Structure, primary peptide bonds

Complete sequence analyses of the picomavirus precursor proteins are not available. However, there have been determinations of amino and carboxyl terminal sequences of capsid polypeptides, which permit educated guesses of the structure of the cleavage region. Obviously, the information obtained is only valid if exopeptidases have not removed terminal residues after the primary peptide bond scission (this latter phenomenon has been described with proinsulin). 

Where helical secondaiy structures are represented by the cylinder model, the /i-strand. structures are visualized by the ribbon model (see the ribbons in Figure 2-124c). The broader side of these ribbons is oriented parallel to the peptide bond. Other representations replace the flat ribbons with flat arrows to visualize the sequence of the primary structure. 

The loss of structure by a protein is called denaturation. This structural change may be a loss of quaternary, tertiary, or secondary structure it may also be degradation of the primary structure by cleavage of the peptide bonds. Even mild heating can cause irreversible denaturation. When we cook an egg, the protein called albumen denatures into a white mass. The permanent waving of hair, which consists primarily of long a helices of the protein keratin, is a result of partial denaturation. 

The primary structure - the sequence of peptide-bonded amino acids in the protein chain and the location of any disulfide bridges. 

Primary structures are stabilized by covalent peptide bonds. Higher orders of structure are stabilized by weak forces—multiple hydrogen bonds, salt (electrostatic) bonds, and association of hydrophobic R groups. 

The essential distinction between the approaches used to formulate and evaluate proteins, compared with conventional low molecular weight drugs, lies in the need to maintain several levels of protein structure and the unique chemical and physical properties that these higher-order structures convey. Proteins are condensation polymers of amino acids, joined by peptide bonds. The levels of protein architecture are typically described in terms of the four orders of structure [23,24] depicted in Fig. 2. The primary structure refers to the sequence of amino acids and the location of any disulfide bonds. Secondary structure is derived from the steric relations of amino acid residues that are close to one another. The alpha-helix and beta-pleated sheet are examples of periodic secondary structure. Tertiary... 

Proteins are built up by aminoacids linked by peptide bonds into a polypeptide chain (Figure 2). The sequence of the aminoacids in the chain is known as the primary structure of the protein. The primary structure of the protein gives rise to the corresponding three-dimensional structure, and the spatial relationships of the constituents are the key for the peptide function. 

The primary structure of a protein is the linear sequence of amino acids linked by peptide bonds. The structural heirarchy of proteins is as follows. 

The amino group of the N-terminal amino acid residue of a peptide will react with the FDNB reagent to form the characteristic yellow DNP derivative, which may be released from the peptide by either acid or enzymic hydrolysis of the peptide bond and subsequently identified. This is of historic interest because Dr F. Sanger first used this reaction in his work on the determination of the primary structure of the polypeptide hormone insulin and the reagent is often referred to as Sanger s reagent. 

The sequence of amino acids in a polypeptide chain is known as the primary structure. This feature is genetically determined and is responsible not only for the final shape of the protein but also for its physical characteristics and, ultimately, for its biological function. Proteins are made up of about 22 amino acids, which are linked by the peptide bond (Figure 11.1), an amide linkage involving the amino group of one amind acid and the carboxyl group of another. 

The H- and C-NMR spectroscopic data support the proposed primary structure of poly(Lys-25). The amide carbonyl resonances are particularly informative as these signals are well resolved in the C-NMR spectrum of poly(Lys-25) (Figure 4). An amide carbonyl resonance is observed at 174.9 ppm for poly(Lys-25) that does not appear in the spectrum of poly(Val-Pro-Gly-Val-Gly) [13]. The position and relative intensity of this resonance are consistent with a lysine amide carbonyl group within a peptide bond [14]. Moreover, the resonances of the amide carbonyl groups for other residues in the pentapeptide repeat are split due to the substitution of a lysine residue at position 4 in every fifth pentapeptide in Lys-25. In addition, the absence of splitting in amide carbonyl group of valine in position 4 (174.5 ppm) supports this assignment, as this residue is replaced by lysine in the fifth pentapeptide of the Lys-25 repeat. The presence of other resonances attributable to the lysine residue can be detected in the H- and C-NMR spectra of the Lys-25 polymer at levels commensurate with its... 

Proteins are polymers of amino acids linked together by peptide bonds the same family of 20 amino acids is employed by all living organisms to construct their proteins. The sequence of amino acids along the chain defines the primary structure of the protein, a species-specific quality. 

Robust peptide-derived approaches aim to identify a small drug-like molecule to mimic the peptide interactions. The primary peptide molecule is considered in these approaches as a tool compound to demonstrate that small molecules can compete with a given interaction. A variety of chemical, 3D structural and molecular modeling approaches are used to validate the essential 3D pharmacophore model which in turn is the basis for the design of the mimics. The chemical approaches include in addition to N- and C-terminal truncations a variety of positional scanning methods. Using alanine scans one can identify the key pharmacophore points D-amino-acid or proline scans allow stabilization of (i-turn structures cyclic scans bias the peptide or portions of the peptide in a particular conformation (a-helix, (i-turn and so on) other scans, like N-methyl-amino-acid scans and amide-bond-replacement (depsi-peptides) scans aim to improve the ADME properties." ... 

Carboxypeptidase A"" (CPA, EC 3.4.17.1) is a proteolytic enzyme that cleaves C-terminal amino acid residues with hydrophobic side chains selectively. Several X-ray structures are available" The active site of CPA consists of a hydrophobic pocket (primary substrate recognition site) that is primarily responsible for the substrate specificity, a guanidinium moiety of Argl45 that forms hydrogen bonds to the carboxylate of the substrate, and Glu270, whose carboxylate plays a critical role, functioning either as a nucleophile to attack the scissUe carboxamide carbonyl carbon of the substrate or as a base to activate the zinc-bound water molecule, which in turn attacks the scissile peptide bond ". However, semiempirical calculations had shown that the direct attack of... 

In a protein the amino acids are joined together in a linear order by amide linkages, also known as peptide bonds. The sequence of the covalently linked amino acids is referred to as the primary level of structure for the protein. In writing the sequence of amino acids in a chain, it is conventional to orient the chain so that the amino acid on the left is the one with a free amino group on its a-carbon, while the last amino acid on the right is the one whose a-carbon carboxylate is free. In other words, the amino- or N-terminus of the peptide chain is written on the left, and the carboxyl-or C-terminus is written on the right. One more convention the term backbone for a protein refers to the series of covalent bonds joining one a-carbon in a chain to the next a-carbon. 

FIGURE 3-16 Levels of structure in proteins. The primary structure consists of a sequence of amino acids linked together by peptide bonds and includes any disulfide bonds. The resulting polypeptide can be coiled into units of secondary structure, such as an cr helix. The he-... 

Unlike polysaccharides, proteins do not have branched chains, but several chains may be linked together via disulphide bridges rather than peptide bonds. The primary structure of ox insulin is shown in Fig. S.A2. The protein consists of two peptide chains which are linked via the formation of the disulphide bridges. Disulphide bridges are formed by the condensation of the thiol groups of two cysteine residues. 

In biological recognition phenomena, protein-protein interactions are of primary importance. In an attempt to mimic these processes, LaBrenz and Kelly [51] synthesized the peptidic host 64. In this receptor, the dibenzofuran template separates the two peptide units by roughly 10 A and allows for the complexation of a guest peptide (65), as depicted in Fig. 21. The complex first forms a three-stranded, antiparallel /J-sheet that is stabilized by hydrogen bonds, electrostatic interactions, and aromatic-aromatic interactions between the dibenzofuran and the benzamide moieties. This complex can further self associate to form more complex structures. This example shows that structurally defined peptide nanostructures can interfere with biological recognition processes and potentially have therapeutic applications. 

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