Mixology of protein solutions and the Vroman effect

Mixing rules stipulating both concentration and distribution of proteins adsorbed to the liquid-vapor (LV) interphase from multicomponent aqueous solutions are derived from a relatively straightforward protein-adsorption model. Accordingly, proteins compete for space within an interphase separating bulk-vapor and bulk-solution phases on a weight, not molar, concentration basis. This results in an equilibrium weight-fraction distribution within the interphase that is identical to bulk solution. However, the absolute interphase concentration of any particular protein adsorbing from an m-component solution is 1/mth that adsorbed from a pure, single-component solution of that protein due to competition with m - 1 constituents. Applied to adsorption from complex biological fluids such as blood plasma and serum, mixing rules suggest that there is no energetic reason to expect selective adsorption of any particular protein from the mixture. Thus, dilute members of the plasma proteome are overwhelmed at the hydrophobic LV surface by the 30 classical plasma proteins occupying the first 5 decades of physiological concentration. Mixing rules rationalize the experimental observations that (i) concentration-dependent liquid-vapor interfacial tension, gammalv, of blood plasma and serum (comprised of about 490 different proteins) cannot be confidently resolved, even though serum is substantially depleted of coagulable proteins (e.g., fibrinogen), and (ii) gammalv of plasma is startlingly similar to that of purified protein constituents. Adsorption-kinetics studies of human albumin (66.3 kDa) and IgM (1000 kDa) binary mixtures revealed that relatively sluggish IgM molecules displace faster-moving albumin molecules adsorbing to the LV surface. This Vroman-effect-like process leads to an equilibrium gammalv reflecting the linear combination of weight/volume concentrations at the surface predicted by theory. Thus, the Vroman effect is interpreted as a natural outcome of protein reorganization to achieve an equilibrium interphase composition dictated by a firm set of mixing rules.     

Toward a microscopic description of molecular electronic systems

The many-body perturbation theory is reformulated within the dielectric function method presented in the preceding paper [12]. The self-energy effects are explicitly considered. These corrections turn out to be important and are calculated to the same level of approximation as the corresponding local-field terms. The method is at the moment applicable to π-electron systems within the zero differential overlap approximation. Explicit calculations of the excitation energies for the benzene molecule, using different parametrizations, are presented. Comparison is made with the results obtained in the random phase approximation (RPA ) and other schemes.     

Fermi level alignment in self-assembled molecular layers: the effect of coupling chemistry

Photoelectron spectroscopy was used to explore changes in Fermi level alignment, within the pi-pi* gap, arising from modifications to the coupling chemistry of conjugated phenylene ethynylene oligomers to the Au surface. Self-assembled monolayers were formed employing either thiol (4,4'-ethynylphenyl-1-benzenethiol or OPE-T) or isocyanide (4,4'-ethynylphenyl-1-benzeneisocyanide or OPE-NC) coupling. The electronic density of states in the valence region of the two systems are nearly identical with the exception of a shift to higher binding energy by about 0.5 eV for OPE-NC. Corresponding shifts appear in C(1s) spectra and in the threshold near E(F). The lack of change in the optical absorption suggests that a rigid shift of the Fermi level within the pi-pi* gap is the major effect of modifying the coupling chemistry. Qualitative consideration of bonding in each case is used to suggest the influence of chemisorption-induced charge transfer as a potential explanation. Connections to other theoretical and experimental work on the effects of varying coupling chemistries are also discussed.     

Solvent resistant nanofiltration: separating on a molecular level

Over the past decade, solvent resistant nanofiltration (SRNF) has gained a lot of attention, as it is a promising energy- and waste-efficient unit process to separate mixtures down to a molecular level. This critical review focuses on all aspects related to this new burgeoning technology, occasionally also including literature obtained on aqueous applications or related membrane processes, if of relevance to understand SRNF better. An overview of the different membrane materials and the methods to turn them into suitable SRNF-membranes will be given first. The membrane transport mechanism and its modelling will receive attention in order to understand the process and the reported membrane performances better. Finally, all SRNF-applications reported so far - in food chemistry, petrochemistry, catalysis, pharmaceutical manufacturing - will be reviewed exhaustively (324 references).     

The molecular level modification of surfaces: from self-assembled monolayers to complex molecular assemblies

The modification of surfaces with self-assembled monolayers (SAMs) containing multiple different molecules, or containing molecules with multiple different functional components, or both, has become increasingly popular over the last two decades. This explosion of interest is primarily related to the ability to control the modification of interfaces with something approaching molecular level control and to the ability to characterise the molecular constructs by which the surface is modified. Over this time the level of sophistication of molecular constructs, and the level of knowledge related to how to fabricate molecular constructs on surfaces have advanced enormously. This critical review aims to guide researchers interested in modifying surfaces with a high degree of control to the use of organic layers. Highlighted are some of the issues to consider when working with SAMs, as well as some of the lessons learnt (169 references).     

Biaxial stretching of pet films: A molecular description

Biaxially oriented poly(ethylene terephthalate) films were prepared under well defined stretching conditions in order to mimic the three stages of the industrial inverse drawing process. Molecular orientation has been characterized through X-ray diffraction and infrared dichroism. The main orientation mechanisms in the constant-speed drawing of an amorphous film as well as in the constant-force transverse drawing of monodrawn samples are described. It is shown that relaxation phenomena dominate the orientation of an amorphous sample. Reorientation along the second drawing direction involves rotation of crystalline blocks along the draw direction and further crystalline growth. The high-temperature heating stage leads to an almost four-fold increase in the size of the crystallites. The orientation of the amorphous phase is controlled by the mechanisms occurring during crystallization (relaxation followed by extension).     

The effect of water displacement on binding thermodynamics: concanavalin A

Interactions at the binding interface of biomolecular complexes are often mediated by ordered water molecules. In this work, we considered two concanavalin A-carbohydrate complexes. In the first, a water molecule is buried at the binding interface. In the second, this water molecule is displaced by a modification of the ligand (Clarke, C.; Woods, R. J.; Gluska, J.; Cooper, A.; Nutley, M. A.; Boons, G. J. J. Am. Chem. Soc. 2001, 123, 12238-12247). We computed the contribution of this water molecule to the thermodynamic properties using statistical mechanical formulas for the energy and entropy and molecular dynamics simulations. Other contributions to the binding affinity, including desolvation, entropy of conformational restriction, and interaction between the ligand and protein, were also computed. The thermodynamic consequences of displacement of the ordered water molecule by ligand modification were in qualitative agreement with experimental data. The free energy contribution of the water molecule (-17.2 kcal/mol; -19.2 enthalpic and +2 entropic) was nearly equivalent to the additional protein-ligand interactions in trimannoside 2 (-18.9 kcal/mol). The two structural ions interact more strongly with the water than with the hydroxyl of trimannoside 2, thus favoring trimannoside 1. The contributions from desolvation and conformational entropy are much smaller but significant, compared to the binding free energy difference. The picture that emerges is that the final outcome of water displacement is sensitive to the details of the binding site and cannot be predicted by simple empirical rules.     

Steric effect: a quantitative description from density functional theory

The concepts of steric energy, steric potential, and steric charge are introduced within the density functional theory framework. The steric energy, representing a hypothetical state with all electrons packed into the lowest orbital and other effects entirely excluded, is a measure of the intrinsic space occupied by an electronic system. It is exclusive, repulsive, and extensive, and it vanishes for homogeneous electron gas. When Bader's zero-flux boundary condition is adopted, atoms in molecules are found to achieve balanced steric repulsion among one another with vanished steric energy density interfaces. A few molecular systems involving conformation changes and chemical reactions have been investigated to examine the relative contribution of the steric and other effects, providing insights for a few controversial topics from a different perspective.     

Isotopomer encapsulation in a cylindrical molecular capsule: a probe for understanding noncovalent isotope effects on a molecular level

Isotope effects for the encapsulation of deuterated versus nondeuterated guests are determined. This system involves the use of social isomers, and the origin of the isotope effect is localized to methyl groups interacting with aromatic rings.     

A molecular description of the evolution of resistance

BACKGROUND: In vitro evolution has been used to obtain nucleic acid molecules with interesting functional properties. The evolution process usually is carried out in a stepwise manner, involving successive rounds of selection, amplification and mutation. Recently, a continuous in vitro evolution system was devised for RNAs that catalyze the ligation of oligonucleotide substrates, allowing the evolution of catalytic function to be studied in real time. RESULTS: Continuous in vitro evolution of an RNA ligase ribozyme was carried out in the presence of a DNA enzyme that was capable of cleaving, and thereby inactivating, the ribozyme. The DNA concentration was increased steadily over 33.5 hours of evolution, reaching a final concentration that would have been sufficient to inactivate the starting population in one second. The evolved population of ribozymes developed resistance to the DNA enzyme, reducing their vulnerability to cleavage by 2000-fold but retaining their own catalytic function. Based on sequencing and kinetic analysis of the ribozymes, two mechanisms are proposed for this resistance. One involves three nucleotide substitutions, together with two compensatory mutations, that alter the site at which the DNA enzyme binds the ribozyme. The other involves enhancement of the ribozyme's ability to bind its own substrate in a way that protects it from cleavage by the DNA enzyme. CONCLUSIONS: The ability to direct the evolution of an enzyme's biochemical properties in response to the behavior of another macromolecule provides insight into the evolution of resistance and may be useful in developing enzymes with novel or enhanced function.