Biomolecules, stability

Reverse micelles are self-organized aggregates of amphiphilic molecules that provide a hydrophilic nano-scale droplet in apolar solvents. This polar core accommodates some hydrophilic biomolecules stabilized by a surfactant shell layer. Furthermore, reverse micellar solutions can extract proteins from aqueous bulk solutions through a water-oil interface. Such a liquid-liquid extraction technique is easy to scale up without a loss in resolution capability, complex equipment design, economic limitations and the impossibility of a continuous mode of operation. Therefore, reverse micellar protein extraction has great potential in facilitating large-scale protein recovery processes from fermentation broths for effective protein production. 

In this section, we briefly describe our hybrid approach for predicting conformations of biomolecules stabilized in solvent [15, 16, 17]. In this approach, the RISM theory is combined with the MC simulated annealing or one of the generalized-ensemble algorithms. Our approach falls into the third category, and both the biomolecule and the solvent are treated on the atomic level. The hybrid approach is implemented for two small peptides as the first step of the research. The solvent effects on the conformational stability of the peptides are discussed and the... 

The IE scheme is nonconservative, with the damping both frequency and timestep dependent [42, 43]. However, IE is unconditionally stable or A-stable, i.e., the stability domain of the model problem y t) = qy t), where q is a complex number (exact solution y t) = exp(gt)), is the set of all qAt satisfying Re (qAt) < 0, or the left-half of the complex plane. The discussion of IE here is only for future reference, since the application of the scheme is faulty for biomolecules. 

One of the most thoroughly investigated examples of polymeric biomolecules in regard to the stabilization of ordered structures by hydration are the DNAs. Only shortly after establishing the double-helix model by Watson and Crick 1953 it became clear, that the hydration shell of DNA plays an important role in stabilizing the native conformation. The data obtained by the authors working in this field up until 1977 are reviewed by Hopfinger155>. 

The covalent bond is the strongest force that holds molecules together (Table 2-1). Noncovalent forces, while of lesser magnitude, make significant contributions to the structure, stability, and functional competence of macromolecules in living cells. These forces, which can be either attractive or repulsive, involve interactions both within the biomolecule and between it and the water that forms the principal component of the surrounding environment. 

In 1994, thiols were firstly used as stabilizers of gold nanoparticles [6a]. Thiols form monolayer on gold surface [18] and highly stable nanoparticles could be obtained. Purification of nanoparticles can be carried out, which makes chemical method of metal nanoparticles a real process for nanomaterial preparation. Various thiol derivatives have been used to functionalize metal nanoparticles [6b, 19]. Cationic and anionic thiol compounds were used to obtain hydrosols of metal nanoparticles. Quaternary ammonium-thiol compounds make the nanoparticle surface highly positively charged [20]. In such cases, cationic nanoparticles were densely adsorbed onto oppositely charged surfaces. DNA or other biomolecule-attached gold nanoparticles have been proposed for biosensors [21]. 

J. H. Crowe, J. F. Carpenter, L. M. Crowe, and T. J. Anchordoguy, Are freezing and dehydration similar stress vectors A comparison of modes of interaction of stabilizing solutes with biomolecules, Cryobiology, 27, 219 (1990). 

The same problem, the stability of the nucleobases, was taken up by Levi and Miller (1998). They wanted to show that a synthesis of these compounds at high temperatures is unrealistic, and thus they took a critical look at the high temperature biogenesis theories, such as the formation of biomolecules at hydrothermal vents (see Sect. 7.2). The half-life of adenine and guanine at 373 K is about a year, that of uracil about 12 years and of the labile cytosine only 19 days. Such temperatures could have easily been reached when planetoids impacted the primeval ocean. 

The question of the stability of the biomolecules is a vital one. Could they really have survived the tremendous energies which would have been set free (in the form of shock waves and/or heat) on the impact of a meteorite Blank et al. (2000) developed a special technique to try and answer this question. They used an 80-mm cannon to produce the shock waves the shocked solution contained the two amino acids lysine and norvaline, which had been found in the Murchison meteorite. Small amounts of the amino acids survived the bombardment , lysine seeming to be a little more robust. In other experiments, the amino acids aminobutyric acid, proline and phenylalanine were subjected to shock waves the first of the three was most stable, the last the most reactive. The products included amino acid dimers as well as cyclic diketopiperazine. The kinetic behaviour of the amino acids differs pressure seems to have a greater effect on the reaction pathway than temperature. As had been recognized earlier, the effect of pressure would have slowed down certain decomposition reactions, such as pyrolysis and decarboxylation (Blank et al., 2001). 

If prebiotic peptides and/or proteins were in fact initially formed in aqueous solution (the hypothesis of biogenesis in the primeval ocean ), the energy problems referred to above would have needed to be solved in order for peptide synthesis to occur. As discussed in Sect. 5.3, there is some initial experimental evidence indicating that the formation of peptide bonds in aqueous media is possible. An important criterion for the evolutionary development of biomolecules is their stability in the aqueous phase. The half-life of a peptide bond in pure water at room temperature is about seven years. The stability of the peptide bond towards cleavage by aggressive compounds was studied by Synge (1945). The following relative hydrolysis rates were determined experimentally, with the relative rate of hydrolysis for the dipeptide Gly-Gly set equal to unity ... 

One problem which had previously been ignored in the dispute on the stability of biomolecules under extreme conditions was the influence of the properties of supercritical water. Water becomes supercritical at temperatures above the critical... 

In general, biomolecules such as proteins and enzymes display sophisticated recognition abilities but their commercial viability is often hampered by their fragile structure and lack of long term stability under processing conditions [69]. These problems can be partially overcome by immobilization of the biomolecules on various supports, which provide enhanced stability, repetitive and continuous use, potential modulation of catalytic properties, and prevention of microbial contaminations. Sol-gel and synthetic polymer-based routes for biomolecule encapsulation have been studied extensively and are now well established [70-72]. Current research is also concerned with improving the stability of the immobilized biomolecules, notably enzymes, to increase the scope for exploitation in various... 

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