Protein peptide bonds from covalent

The high growth temperatures of archaeal thermophiles raise questions not only about the stability of the protein conformation but also about the protection of the peptide chain from covalent damage which occurs in mesophilic proteins. As shown by several authors [22-28] these chemical modifications mainly comprise, (a) deamidation of Asn and, to a minor extent. Gin (b) hydrolysis of Asp-containing peptide bonds (limited to the acidic pH range) and Asn-X bonds (c) destruction of cysteine and cystine residues. 

Chemically, proteins are unbranched polymers of amino acids linked head to tail, from carboxyl group to amino group, through formation of covalent peptide bonds, a type of amide linkage (Figure 5.1). 

Macromolecules are formed from many fragments of smaller molecules which are connected to each other by covalent bonds. For example, protein molecules are assembled from amino acids which are interconnected by peptide bonds (see Fig. 4.1). Typical amino acids are given in Fig. 4.2. 

Finally, special mention must be made of Cys, which, when present alone, can be considered to belong to the polar uncharged group described above. It can, however, when correctly positioned within the three-dimensional (3-D) structure of a protein, form disulfide bridges with another Cys residue (Figure 4.2). These are the only covalent bonds, apart from the peptide bond of course, that we usually find in proteins2. 

This enzyme (RNase A) is a single chain protein of 124 amino acid residues, cross-linked by four intrachain disulfide bonds. Limited proteolysis of the enzyme cuts a single peptide bond between residues 20 and 21 (Richards and Vithayathil, 1959). The derived protein, RNase S, retains enzymic activity although the N-terminal peptide of 20 amino acids (S-peptide) is no longer covalently attached to the balance of the molecule (S-protein). Removal of S-peptide from... 

There are many instances where a problem in protein chemistry or biology can be studied efficiently and effectively by semisynthesis. For this section, semisynthesis means the combination of a synthetic peptide with a large protein segment derived from natural sources. The combination can be by a covalent peptide bond or, in certain cases, by a specific... 

Protein catabolism begins with hydrolysis of the covalent peptide bonds that link successive amino acid residues in a polypeptide chain (fig. 22.3). This process is termed proteolysis, and the enzymes responsible for the action are called proteases. In humans and many other animals, proteolysis occurs in the gastrointestinal tract this type of proteolysis results from proteases secreted by the stomach, pancreas, and small intestine. 

Figure 3. Structure of peptide and isopeptide bonds resulting from covalent attachment of amino acids to proteins by chemical methods. In isopeptide bond formation Rt = -CH2- or -CH2CH2- of aspartic or glutamic acid and R2 = -(CH2)n- of lysine.

TMC-95A, a cydic peptide metabolite from Apiospra montagnei, is a potent competitive inhibitor of all active sites and forms characteristic hydrogen bonds with the protein backbone. The crystal structure of the yeast 20S proteasome in complex with TMC-95A indicates a non-covalent linkage to the active y -subunits the N-terminal threonine residues are not modified. The TMC-95A backbone adopts a -conformation and extends the -strand SI by the generation of an antiparallel P-sheet. This stmcture is similar to that seen with the aldehyde and epoxyketone inhibitors. An interactions of TMC-95A are formed with main-chain atoms and strictly conserved residues of the 20S proteasome. 

The system of intraglobular residue-residue contacts of a protein of N residues may be represented as an N x N matrix of the carbon-alphas, whose elements are ones (contact) or zeros (lack of contact). Any reasonable definition of contact provides ones in the positions (i, i + l)that correspond to a peptide bond between two adjacent residues in the sequence. The same is true for the residues corresponding to the pair of cysteines forming a disulfide bond (these data may not be available as input and may be used as a test of correct prediction). This set of contacts describes the sequential covalent topology and is a constant part of the contact matrix which does not depend on the spatial structure of the polypeptide chain however, any additional information on existing intraglobular contacts (e.g., from NMR data or disulfide linkage) can easily be introduced in the constant part of the contact matrix A ... 

From a purely chemical point of view, the fundamental fact is that proteins contain covalent bonds which are split by rather drastic means and more labile, noncovalent bonds which may be split or at least altered by denaturation alone. Two types of covalent structures exist, involving peptide bonds and disulfide bridges respectively. Both structures should be clearly differentiated since they are destroyed by quite different chemical treatments (hydrolysis for the first, oxidation or reduction for the second). They will be called for this reason, respectively, the primary and the secondary structures. Conversely, several inter- or intrachain, noncovalent... 

Primary structure refers to the identity and specific order of amino acid residues in the polypeptide cham. This sequence, which depends exclusively on covalent (peptide) bonds, is predetermined by the DNA coding (see Chapter 36) the tliree-dimensional structure and any special biological properties of the protein follow automatically from this amino acid sequence that folds itself into the most stable structure possible under physiological conditions. 

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