Hydrophobic effects collapse

Fig. 5. Protein folding. The unfolded polypeptide chain collapses and assembles to form simple structural motifs such as p-sheets and a-helices by nucleation-condensation mechanisms involving the formation of hydrogen bonds and van der Waal s interactions. Small proteins (eg, chymotrypsin inhibitor 2) attain their final (tertiary) structure in this way. Larger proteins and multiple protein assemblies aggregate by recognition and docking of multiple domains (eg, p-barrels, a-helix bundles), often displaying positive cooperativity. Many noncovalent interactions, including hydrogen bonding, van der Waal s and electrostatic interactions, and the hydrophobic effect are exploited to create the final, compact protein assembly. Further structural...

Abstract We discuss recent experiments and theories concerning protein collapse and folding. Experiments using multicomponent solutions have revealed much about the mechanism of folding. Simulation and theory have been used to interpret thermodynamic and fluorescence correlation spectroscopy experimental results. We consider the theoretical arguments using variations of the free energy with respect to fluctuations in number and composition to consider recent experiments. We find new measures of protein stability tendencies offer a different view than the often poorly defined hydrophobic effect. 

An essential feature of proteins is that they spontaneously fold into well-defined, three-dimensional structures. The single most important contributor to protein folding is the hydrophobic effect. It is imperative that amino acids such as leucine and valine, which have hydrophobic side chains, bury those side chains in the core of the protein, away from the aqueous environment of the cell. This hydrophobic collapse is a key early event in the process... 

With the repulsive LJ potential, polymer collapse due to hydrophobic effect is not addressed. The same form of Equation 4.21 is also used to capture the nonelectrostatic excluded volume interactions among the polymer beads and counterions, the difference appearing in the choice of the hardcore distance a. The electrostatic interaction among the charged beads and ions is taken to be the Coulomb energy,... 

Stoichiometric [40], whereas for single-stranded DNA it is not [41]. Studies on spermine and lipospermine binding to DNA were conducted and reported [42] to assess the importance of contribution of hydrophobic effects on DNA collapse. While ITC measurements showed a larger DNA binding affinity for the hydro-phobic lipospermine than spermine, electron micrographs showed that lipospermine was incapable of condensing DNA into toroidal structures. 

Cationic surfactants at low concentrations do not affect the gd volume, but effectively collapsed the gel from a critical aggregation concentration (cac), which decreases with increasing length of the hydrophobic tail (Figure 10.14). This is because at the cac the surfactants start to form micelles, which act as multivalent counterions, and thus cause a very important osmotic deswelling. 

Electrostatic effects have long been recognized in commercial HPLC columns for SEC of proteins (15,21,22). The usual remedy is to add 100 mM salt to the mobile phase. This works here too the Lys and Asp peaks collapse into the Gly peak with 100 mM salt (Eig. 8.8). High concentrations of sodium sulfate were added to determine the role played in SEC by hydrophobic interactions (sodium sulfate, a structure-forming salt, strengthens such interactions). Sodium sulfate increased the retention only of the most hydrophobic amino acids to any extent, and then only when the concentration approached 1 M. Clearly, hydrophobic interaction cannot account for the elution order of amino acids on PolyHEA. 

The above statements are adequate for liquid defoamers that are insoluble in the bulk. Experience has proven, however, that certain dispersed hydrophobic solids can greatly enhance the effectiveness of defoaming. A strong correlation between the effectiveness of a defoamer and the contact angle for silicone-treated silica in hydrocarbons has been established [300]. It is believed that the dewetting process of the hydrophobic silica causes the collapse of a foam by the direct mechanical shock occurring by this process. 

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