Side chains properties

Evolution has provided the cell with a repertoire of 20 amino acids to build proteins. The diversity of amino acid side chain properties is enormous, yet many additional functional groups have been selectively chosen to be covalently attached to side chains and this further increases the unique properties of proteins. Diese additional groups play a regulatory role allowing the cell to respond to changing cellular conditions and events. Known covalent modifications of proteins now include phosphorylation, methylation, acetylation, ubi-quitylation, hydroxylation, uridylylation and glycosyl-ation, among many others. Intense study in this field has shown the addition of a phosphate moiety to a protein... 

Although the most stimulatory amino acids were identical in the dog (e.g.,L-cysteine, L-proline, L-lysine, L-histidine and L-alanine), interspecies differences could be related to the side chain properties of the amino acids. Thus, amino acids with hydrophobic side chains were normally inactive or inhibitory in the cat, but were often excitatory in the dog. Conversely, amino acids with acidic side chains tended to be somewhat more excitatory in the cat. 

The shapes of the pressure-area isotherms of monolayers of synthetic polypeptides in the a-helical conformation depend on the nature of the side chain interactions. Poly(y-n-decyl-iu-glutamate), poly(i.-leucine), poly(iu-norleucine), and poly(iu-methionine) show differences related to side chain flexibility and dipolar interactions. Comparison of the isotherms of monolayers of the enantiomorphic and racemic forms of polymers [poly(alanine), poly(y-benzyl-glutamate), poly( /3-benzyl-aspartate), poly( e-benzyloxycarbonyllysine )] similarly show features related to side chain properties. The results support the view that when a monolayer consists of a-helices, the shape of the isotherm depends on the difference between the energies of interaction of parallel and antiparallel molecules. These conclusions are discussed in relation to proteins. 

Fig. 3. Alignment of simplified apoLp-IlI sequences. The sequences in Fig. 2 were simplified by grouping amino acids with similar side-chain properties G = G, S, T D = D, E, N, Q H = H, K, R I = A, L, I, M, V, F, Y, W P = P. The asterisks indicate residues with similar side-chain properties found in all four sequences. Species acronyms as in legend to Fig. 2.

As discussed earlier in Section II, 5, only for typical mammalian collagen is chemical evidence reasonably complete. Table VI adds to the chemical data summarized by Bowes and Kenten (40) several side-chain properties which are useful in considering these appendages in relation to space filling characteristics and ability to scatter X-rays. 

There are several ways to think about the amino acid residues in proteins their length and size, their hydrophobicity or hydrophilicity, their charge and ionization state, their hydrogen-bonding potential and their possible metalbinding potentials [73-75]. It is possible to gain or lose charge, hydrophobicity or hydrophilicity in a controlled way, as is required in the active site of an enzyme. This is done by appropriate choices of amino acids with specific side-chain properties. Therefore amino acids must be chosen with care when a... 

Amino acids were characterized by a principal component analysis of their side-chain properties [170, 171] first, for 20 coded amino acids three principal components Zj, Z2 and Zj were derived (interpreted as being related to hydrophilicity, side-chain bulk, and electronic properties) [170] and afterwards new z scales resulted [171] from a partial least squares (PLS) analysis of the side-chain properties of these amino acids and additional 35 noncoded (unnatural) amino acids. The use of these scales (instead of the original variables) was recommended for structure-activity analyses. 

Schroen CGP, Nierstrasz VA, Kroon PJ et aL (1999) Thermodynamically controlled synthesis of 13-lactam antibiotics. Equilibrium concentrations and side-chain properties. Enzyme Microb Technol 24 489-506... 

In this following section the modification of structure and properties of the derivatives of HPC as a function of their side-chain properties will be presented. 

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