Peptide bonds nature

Depsipeptide polypeptides which contain ester bonds as well as peptide bonds. Naturally occurring D. are usually cyclic peptides, also called peptolides, which generally have a- or p-hydroxyacids as hetero-components. In the wider sense, this class also includes 0-peptides and peptide lactones. The most important peptide lactones are the Actinomycins (see), Etamycin (see) and Echinomycin (see) the peptolides include the Enniatins (see), Valinomycin (see), Sporidesmo-lides (see), Serratamolide (see), Esperin (see), etc. D. are metabolic products of microorganisms which often have very high antibiotic activity. Many D. can be chemically synthesized by methods very similar to those used in the chemical synthesis of peptides. 

Most reactions in cells are carried out by enzymes [1], In many instances the rates of enzyme-catalysed reactions are enhanced by a factor of a million. A significantly large fraction of all known enzymes are proteins which are made from twenty naturally occurring amino acids. The amino acids are linked by peptide bonds to fonn polypeptide chains. The primary sequence of a protein specifies the linear order in which the amino acids are linked. To carry out the catalytic activity the linear sequence has to fold to a well defined tliree-dimensional (3D) stmcture. In cells only a relatively small fraction of proteins require assistance from chaperones (helper proteins) [2]. Even in the complicated cellular environment most proteins fold spontaneously upon synthesis. The detennination of the 3D folded stmcture from the one-dimensional primary sequence is the most popular protein folding problem. 

ENZYMATIC ANALYSIS WITH CARBOXYPEPTIDASES. Carboxypeptidases are enzymes that cleave amino acid residues from the C-termini of polypeptides in a successive fashion. Four carboxypeptidases are in general use A, B, C, and Y. Carboxypeptidase A (from bovine pancreas) works well in hydrolyzing the C-terminal peptide bond of all residues except proline, arginine, and lysine. The analogous enzyme from hog pancreas, carboxypeptidase B, is effective only when Arg or Lys are the C-terminal residues. Thus, a mixture of carboxypeptidases A and B liberates any C-terminal amino acid except proline. Carboxypeptidase C from citrus leaves and carboxypeptidase Y from yeast act on any C-terminal residue. Because the nature of the amino acid residue at the end often determines the rate at which it is cleaved and because these enzymes remove residues successively, care must be taken in interpreting results. Carboxypeptidase Y cleavage has been adapted to an automated protocol analogous to that used in Edman sequenators. 

Why should the cores of most globular and membrane proteins consist almost entirely of a-helices and /3-sheets The reason is that the highly polar N—H and C=0 moieties of the peptide backbone must be neutralized in the hydrophobic core of the protein. The extensively H-bonded nature of a-helices and /3-sheets is ideal for this purpose, and these structures effectively stabilize the polar groups of the peptide backbone in the protein core. 

Zhang, B., and Cecil, T. R., 1997. Peptide bond formation by in vitro selected ribozymes. Nature 59 99- 99. 

Relatively few heteroaromatic N-oxides occur in nature. The chemistry of compounds that contain the oxidized peptide bond (the so-called hydroxamic acids) and their role in iron metabolism have been reviewed (67SC1443). Another review deals with the natural occurrence of N-oxides (68MI1). 

Other interesting examples of proteases that exhibit promiscuous behavior are proline dipeptidase from Alteromonas sp. JD6.5, whose original activity is to cleave a dipeptide bond with a prolyl residue at the carboxy terminus [121, 122] and aminopeptidase P (AMPP) from E. coli, which is a prohne-specific peptidase that catalyzes the hydrolysis of N-terminal peptide bonds containing a proline residue [123, 124]. Both enzymes exhibit phosphotriesterase activity. This means that they are capable of catalyzing the reaction that does not exist in nature. It is of particular importance, since they can hydrolyze unnatural substrates - triesters of phosphoric acid and diesters of phosphonic acids - such as organophosphorus pesticides or organophosphoms warfare agents (Scheme 5.25) [125]. 

Biosynthesis of the polypeptide chain is realised by a complicated process called translation. The basic polypeptide chain is subsequently chemically modified by the so-called posttranslational modifications. During this sequence of events the peptide chain can be cleaved by directed proteolysis, some of the amino acids can be covalently modified (hydroxylated, dehydrogenated, amidated, etc.) or different so-called prosthetic groups such as haem (haemoproteins), phosphate residues (phosphoproteins), metal ions (metal-loproteins) or (oligo)saccharide chains (glycoproteins) can be attached to the molecule by covalent bonds. Naturally, one protein molecule can be modified by more means. 

Hydrolysis reactions occur by nucleophilic attack at a carbon single bond, involving either the water molecule directly or the hydronium or hydroxyl ion. The most favorable conditions for hydrolysis, e.g. acidic or alkaline solutions, depend on the nature of the bond which is to be cleaved. Mineral surfaces that have Bronsted acidity have been shown to catalyze hydrolysis reactions. Examples of hydrolysis reactions which may be catalyzed by the surfaces of minerals in soils include peptide bond formation by amino acids which are adsorbed on clay mineral surfaces and the degradation of pesticides (see Chapter 22). 

When forming a bond, the nature of the substituent at the carboxyl function of the residue providing the amino group is irrelevant to the reaction that is, it may be a protector or the nitrogen atom of an amide or peptide bond. In contrast, the nature of the substituent on the amino function of the residue providing the carboxyl group... 

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