Solvent-exposed side-chains, increased

The total S AS A calculated for both CT and CTWAT are lower relative to the X-ray structure while in CTMONO the SASA is increased relative to the X-ray structure.(Table 1) The protein, when placed in a non-aqueous media, have repositioned its solvent exposed side chains which results in a net reduction of SASA. Thus, the exposed surface area for the hydrophobic residues increased, while that of the polar residues decreased significantly. Both the CT and CTWAT systems experienced about 5% increase while CTMONO experiences a 4% increase for the SASA of the hydrophobic residues. This is in accord with the expectation of "like dissolves like". The hydrophobic side chains of CT reorient themselves on the surface and become more exposed to hexane, while the charged residues fold inward. 

It can be seen from these data that the larger hydrophobic side chains are the most buried with the exception that cystine also tends to be quite inaccessible with 26, 72, 84, and 110 completely buried. All of the alanines are exposed, three of the four prolines are very exposed, three of the valines are completely buried as are Met 30, Phe 46, and Ser 90. Phenylalanine 8 is only accessible via a tunnel from the surface which is in fact occupied and blocked by one well-defined solvent molecule. The various residues of each polar amino acid have a wide range of exposure, but the larger residues tend to be most accessible with the exception of the tyrosines, which are quite variable. Residues in the active site region, 11, 12, 41, 43, 44, 45, 119, 120, 121, and 123, tend to be the extremes within each residue type but it should be noted that the motion of His 119 to the active position proposed later (Section VI) would increase the exposure of 11, 12, 41, and 44 and decrease the exposure of 121 and 109 in particular. The hydrophilic residues and especially the hydrophilic portions of these residues are generally ex-... 

The intrinsic fluorescence of the eight tryptophanyl residues in MBP can be used to measure its reversible unfolding/refolding reactions. When unfolded by incubation in a denaturant such as guanidinium hydrochloride, the side chains of the tryptophanyl residues are exposed to solvent and their fluorescence is quenched. On dilution of the denaturant, the subsequent refolding reaction can be monitored by the increase in fluorescence that results from burial of the side chains in the interior of the protein and their shielding from solvent (Liu et al., 1988, 1989). 

Our studies have shown that both hydration and the placement of "essential" water molecules affect the RMS deviation, but not RMS fluctuation, of the protein when placed in a non-aqueous environment. As hydration increases, the structural similarities of the protein to the crystal structure increases. Although the deviation of the protein from the X-ray structure is higher in organic solvent than in water, the flexibility of the protein is higher in water. The protein remained spherical and the major movement is due to the folding back of the hydrophilic side chains on the protein surface exposed to hexane. The placement of bound water molecules affects the "local" mobility of the protein, mainly the surface loops. The total... 

Both native and formalin-fixed RNase A undergo a structural transition from the native a -i- P to a nearly all-P conformation as ethanol concentration is increased to >80%. The transition from the native to an all-P conformation at high ethanol concentrations is characteristic of most soluble proteins and is driven by the disruption of water structure by ethanol and the associated energetically unfavorable interaction of ethanol with the peptide backbone. The response of most proteins to this situation is to form P-sheets to sequester the peptide bonds away from the solvent while exposing nonpolar side chains to the alcohol. This secondary structural transformation is typically accompanied by a significant disruption (collapse) of tertiary structure as was observed for RNase A in the above studies. This new protein conformation is further stabilized by the formation of intermolecular hydrogen bonds between geometrically compatible hydrophobic p-sheets, which then leads... 

Photopatterning is commonly based on the solubility difference between exposed and unexposed portions as a result of the main chain (chain scission and crossUnking) or side chain (pendant) reactions. An increased or a decreased solubility leads to the positive or negative pattern, respectively. Photo-patternable PI systems are classified into the PAA-exposure type, where patterning is performed at the PAA stage, then cured, and the Pl-exposure type in which Pis themselves have both photosensitivity and developability by adequate solvents. 

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