GTP binding and intramolecular regulation by the ROC domain of Death Associated Protein Kinase 1

The ROCO proteins are a family of large, multidomain proteins characterised by the presence of a Ras of complex proteins (ROC) domain followed by a COR, or C-terminal of ROC, domain. It has previously been shown that the ROC domain of the human ROCO protein Leucine Rich Repeat Kinase 2 (LRRK2) controls its kinase activity. Here, the ability of the ROC domain of another human ROCO protein, Death Associated Protein Kinase 1 (DAPK1), to bind GTP and control its kinase activity has been evaluated. In contrast to LRRK2, loss of GTP binding by DAPK1 does not result in loss of kinase activity, instead acting to modulate this activity. These data highlight the ROC domain of DAPK1 as a target for modifiers of this proteins function, and casts light on the role of ROC domains as intramolecular regulators in complex proteins with implications for a broad range of human diseases.

Binding properties and adhesion-mediating regions of the major sheath protein of Treponema denticola ATCC 35405

There is growing evidence that a number of oral Treponema species, in particular Treponema denticola, are associated with the progression of human periodontal disease. The major sheath (or surface) protein (Msp) of T. denticola is implicated in adhesion of bacteria to host cells and tissue proteins and is likely to be an important virulence factor. However, the binding regions of the Msp are not known. We have purified from Escherichia coli recombinant Msp (rMsp) polypeptides corresponding to the following: full-length Msp (rMsp) minus 13 N-terminal amino acid (aa) residues, an amino-terminal fragment (rN-Msp, 189 aa residues), a 57-aa residue segment from the central region (rV-Msp), and a C-terminal fragment (rC-Msp, 272 aa residues). rMsp (530 aa residues) bound to immobilized fibronectin, keratin, laminin, collagen type 1, fibrinogen, hyaluronic acid, and heparin. The N- and V-region polypeptides, but not rC-Msp, also bound to these substrates. Binding of rMsp to fibronectin was targeted to the N-terminal heparin I/fibrin I domain. Antibodies to the N-region or V-region polypeptides, but not antibodies to the rC-Msp fragment, blocked adhesion of T. denticola ATCC 35405 cells to a range of host protein molecules. These results suggest that the N-terminal half of Msp carries epitopes that are surface exposed and that are involved in mediating adhesion. Binding of rMsp onto the cell surface of low-level fibronectin-binding Treponema isolates conferred a 10-fold increase in fibronectin binding. This confirms that Msp functions autonomously as an adhesin and raises the possibility that phenotypic complementation of virulence functions might occur within mixed populations of Treponema species.

Synthesis, characterization, crystal structure, and DNA-binding of ruthenium(II) complexes of heterocyclic nitrogen ligands resulting from a benzimidazole-based quinazoline derivative

The reaction of cis-[RuCl2(dmso)(4)] with [6-(2-pyridinyl)-5,6-dihydrobenzimidazo[1,2-c] quinazoline] (L) afforded in pure form a blue ruthenium(II) complex, [Ru(L-1)(2)] (1), where the original L changed to [2-(1H-benzoimidazol-2-yl)-phenyl]-pyridin-2-ylmethylene-amine (HL1). Treatment of RuCl3 center dot 3H(2)O with L in dry tetrahydrofuran in inert atmosphere led to a green ruthenium(II) complex, trans-[RuCl2(L-2)(2)] (2), where L was oxidized in situ to the neutral species 6-pyridin-yl-benzo[4,5]imidazo[1,2-c] quinazoline (L-2). Complex 2 was also obtained from the reaction of RuCl3 center dot 3H(2)O with L-2 in dry ethanol. Complexes 1 and 2 have been characterized by physico-chemical and spectroscopic tools, and 1 has been structurally characterized by single-crystal X-ray crystallography. The electrochemical behavior of the complexes shows the Ru(III)/Ru(II) couple at different potentials with quasi-reversible voltammograms. The interaction of these complexes with calf thymus DNA by using absorption and emission spectral studies allowed determination of the binding constant K-b and the linear Stern-Volmer quenching constant K-SV

Mutual binding of polymer end-groups by complementary π–π-stacking: a molecular “Roman Handshake”

Self-complementary tweezer-molecules based on a naphthalenediimide core self-assemble into supramolecular dimers through mutual π–π-stacking and hydrogen bonding. The resulting motif is extremely stable in solution (Ka = 105 M−1), and its attachment to one terminal position of a poly(ethylene glycol) chain leads to a doubling of the polymer's apparent molecular weight.

Metalloporphyrin anion sensors: the effect of the metal centre on the anion binding properties of amide-functionalised and tetraphenyl metalloporphyrins

This article describes the synthesis and anion binding properties of a series of ‘picket fence’ metalloporphyrin complexes, within which the metal centre is systematically varied. The porphyrin structure contains four amide bonds and is the same for each metal. The anion binding properties of these receptors are further contrasted with those of their tetraphenylporphyrin congeners to elucidate both the effect of the metal centre and the influence of the amide groups on the anion recognition process. Anion binding was demonstrated using UV/visible and 1H NMR spectroscopies, electrochemistry and luminescence. The metal centre was found to be highly influential in the strength and selectivity of binding; for example, the cadmium and mercury complexes exhibited far greater affinities for anions than the zinc complexes in competitive solvents such as DMSO. The amide functionalities were found to enhance the anion binding process.

Interaction of anthocyanins with human serum albumin: influence of pH and chemical structure on binding

The affinity of anthocyanins for human serum albumin (HSA) was determined by a fluorescence quenching method. The effects of pH and structure of anthocyanins on the binding constants were studied. The constants for binding of anthocyanins to HSA ranged from 1.08 x 10^5 M-1 to 13.16 x 10^5 M-1. A hydrophobic effect at acidic pH was shown by the relatively high positive entropy values under the conditions studied. Electrostatic interactions including hydrogen bonding contributed to the binding at pH 7.4. The effect of structure of anthocyanins on the affinity was pH dependent, particularly the effect of additional hydroxyl substituents. Hydroxyl substituents and glycosylation of anthocyanins decreased the affinity for binding to HSA at lower pH (especially pH 4), but increased the strength of binding at pH 7.4. In contrast, methylation of a hydroxyl group enhanced the binding at acidic pH, while this substitution reduced the strength of binding at pH 7.4. This paper has shown that changes in anthocyanin structure or reductions in pH, which may occur in the region of inflammatory sites, have an effect of the binding of anthocyanins to HSA.

Selected wheat seed defense proteins exhibit competitive binding to model microbial lipid interfaces

Puroindolines (Pins) and purothionins (Pths) are basic, amphiphilic, cysteine-rich wheat proteins that play a role in plant defense against microbial pathogens. We have examined the co-adsorption and sequential addition of Pins (Pin-a, Pin-b and a mutant form of Pin-b with Trp-44 to Arg-44 substitution) and β-purothionin (β-Pth) model anionic lipid layers, using a combination of surface pressure measurements, external reflection FTIR spectroscopy and neutron reflectometry. Results highlighted differences in the protein binding mechanisms, and in the competitive binding and penetration of lipid layers between respective Pins and β-Pth. Pin-a formed a blanket-like layer of protein below the lipid surface that resulted in the reduction or inhibition of β-Pth penetration of the lipid layer. Wild-type Pin-b participated in co-operative binding with β-Pth, whereas the mutant Pin-b did not bind to the lipid layer in the presence of β-Pth. The results provide further insight into the role of hydrophobic and cationic amino acid residues in antimicrobial activity.

Dopant-vacancy binding effects in Li-doped magnesium hydride

We use a combination of ab initio calculations and statistical mechanics to investigate the substitution of Li+ for Mg2+ in magnesium hydride (MgH2) accompanied by the formation of hydrogen vacancies with positive charge (with respect to the original ion at the site). We show that the binding energy between dopants and vacancy defects leads to a significant fraction of trapped vacancies and therefore a dramatic reduction in the number of free vacancies available for diffusion. The concentration of free vacancies initially increases with dopant concentration but reaches a maximum at around 1 mol % Li doping and slowly decreases with further doping. At the optimal level of doping, the corresponding concentration of free vacancies is much higher than the equilibrium concentrations of charged and neutral vacancies in pure MgH2 at typical hydrogen storage conditions. We also show that Li-doped MgH2 is thermodynamically metastable with respect to phase separation into pure magnesium and lithium hydrides at any significant Li concentration, even after considering the stabilization provided by dopant-vacancy interactions and configurational entropic effects. Our results suggest that lithium doping may enhance hydrogen diffusion hydride but only to a limited extent determined by an optimal dopant concentration and conditioned to the stability of the doped phase.

Investigation of milk proteins binding to the oral mucosa

High protein dairy beverages are considered to be mouth drying. The drying sensation may be due to the product protein content; however the mechanism of this mouth drying is uncertain. This study investigated the potential adhesion of milk proteins to porcine oral mucosal tissues and their resistance to wash out with simulated saliva was monitored using fluorescence microscopy. Cadein was found to be more adhesive to porcine mucosa then lactogloubulin. Some investigation into the reason for this difference in mucoadhesion was conducted by thiol-content analysis, rheology and zeta-potential measurements. The higher viscosity of casein solution and smaller zeta-potential is believed to be responsible for its better retention on mucosal surfaces. These findings suggest that casein and whey protein are both capable of binding and eliciting mouth drying in high protein dairy beverages.

Variable binding and coreference in sentence comprehension: evidence from eye movements

The hypothesis that pronouns can be resolved via either the syntax or the discourse representation has played an important role in linguistic accounts of pronoun interpretation (e.g. Grodzinsky & Reinhart, 1993). We report the results of an eye-movement monitoring study investigating the relative timing of syntactically-mediated variable binding and discourse-based coreference assignment during pronoun resolution. We examined whether ambiguous pronouns are preferentially resolved via either the variable binding or coreference route, and in particular tested the hypothesis that variable binding should always be computed before coreference assignment. Participants’ eye movements were monitored while they read sentences containing a pronoun and two potential antecedents, a c-commanding quantified noun phrase and a non c-commanding proper name. Gender congruence between the pronoun and either of the two potential antecedents was manipulated as an experimental diagnostic for dependency formation. In two experiments, we found that participants’ reading times were reliably longer when the linearly closest antecedent mismatched in gender with the pronoun. These findings fail to support the hypothesis that variable binding is computed before coreference assignment, and instead suggest that antecedent recency plays an important role in affecting the extent to which a variable binding antecedent is considered. We discuss these results in relation to models of memory retrieval during sentence comprehension, and interpret the antecedent recency preference as an example of forgetting over time.

Analysis of tyrosine phosphorylation and phosphotyrosine-binding proteins in germinating seeds from Scots pine

Protein tyrosine phosphorylation in angiosperms has been implicated in various physiological processes, including seed development and germination. In conifers, the role of tyrosine phosphorylation and the mechanisms of its regulation are yet to be investigated. In this study, we examined the profile of protein tyrosine phosphorylation in Scots pine seeds at different stages of germination. We detected extensive protein tyrosine phosphorylation in extracts from Scots pine (Pinus sylvestris L.) dormant seeds. In addition, the pattern of tyrosine phosphorylation was found to change significantly during seed germination, especially at earlier stages of post-imbibition which coincides with the initiation of cell division, and during the period of intensive elongation of hypocotyls. To better understand the molecular mechanisms of phosphotyrosine signaling, we employed affinity purification and mass spectrometry for the identification of pTyr-binding proteins from the extracts of Scots pine seedlings. Using this approach, we purified two proteins of 10 and 43 kDa, which interacted specifically with pTyr-Sepharose and were identified by mass spectrometry as P. sylvestris defensin 1 (PsDef1) and aldose 1-epimerase (EC:5.1.3.3), respectively. Additionally, we demonstrated that both endogenous and recombinant PsDef1 specifically interact with pTyr-Sepharose, but not Tyr-beads. As the affinity purification approach did not reveal the presence of proteins with known pTyr binding domains (SH2, PTB and C2), we suggest that plants may have evolved a different mode of pTyr recognition, which yet remains to be uncovered.

A mathematical model of the sterol regulatory element binding protein 2 cholesterol biosynthesis pathway

Cholesterol is one of the key constituents for maintaining the cellular membrane and thus the integrity of the cell itself. In contrast high levels of cholesterol in the blood are known to be a major risk factor in the development of cardiovascular disease. We formulate a deterministic nonlinear ordinary differential equation model of the sterol regulatory element binding protein 2 (SREBP-2) cholesterol genetic regulatory pathway in an hepatocyte. The mathematical model includes a description of genetic transcription by SREBP-2 which is subsequently translated to mRNA leading to the formation of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR), a main precursor of cholesterol synthesis. Cholesterol synthesis subsequently leads to the regulation of SREBP-2 via a negative feedback formulation. Parameterised with data from the literature, the model is used to understand how SREBP-2 transcription and regulation affects cellular cholesterol concentration. Model stability analysis shows that the only positive steady-state of the system exhibits purely oscillatory, damped oscillatory or monotic behaviour under certain parameter conditions. In light of our findings we postulate how cholesterol homestasis is maintained within the cell and the advantages of our model formulation are discussed with respect to other models of genetic regulation within the literature.

Bridge-localized HOMO-binding character of divinylanthracene-bridged dinuclear ruthenium carbonyl complexes: spectroscopic, spectroelectrochemical, and computational studies

The electronic properties of four divinylanthracene-bridged diruthenium carbonyl complexes [{RuCl(CO)(PMe3)3}2(μ[BOND]CH[DOUBLE BOND]CHArCH[DOUBLE BOND]CH)] (Ar=9,10-anthracene (1), 1,5-anthracene (2), 2,6-anthracene (3), 1,8-anthracene (4)) obtained by molecular spectroscopic methods (IR, UV/Vis/near-IR, and EPR spectroscopy) and DFT calculations are reported. IR spectroelectrochemical studies have revealed that these complexes are first oxidized at the noninnocent bridging ligand, which is in line with the very small ν(C[TRIPLE BOND]O) wavenumber shift that accompanies this process and also supported by DFT calculations. Because of poor conjugation in complex 1, except oxidized 1+, the electronic absorption spectra of complexes 2+, 3+, and 4+ all display the characteristic near-IR band envelopes that have been deconvoluted into three Gaussian sub-bands. Two of the sub-bands belong mainly to metal-to-ligand charge-transfer (MLCT) transitions according to results from time-dependent DFT calculations. EPR spectroscopy of chemically generated 1+–4+ proves largely ligand-centered spin density, again in accordance with IR spectra and DFT calculations results.

GTP binding controls complex formation by the human ROCO protein MASL1

The human ROCO proteins are a family of multi-domain proteins sharing a conserved ROC-COR supra-domain. The family has four members: leu- cine-rich repeat kinase 1 (LRRK1), leucine-rich repeat kinase 2 (LRRK2), death-associated protein kinase 1 (DAPK1) and malignant fibrous histiocy- toma amplified sequences with leucine-rich tandem repeats 1 (MASL1). Previous studies of LRRK1/2 and DAPK1 have shown that the ROC (Ras of complex proteins) domain can bind and hydrolyse GTP, but the cellular consequences of this activity are still unclear. Here, the first biochemical characterization of MASL1 and the impact of GTP binding on MASL1 complex formation are reported. The results demonstrate that MASL1, similar to other ROCO proteins, can bind guanosine nucleotides via its ROC domain. Furthermore, MASL1 exists in two distinct cellular com- plexes associated with heat shock protein 60, and the formation of a low molecular weight pool of MASL1 is modulated by GTP binding. Finally, loss of GTP enhances MASL1 toxicity in cells. Taken together, these data point to a central role for the ROC/GTPase domain of MASL1 in the reg- ulation of its cellular function.