Protein self assembly, thermodynamics

In principle, the expressions for pair potentials, osmotic pressure and second virial coefficients could be used as input parameters in computer simulations. The objective of performing such simulations is to clarify physical mechanisms and to provide a deeper insight into phenomena of interest, especially under those conditions where structural or thermodynamic parameters of the studied system cannot be accessed easily by experiment. The nature of the intermolecular forces responsible for protein self-assembly and phase behaviour under variation of solution conditions, including temperature, pH and ionic strength, has been explored using this kind of modelling approach (Dickinson and Krishna, 2001 Rosch and Errington, 2007 Blanch et al., 2002). 

As noted earlier, microtubule elongation has been characterized largely with respect to the involvement of guanine nucleotides and the modes of drug inhibition of microtubule formation. There have also been a number of important studies on the influence of microtubule-associated proteins and solution variables on the kinetics and thermodynamics of microtubule self-assembly. Of these, the characterization of the so-called mitotic spindle poisons has been particularly complex because of the variety of agents and the diversity of systems studied. For this reason, we shall concentrate on the other factors affecting the elongation process. 

Polynuclear Fe-M-S Complexes from "spontaneous self assembly" reactions. Synthetic analog clusters for the Fe2S2 and Fe4S4 centers in the Fe/S proteins (ferredoxins) have been obtained by procedures that are based on the concept of "spontaneous self assembly". The latter (30) assumes that the cores of the Fe/S centers are thermodynamically stable units that should be accessible fiom appropriate reagents even in the absence of a protein environment. 

The threshold concentration of monomer that must be exceeded for any observable polymer formation in a self-assembling system. In the context of Oosawa s condensation-equilibrium model for protein polymerization, the cooperativity of nucleation and the intrinsic thermodynamic instability of nuclei contribute to the sudden onset of polymer formation as the monomer concentration reaches and exceeds the critical concentration. Condensation-equilibrium processes that exhibit critical concentration behavior in vitro include F-actin formation from G-actin, microtubule self-assembly from tubulin, and fibril formation from amyloid P protein. Critical concentration behavior will also occur in indefinite isodesmic polymerization reactions that involve a stable template. One example is the elongation of microtubules from centrosomes, basal bodies, or axonemes. 

Self-assembly is the spontaneous organization of molecules into stable, well-defined structures with the driving forces being noncovalent associations. The final structure is normally near or at the thermodynamic equilibrium arrangement allowing it to form spontaneously. Such formations can be done under conditions where defects are either minimized or eliminated. In nature, self-assembly is common as in the folding of proteins, formation of the DNA double helix, etc. 

Gray HB, Winkler JR (1996) Electron transfer in proteins. Annu Rev Biochem 65 537 Fedurco M (2000) Redox reactions of heme-containing metalloproteins dynamic effects of self-assembled monolayers on thermodynamics and kinetics of cytochrome c electron-transfer reactions. Coord Chem Rev 209 263... 

The simplest way in which a process occurs by itself is when it is under thermodynamic control. The folding of a protein, or the self-assembly of micelles at the critical micelle concentration (cmc) are examples of spontaneous processes the latter are characterized by a negative free-energy change, as the self-orgaiuzed product has a lower energy than the single components. ... 

The weak physical forces that hold together self-assembled nanoparticles are, of course, susceptible to disruption under the influence of thermodynamic and/or mechanical stresses. Hence some workers have investigated ways to reinforce nanoscale structures via covalent bonding. For instance, improved stability of protein nanoparticles, in particular, casein micelles, can be achieved by enzymatic cross-linking with the enzyme transglutaminase, which forms bonds between protein-bound glutamine and lysine residues. By this means native casein micelles can be converted from semi-reversible association colloids into permanent nanogel particles (Huppertz and de Kruif, 2008). 

In line with the general increase in thermodynamic affinity of surfactant-protein particles for the aqueous medium, a marked increase in the solubility of soy protein has been observed in response to interactions with SDS (Malhotra and Coupland, 2004). In contrast, however, the self-assembly of the globular protein legumin, as modified by the anionic... 

We have seen earlier in this chapter how the self-assembly of casein systems is sensitively affected by temperature. Another thermodynamic variable that can affect protein-protein interactions in aqueous media is the hydrostatic pressure. Static high-pressure treatment causes the disintegration of casein micelles due to the dismption of internal hydro-phobic interactions and the dissociation of colloidal calcium phosphate. This phenomenon has been used to modify the gelation ability of casein without acidification as a consequence of exposure of hydrophobic parts of the casein molecules into the aqueous medium from the interior of the native casein micelles (Dickinson, 2006). High-pressure treatment leads to a reduction in the casein concentration required for gelation under neutral conditions, especially in the presence of cosolutes such as sucrose (Abbasi and Dickinson, 2001, 2002, 2004 Keenan et al., 2001). 

Nowadays it is well established that the interactions between different macromolecular ingredients (i.e., protein + protein, polysaccharide + polysaccharide, and protein + polysaccharide) are of great importance in determining the texture and shelf-life of multicomponent food colloids. These interactions affect the structure-forming properties of biopolymers in the bulk and at interfaces thermodynamic activity, self-assembly, sin-face loading, thermodynamic compatibility/incompatibility, phase separation, complexation and rheological behaviour. Therefore, one may infer that a knowledge of the key physico-chemical features of such biopolymer-biopolymer interactions, and their impact on stability properties of food colloids, is essential in order to be able to understand and predict the functional properties of mixed biopolymers in product formulations. 

We saw in Figure 1.2c that supramolecular chemistry is not just about solid state or solution host-guest chemistry but increasingly emphasises self-assembly and the construction of multi-nanometre scale devices and ultimately materials based on nanometre-scale components (a nanometre is 10 9 of a metre). Strict supramolecular self-assembly (Chapter 10) involves the spontaneous formation of a multi-component aggregate under thermodynamically controlled conditions based on information encoded within the individual building blocks (referred to as tectons ) themselves. The aggregate might comprise only one kind of molecule (as in the multiple copies of the same protein that comprise... 

In a strict self-assembly process, the final product is produced entirely spontaneously when the components are mixed together in the correct ratios under a given set of conditions of temperature, pH, concentration etc. The product formation must be completely reversible and represent the thermodynamic minimum for the system. In essence, all the information necessary for the assembly to occur is coded into the constituent parts. The concept of strict self-assembly is rooted in the Thermodynamic Hypothesis of Afinison who suggested that under physiological conditions the native structure of a protein is... 

Hydrophobic and osmophobic effects are important not only in the folding of individual polypeptide chains into compact globular proteins, but also in the assembly of multiprotein complexes. Osmophobic effects are noted, for instance, in the self-assembly of subunits of the glycolytic enzyme phosphofructokinase (PFK). Self-assembly is enhanced by the presence of stabilizing organic cosolvents such as trimethylamine-A-oxide (TMAO) (Hand and Somero, 1982). As discussed later, self-assembly driven by osmophobic effects results from the thermodynamic favorability of minimizing the surface area on the proteins that is in contact with the cosolvent. 

Many other examples of outwardly complex molecular structures, whose salient architectural features appear to self-assemble from their constituent building blocks, have been documented [16]. The formation of the DNA double helix from its constituent chains is perhaps the quintessential example, whilst the perfect reconstitution of the intact tobacco mosaic virus from its constituent RNA and protein monomers also exhibits all the hallmarks of a cooperative self-assembly process [17]. The same is true of ribonuclease. Reconstitution of this enzyme in the presence of mercaptoethanol, to allow reversible exchange of the four disulfide bridges, proceeds smoothly to generate eventually only the active conformation from many possible isomeric states [18], In each of these cases, the thermodynamic stability of the product is vital in directing its synthesis. These syntheses could therefore be termed product-directed. 

Bioenergetics of Self-Assembly Energetics of Protein Folding Ligand-Operated Membrane Channels Protein-Protein Interactions Thermodynamics in Living Systems... 

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