Asymmetry in the Multiprotein Systems of Molecular Biology

Signaling in living systems needs to achieve high specificity, to be reversible, and to achieve high signal to noise. Signaling mediated by multiprotein systems has evolved that avoids the requirement for high-affinity binary complexes that would be difficult to reverse and which, in the overcrowded cell, would lead to excessive noise in the system. Symmetrical structures are only occasionally formed. When they are, it is principally to colocate components, for example, the tyrosyl kinases of growth factors, where dimers form. Symmetry is, however, often broken, presumably to create more sensitivity and specificity in the signaling system by assembling other components, into higher-order multiprotein systems. The binding of a single heparin to two 1:1 FGF:FGFR complexes is an example, as is the binding of a single ligase to the Xrcc4 dimer, perhaps so creating a further DNA-binding site.     

Charge-transfer mechanism for cytochrome c adsorbed on nanometer thick films. Distinguishing frictional control from conformational gating

Using nanometer thick tunneling barriers with specifically attached cytochrome c, the electron-transfer rate constant was studied as a function of the SAM composition (alkane versus terthiophene), the omega-terminating group type (pyridine, imidazole, nitrile), and the solution viscosity. At large electrode-reactant separations, the pyridine terminated alkanethiols exhibit an exponential decline of the rate constant with increasing electron-transfer distance. At short separations, a plateau behavior, analogous to systems involving -COOH terminal groups to which cytochrome c can be attached electrostatically, is observed. The dependence of the rate constant in the plateau region on system properties is investigated. The rate constant is insensitive to the mode of attachment to the surface but displays a significant viscosity dependence, change with spacer composition (alkane versus terthiophene), and nature of the solvent (H(2)O versus D(2)O). Based on these findings and others, the conclusion is drawn that the charge-transfer rate constant at short distance is determined by polarization relaxation processes in the structure, rather than the electron tunneling probability or large-amplitude conformational rearrangement (gating). The transition in reaction mechanism with distance reflects a gradual transition between the tunneling and frictional mechanisms. This conclusion is consistent with data from a number of other sources as well.     

Polypropylene ionic thermoplastic elastomers: Synthesis and properties

Polypropylene ionic thermoplastic elastomers have been prepared by melt radical grafting of maleic anhydride onto polypropylene in the presence of N-bromosuccinimide followed by neutralization of the resulting elastomeric grafted polypropylene using sodium salts. Sodium hydroxide and sodium acetate were compared in aqueous solution, as anhydrous or hydrated powders. The neutralization reaction was followed by Fourier transform infrared spectroscopy, allowing the development of a method to determine the effective neutralization degree. Important physical changes were recorded upon neutralization. Especially thermal stability, shear storage modulus and complex viscosity in the flow region were largely increased as a function of the neutralization degree.     

Mechanistic pathways for the reaction of quercetin with hydroperoxy radical

The extensive theoretical study of the interaction of one of the most abundant and reactive flavonols, quercetin, with hydroperoxy radical (HOO·), using the M052X/6-31 + Gd, p level of theory, was performed. Results indicating that quercetin is not a planar molecule are in accord with the X-ray analysis. The applied method successfully reproduces the bond dissociation enthalpy, and reveals that the reaction of quercetin with the hydroperoxy radical is governed by a hydrogen atom transfer mechanism. It is confirmed that the 3′OH and 4′OH are the most reactive sites, and that the reaction in the 3′OH position is faster than that in the 4′OH position.     

Fast reduction of a copper center in laccase by nitric oxide and formation of a peroxide intermediate

The rapid reduction of one of the copper atoms (type 2) of tree laccase by nitric oxide (NO) has been detected. Addition of NO to native laccase in the presence of oxygen leads to EPR changes consistent with fast reduction and slow reoxidation of this metal center. These events are paralleled by optical changes that are reminiscent of formation and decay of the peroxide intermediate in a fraction of the enzyme population. Formation of this species is only possible if the trinuclear copper cluster (type 2 plus type 3) is fully reduced. This condition can only be met if, as suggested previously, a fraction of the enzyme contains both type 3 coppers already reduced before addition of NO. Our data are consistent with this assumption. We have suggested recently that fast reduction of copper is the mechanism by which NO interacts with the oxidized dinuclear center in cytochrome c oxidase. The present experiments using laccase strongly support this view and suggest this reaction as a general mechanism by which copper proteins interact with NO. In addition, this provides an unexploited way to produce a stable peroxide intermediate in copper oxidases in which the full complement of copper atoms is present. This enables the O-O scission step in the catalytic cycle to be studied by electron addition to the peroxide derivative through the native electron entry site, type 1 copper.     

Local dense structural heterogeneities in liquid water from ambient to 300 MPa pressure: evidence for multiple liquid-liquid transitions.

Difference and double-difference near-infrared DO-D and HO-H stretching overtone (2nuOD and 2nuOH) spectroscopy and a rigorous (physically substantiated) band deconvolution technique were applied to reveal three different kinds of inherent (interstitial) structures of liquid water, which determine its high density (compared to ice lh under ambient conditions), its compressibility (under hydrostatic pressure, up to 300MPa), and its high fragility (manifested under temperature variation). Our data processing allowed the rigorous discrimination of up to six vibrational components. On the basis of an extensive comparative analysis combined with available structural data (X-ray and neutron scattering) and molecular dynamics (MD) simulations for liquid water, as well as with experimental and computed data for small non-tetrahedrally arranged water clusters, the major four components could be ascribed to: i) The basic lh icelike substructure; ii) the temperature-dependent remote interstitial "defects" due to tetrahedral displacements (primarily responsible for transport properties); iii) the interstitial "defects" most probably arranged in quasiplanar noncyclic tetramers (totally absent in the ice structure); and iv) the interstitial "defects" formed with increasing pressure, probably arranged in cubic water octamers and composed of two pairs of noncyclic and cyclic tetramer fragments. The latter structures include, essentially, bent hydrogen bonds stabilized by resonance effects.     

A single-site model for divalent transition and heavy metal adsorption over a range of metal concentrations

Metal adsorption data over a range of surface coverages typically are characterized by curvilinear metal adsorption isotherms. These isotherms generally have a slope of 1 at low surface coverage and a shallower slope at higher surface coverages. The curvature of metal adsorption isotherms with increasing surface coverage is frequently interpreted in terms of sequential adsorption onto different types of surface sites, multinuclear surface complexation, or nonideality of metal adsorption. We demonstrate that the curvature of metal adsorption isotherms can also be attributed to changes in surface charge and potential that depend on the predominant type of metal surface complex. A single-site extended triple-layer model is used to reinterpret previously studied metal adsorption isotherms and pH edges for a wide variety of metals (Cd2+, Co2+, Cu2+, Pb2+, and Zn2+) and solids (goethite, hydrous ferric oxide, corundum, and magnetite) in different electrolyte solutions (NaNO3 and NaClO4). Only metal adsorption on ferrihydrite at very low surface coverages is not consistent with the single-site triple-layer model. This discrepancy might be explained if ferrihydrite is in fact not a single phase but a mixture of two or more phases. Metal surface coverages ranging from 10(-4) to 10.2 mmol/m2 on the other minerals can be accounted for with a single-site extended triple-layer model if appropriate metal adsorption reactions are chosen. In addition, several examples suggest that, within the context of the model, surface complexation schemes can be established that describe metal adsorption over both a wide range of surface coverage and a wide range of ionic strength.     

An improved capillary electrophoresis method for in vitro monitoring of the challenging early steps of Aβ1–42 peptide oligomerization: Application to anti‐Alzheimer's drug discovery

We report an improved CE method to monitor in vitro the self‐assembly of monomeric amyloid β‐peptide (42 amino acids amyloid β‐peptide, Aβ_1–42) and in particular the crucial early steps involved in the formation of the neurotoxic oligomers. In order to start the kinetics from the beginning, sample preparation was optimized to provide samples containing exclusively the monomeric form. The CE method was also improved using a dynamic coating and by reducing the separation distance. Using this method, the disappearance of the monomer as well as the progressive formation of four species during the self‐assembly process can now be monitored and quantified over time. The hydrodynamic radius of the species present at the initial kinetics step was estimated around 1.8 nm by Taylor dispersion analysis while SDS‐PAGE analyses showed the predominance of the monomer. These results confirmed that the Aβ_1–42 species present at this initial time was the monomer. Methylene blue, an anti‐Alzheimer disease candidate, was then evaluated. In spite of an oligomerization inhibition, the enhanced disappearance of the Aβ_1–42 monomer provoked by methylene blue was demonstrated for the first time. This method, allowing the monomeric and smallest oligomeric species to be monitored, represents a new accurate and precise way to evaluate compounds for drug discovery.