Proteins surface

Protein adsorption has been studied with a variety of techniques such as ellipsome-try [107,108], ESCA [109], surface forces measurements [102], total internal reflection fluorescence (TIRE) [103,110], electron microscopy [111], and electrokinetic measurement of latex particles [112,113] and capillaries [114], The TIRE technique has recently been adapted to observe surface diffusion [106] and orientation [IIS] in adsorbed layers. These experiments point toward the significant influence of the protein-surface interaction on the adsorption characteristics [105,108,110]. A very important interaction is due to the hydrophobic interaction between parts of the protein and polymeric surfaces [18], although often electrostatic interactions are also influential [ 116]. Protein desorption can be affected by altering the pH [117] or by the introduction of a complexing agent [118]. 

Kovacs H, A E Mark and W F van Gunsteren 1997. Solvent Structure at a Hydrophobic Protein Surface. Proteins Structure, Function and Genetics 27 395-404. 

In HIC, the hydrophobic interactions are relatively weak, often driven by salts in moderate concentration (I to 2 M), and depend primarily on the exposed residues on or near the protein surface preservation of the native, biologically active state of the protein is an important feature of HIC. Elution can be achieved differentially by decreasing salt concentration or increasing the concentration of polarity perturbants (e.g., ethylene glycol) in the eluent. 

The thioredoxin domain (see Figure 2.7) has a central (3 sheet surrounded by a helices. The active part of the molecule is a Pa(3 unit comprising p strands 2 and 3 joined by a helix 2. The redox-active disulfide bridge is at the amino end of this a helix and is formed by a Cys-X-X-Cys motif where X is any residue in DsbA, in thioredoxin, and in other members of this family of redox-active proteins. The a-helical domain of DsbA is positioned so that this disulfide bridge is at the center of a relatively extensive hydrophobic protein surface. Since disulfide bonds in proteins are usually buried in a hydrophobic environment, this hydrophobic surface in DsbA could provide an interaction area for exposed hydrophobic patches on partially folded protein substrates. 

Most sequence-specific regulatory proteins bind to their DNA targets by presenting an a helix or a pair of antiparallel p strands to the major groove of DNA. Recognition of the TATA box by TBP is therefore exceptional it utilizes a concave pleated sheet protein surface that interacts with the minor groove of DNA. Since the minor groove has very few sequence-specific... 

Figure 12.2 (a) Schematic drawing of membrane proteins in a typical membrane and their solubilization by detergents. The hydrophilic surfaces of the membrane proteins are indicated by red. (b) A membrane protein crystallized with detergents bound to its hydrophobic protein surface. The hydrophilic surfaces of the proteins and the symbols for detergents are as in (a). (Adapted from H. Michel, Trends Biochem. Sci. 8 56-59, 1983.)... 

Hydrophobic bonds, or, more accurately, interactions, form because nonpolar side chains of amino acids and other nonpolar solutes prefer to cluster in a nonpolar environment rather than to intercalate in a polar solvent such as water. The forming of hydrophobic bonds minimizes the interaction of nonpolar residues with water and is therefore highly favorable. Such clustering is entropically driven. The side chains of the amino acids in the interior or core of the protein structure are almost exclusively hydrophobic. Polar amino acids are almost never found in the interior of a protein, but the protein surface may consist of both polar and nonpolar residues. 

One general benefit of subunit association is a favorable reduction of the protein s surface-to-volume ratio. The surface-to-volume ratio becomes smaller as the radius of any particle or object becomes larger. (This is because surface area is a function of the radius squared and volume is a function of the radius cubed.) Because interactions within the protein usually tend to stabilize the protein energetically and because the interaction of the protein surface with... 

Protein crystals contain between 25 and 65 vol% water, which is essential for the crystallisation of these biopolymers. A typical value for the water content of protein crystals is 45% according to Matthews et al. l49,150). For this reason it is possible to study the arrangement of water molecules in the hydration-shell by protein-water and water-water interactions near the protein surface, if one can solve the structure of the crystal by X-ray or neutron diffraction to a sufficiently high resolution151 -153). 

NDO can be classified as class III dioxygenase the electron transfer chain involves a Rieske-type ferredoxin. Electrons enter NDO through the Rieske-type cluster of the dioxygenase. Kauppi et al. (11) have suggested that the binding site of NDO for the ferredoxin involves the 6 strands 10 and 12 of the Rieske domain as well as residues from the catalytic domain that form a depression in the protein surface close to Cys 101, which is a ligand of the Rieske cluster. In Rieske proteins from be complexes, access to this side of the cluster is blocked by an acidic surface residue (Asp 152 in the ISF, Glu 120 in RFS). 

It is necessary to note that the initial conditions of the samples in solution were absolutely different. RC was extracted from the membranes by detergent (lauryldimethy-lamineoxide—LDAO) the solution contains the individual protein molecules surrounded by a detergent belt shielding the hydrophobic areas of the protein surface. In the case of BR the situation is different. BR is the main part of purple membranes (about 80%) and is already close packed in it. It is difficult to extract BR in the form of individual molecules, for they are very unstable (Okamura et al. 1974). Thus, the initial solution of BR was in reality the solution of sonicated membrane fragments. 

Chromatographic Development The basic concepts of chromatographic separations are described elsewhere in this handbook. Proteins differ from small solutes in that the large number of charged and/or hydrophobic residues on the protein surface provide multiple... 

Achieving fast electron transfer to enzyme active sites need not be complicated. As mentioned above, many redox enzymes incorporate a relay of electron transfer centers that facilitate fast electron transfer between the protein surface and the buried active site. These may be iron-sulfur clusters, heme porphyrin centers, or mononuclear... 

Separations in hydrophobic interaction chromatography have been modeled as a function of the ionic strength of the buffer and of the hydrophobicity of the column, and tested using the elution of lysozyme and ovalbumin from octyl-, butyl- and phenyl-Sepharose phases.2 The theoretical framework used preferential interaction analysis, a theory competitive to solvophobic theory. Solvophobic theory views protein-surface interaction as a two-step process. In this model, the protein appears in a cavity in the water formed above the adsorption site and then adsorbs to the phase, with the free energy change... 

Properly folded native proteins tend to aggregate less than when unfolded. Solution additives that are known to stabilize the native proteins in solution may inhibit aggregation and enhance solubility. A diverse range of chemical additives are known to stabilize proteins in solution. These include salts, polyols, amino acids, and various polymers. Timasheff and colleagues have provided an extensive examination of the effects of solvent additives on protein stability [105]. The unifying mechanism for protein stabilization by these cosolvents is related to their preferential exclusion from the protein surface. With the cosolvent preferentially excluded, the protein surface is... 

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