The role of protein “Stability patches” in molecular recognition: A case study of the human growth hormone‐receptor complex

Dynamic characteristics of protein surfaces are among the factors determining their functional properties, including their potential participation in protein‐protein interactions. The presence of clusters of static residues—“stability patches” (SPs)—is a characteristic of protein surfaces involved in intermolecular recognition. The mechanism, by with SPs facilitate molecular recognition, however, remains unclear. Analyzing the surface dynamic properties of the growth hormone and of its high‐affinity variant we demonstrated that reshaping of the SPs landscape may be among the factors accountable for the improved affinity of this variant to the receptor. We hypothesized that SPs facilitate molecular recognition by moderating the conformational entropy of the unbound state, diminishing enthalpy–entropy compensation upon binding, and by augmenting the favorable entropy of desolvation. SPs mapping emerges as a valuable tool for investigating the structural basis of the stability of protein complexes and for rationalizing experimental approaches, such as affinity maturation, aimed at improving it. © 2015 Wiley Periodicals, Inc.     

Hall effect and conduction anisotropy in the organic conductor (TMTSF)2PF6

Both the Hall effect and the ab(')-plane conduction anisotropy are directly addressing the unconventional normal phase properties of the Bechgaard salt (TMTSF)2PF6. We found that the dramatic reduction of the carrier density deduced from recent optical data is not reflected in an enhanced Hall resistance. The pressure and temperature dependence of the b(')-direction resistivity reveal isotropic relaxation time and do not require explanations beyond the Fermi liquid theory. Our results allow a coherent-diffusive transition in the interchain carrier propagation, however the possible crossover to Luttinger liquid behavior is placed at an energy scale above room temperature.     

Measurement of the surface potential of individual crystal planes of hematite

A device for measuring surface potentials of individual crystal planes was constructed. The surface potentials of the (0 1 2), (1 0 -2), (1 1 3), and (1 1 -3) crystal planes of hematite were measured as a function of pH at different sodium nitrate concentrations. Results of measurement enabled differentiation between the planes, showing agreement with the surface potentials obtained with a single-crystal hematite electrode. At low ionic strength there was no significant difference in potential between the crystal planes, whereas at relatively high ionic strength the difference was noticeable. In the absence of counterion association, but also in the case of their symmetric association taking place, point of zero potential (pH(pzp)) coincides with other zero points, i.e., with the isolectric point (pH(iep)) and the point of zero charge (pH(pzc)). If the counterion affinities toward association are not equal, the pH(pzp) is shifted in the same directions as the pH(pzc). The shift in the point of zero potential to the basic region was more pronounced for the (1 1 -3) plane than for the (1 0 -2) one, indicating a higher affinity of anions for association with oppositely charged surface groups compared to cations. It was demonstrated that measurements of surface potentials of individual crystal planes could help to better understand the equilibrium at solid/liquid interfaces.     

Optimal position of solute for simulations

It is shown that, by optimizing the placement of a solute in a solvent droplet or in a periodic simulation cell, the number of solvent molecules can be reduced without affecting the quality of the simulation. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 812–815, 1997     

Modeling dimerizations of transmembrane proteins using Brownian dynamics simulations

The dimerizations of membrane proteins, Outer Membrane Phospholipase A (OMPLA) and glycophorin A (GPA), have been simulated by an adapted Brownian Dynamics program. To mimic the membrane protein environment, we introduced a hybrid electrostatic potential map of membrane and water for electrostatic interaction calculations. We added a van der Waals potential term to the force field of the current version of the BD program to simulate the short-range interactions of the two monomers. We reduced the BD sampling space from three dimensions to two dimensions to improve the efficiency of BD simulations for membrane proteins. The OMPLA and GPA dimers predicted by our 2D-BD simulation and structural refinement is in good agreement with the experimental structures. The adapted 2D-BD method could be used for prediction of dimerization of other membrane proteins, such as G protein-coupled receptors, to help better understanding of the structures and functions of membrane proteins.     

Charging of water at inert and hydrophobic surfaces. Effect on interfacial properties of silver halides

Isoelectric point of silver halides depends on pH due to charging of interfacial water layer. The isoelectric point of water at inert and hydrophobic surfaces lies at pH≈3 so that water at surfaces is negatively charged in the pH region above 4. Consequently the electroneutrality point of silver halides pAg_eln in aqueous environment, with respect to adsorption of silver and halide ions, does not correspond to the isoelectric point pAg_iep measured at pH≈6, as previously assumed. The effect of assumed value of pAg_iep was examined. The equilibrium constants for adsorption of silver and halide ions on silver chloride and silver bromide were calculated for the range of assumed pAg_iep values ranging from isoelectric points measured at pH=6 to pH=3. The values of pAg_iep obtained at pH=3 was taken as pAg_eln and the corresponding equilibrium constants of interfacial reactions were obtained.     

Synthesis of gold nanoparticles by microemulsion assisted photoreduction method

A new, clean, cost-effective and rapid method for the synthesis of stable spherical gold nanoparticles (AuNPs) is developed. This novel technique combines microemulsion as one of soft-nanotechnology techniques of wet chemistry, with photo-physics of UV-radiation in a unique versatile method to design and obtain controlled nanostructures for multifunctional materials. Based on a phase diagram in ternary water/Brij 30/n-heptane system pristine, and thiol functionalized, gold nanoparticles were obtained by a microemulsion assisted photoreduction technique, allowing increased flexibility during the synthesis and selection of materials. The spherical nanoparticles obtained by this route show a homogeneous size distribution, with an average diameter of 11 nm, for pristine gold nanoparticles and of 12 nm, for functionalized species. The evolution of the system at the nanoscale has been studied using, in tandem, UV-VIS and DLS measurements. The structure, size and shape of the final nanoparticles obtained have been evaluated by adequate instrumental techniques: FTIR, XRD and TEM image analysis. Kinetic studies have also been performed in order to follow the evolution of nanospecies during irradiation procedure.     

Influence of interfacial water layer on surface properties of silver halides: effect of pH on the isoelectric point

The hypothesis that pH dependent charge of interfacial water affects electrokinetic charge and electrokinetic potential of hydrophobic colloids, but not the (inner) surface potential was tested. It was found that isoelectric points of silver chloride, bromide and iodide shift to the higher pAg values in the acidic solutions, but that surface potential did not depend on pH. Isoelectric points of water at inert surfaces lie in the range 2相似文献   

The effect of electrolytes on the surface potential at the rutile/aqueous interface

The method for evaluation of surface potential from the electrode potential of single crystal electrodes is refined. The effect of NaCl and LiCl concentrations on the dependency of the surface potential of TiO₂ on pH was examined. The point of zero potential was shifted to lower pH values in the presence of NaCl and to higher pH values in the presence of LiCl. The interpretation of the data based on the Surface Complexation Model suggested that at 0 0 1 crystal plane of rutile, sodium ions as counterions have more pronounced affinity for association with negatively charged surface groups with respect to the lithium ions.