Ring Oligomers Research Articles

Structure-Activity Relationships for the N-Me- Versus N-H-Amide Modification to Macrocyclic ent-Verticilide Antiarrhythmics.

The synthesis of all N-Me and N-H analogues of ent-verticilide is described, enabling a structure-activity relationship study based on cardiac ryanodine receptor (RyR2) calcium ion channel inhibition. The use of permeabilized cardiomyocytes allowed us to correlate the degree of N-methylation with activity without concern for changes in passive membrane permeability that these modifications can cause. A key hypothesis was that the minimal pharmacophore may be repeated in this cyclic oligomeric octadepsipeptide (a 24-membered macrocycle), opening the possibility that target engagement will not necessarily be lost with a single N-Me → N-H modification. The effect in the corresponding 18-membered ring oligomer (ent-verticilide B1) was also investigated. We report here that a high degree of N-methyl amide content is critical for activity in the ent-verticilide series but not entirely so for the ent-verticilide B1 series.

Monte Carlo simulation of the surface-assisted self-assembly of metal-organic precursors comprising phenanthrene building blocks

Surface-assisted fabrication of carbon-based covalent architectures has been a promising pathway to low-dimensional materials with special physicochemical properties and functions. In this contribution, the Monte Carlo simulation method was used to predict the formation of metal-organic precursors preceding the covalent Ullmann coupling of halogenated phenanthrene monomers. To that end, the coarse-grained model of adsorbing (111) surface, phenanthrene molecules and linking adatoms was proposed, in which the monomers were equipped with active centers providing directional metal-linker interactions. The simulations performed for various intramolecular distributions of active centers in the phenanthrene unit (corresponding to halogen positions) resulted in diverse metal-organic superstructures, including chains, ring oligomers, triangular and windmill trimers, ladders, and periodic and aperiodic networks. For those molecules which were chiral in 2D the corresponding calculations in enantiopure and racemic overlayers were also carried out. These simulations resulted in characteristic examples of both advantageous and adverse effect of the opposite enantiomer on the ordering in racemic systems. Our theoretical findings provided some hints on how to halogenate monomeric phenanthrene units to create polymeric architectures with presumed structural features, such as topology, periodicity, connectivity, ramification and porosity.

Modeling of mutant superoxide dismutase 1 octamers with cross-linked disulfide bonds.

Mutant superoxide dismutase 1 (SOD1) may form cyclic structures due to its greater instability from aberrant demetallization and oxidation of cysteine bonds. This cyclic structure may allow SOD1 to form ion channels on membranes such as the mitochondrial membrane, causing imbalances in the concentration of intracellular ions as a potential mechanism for the progressive neuron death involved in amyotrophic lateral sclerosis (ALS). Using docking programs within modeling software, models of mutant SOD1 dimers and eventually ring oligomers were constructed based on known descriptions of such structures in addition to information on the orientation of the models associated with a membrane. The resulting structure consists of a ring of four demetallated mutant SOD1 dimers with cross-linked disulfide bonds. Stability of the octamer model was supported by the molecular dynamics simulations. Further analysis of the octamer model indicated that its inner- and outer-pore diameters were stable, matching the dimensions of known SOD1 ion channels.

Novel features of centriole polarity and cartwheel stacking revealed by cryo‐tomography

Centrioles are polarized microtubule‐based organelles that seed the formation of cilia, and which assemble from a cartwheel containing stacked ring oligomers of SAS‐6 proteins. A cryo‐tomography map of centrioles from the termite flagellate Trichonympha spp. was obtained previously, but higher resolution analysis is likely to reveal novel features. Using sub‐tomogram averaging (STA) in T. spp. and Trichonympha agilis, we delineate the architecture of centriolar microtubules, pinhead, and A‐C linker. Moreover, we report ~25 Å resolution maps of the central cartwheel, revealing notably polarized cartwheel inner densities (CID). Furthermore, STA of centrioles from the distant flagellate Teranympha mirabilis uncovers similar cartwheel architecture and a distinct filamentous CID. Fitting the CrSAS‐6 crystal structure into the flagellate maps and analyzing cartwheels generated in vitro indicate that SAS‐6 rings can directly stack onto one another in two alternating configurations: with a slight rotational offset and in register. Overall, improved STA maps in three flagellates enabled us to unravel novel architectural features, including of centriole polarity and cartwheel stacking, thus setting the stage for an accelerated elucidation of underlying assembly mechanisms.

Why Do B-P and Al-P Polymers Differ? Structures, Stability, and Electronic Properties of Chain and Ring [H2 PEH2 ]n Oligomers (E=B, Al; n=1-15).

Chain and ring [H2 PEH2 ]n oligomers (E=B, Al; n=2-15) have been computationally studied at the B3LYP/def2-TZVP level of theory. A strong tendency to cyclization was found for the chain Al-P oligomers with n>7, whereas analogous long B-P oligomers can exist as chain structures. Subsequent oligomerization enthalpies approach each other very closely for the ring and chain oligomers with an increase of n. However, these oligomers have very different electronic properties with band gaps below 0.2 eV for the chain [H2 PBH2 ]15 and more than 5 eV for the ring isomer [H2 PEH2 ]15 . The molecular orbitals in the ring oligomers are highly delocalized, whereas for the chain isomers, the HOMO and LUMO are localized at the different ends of the oligomeric chain.

To Be Fibrils or To Be Nanofilms? Oligomers Are Building Blocks for Fibril and Nanofilm Formation of Fragments of Aβ Peptide.

To identify the key stages in the amyloid fibril formation we studied the aggregation of amyloidogenic fragments of Aβ peptide, Aβ(16-25), Aβ(31-40), and Aβ(33-42), using the methods of electron microscopy, X-ray analysis, mass spectrometry, and structural modeling. We have found that fragments Aβ(31-40) and Aβ(33-42) form amyloid fibrils in the shape of bundles and ribbons, while fragment Aβ(16-25) forms only nanofilms. We are the first who performed 2D reconstruction of amyloid fibrils by the Markham rotation technique on electron micrographs of negatively stained fragments of Aβ peptide. Combined analysis of the data allows us to speculate that both the fibrils and the films are formed via association of ring-shaped oligomers with the external diameter of about 6 to 7 nm, the internal diameter of 2 to 3 nm, and the height of ∼3 nm. We conclude that such oligomers are the main building blocks in fibrils of any morphology. The interaction of ring oligomers with each other in different ways makes it possible to explain their polymorphism. The new mechanism of polymerization of amyloidogenic proteins and peptides, described here, could stimulate new approaches in the development of future therapeutics for the treatment of amyloid-related diseases.

Molecular mechanism of amyloid formation by Ab peptide: review of own works

TA characteristic feature of amyloid structures is polymorphism. The study of amyloid structures and their formation process was carried out for synthetic and recombinant Ab(1-40) and Ab(1-42) peptide preparations. In the study of these peptides, we recognized fibrils of different morphologies. We observed fibrillar formations in the form of single fibrils, ribbons, bundles, bunches, and clusters. Polymorphism of fibrils was observed not only when the environmental conditions changed, but under the same conditions and this was a common characteristics of all amyloid formations. Fibrils of Ab(1-40) peptides tended to form aggregates of fibrils in the form of ribbons, while Ab(1-42) peptide under the same conditions polymerized in the form of rough fibrils of different diameters and tends to branch. We assume that the formation of fibrils of Ab(1-40) and Ab(1-42) peptides occurs according to a simplified scheme: a destabilized monomer ® a ring oligomer ® a mature fibril consisting of ring oligomers. Proceeding from the proposition that the ring oligomer is the main building block of amyloid fibril (similar to the cell in the body), it is easy to explain fibril polymorphism, as well as fragmentation of mature fibrils under various external influences, branching and irregularity of diameter (surface roughness) of fibrils. One aspect of the study of amyloidogenesis is the determination of the regions of the protein chain forming the core of the amyloid fibril. We theoretically predicted amyloidogenic regions for two isoforms of Ab peptides capable of forming an amyloid structure: 16-21 and 32-36 residues. Using the method of tandem mass spectrometry, these regions were determined experimentally. It was shown that the regions of Ab(1-40) peptide from 16 to 22 and from 28 to 40 residues were resistant to the action of proteases, i.e. its formed the core of the amyloid fibril. For Ab(1-42) peptide the whole sequence is not available for the action of proteases, which indicates a different way of associating ring oligomers in the formation of fibrils. Based on electron microscopy and mass spectrometry data we proposed a molecular model of the fibril formed by Ab(1-40) and Ab(1-42) peptides.

Rosetta Stone for Amyloid Fibrils: The Key Role of Ring-Like Oligomers in Amyloidogenesis

Deeper understanding of processes of protein misfolding, aggregation, formation of oligomers, protofibrils, and fibrils is crucial for the development of future medicine in treatment of amyloid-related diseases. While numerous reports illuminate the field, the above processes are extremely complex, as they depend on many varying parameters, such as the peptide concentration, temperature, pH, presence of metal ions, lipids, and organic solvents. Different mechanisms of amyloid fibril formation have been proposed, but the process of the oligomer-to-fibril transition is the least agreed upon. Our studies of a number of amyloidogenic proteins and peptides (insulin, Aβ peptides, the Bgl2 protein from the yeast cell wall), as well as their amyloidogenic fragments, have allowed us to propose a model of the fibril structure generation. We have found that the main building block of fibrils of any morphology is a ring-like oligomer. The varying models of interaction of ring oligomers with each other revealed in our studies make it possible to explain their polymorphism. Crucially, the amino acid sequence determines the oligomer structure for the given protein/peptide.

Calcium Sensitive Ring-Like Oligomers of Synaptotagmin 1: Implications for Neurotransmitter Release

The synaptic vesicle protein, Synaptotagmin-1 (Syt1) is required to couple Ca2+ influx to the membrane fusion machinery. However, the structural mechanism underlying this process is unclear. Using negative stain electron microscopy, we find that the Syt1 assembles into ring-like oligomeric structures on lipid monolayers under physiological ionic strength and lipid composition in the absence of free Ca2+. These rings oligomers vary in diameter between 19 - 42 nm (with an average size of 30 ± 5 nm), corresponding to 12- 25 molecules of Syt1. The ring-like oligomers are sensitive to Ca2+ and are disrupted rapidly by the physiological concentrations of free Ca2+. Analogous ring-like oligomers assemble from the C2AB domains of other Syt isoforms (Syt2, Syt7, Syt9) as well as related C2 domain containing protein, Doc2B and extended Synaptotagmins (E-Syts). Evidently, the circular oligomerization is a general and conserved structural aspect of many C2 domain proteins, including Synaptotagmins. Further, we find that both Syt1 ring formation and its disruption by Ca2+ principally involve well-established functional surfaces of the C2B domain which are important for neurotransmission. This includes the Ca2+ -independent binding of the polybasic motif of C2B domain with phosphatidylinositol 4,5-bisphosphate (PIP2) as a prerequisite for rings to assemble. This suggests that ring formation may be triggered at a very early step in synaptic vesicle docking, as C2B-PIP2 interaction is required for docking in vivo. Ca2+ binding to the C2B domain and re-orientation/insertion into the membrane, both required for triggering synaptic transmission, disrupts the ring oligomers. We advance a simple and novel mechanism wherein Syt1 ring oligomer act as reversible washer/spacer to synchronize neurotransmitter release to Ca2+ influx. Supporting this hypothesis, we find mutations in Syt1 that specifically disrupt the ring oligomer formation results in dysregulation neuroexocytosis in PC12 cells.

Statistical Ring Catenation under Thermodynamic Control: Should the Jacobson-Stockmayer Cyclization Theory Take into Account Catenane Formation?

An extension of the Jacobson-Stockmayer theory is presented to include the reversible formation of [2]catenanes in a ring-chain system under thermodynamic control. The extended theory is based on the molar catenation constant, measuring the ease of catenation of two ring oligomers, whose expression was obtained in a previous work. Two scenarios have been considered: that of "thick" (hydrocarbon-like) chains and that of "thin" (DNA-like) chains. In the case of "thick" chains, the formation of catenanes can be neglected, unless in the unlikely case of a very large value of the equilibrium constant for linear propagation (K ≈ 108 mol-1 L, or larger). For K tending to infinity, the system becomes a chain-free system where only ring-catenane equilibria occur. Under this condition, there is a critical concentration below which only rings are present at equilibrium and above which the ring fraction remains constant, and the excess monomer is converted only into catenanes. In the case of "thin" chains, the formation of catenanes cannot be neglected even for values of K as low as 102 mol-1 L, thus justifying the use of the extended theory.

Insulin and Lispro Insulin: What is Common and Different in their Behavior?

There are different insulin analogues with various pharmacokinetic characteristics, such as, rapid-acting, long-acting, or intermediate-acting analogues. Since insulin tends to form amyloid aggregates, it is of particular interest to measure characteristic times of formation of amyloid aggregates and compare those to action times for insulin and its analogues. For the study we have chosen one of the insulin analogues - insulin Lispro, which is a fast acting insulin analog. It is usually thought of amyloid aggregation as a nucleation-dependent process. We have estimated the size of the primary nucleus to be one monomer and the size of the secondary nucleus to be around zero in both insulin and Lispro insulin aggregation processes. The main structural element of insulin and Lispro insulin amyloid fibrils is a rounded ring oligomer of about 6-7 nm in diameter, about 2-3 nm in height and about 2 nm in diameter of the hole. Fibrils of several μm in length are produced due to interaction of such oligomers. The packing of ring oligomers in fibrils differs because of the difference in their orderliness. Though the initial stages of fibril formation (monomer, oligomer) are similar, the further process depends on the unique sequence of each peptide. Namely the sequence affects the final morphology of mature amyloids. These observations allow us to conclude that formation of fibrils by short peptides occurs via and by means of oligomer ring structures. Such an important issue as the nature of polymorphism of insulin amyloid fibrils has been settled by us. The role of early oligomeric aggregates in such processes as nucleation and aggregation of amyloid fibrils has been examined.

One of the possible mechanisms of amyloid fibrils formation based on the sizes of primary and secondary folding nuclei of Aβ40 and Aβ42.

In the presented paper, theoretical as well as electron microscopy and X-ray diffraction experimental approaches were employed for studding the process of Aβ amyloid formation. Using quantitative estimates of a number of monomers which form the nuclei of amyloid fibrils the sizes of folding nuclei of amyloid fibrils for Aβ40 and 42 have been determined for the first time. We have shown that the size of the primary nucleus of Aβ42 peptide fibrils corresponds to 3 monomers, the size of the secondary nucleus for this peptide is 2 monomers. Applying the same analysis to Aβ40 we conclude that the size of the primary nucleus is 2 monomers, and the size of the secondary nucleus is one monomer. Summation of our theoretical and experimental results has allowed us to propose a new model of the structural organization of amyloid fibrils. Our model suggests that the generation of fibrils takes place along the following simplified pathway: a monomer→a ring oligomer→a mature fibril consisting of ring oligomers. These data shed more light upon our understanding of what sizes of the oligomers could represent main targets for future therapies (tetramers for Aβ42 and trimers for Aβ40), and aid in the development of inhibitors of Aβ40 and 42 oligomer formation.

Catenation Equilibria Between Ring Oligomers and Their Relation to Effective Molarities: Models From Theories and Simulations

Five models are discussed giving the equilibrium constant for the catenation of two ring oligomers as a function of their Effective Molarity (EM), the physico-chemical parameter expressing the ease of cyclization of a chain. The first three models (A–C) are derived from the revision of previous theories of catenation, that neglect excluded volume effects. A fourth model (D) is obtained from the results of Monte Carlo simulations by Deguchi and co, that can also account for excluded volume effects. Finally, a fifth model (E) is introduced which has the same functional form of models A, B, D, but is parameterized using the available experimental catenation constant.

Biosourced Amphiphilic Degradable Elastomers of Poly(glycerol sebacate): Synthesis and Network and Oligomer Characterization

Glycerol (G, a triol) and sebacic acid (S, an α,ω-dicarboxylic acid) were condensed in the bulk to obtain poly(glycerol sebacate) (PGS) cross-linked elastomers which were characterized in terms of their swelling, thermal, and mechanical properties. The soluble precursors to the elastomers were characterized in terms of their size, size distribution, and composition. In particular, G–S mixtures of five different compositions (molar G:S ratio = 2:1, 2:2, 2:3, 2:4, and 2:5) were copolymerized in the bulk at 120 °C in a three-step strategy (first step under inert gas atmosphere, followed by two steps in vacuo). When the G:S molar ratio was equal to (2:3) or close to (2:4), the stoichiometrically matched, network formation took place from the second condensation step, whereas three reaction steps were necessary for network formation far from stoichiometry, at G:S molar ratios equal to 2:2 and 2:5; at a G:S molar ratio of 2:1, no network formation was observed at all. Network composition also proved to be an important structural property, directly influencing the swelling and thermomechanical behavior of the elastomers. In particular, at the stoichiometrically matched G:S ratio of 2:3, corresponding to the cross-linking density maximum, the sol fraction extracted from the elastomers and the elastomer degree of swelling in aqueous media and in organic solvents presented a minimum, whereas the storage moduli of PGS elastomeric membranes in the dry state, measured within the temperature range between 35 and 140 °C, exhibited a maximum. The molecular weights of all soluble network precursors were found to be below 5000 g mol–1 (gel permeation chromatography), containing but traces of ring oligomers (electron-spray ionization mass spectrometry). 1H NMR spectroscopy indicated that the precursor composition was close to that expected on the basis of the G:S feed ratio and that monomer-to-polymer conversion increased from the first to the second condensation step.

Engineered Rings of Mixed Yeast Lsm Proteins Show Differential Interactions with Translation Factors and U-Rich RNA

The Lsm proteins organize as heteroheptameric ring assemblies capable of binding RNA substrates and ancillary protein factors. We have constructed simplified Lsm polyproteins that organize as multimeric ring structures as analogues of the functional Lsm complexes. Polyproteins Lsm[2+3], Lsm[4+1], and Lsm[5+6] incorporate natural sequence extensions as linker peptides between the core Lsm domains. In solution, the recombinant products organize as stable ring oligomers (75 A wide, 20 A pores) in discrete tetrameric and octameric forms. Following immobilization, the polyproteins successfully act as affinity pull-down ligands for proteins within yeast lysate, including native Lsm proteins. Interaction partners were consistent with current models of the mixed Lsm ring assembly in vivo but also suggest that dynamic rearrangements of Lsm protein complexes can occur. The Lsm polyprotein ring complexes were seen in gel shift assays to have a preference for U-rich RNA sequences, with tightest binding measured for Lsm[2+3] with U(10). Polyprotein rings containing truncated forms of Lsm1 and Lsm4 were found to associate with translation, initiation, and elongation protein factors in an RNA-dependent manner. Our findings suggest Lsm1 and/or Lsm4 can interact with translationally active mRNA.

Aluminum−Nitrogen Rings and Cages with Organic Handles: A Theoretical Study

The structures and stability of monomeric and oligomeric compounds resulting from the elimination of 2 mol of HBr from the AlBr(3)en complex have been studied theoretically at the B3LYP/LANL2DZ(d,p) level of theory. Two series of the ring and cage oligomer compounds were considered: imino [AlBrNCH(2)CH(2)NH(2)](n), n = 1-4, 6 (I(n)), and isomeric amido [AlBrNHCH(2)CH(2)NH](n), n = 1-3 (A'(n)), species. In all cases the amido isomers are 95-295 kJ mol(-1) more stable compared to their imino counterpairs. Intramolecular donor-acceptor interactions play an important role in the stabilization of the structure. Possible pathways of the polymerization have also been explored. Although the generation of the oligomers via HBr elimination in the gas phase is predicted to be thermodynamically unfavorable, operation of such reactions in the condensed phase is feasible. Substitution of bromine by hydrogen makes H(2) elimination reactions thermodynamically favorable. This opens a perspective for the synthesis of novel ladder-type oligomers with a continuous (AlN)(n) core supported by C(2)H(4) balustrade and imino cages with C(2)H(4) handles.

Phospholamban Oligomerization, Quaternary Structure, and Sarco(endo)plasmic Reticulum Calcium ATPase Binding Measured by Fluorescence Resonance Energy Transfer in Living Cells

Phospholamban (PLB) oligomerization, quaternary structure, and sarco(endo)plasmic reticulum calcium ATPase (SERCA) binding were quantified by fluorescence resonance energy transfer (FRET) in an intact cellular environment. FRET between cyan fluorescent protein-PLB and yellow fluorescent protein-PLB in AAV-293 cells showed hyperbolic dependence on protein concentration, with a maximum efficiency of 45.1 +/- 1.3%. The observed FRET corresponds to a probe separation distance of 58.7 +/- 0.5A(,) according to a computational model of intrapentameric FRET. This is consistent with models of the PLB pentamer in which cytoplasmic domains fan out from the central bundle of transmembrane helices. An I40A mutation of PLB did not alter pentamer conformation but increased the concentration of half-maximal FRET (K(D)) by >4-fold. This is consistent with the previous observation that this putatively monomeric mutant still oligomerizes in intact membranes but forms more dynamic pentamers than wild type PLB. PLB association with SERCA, measured by FRET between cyan fluorescent protein-SERCA and yellow fluorescent protein-PLB, was increased by the I40A mutation without any detectable change in probe separation distance. The data indicate that the regulatory complex conformation is not altered by the I40A mutation. A naturally occurring human mutation (L39Stop) greatly reduced PLB oligomerization and SERCA binding and caused mislocalization of PLB to the cytoplasm and nucleus. Overall, the data suggest that the PLB pentamer adopts a "pinwheel" shape in cell membranes, as opposed to a more compact "bellflower" conformation. I40A mutation decreases oligomerization and increases PLB binding to SERCA. Truncation of the transmembrane domain by L39Stop mutation prevents anchoring of the protein in the membrane, greatly reducing PLB binding to itself or its regulatory target, SERCA.

Template effect of vancomycin aglycon in the oxidative oligomerization of 1,6-dithio- d-mannitol: A MALDI-TOF MS and solvent effect study

Oxidative oligomerization of 1,6-dithio- d-mannitol (DTM) using air as oxidant is reported. It was found that both ring and chain oligomers were formed with a degree of polymerization up to 11–12 as determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). It was found that the relative amounts of rings to chains were significantly dependent on the solvent employed: in water or in dimethyl formamide (DMF) yielded ring oligomers with a relative amount of higher than 90% (on the average), and almost exclusive formation of chain oligomers was observed in methanol or in dioxane. The oxidative oligomerization of DTM was also carried out in the presence of vancomycin aglycon as a template. It was observed that in water the vancomycin aglycon induced the exclusive formation of chain oligomers from DTM. The non-covalent, strong interaction existing between the vancomycin aglycon and the chain dimer of DTM was further supported by electrospray ionization mass spectrometry (ESI-MS).

Ring and cage compounds from complexes of group 13 metal halides with ethylenediamine: Experiment and theory

Formation of gaseous ring and cage compounds by thermolysis of the complexes between group 13 metal halides MX 3 and ethylenediamine (en) has been observed experimentally by mass spectrometry method (M = Al, Ga; X = Cl, Br, I) and studied theoretically. Existence of gaseous associates with molecular weight of 600–900 amu was observed for all studied systems. The abundance of the high molecular weight species decreases in order AlBr 3 > AlI 3 > GaCl 3 > GaBr 3. For aluminum compounds, formation of carbon-free cubane-type clusters was evidenced. Theoretical ab initio studies at B3LYP/LANL2DZ(d,p) level of theory have been performed for the series of the ring and cage oligomer compounds in Al 2Br 6-en system. A mechanistic pathway of the formation of inorganic rings and cages by subsequent HBr elimination and oligomerization reactions has been proposed. It is concluded that elimination reactions take place in the condensed phase.

The Mdm2 RING domain C-terminus is required for supramolecular assembly and ubiquitin ligase activity

Mdm2, a key negative regulator of the p53 tumor suppressor, is a RING-type E3 ubiquitin ligase. The Mdm2 RING domain can be biochemically fractionated into two discrete species, one of which exists as higher order oligomers that are visible by electron microscopy, whereas the other is a monomer. Both fractions are ATP binding and E3 ligase activity competent, although the oligomeric fraction exhibits lower dependence on the E2 component of ubiquitin polymerization reactions. The extreme C-terminal five amino acids of Mdm2 are essential for E3 ligase activity in vivo and in vitro, as well as for oligomeric assembly of the protein. A single residue (phenylalanine 490) in that sequence is critical for both properties. Interestingly, the C-terminus of the Mdm2 homologue, MdmX (itself inert as an E3 ligase), can fully substitute for the equivalent segment of Mdm2 and restore its E3 activity. We further show that the Mdm2 C-terminus is involved in intramolecular interactions and can set up a platform for direct protein-protein interactions with the E2.