Protein side-chain peptides

The most important aspect of Table 27.1 is that the 20 anino acids that occur in proteins share the common feature of being a-anino acids, and the differences fflnong them are in their side chains. Peptide bonds linking carboxyl and a-anino groups characterize the structure of proteins, but it is the side chains that are mainly responsible for theh properties. The side chains of the 20 commonly occuning amino acids encompass both large and small differences. The major differences between amino acid side chains concern ... 

Similarly to their (33-counterparts, short 32-peptides have been shown to exhibit extraordinary tendencies to adopt stable secondary structures. Again, interest has, to date, focused on those 32-amino acids which bear protein side chains.15 7 This interest has resulted in the development of methodology based on Evans work 18 for the synthesis of these (3-amino acids bearing a substituent on C2. 

The synthesis of (3-peptides bearing substituents at both C2 and C3 atoms has seen the most widespread interest. Stable secondary structures have once again been observed in these classes of (3-peptides. They can be divided into three classes (1) those bearing protein side chains (2) those carrying a cycloalkyl ring 19-21 and (3) those with allyl substituents 22 (Scheme 9). 

Scheme 10 Synthesis of 32 3-Peptides with Protein Side Chains 71...

Fischer (1906) recognized the possibility of linkages between active side chains. Pauling and Niemann (1939) suggested that covalent cross-links such as disulfide bridges, side-chain ester links, and side-chain peptide links might be partly responsible for the configurational stability of proteins. 

Several factors affect the volatility and stability of a peptide derivative, not least of these being the number and nature of the constituent amino acids. Heterocyclic and aromatic amino acids reduce volatility while those containing sulphur tend to decrease the thermal stability. Small naturally occurring peptides which are not derived from proteins often contain only aliphatic amino acids which lack functional groups in the side chains. Peptides of this type of up to about ten amino acids, after conversion to suitable derivatives, are amenable to analysis by mass spectrometry, e.g. [164]. A variety of derivatives has been reported and include N-trifluoroacetyl peptide esters [136,165], N-acetyl peptide esters [166-168], aromatic N-acyl peptide esters [169-172], and per-methylated N-acyl peptides [173]. The principal modes of the electron impact induced fragmentation of these peptide derivatives are well established and have been summarised in recent reviews [174,175]. Although the spectra of the permethylated derivatives [176] are perhaps the simplest and easiest to interpret and are now frequently used, the N-acyl peptide esters have been widely and successfully employed. 

The vibrational transitions of protein side-chain groups are highly localized (Table 7.7), therefore they can be applied directly to investigate the side chains of peptides and proteins (Singh, 2000). 

From these results, we propose that in EPR signals from wheat flour the dominant center line is from nitrogen-centered radicals produced during heat-induced peptide scission, down-fleld peaks and shoulders are from sulfur radicals induced by shear scission of disulfide bonds, and the line broadening and wings are from protein side chain nitrogen or oxyl radicals transferred from oxidizing lipids. 

Membrane protein side chains (for example, Lys- CH2 Val- CH2) have been shown to possess fast ( is) motions from measurements of specifically deuterated residues in bacteriorhodopsin, even though the membrane environment was relatively rigid and crystalline. Similar approaches showed that the a-CH group rotation is fast (t (is) for membrane-bound, specifically deuterated retinal in the same protein, even at —60°C. Somewhat slower motions (in the ms range) occur in peptide backbones of membrane proteins. 

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