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PubMed2004

Self-protection: the advantage of radical oligomeric mixtures in organic synthesis.

Atom-transfer radical oligomers of allyl iodoacetates were converted to 4-pentenoic acids upon treatment with zinc. Reactions of the radical oligomers of various omega-alkenyl iodoacetates with Grignard reagents afforded the corresponding substituted tetrahydrofuran derivatives. These results indicated that radical oligomeric mixtures not only serve as versatile intermediates in organic synthesis, but also exhibit unique advantages in that the oligomeric mixtures are self-protected and the deoligomerization functions as the simultaneous deprotection.

Journal Article↗
PubMed1996

Solid and Solution Phase Organic Syntheses of Oligomeric Thioureas.

In order to study supramolecular architectures built from unnatural oligomeric and polymeric structures, one must first have an efficient synthetic strategy to produce them. Oligomers built from thiourea groups should form complex secondary and tertiary structures due to the hydrogen-bonding capabilities of the thioureas. Herein, both solution and solid phase synthetic procedures that yield oligomeric thioureas are described. They rely on the coupling of an isothiocyanate with an amine to produce the thiourea linkage. The monomers are derived from simple diamines. Higher yields are achieved using the solid phase method due to the ability to easily monitor the extent of reaction, to use a large excess of reagent, and to perform purification after cleavage from the solid support. A variety of oligomers are given as examples. The procedure is quite general, should be easily extended to complex monomers, and will allow the investigation of intramolecular and intermolecular interactions.

Journal Article↗
PubMed2005

Thermal chemistry of styrene on Si(100)2x1 and modified surfaces: electron-mediated condensation oligomerization and posthydrogenation reactions.

The room-temperature (RT) adsorption and surface reactions of styrene on Si(100)2x1 have been investigated by thermal desorption spectrometry, low-energy electron diffraction, and Auger electron spectroscopy. Styrene is found to adsorb on Si(100)2x1 at a saturation coverage of 0.5 monolayer, which appears to have little effect on the 2x1 reconstructed surface. The chemisorption of styrene on the 2x1 surface primarily involves bonding through the vinyl group, with less than 15% of the surface moiety involved in bonding through the phenyl group. Except for the 2x1 surface where molecular desorption is also observed, the adsorbed styrene is found to undergo, upon annealing on the 2x1, sputtered and oxidized Si(100) surfaces, different thermally induced processes, including hydrogen abstraction, fragmentation, and/or condensation oligomerization. Condensation oligomerization of styrene has also been observed on Si(100)2x1 upon irradiation by low-energy electrons. In addition, large postexposure of atomic hydrogen to the chemisorbed styrene leads to Si-C bond cleavage and the formation of phenylethyl adspecies. Hydrogen therefore plays a decisive role in stabilizing and manipulating the processes of different surface reactions by facilitating different surface structures of Si.

Adsorption↗
PubMed2006

Evaluation of force fields for molecular simulation of polyhedral oligomeric silsesquioxanes.

Polyhedral oligomeric silsesquioxanes (POSS) are nanometer-size molecules suitable for the production of organic-inorganic nanocomposite materials. These organic-inorganic nano-building blocks show promise for enabling the production of polymeric materials of exceptional mechanical properties as well as novel composite materials. While the experimental studies of these materials have rapidly evolved in the past decade, their theoretical investigation is still in its infancy. Toward the validation of force fields for the molecular simulation of POSS-containing systems, we present the charge-transfer reactive (CTR) force field for the molecular simulation of polyhedral oligomeric silsesquioxane (POSS) molecules and compare the ability of this, and several force fields taken from the literature, to predict the thermophysical properties of POSS-containing systems. The literature force fields compared include the universal force field (UFF) and the COMPASS and Hybrid-COMPASS force fields. Predictions from molecular dynamics simulations of the structural parameters (unit cell vectors), melting temperature, and FT-IR spectra of crystals of POSS monomers are presented. The POSS monomers investigated are octahydride, octamethyl, and octapropyl POSS. Predicted quantities are compared to experimental results where available and provide molecular-level physical insight into several aspects of the behavior of POSS molecules. While all the force fields tested perform reasonably well, our results indicate that the Hybrid-COMPASS and CTR force fields predict structural properties that are in good agreement with experimental data.

Journal Article↗
PubMed2006

Mechanism of oligomerization reactions of silica.

The mechanism of the oligomerization reaction of silica, the initial step of silica formation, has been studied by quantum chemical techniques. The solvent effect is included by using the COSMO model. The formation of various oligomers (from dimer to tetramer) was investigated. The calculations show that the anionic pathway is kinetically preferred over the neutral route. The first step in the anionic mechanism is the formation of the SiO-Si linkage between the reactants to form a five-coordinated silicon complex, which is an essential intermediate in the condensation reaction. The rate-limiting step is water removal leading to the oligomer product. The activation energies for dimer and trimer formation ( approximately 80 kJ/mol) are significantly higher than those of the subsequent oligermerization. The activation energies for the ring closure reaction ( approximately 100 kJ/mol) are even higher. The differences in activation energies can be related to the details in intra- and intermolecular hydrogen bonding of the oligomeric complexes.

Journal Article↗
PubMed2003

Deoligomerization: a new route to lactams from unsaturated amides via radical oligomerization.

[reaction: see text] Triethylborane-initiated atom transfer radical oligomerization of N-allyl or N-(3-butenyl)iodoacetamides followed by treatment with hydrochloric acid and subsequent neutralization with K(2)CO(3) led to the formation of the corresponding 5-hydroxyl-substituted delta-lactams or caprolactams, respectively. This oligomerization-deoligomerization sequence serves as an alternative to the corresponding intramolecular cyclization reactions.

Amides↗
PubMed2005

MALDI TOF mass study on oligomerization of Pd(OAc)2(L)2 (L = pyridine derivatives): relevance to Pd black formation in Pd-catalyzed air oxidation of alcohols.

[reaction: see text] Oligomerization of Pd(OAc)2(L)2 (L = pyridine derivatives), a catalyst for the air oxidation of alcohols, is studied with MALDI TOF mass, using dithranol as the matrix. The degree of the Pd oligomerization is influenced by the pyridine ligands, and this ligand effect is similar to one observed for Pd black formation in the catalysis.

Journal Article↗
PubMedDate not supplied

Synthesis of 2'-deoxy-7,8-dihydro-8-oxoguanosine and 2'-deoxy-7,8-dihydro-8-oxoadenosine and their incorporation into oligomeric DNA.

Reliable methods have been developed for the synthesis of the 3'-O-[(diisopropylamino) (2-cyanoethoxy)phosphino]-5'-O-(4,4'- dimethoxytrityl) derivatives of 2'-deoxy-7,8-dihydro-8-oxoguanosine (8-oxo-dGuo, 1) and 2'-deoxy-7,8-dihydro-8-oxoadenosine (8-oxo-dAdo, 2), and for the efficient incorporation of the latter into oligomeric DNA. Both methods rely on the conversion of the 2'-deoxy-8-bromopurine nucleosides 3 and 10 to their corresponding 2'-deoxy-8-(benzyloxy) nucleosides 4 and 12 followed by catalytic hydrogenation to generate the 8-oxo function at the C-8 position. The preparation of the phosphoramidites 8 and 19 required for the synthesis of a series of DNA oligomers was carried out under strictly anhydrous conditions. Failure to keep the systems dry resulted in great difficulties during the purification procedures, and erratic results when DNA synthesis was attempted. In the preparation of the DNA itself, it was found to be extremely important during the ammonia deprotection step to add an antioxidant. Otherwise aerial oxidation resulted in almost complete loss of the oligomer. However, when these special conditions were followed, oligomeric DNA containing 8-oxo-dGuo and 8-oxo-dAdo residues could be prepared in excellent yield. Analysis of selected DNA oligomers by enzymatic degradation and mass spectroscopic analysis confirmed the designated sequences and compositions.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed2000

The oligomeric subunit C rotor in the fo sector of ATP synthase: unresolved questions in our understanding of function.

We have proposed a model for the oligomeric c-rotor of the F(o) sector of ATP synthase and its interaction with subunit a during H+-transport driven rotation. The model is based upon the solution structure of monomeric subunit c, determined by NMR, and an extensive series of cross-linking distance constraints between c subunits and between subunits c and a. To explain the complete set of cross-linking data, we have suggested that the second transmembrane helix rotates during its interaction with subunit a in the course of the H+-translocation cycle. The H+-transport coupled rotation of this helix is proposed to drive the stepwise movement of the c-oligomeric rotor. The model is testable and provides a useful framework for addressing questions raised by other experiments.

Bacterial Proton-Translocating ATPases↗
PubMed1999

Oligomerization of deoxyguanosine 5'-phosphoro-2-methylimidazolide on a polycytidylate template.

The oligomerization of deoxyguanosine 5'-phosphoro-2-methylimidazolide on a polycytidylate template is much less efficient than the oligomerization of the corresponding activated ribonucleotide. Nonetheless oligomers containing up to eight nucleotide residues are detected. The products are 3'-5'-linked oligodeoxyribonucleotides capped at the 5'-terminus with a pyrophosphate-linked monomer.

Chromatography, High Pressure Liquid↗
PubMed1998

An asymmetric deuterium labeling strategy to identify interprotomer and intraprotomer NOEs in oligomeric proteins.

A major difficulty in determining the structure of an oligomeric protein by NMR is the problem of distinguishing inter- from intraprotomer NOEs. In order to address this issue in studies of the 27 kD compact trimeric domain of the MHC class II-associated invariant chain, we compared the 13C NOESY-HSQC spectrum of a uniformly 13C-labeled trimer with the spectrum of the same trimer labeled with 13C in only one protomer, and with deuterium in the other two protomers. The spectrum of the unmixed trimer included both inter- and intraprotomer NOEs while the spectrum of the mixed trimer included only intraprotomer peaks. NOEs clearly absent from the spectrum of the mixed trimer could be confidently assigned to interprotomer interactions. Asymmetrically labeled trimers were isolated by refolding a 13C-labeled shorter form of the protein with a 2H-labeled longer form, chromatographically purifying trimers with only one short chain, and then processing the trypsin to yield only protomers with the desired N- and C-termini. In contrast to earlier studies, in which statistical mixtures of differently labeled protomers were analyzed, our procedure generated only a well-defined 1:2 oligomer, and no other mixed oligomers were present. This increased the maximum possible concentration of NMR-active protomers and thus the sensitivity of the experiments. Related methods should be applicable to many oligomeric proteins, particularly those with slow protomer exchange rates.

Antigens, Differentiation, B-Lymphocyte↗
PubMed2001

Na/K-ATPase as an oligomeric ensemble.

Differences in the kinetic behavior and properties of monomeric and oligomeric forms of membrane-bound Na/K-ATPase are analyzed. It is concluded that enzyme molecules within oligomeric complexes are affected by extrinsic signals that result in change of enzyme activity, whereas the individual (protomeric) state is insensitive to these signals. Some of the major factors of such regulation are microviscosity of the lipid environment, reactive oxygen species, and intracellular protein kinases.

Adenosine Triphosphate↗
PubMed2000

An unsolved problem of the clonal selection theory and the model of an oligomeric B-cell antigen receptor.

The B cell antigen receptor (BCR) plays a central role in the development, survival and activation of B lymphocytes. As the pre-BCR, it controls allelic exclusion of heavy chains and the expansion of pre-B cells. As the BCR, it controls the positive and negative selection of immature B cells as well as the survival and activation of mature B cells. Recent studies of receptors have shown that it is the ligand that brings them into the conformation necessary for signaling. How the multiple and structurally diverse antigens could fulfill this task for the BCR is unknown, and we regard this as an unsolved problem of Burnet's clonal selection theory This question and our recent biochemical studies lead us to propose a new model for the BCR, according to which the BCR exists as a precise oligomeric complex on the B cell surface. In this form, it can signal positive selection and survival of B cells. Binding to self- or foreign antigen results in a distortion of the oligomeric complex that gives the signal for negative selection of immature and activation of mature B cells.

Animals↗
PubMed1998

Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP.

N-ethylmaleimide-sensitive factor (NSF) is a hexameric ATPase which primes and/or dissociates SNARE complexes involved in intracellular fusion events. Each NSF protomer contains three domains: an N-terminal domain required for SNARE binding and two ATPase domains, termed D1 and D2, with D2 being required for oligomerization. We have determined the 1.9 A crystal structure of the D2 domain of NSF complexed with ATP using multi-wavelength anomalous dispersion phasing. D2 consists of a nucleotide binding subdomain with a Rossmann fold and a C-terminal subdomain, which is structurally unique among nucleotide binding proteins. There are interactions between the ATP moiety and both the neighboring D2 protomer and the C-terminal subdomain that may be important for ATP-dependent oligomerization. Of particular importance are three well-ordered and conserved lysine residues that form ionic interactions with the beta- and gamma-phosphates, one of which likely contributes to the low hydrolytic activity of D2.

Adenosine Triphosphatases↗
PubMed1988

Homologous plant and bacterial proteins chaperone oligomeric protein assembly.

An abundant chloroplast protein is implicated in the assembly of the oligomeric enzyme ribulose bisphosphate carboxylase-oxygenase, which catalyses photosynthetic CO2-fixation in higher plants. The product of the Escherichia coli groEL gene is essential for cell viability and is required for the assembly of bacteriophage capsids. Sequencing of the groEL gene and the complementary cDNA encoding the chloroplast protein has revealed that these proteins are evolutionary homologues which we term 'chaperonins'. Chaperonins comprise a class of molecular chaperones that are found in chloroplasts, mitochondria and prokaryotes. Assisted post-translational assembly of oligomeric protein structures is emerging as a general cellular phenomenon.

Adenosine Triphosphatases↗
PubMed2001

Crystal structure of the human prion protein reveals a mechanism for oligomerization.

The pathogenesis of transmissible encephalopathies is associated with the conversion of the cellular prion protein, PrP(C), into a conformationally altered oligomeric form, PrP(Sc). Here we report the crystal structure of the human prion protein in dimer form at 2 A resolution. The dimer results from the three-dimensional swapping of the C-terminal helix 3 and rearrangement of the disulfide bond. An interchain two-stranded antiparallel beta-sheet is formed at the dimer interface by residues that are located in helix 2 in the monomeric NMR structures. Familial prion disease mutations map to the regions directly involved in helix swapping. This crystal structure suggests that oligomerization through 3D domain-swapping may constitute an important step on the pathway of the PrP(C) --> PrP(Sc) conversion.

Crystallography, X-Ray↗
PubMed2004

Membrane-dependent conformational changes initiate cholesterol-dependent cytolysin oligomerization and intersubunit beta-strand alignment.

Cholesterol-dependent cytolysins are bacterial protein toxins that bind to cholesterol-containing membranes, form oligomeric complexes and insert into the bilayer to create large aqueous pores. Membrane-dependent structural rearrangements required to initiate the oligomerization of perfringolysin O monomers have been identified, as have the monomer-monomer interaction surfaces, using site-specific mutagenesis, disulfide trapping and multiple fluorescence techniques. Upon binding to the membrane, a structural element in perfringolysin O moves to expose the edge of a previously hidden beta-strand that forms the monomer-monomer interface and is required for oligomer assembly. The beta-strands that form the interface each contain a single aromatic residue, and these aromatics appear to stack, thereby aligning the transmembrane beta-hairpins of adjacent monomers in the proper register for insertion. Collectively, these data reveal a novel membrane binding-dependent mechanism for regulating cytolysin monomer-monomer association and pore formation.

Bacterial Toxins↗
PubMed2000

Subcellular localization and CARD-dependent oligomerization of the death adaptor RAIDD.

RAIDD, a caspase recruitment domain (CARD) containing molecule, interacts with procaspase-2 in a CARD-dependent manner. This interaction has been suggested to mediate the recruitment of caspase-2 to the tumour necrosis factor receptor 1 (TNFR1). In this paper we have studied the subcellular localization of RAIDD and its interaction with caspase-2. We demonstrate that endogenous RAIDD is mostly localized in the cytoplasm and to some extent in the nucleus. RAIDD localization is not affected by TNF-treatment of HeLa cells, but in cells ectopically expressing caspase-2, a fraction of RAIDD is recruited to the nucleus. In transfected cells, coexpression of RAIDD and caspase-2 leads to CARD-dependent colocalization of the two proteins to discrete subcellular structures. We further show that overexpression of the RAIDD-CARD results in the formation of filamentous structures due to CARD-mediated oligomerization. These structures were similar to death effector filaments (DEFs) formed by FADD and FLICE death effector domains (DEDs), and partially colocalized with DEFs. Our results suggest that similar to the DED, the RAIDD-CARD has the ability to form higher order complexes, believed to be important in apoptotic execution. We also present evidence that RAIDD-CARD oligomerization may be regulated by intramolecular folding of the RAIDD molecule.

Apoptosis↗