Protein side-chains 200 INDEX

Amino acid Three- letter code One- letter code Mass of residue in. b proteins Accessible surface area, 2 nm Hydrophobicity index ionizable side chain Occurrence in n/ proteins, /o Relative mutabihty... 

Two of the hydrophihcity scales in Table 2 were derived from experimental measures of the behavior of amino acids in various solvents, namely partitioning coefficients [K-D index of Kyte and Doolittle (30)] or mobility in paper chromatography [Rf index of Zimmerman et al. (31)]. By contrast, the Hp index was obtained from quantum mechanics (QM) calculations of electron densities of side chain atoms in comparison with water (32). The Hp index is correlated highly with these two established hydrophobicity scales (Table 4). Therefore, like the polarizability index, it is possible to represent fundamental chemical properties of amino acids (hydrophUicity, Hp) with parameters derived from ab initio calculations of electronic properties. However, in contrast to polarizabihty (steric effects), hydrophihcity shows significant correlation with preference for secondary structure. Thus, hydrophobic amino acids prefer fi-strands (and fi-sheet conformations) and typically are buried in protein structures, whereas hydrophilic residues are found commonly in turns (coil structure) at the protein surface. 

Prom the electron paramagnetic resonance (EPR) spectmm of the nitroxide side chain, four primary parameters are obtained 1) solvent accessibility, 2) mobility of the R1 side chain, 3) a polarity index for its immediate environment, and 4) the distance between R1 and another paramagnetic center in the protein. Solvent accessibility of the side chain is determined from the collision frequency of the nitroxide with paramagnetic reagents in solution. The mobility, polarity, and distances are deduced from the EPR spectral line shape. For regular secondary stmc-tures, accessibility, mobility, and polarity are periodic functions of sequence position. The period and the phase of the function reveal the type of secondary stmcture and its orientation within the protein, respectively (71, 74). In the case of membrane proteins, the topography of the secondary stmcture with respect to the membrane surface can also be described (75, 76). 

To answer these questions, we have analyzed the frequency of appearance of various amino acid residues at the loci near the sessile bond in protein substrates (4). This was statistically analyzed for more than 500 amino acid sequences in which the peptic hydrolytic sites are known. The calculated specificity indices, Sij for some of the residues (i) and positions (j) are shown in Table I. This index is a measure of the preferability, undesirability, or indifference for a given amino acid side chain. The calculation included ten residues on each side of the hydrolyzed bond. We also... 

---