Amides in proteins

Enzymatic Hydrolysis Reactions of Esters. Xenobiotic compounds containing esters or other acid derivatives in their structures (e.g., amides, carbamates, ureas, etc., see Table 17.3) are often readily hydrolyzed by microorganisms. To understand how enzymatic steps can be used to transform these substances, it is instructive to consider the hydrolases (i.e., enzymes that catalyze hydrolysis reactions) used by organisms to split naturally occurring analogs (e.g., fatty acid esters in lipids or amides in proteins). The same chemical processes, and possibly even some of the same enzymes themselves, are involved in the hydrolysis of xenobiotic substrates. 

An improved quantitative understanding of the aggregate of fundamental factors that govern the HX of individual amides in proteins is needed to fully harness the wealth of information on local stmcture and d5mamics that is resident in protein HX kinetics. Thus, a direct and simple structural interpretation of observed HX rates in native proteins should be approached with utmost caution. This latter point was also recently highlighted by Englander et al. [40,41]. 

N-H [vN-H and amide II deformation (N-H in-plane bending) combination] for secondary amides in proteins CONHj combination of amide A and amide II N-H stretching and C=0 stretching (amide I) combination N-H (vN-H and 5N-H combination) for gamma-valerolactam N-H combination band found in the spectrum of native RNase A (C=0 amide I band)... 

N-H from secondary amide in proteins N-H (2v) stretching from secondary amide in proteins N-H from protein ... 

N-H combination band from secondary amides in proteins 2060 4850... 

Proteins are large biomolecules made up of a-amino acid residues linked together by amide, or peptide, bonds. Chains with fewer than 50 amino acids are often called peptides, while the term protein is reserved for larger chains. Twenty amino acids are commonly found in proteins all are a-amino acids, and all except glycine have stereochemistry similar to that of l sugars. In neutral solution, amino acids exist as dipolar zwitterions. 

Amide derivatives have proved especially useful sugars for study by c.d. spectroscopy. The amide substituent is the same as the chromophore found in proteins, so that its optical properties have been extensively studied both experimentally and theoretically. 2-Acetamido sugars are found in many glycoproteins. The structure of 2-acetamido-2-deoxy-a-D-glucopyranose is given as an example in formula 7. 

Although the ROA spectra of typical /1-sheet proteins share some of the features observed in /3-sheet poly-L-lysine, there are also some differences, especially in the amide I region. This is because the /1-sheet in proteins tends to be twisted and irregular, whereas that in polypeptides tends to be extended, multistranded and relatively flat. 

Fig. 7.17 Bend structure resulting from the HF/4-21G geometry refinement of a type-II bend of N-formyl pentaglycine amide. The torsional angles in this structure are not common in proteins due to the effects of the end groups on the dihedral angles in the bend.

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