. Induction of thymine dimers was higher in the mitotic phase and the middle of the S phase than in the G₁ phase and from the late S phase to the early G₂ phase which are rather insensitive to UV. However, there is no significant difference in excision rate of UV-induced thymine dimers from the irradiated cells through the cell cycle. These findings indicate that the cyclic variation of UV-survivals during the cell cycle may be due to differences in the amount of thymine dimers in cellular DNA induced by UV-irradiation.     

Multiple Recognition Motifs in Nucleoporin Nup159 Provide a Stable and Rigid Nup159-Dyn2 Assembly

Dyn2 is the yeast ortholog of the molecular hub LC8, which binds disordered proteins and promotes their self-association and higher order assembly. Dyn2 is proposed to dimerize and stabilize the Nup82-Nsp1-Nup159 complex of the nuclear pore assembly through its interaction with nucleoporin Nup159. Nup159 has six LC8 recognition motifs separated by short linkers. NMR experiments reported here show that the Dyn2 binding domain of Nup159 is intrinsically disordered and that binding of one equivalent of Dyn2 dimer aligns two Nup159 chains along the full Dyn2 binding domain to form a bivalent scaffold that promotes binding of other Dyn2 dimers. Isothermal titration calorimetry of Dyn2 binding to Nup constructs of increasing lengths determine that the third LC8 recognition motifs does not bind Dyn2. A new approach to identifying active LC8 recognition motifs based on NMR-detected β-sheet propensities is presented. Isothermal titration calorimetry experiments also show that, due to unfavorable entropy changes, a Nup-Dyn2 complex with three Dyn2 dimers is more stable than the wild-type complex with five Dyn2 dimers. The calorimetric results argue that, from a thermodynamics perspective, only three Dyn2 dimers are needed for optimal stability and suggest that the evolutionary adaptation of multiple tandem LC8 recognition motifs imparts to the complex other properties such as rigidity and a kink in the rod-like structure. These findings extend the repertoire of functions of intrinsically disordered protein to fine-tuning and versatile assembly of higher order macromolecular complexes.     

Gβ3 forms distinct dimers with specific Gγ subunits and preferentially activates the β3 isoform of phospholipase C

Heterotrimeric G proteins regulate multiple effectors of which some are mediated via the Gβγ dimers. There is evidence to suggest that the functions of Gβγ dimers are not shared by all possible permutations of Gβγ complexes. Here, we report our efforts in defining the formation of distinct Gβγ dimers and their functional differences in activating phospholipase Cβ (PLCβ) isoforms. Co-immunoprecipitation assays using Cos-7 cells transiently expressing 48 different combinations of Gβ_(1–4) and Gγ_{(1–5, 7–13)} subunits showed that Gβ₁ and Gβ₄ could form dimers with all known Gγ subunits, whereas several dimers could not be observed for Gβ₂ and Gβ₃. All Gβ₁γ and Gβ₂γ dimers significantly stimulated PLCβ isoforms (PLCβ₂ ≥ PLCβ₃ > PLCβ₁), but Gβ₃γ and Gβ₄γ dimers were poor activators of PLCβ₁ and exhibited preference for PLCβ₃ and PLCβ₂, respectively. All Gβ subunits revealed to date contain the previously identified PLCβ₂-interacting residues, but their neighboring residues in the proposed 3-D structures are different. To test if differences in these neighboring residues affect the interactions with PLCβ isoforms, we generated several Gβ₃ mutants by replacing one or more of these residues with their Gβ₁ counterparts. One of these mutants (M120I, S140A and A141G triple mutant) acquired enhanced PLCβ₂-activating functions when co-expressed with different Gγ subunits, while the corresponding stimulation on PLCβ₃ was not altered. Taken together, our results show that the exact composition of a Gβγ dimer can determine its selectivity for activating PLCβ isoforms, and certain residues in Gβ₃ may account for the preferential stimulation of PLCβ₃ by Gβ₃γ dimers.     

An examination of structural interactions presumed to be of importance in the stabilization of phospholipase A2 dimers based upon comparative protein sequence analysis of a monomeric and dimeric enzyme from the venom ofAgkistrodon p. piscivorus

Phospholipases A₂ may exist in solution both as monomers and dimers, but enzymes that form strong dimers (K _D approximately 10^–9 M) have been found, thus far, only in venoms of the snake family Crotilidae. The complete amino acid sequences of a basic monomeric and an acidic dimeric phospholipase A₂ fromAgkistrodon piscivorus piscivorus (American cotton-mouth water moccasin) venom have been determined by protein sequencing methods as part of a search for aspects of structure contributing to formation of stable dimers. Both the monomeric and dimeric phospholipases A₂ are highly homologous to the dimeric phospholipases A₂ fromCrotalus atrox andCrotalus adamanteus venoms, and both have the seven residue carboxy-terminal extension characteristic of the crotalid and viperid enzymes. Thus, it is clear that the extension is not a prerequisite for dimerization. Studies to date have revealed two characteristic features of phosphilipases A₂ that exist in solution as strong dimers. One is the presence in the dimers of a Pro-Pro sequence at position 112 and 113 which just precedes the seven residue carboxy-terminal extension (residues 116–122). The other is a low isoelectric point; only the acidic phospholipases A₂ have been observed, thus far, to form stable dimers. These, alone or together, may be necessary, though not sufficient conditions for phospholipase A₂ dimer formation. Ideas regarding subunit interactions based upon crystallographic data are evaluated relative to the new sequence information on the monomeric and dimeric phospholipases A₂ fromA. p. piscivorus venom.     

Mitochondrial permeability transition involves dissociation of F1FO ATP synthase dimers and C‐ring conformation

The impact of the mitochondrial permeability transition (MPT) on cellular physiology is well characterized. In contrast, the composition and mode of action of the permeability transition pore complex (PTPC), the supramolecular entity that initiates MPT, remain to be elucidated. Specifically, the precise contribution of the mitochondrial F₁F_O ATP synthase (or subunits thereof) to MPT is a matter of debate. We demonstrate that F₁F_O ATP synthase dimers dissociate as the PTPC opens upon MPT induction. Stabilizing F₁F_O ATP synthase dimers by genetic approaches inhibits PTPC opening and MPT. Specific mutations in the F₁F_O ATP synthase c subunit that alter C‐ring conformation sensitize cells to MPT induction, which can be reverted by stabilizing F₁F_O ATP synthase dimers. Destabilizing F₁F_O ATP synthase dimers fails to trigger PTPC opening in the presence of mutants of the c subunit that inhibit MPT. The current study does not provide direct evidence that the C‐ring is the long‐sought pore‐forming subunit of the PTPC, but reveals that PTPC opening requires the dissociation of F₁F_O ATP synthase dimers and involves the C‐ring.     

The chemistry of thiamine: Studies on the dimerization of thiazolium salts

In this communication we report on our studies into the previously undetected dimerization chemistry of thiazolium salts. Thiazolium salts with electron-withdrawing substituents, such as 3,4-dimethyl-5-ethoxycarbonylthiazolium iodide, yield acid- and oxygen-sensitive ethylenic dimers under conditions originally used to detect the dimerization of 3-methylbenzothiazolium iodide. The 5-ethoxycarbonyl-4-methyl-3-phenylmethylthiazolium and 5-(2-O-triphenylmethyl-hydroxyethyl)-4-methyl-3-phenylmethylthiazolium bromides yield stable rearranged dimers, rather than the labile ethylenic dimers, under identical conditions. 4-Methyl-5-(2-hydroxyethyl)-3-phenylmethylthiazolium bromide and thiamine hydrochloride yield rearranged dimers which were isolated as their N,O-ketal derivatives when these salts were heated in aprotic solution in the presence of DBN and K₂CO₃, respectively. Rearrangement of the ethylenic dimer of 3-phenylmethylbenzothiazolium bromide to 2-(benzothiazol-2-yl)-2,3-diphenylmethylbenzothiazoline (J. Baldwin, S. E. Branz, and J. A. Walker (1977) J. Org. Chem. 42, 4142) demonstrates that rearranged dimers of these thiazolium salts are produced via a mechanism involving 1,3-sigmatropic rearrangement of intermediate ethylenic dimers. Based on literature precedent we argue that this dimerization chemistry demonstrates the nucleophilic carbene nature of C-2 deprotonated thiazolium salts in aprotic basic solution.     

An examination of structural interactions presumed to be of importance in the stabilization of phospholipase A2 dimers based upon comparative protein sequence analysis of a monomeric and dimeric enzyme from the venom ofAgkistrodon p. piscivorus

Phospholipases A₂ may exist in solution both as monomers and dimers, but enzymes that form strong dimers (K _D approximately 10^?9 M) have been found, thus far, only in venoms of the snake family Crotilidae. The complete amino acid sequences of a basic monomeric and an acidic dimeric phospholipase A₂ fromAgkistrodon piscivorus piscivorus (American cotton-mouth water moccasin) venom have been determined by protein sequencing methods as part of a search for aspects of structure contributing to formation of stable dimers. Both the monomeric and dimeric phospholipases A₂ are highly homologous to the dimeric phospholipases A₂ fromCrotalus atrox andCrotalus adamanteus venoms, and both have the seven residue carboxy-terminal extension characteristic of the crotalid and viperid enzymes. Thus, it is clear that the extension is not a prerequisite for dimerization. Studies to date have revealed two characteristic features of phosphilipases A₂ that exist in solution as strong dimers. One is the presence in the dimers of a Pro-Pro sequence at position 112 and 113 which just precedes the seven residue carboxy-terminal extension (residues 116–122). The other is a low isoelectric point; only the acidic phospholipases A₂ have been observed, thus far, to form stable dimers. These, alone or together, may be necessary, though not sufficient conditions for phospholipase A₂ dimer formation. Ideas regarding subunit interactions based upon crystallographic data are evaluated relative to the new sequence information on the monomeric and dimeric phospholipases A₂ fromA. p. piscivorus venom.     

Cardiolipin affects the supramolecular organization of ATP synthase in mitochondria

F₁F₀ ATP synthase forms dimers that tend to assemble into large supramolecular structures. We show that the presence of cardiolipin is critical for the degree of oligomerization and the degree of order in these ATP synthase assemblies. This conclusion was drawn from the statistical analysis of cryoelectron tomograms of cristae vesicles isolated from Drosophila flight-muscle mitochondria, which are very rich in ATP synthase. Our study included a wild-type control, a cardiolipin synthase mutant with nearly complete loss of cardiolipin, and a tafazzin mutant with reduced cardiolipin levels. In the wild-type, the high-curvature edge of crista vesicles was densely populated with ATP synthase molecules that were typically organized in one or two rows of dimers. In both mutants, the density of ATP synthase was reduced at the high-curvature zone despite unchanged expression levels. Compared to the wild-type, dimer rows were less extended in the mutants and there was more scatter in the orientation of dimers. These data suggest that cardiolipin promotes the ribbonlike assembly of ATP synthase dimers and thus affects lateral organization and morphology of the crista membrane.     

Self-association of adenine-dependent hairpin ribozymes

Hairpin ribozymes are flexible molecules that catalyse reversible self-cleavage after the docking of two independently folded internal loops, A and B. The activities, self-association and structures in solution of two 85 base adenine-dependent hairpin ribozymes (ADHR1 and ADHR2) were studied by native gel electrophoresis, analytical centrifugation, and small angle neutron scattering. Bi-molecular RNA interactions such as linear–linear, loop–loop, loop–linear or kissing interactions have been found to be important in the control of various biological functions, and hairpin loops present rich potential for establishing both intra- and intermolecular interactions through standard Watson-Crick base pairing or non-canonical interactions. Similar results were obtained for ADHR1 and ADHR2. At room temperature, they indicated end-to-end self-association of the ribozymes in rod-like structures with a cross-section corresponding to two double strands side-by-side. Dimers, which predominate at low concentration (∼0.1 mg/ml), associate into longer rods, with increasing concentration (∼1 mg/ml). Above 65°C, the dimers and rods dissociated into compact monomers, with a radius of gyration similar to that of tRNA (about 70 bases). The dimers were non-active for catalysis, which suggests that dimer formation, probably by preventing the correct docking of loops A and B, could act as an inhibition mechanism for the regulation of hairpin ribozyme catalysis.     

Synthesis of Oleanolic Acid Dimers as Inhibitors of Glycogen Phosphorylase

Recently, oleanolic acid was found to be an inhibitor of glycogen phosphorylase. For further structural modification, we have synthesized several dimers of oleanolic acid by using amide, ester, or triazole linkage with click chemistry. The click chemistry was shown to be the most efficient method for the dimer synthesis. Nearly quantitative yield of triazole‐linked dimers was obtained. Biological evaluation of the synthesized dimers as inhibitors of glycogen phosphorylase has been described. Four of six dimers exhibited inhibitory activity against rabbit muscle glycogen phosphorylase a (RMGPa), with compounds 2 and 7 as the most potent inhibitors, which displayed an IC₅₀ value (ca. 3 μM ) lower than that of oleanolic acid (IC₅₀=14 μM ).