Strength Of Dimerization Research Articles

Cysteine‐Mediated Dimerization of the Transmembrane Domain of Mucin 16

Mucins are proteins in the epithelial tissue that produce mucus barriers to provide moisture and also prevent harmful, foreign material from entering the cell. These proteins are heavily glycosylated, and can be secreted to the extracellular space or be embedded in the plasma membrane. The overexpression of transmembrane mucins have been correlated with the development of cancerous growths. For example, the transmembrane mucins mucin 1 (MUC1) and mucin 16 (MUC16) have been associated with breast and ovarian cancer, respectively.The role of MUC1 in tumor progression has been extensively studied. Dimerization of MUC1 leads to its trafficking to the nucleus where it can alter the expression of genes that regulate cell growth. The cysteine‐glutamine‐cysteine (CQC) motif in the cytosolic juxtamembrane domain of MUC1 is the main driving force of this dimerization, primarily through the formation of disulfide bonds. Contrary to MUC1, there is not much information regarding the possible intracellular role of MUC16 in tumor formation and progression. Similar to MUC1, MUC16 also has two cysteine residues at or near the juxtamembrane domain. Furthermore, recent studies have observed the presence of MUC16 in the nucleus. Thus, we hypothesized that there may be a similarity in the mechanism of trafficking of MUC1 with that of MUC16.We are using the ToxR activity assay to assess the dimerization of the transmembrane domains of MUC1 and MUC16 with and without the juxtamembrane cysteines. Our preliminary results show that, in the presence of the cysteine residues, the transmembrane domain of MUC16 dimerizes as strongly as that of MUC1. Our results also show that the strength of dimerization, in both MUC1 and MUC16 are associated with the formation of disulfide bonds. These results suggest a possible mechanism of MUC16 nuclear trafficking, similar to that of MUC1, involving cysteine‐mediated dimerization.Support or Funding InformationNicholas & Susan Nicholaides Research Fellowship, and the SJU Summer Scholars ProgramThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Selective Dimerization Control in a Redox-Responsive Ureidopyrimidinone Supramolecular Assembly

Supramolecular polymers can be formed through directional intermolecular interactions between designated molecular subunits in order to achieve dynamic behavior. The strength of these intermolecular interactions can be altered through the use of external signals such as light absorption, changes in temperature and/or pH, or in an almost unexplored caveat, the application of voltage. Such is one of the important goals in supramolecular chemistry: the development of stimuli-responsive systems where the strength of intermolecular interactions can be perturbed through the use of external signals. Applications of supramolecular chemistry include self-healing polymers and gels, controlled release of entrapped molecules, and the development of smart materials. Ureidopyrimidinones (UPy) – introduced by Meijer and coworkers – can form two self-complementary 4 hydrogen bond arrays with binding motifs AADD or ADAD and have a relatively small dissociation constant of 10-6. Due to their directionality and strength of dimerization, UPys have been widely imployed as polymer cross-linkers in oligomerization and also as capping agents in chain termination. In these cases, association and/or dissociation of UPy hydrogen bonded complexes are influenced by external signals that were previously described. However, the application of voltage to affect binding of the UPy supramolecular complex is a relatively new approach towards dimerization control. In order for UPy to show electrochemical responsiveness, an electroactive substituent needs to be attached to the UPy framework. We have prepared and characterized such a system in which a ferrocene (Fc) is attached to the pyrimidone ring in the UPy. Concentration and scan-rate-dependent cyclic voltammetry and diffusion coefficient data from bulk electrolysis coupled with steady-state voltammetry indicate a square scheme mechanism for the UPyFc / UPyFc+ redox couple in dichloromethane. The fully reduced UPyFc exists as a dimer. Upon oxidation to UPyFc+, the dimer breaks apart to form the monomer. However, it is unknown how conversion between the AADD and ADAD binding motifs – due to tautomerization – factors into the square scheme mechanism. Nonetheless CV simulations with a simple square scheme mechanism (neglecting tautomerization) provide reasonable fits to the experimental data. Importantly, the overall process appears to be completely chemically reversible even over the relatively long time scale of bulk electrolysis. Based off of this preliminary work, syntheses of covalently-linked UPyFc oligomers are underway with the goal of creating a redox-responsive supramolecular polymer whose physical properties can be altered upon oxidation. As it has been confirmed that the fully reduced UPyFc exists as a dimer, the physical properties of the material should reflect this dimerization by showing rigidity or in some cases, a highly viscous material. Upon oxidation, dimerization should cease, causing the ferrocene-UPy oligomer to break apart and show physical properties that reflect a loss in rigidness and greater fluid, thereby achieving a more selective process of perturbing electrostatic interactions in supramolecular assemblies.

Evidence for Electronically Driven Ferroelectricity in a Strongly Correlated Dimerized BEDT-TTF Molecular Conductor.

By applying measurements of the dielectric constants and relative length changes to the dimerized molecular conductor κ-(BEDT-TTF)_{2}Hg(SCN)_{2}Cl, we provide evidence for order-disorder type electronic ferroelectricity that is driven by the charge order within the (BEDT-TTF)_{2} dimers and stabilized by a coupling to the anions. According to our density functional theory calculations, this material is characterized by a moderate strength of dimerization. This system thus bridges the gap between strongly dimerized materials, often approximated as dimer-Mott systems at 1/2 filling, and nondimerized or weakly dimerized systems at 1/4 filling, exhibiting a charge order. Our results indicate that intradimer charge degrees of freedom are of particular importance in correlated κ-(BEDT-TTF)_{2}X salts and can create novel states, such as electronically driven multiferroicity or charge-order-induced quasi-one-dimensional spin liquids.

Enhancement of electron correlation due to the molecular dimerization in organic superconductorsβ−(BDA-TTP)2X(X=I3, SbF6)

We perform a first principles band calculation for quasi-two-dimensional organic superconductors $\beta$-(BDA-TTP)$_{2}$I$_{3}$ and $\beta$-(BDA-TTP)$_{2}$SbF$_{6}$. The first principles band structures between the I$_{3}$ and SbF$_{6}$ salts are apparently different. We construct a tight-binding model for each material which accurately reproduces the first principles band structure. The obtained transfer energies give the differences such as (i) larger dimerization in the I$_{3}$ salt than the SbF$_{6}$ salt, and (ii) different signs and directions of the inter-stacking transfer energies. To decompose the origin of the difference into the dimerization and the inter-stacking transfer energies, we adopt a simplified model by eliminating the dimerization effect and extract the difference caused by the inter-stacking transfer energies. From the analysis using the simplified model, we find that the difference of the band structure comes mainly from the strength of dimerization. To compare the strength of the electron correlation having roots in the band structure, we calculate the physical properties originated from the effect of the electron correlation such as the spin susceptibility applying two particle self-consistent (TPSC) method. We find that the maximum value of the spin susceptibility of the I$_{3}$ salt is larger than that of the SbF$_{6}$ salt. Hypothetically decreasing the dimerization within the model of the I$_{3}$ salt, the spin susceptibility takes almost the same value as that of the SbF$_6$ salt for the same magnitude of the dimerization. We expect that the different ground state between the I$_{3}$ and SbF$_{6}$ salt mainly comes from the strength of the dimerization which is apparently masked in the band calculation along a particular $k$-path.

Topology, Dimerization, and Stability of the Single-Span Membrane Protein CadC

Under acid stress, Escherichia coli induce expression of CadA (lysine decarboxylase) and CadB (lysine/cadaverine antiporter) in a lysine-rich environment. The ToxR-like transcriptional activator CadC controls expression of the cadBA operon. Using a novel signal peptidase I (SPase I) cleavage assay, we show that CadC is a type II single-span membrane protein (S-SMP) with a cytoplasmic DNA-binding domain and a periplasmic sensor domain. We further show that, as long assumed, dimerization of the sensor domain is required for activating the cadBA operon. We prove this using a chimera in which the periplasmic domain of RodZ—a type II membrane protein involved in the maintenance of the rod shape of E. coli—replaces the CadC sensor domain. Because the RodZ periplasmic domain cannot dimerize, the chimera cannot activate the operon. However, replacement of the transmembrane (TM) domain of the chimera with the glycophorin A TM domain causes intramembrane dimerization and consequently operon activation. Using a low-expression protocol that eliminates extraneous TM helix dimerization signals arising from protein over-expression, we enhanced dramatically the dynamic range of the β-galactosidase assay for cadBA activation. Consequently, the strength of the intramembrane dimerization of the glycophorin A domain could be compared quantitatively with the strength of the much stronger periplasmic dimerization of CadC. For the signal peptidase assay, we inserted an SPase I cleavage site (AAA or AQA) at the periplasmic end of the TM helix. Cleavage occurred with high efficiency for all TM and periplasmic domains tested, thus eliminating the need for the cumbersome spheroplast-proteinase K method for topology determinations.

Differential Stability of the Crystallographic Interfaces of Mu- and Kappa-Opioid Receptors

The recent mu-opioid receptor (MOPr) and kappa-opioid receptor (KOPr) crystal structures have inspired hypotheses of physiologically relevant dimerization contacts, specifically: a closely packed interface involving transmembrane (TM) helices TM5 and TM6, and a less compact interface, involving TM1, TM2, and helix 8 (H8). While the former was only found in MOPr crystals, similar arrangements of the latter were identified for both KOPr and MOPr. The relevance of these interfaces outside of a crystal lattice is called into question by the possibility that they might be influenced by the specific crystallization conditions. In this study, we have employed umbrella sampling molecular dynamics simulations of coarse-grained representations of the interacting MOPr or KOPr crystallographic structures, in the absence of the T4 lysozyme, and in an explicit lipid-water environment, to determine the strength of receptor dimerization at the different crystallographic interfaces. We note that the shape of the interface plays a dominant role in the strength of the interaction, and the pattern of contacting residues defines the shape of the potential of mean force. This information can be used to guide experiments aimed at exploring the role of dimerization in opioid receptor function.

Theoretical investigation on the 2e/12c bond and second hyperpolarizability of azaphenalenyl radical dimers: Strength and effect of dimerization

An increasing number of chemists have focused on the investigations of two-electron/multicenter bond (2e/mc) that was first introduced to describe the structure of radical dimers. In this work, the dimerization of two isoelectronic radicals, triazaphenalenyl (TAP) and hexaazaphenalenyl (HAP) has been investigated in theory. Results show TAP2 is a stable dimer with stronger 2e/12c bond and larger interaction energy, while HAP2 is a less stable dimer with larger diradical character. Interestingly, the ultraviolet-visible absorption spectra suggest that the dimerization induces a longer wavelength absorption in visible area, which is dependent on the strength of dimerization. Significantly, the amplitude of second hyperpolarizability (γ(yyyy)) of HAP2 is 1.36 × 10(6) a.u. that is larger than 7.79 × 10(4) a.u. of TAP2 because of the larger diradical character of HAP2. Therefore, the results indicate that the strength of radical dimerization can be effectively detected by comparing the magnitude of third order non-linear optical response, which is beneficial for further theoretical and experimental studies on the properties of complexes formed by radical dimerization.

Crossover from Metal to Insulator and Charge Order Transition of (TMTTF)2SbF6 under Constant Pressure

Crossover from Metal to Insulator and Charge Order Transition of (TMTTF)₂SbF₆ under Constant Pressure

Stable and Unstable Cadherin Dimers: Mechanisms of Formation and Roles in Cell Adhesion

Numerous attempts to elucidate the strength of cadherin dimerization that mediates intercellular adhesion have produced controversial and inconclusive results. To clarify this issue, we compared E-cadherin dimerization on the surface of living cells with how the same process unfolds on agarose beads. In both cases, dimerization was monitored by the same site-specific cross-linking assay, greatly simplifying data interpretation. We showed that on the agarose surface under physiological conditions, E-cadherin produced a weak dimer that immediately dissociated after the depletion of calcium ions. However, either at pH 5 or in the presence of cadmium ions, E-cadherin produced a strong dimer that was unable to dissociate upon calcium depletion. Both types of dimers were W156-dependent. Remarkably, only the strong dimer was found on the surface of living cells. We also showed that the intracellular cadherin region, the clustering of which through catenins had been proposed as stabilizer of weak intercadherin interactions, was not needed, in fact, for cadherin junction assembly. Taken together, our data present convincing evidence that cadherin adhesion is based on high-affinity cadherin-cadherin interactions.

Tandem GxxxG motifs and intermonomer hydrogen bonds stabilize BNIP3 transmembrane domain homodimerization

Knowledge of how the transmembrane domains (TMDs) of single-span membrane proteins form stable helix-helix associations can provide insights into understanding membrane protein folding and stability. To enrich this knowledge, we have explored the specificity and stability of BNIP3 TMD dimerization. Using saturation mutagenesis, we have found that this dimerization is mediated by small residues A176, G180, and G184, which allow close approach of the TMD helices, and by polar residues H173 and S172, which mediate intermonomer hydrogen bonding, and that the sequence context flanking these five critical residues also affects the strength of dimerization. Currently, we are using solution NMR to determine the structure of the BNIP3 TMD dimer, which will reveal how the elements of this sequence cooperate to support dimerization and provide a context to interpret the saturation mutagenesis results. This work is supported by Robert A. Welch Foundation grant C-1513 and by NIH grant R01 GM067850.

Dynamics and transport in random quantum systems governed by strong-randomness fixed points

We present results on the low-frequency dynamical and transport properties of random quantum systems whose low temperature $(T),$ low-energy behavior is controlled by strong-disorder fixed points. We obtain the momentum- and frequency-dependent dynamic structure factor in the random singlet (RS) phases of both spin-1/2 and spin-1 random antiferromagnetic chains, as well as in the random dimer and Ising antiferromagnetic phases of spin-1/2 random antiferromagnetic chains. We show that the RS phases are unusual ``spin metals'' with divergent low-frequency spin conductivity at $T=0,$ and we also follow the conductivity through ``metal-insulator'' transitions tuned by the strength of dimerization or Ising anisotropy in the spin-1/2 case, and by the strength of disorder in the spin-1 case. We work out the average spin and energy autocorrelations in the one-dimensional random transverse-field Ising model in the vicinity of its quantum critical point. All of the above calculations are valid in the frequency-dominated regime $\ensuremath{\omega}\ensuremath{\gtrsim}T,$ and rely on previously available renormalization group schemes that describe these systems in terms of the properties of certain strong-disorder fixed-point theories. In addition, we obtain some information about the behavior of the dynamic structure factor and dynamical conductivity in the opposite ``hydrodynamic'' regime $\ensuremath{\omega}<T$ for the special case of spin-1/2 chains close to the planar limit (the quantum $x\ensuremath{-}y$ model) by analyzing the corresponding quantities in an equivalent model of spinless fermions with weak repulsive interactions and particle-hole symmetric disorder.

Dynamics and transport in random antiferromagnetic spin chains

We present the first results on the low-frequency dynamical and transport properties of random antiferromagnetic spin chains at low temperature (T). We obtain the momentum and frequency dependent dynamic structure factor in the random singlet (RS) phases of both spin-1/2 and spin-1 chains, as well as in the random dimer phase of spin-1/2 chains. We also show that the RS phases are unusual "spin-metals" with divergent low-frequency conductivity at T = 0, and follow the spin conductivity through "metal-insulator" transitions tuned by the strength of dimerization or Ising anisotropy in the spin-1/2 case and by the strength of disorder in the spin-1 case.

Carboxyl-terminal domain dimer interface mutant 434 repressors have altered dimerization and DNA binding specificities

Strong dimerization of the repressor, mediated by the carboxyl (C)-terminal domain, is a prerequisite for forming a specific complex with DNA and cooperative DNA binding to form tetramers. We have generated a computer model of the C-terminal domain of the 434 repressor based on the crystal structure of the homologous UmuD′ protein. This model predicts that residues in the primary sequence between 93 and 168 contribute to the dimer interface. We changed several amino acid residues located in this region. Gel filtration and crosslinking assays were used to characterize the strength and specificity of dimerization of the purified repressor C-terminal domain dimer interface mutants. These results indicate that amino acid residues K121, H139, D161 and N163 contribute to the strength and/or specificity of dimerization. The relative affinity of the bacteriophage 434 repressor for 434 operators is determined, in part, by the repressor’s ability to detect sequence-dependent structural alterations in the non-contacted region at the center of an operator site. We find that the relative ability of C-terminal domain dimer interface mutant repressors to dimerize does not necessarily predict their relative abilities to bind DNA, and that these proteins are deficient in detecting non-contacted base-dependent differences in operator strength. Our results show that the structure of the DNA in complex with these mutant proteins differs from that found in wild-type repressor-operator complexes, even though the sites of these mutations lie in a separate domain from that which contacts the DNA. These observations demonstrate that the structural integrity of the C-terminal domain dimer interface is required to appropriately orient the DNA binding information contained within the DNA-contacting N-terminal domain.