Side chains peptide-like

The exact disposition of the side chains in a globular protein is difficult to define in solution. Although it is likely that the peptide main chain (backbone) of the protein is relatively rigid, the side chains have been shown to be undergoing motion of several different types (see lysozyme, peroxidase, and carboxypeptidase). This means that the full definition of atomic positions in the structure requires a knowledge of the time dependence of their coordinates. The motion of side chains is likely to be different in the crystal and solution states, but this difference may well... 

Figure 14.2 Models of a collagen-like peptide with a mutation Gly to Ala in the middle of the peptide (orange). Each polypeptide chain is folded into a polyproline type II helix and three chains form a superhelix similar to part of the collagen molecule. The alanine side chain is accommodated inside the superhelix causing a slight change in the twist of the individual chains, (a) Space-filling model, (b) Ribbon diagram. Compare with Figure 14.1c for the change caused by the alanine substitution. (Adapted from J. Bella et al.. Science 266 75-81, 1994.)...

Elastase-like proteinases are serine proteinases that recognized peptide residues with linear aliphatic side chains (alanyl, valyl, leucyl or isoleucyl residues) and that effect hydrolysis of the polypeptide chain on the carboxy-terminal side of these residues. Examples of elastase-like proteinase are pancreatic elastase, neutrophil elastase and proteinase-3. 

Trypsin-like proteinases are serine proteinases that recognized peptide residues with positively charged side chains (arginyl or lysyl residues) and that effect... 

If peptide residues are converted to peptoid residues, the conformational heterogeneity of the polymer backbone is likely to increase due to cis/trans isomerization at amide bonds. This will lead to an enhanced loss of conformational entropy upon peptoid/protein association, which could adversely affect binding thermodynamics. A potential solution is the judicious placement of bulky peptoid side chains that constrain backbone dihedral angles. 

In contrast to the lability of certain dN adducts formed by the BHT metabolite above, amino acid and protein adducts formed by this metabolite were relatively stable.28,29 The thiol of cysteine reacted most rapidly in accord with its nucleophilic strength and was followed in reactivity by the a-amine common to all amino acids. This type of amine even reacted preferentially over the e-amine of lysine.28 In proteins, however, the e-amine of lysine and thiol of cysteine dominate reaction since the vast majority of a-amino groups are involved in peptide bonds. Other nucleophilic side chains such as the carboxylate of aspartate and glutamate and the imidazole of histidine may react as well, but their adducts are likely to be too labile to detect as suggested by the relative stability of QMs and the leaving group ability of the carboxylate and imidazole groups (see Section 9.2.3). 

The N-terminal peptide fragment of des-angiotensinogen Val-Ile-His-Asn contains two strongly hydrophobic amino acid residues on the N-terminal site of His-3. The potentiometric data have shown that the NiH.2L complex with this albumin-like sequence is more than two orders of magnitude more stable than the respective complex with Gly-Gly-His.1744 The NMR-based molecular structure has shown that the side chains of Val-1 and lie-2 form a well-ordered hydrophobic fence (Figure 21) shielding one side of the coordination plane from the bulk of... 

Fig. 5. Comparison of ab initio, DFT/BPW91/6-31G -computed IR and VCD spectra over the amide I, II, and III regions for model peptides (of the generic sequence Ac-Alaw-NHCH3). These are designed to reproduce the major structural features of an o -helix (top left, n— 6, in which the center residue is fully H-bonded), a 3i helix (PLP Il-like, top right, n— 4), and an antiparallel /1-sheet (n= 2, 3 strands, central residue fully H-bonded) in planar (bottom left) and twisted (bottom right) conformations. The computations also encompass all the other vibrations in these molecules, but those from the CH3 side chains were shifted by H/D exchange (CH3) to reduce interference with the amide modes.

Fig. 10. Electron density projection along -strand direction—hydrogen-bonding direction (a-axis) horizontal, and intersheet direction (c-axis) vertical—and skeletal models of polyGln8 (Q8) and polyGln45 (Q45) assemblies. The unit cell for both peptides was monoclinic, with lattice constants a = 9.73 A, b = 7.14 A, c = 8.16 A, and y = 95.7° for Q8, and a = 9.66 A, b = 7.10 A, c = 8.33 A, and y = 94.0° for Q45. The side chains are nearly overlapped in the hydrogen-bonding direction. This difference in side chain conformation and disorder likely accounts for the differences in observed intensity between their diffraction patterns.

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