Protein covalent links between chains

Asparagine and glutamine are the amides of two other amino acids also found in proteins, aspartate and glutamate, respectively, to which asparagine and glutamine are easily hydrolyzed by acid or base. Cysteine is readily oxidized to form a covalently linked dimeric amino acid called cystine, in which two cysteine molecules or residues are joined by a disulfide bond (Fig. 3-7). The disulfide-linked residues are strongly hydrophobic (nonpolar). Disulfide bonds play a special role in the structures of many proteins by forming covalent links between parts of a protein molecule or between two different polypeptide chains. 

In addition to these noncovalent interactions, disulfide bonds form covalent links between the side chains of cysteines. When such bonds form, they restrict the folding patterns available to polypeptide chains. There are specialized laboratory methods for determining the number and positions of disulfide links in a given protein. Information about the locations of disulfide links can then be combined with knowledge of the primary structure to give the complete covalent structure of the protein. Note the subtle difference here The primary structure is the order of amino acids, whereas the complete covalent structure also specifies the positions of the disulfide bonds (Figure 4.13). 

Many membrane functions can be directly related to the physical properties of the liquid-crystalline lipid bilayer. Variations in curvature and area per unit mass and diffusion properties can thus be explained by the liquid-crystal model. Membrane proteins contain hydrophobic segments in an alpha-helical conformation which constitute the anchor in the hydrophobic core of the bilayer. The proteins contain short chains of sugar groups on the outer surface of the plasma membrane and this surface zone is involved in recognition phenomena. A covalent link between the peptide and the oligo-... 

Proteins are biopolymers formed by one or more continuous chains of covalently linked amino acids. Hydrogen bonds between non-adjacent amino acids stabilize the so-called elements of secondary structure, a-helices and / —sheets. A number of secondary structure elements then assemble to form a compact unit with a specific fold, a so-called domain. Experience has shown that a number of folds seem to be preferred, maybe because they are especially suited to perform biological protein function. A complete protein may consist of one or more domains. 

FIGURE 18.32 Biotin is covalently linked to a protein via the e-amino group of a lysine residue. The biotin ring is thus tethered to the protein by a 10-atom chain. It functions by carrying carboxyl groups between distant sites on biotin-dependent enzymes. 

When a biomolecular system is separated into QM and MM regions one must usually cut amino acid side chains or the protein backbone at covalent bonds (Fig. 5.2 a). The construction of the covalent boundary between the QM and MM parts is key to accurate results from QM/MM calculations. Because there is no unique way to treat the covalent boundary, several different approaches have been described. In the first applications of coupled QM/MM simulations link atoms were used to create the covalent QM/MM boundary (Fig. 5.2b). Link atoms are atoms added to the QM part to fill the broken valences of the boundary QM atoms. These atoms are placed along the broken QM/MM bond at a distance appropriate for the QM bond added. The link atoms have usually been hydrogen atoms but methyl groups and pseudohalogen atoms have also been used [35]. 

Disulfide bridges are, of course, true covalent bonds (between the sulfurs of two cysteine side chains) and are thus considered part of the primary structure of a protein by most definitions. Experimentally they also belong there, since they can be determined as part of, or an extension of, an amino acid sequence determination. However, proteins normally can fold up correctly without or before disulfide formation, and those SS links appear to influence the structure more in the manner of secondary-structural elements, by providing local specificity and stabilization. Therefore, it seems appropriate to consider them here along with the other basic elements making up three-dimensional protein structure. 

The strength of fibrous proteins is enhanced by covalent cross-links between polypeptide chains within the multihelical ropes and between adjacent chains in a supramolecular assembly. In a-keratins, the cross-links stabilizing quaternary structure are disulfide bonds (Box 4-2). In the hardest and toughest a-keratins, such as those of rhinoceros horn, up to 18% of the residues are cysteines involved in disulfide bonds. 

Some membrane proteins contain one or more covalently linked lipids of several types long-chain fatty acids, isoprenoids, sterols, or glycosylated derivatives of phosphatidylmositol, GPI (Fig. 11-14). The attached lipid provides a hydrophobic anchor that inserts into the lipid bilayer and holds the protein at the membrane surface. The strength of the hydrophobic interaction between a bilayer and a single hydrocarbon chain linked to a protein is barely enough to anchor the protein securely, but many proteins have more than one attached... 

Polymeric carbohydrates are major structural components in plant and bacterial cell walls and in the extracellular matrix of vertebrates. Branched-chain polymeric carbohydrates covalently linked to proteins are used to give proteins unique signatures that guide them to their final destination and that facilitate specific interactions between free proteins or proteins attached to cells. 

A protein is a linear sequence of amino acids linked together by peptide bonds. The peptide bond is a covalent bond between the oi-amino group of one amino acid and the a-carboxyl group of another. The peptide bond has partial double bond character and is nearly always in the trans configuration. The backbone conformation of a polypeptide is specified by the rotation angles about the Ca-N bond phi, (j>) and Ca-C bond psi, amino acid residues. The sterically allowed values of 0 and yr are visualized in a Ramachandran plot. When two amino acids are joined by a peptide bond they form a dipeptide. Addition of further amino acids results in long chains called oligopeptides and polypeptides. 

The primary level of structure in a protein is the linear sequence of amino acids as joined together by peptide bonds. This sequence is determined by the sequence of nucleotide bases in the gene encoding the protein (see Topic HI). Also included under primary structure is the location of any other covalent bonds. These are primarily disulfide bonds between cysteine residues that are adjacent in space but not in the linear amino acid sequence. These covalent cross-links between separate polypeptide chains or between different parts of the same chain are formed by the oxidation of the SH groups on cysteine residues that are juxtaposed in space (Fig. 4). The resulting disulfide is called a cystine residue. Disulfide bonds are often present in extracellular proteins, but are rarely found in intracellular proteins. Some proteins, such as collagen, have covalent cross-links formed between the side-chains of Lys residues (see Topic B5). 

Proteins containing more than one polypeptide chain, such as hemoglobin (see Topic B4), exhibit a fourth level of protein structure called quaternary structure (Fig. 8). This level of structure refers to the spatial arrangement of the polypeptide subunits and the nature of the interactions between them. These interactions may be covalent links (e.g. disulfide bonds) or noncovalent interactions (electrostatic forces, hydrogen bonding, hydrophobic interactions). 

Synthesis of aminoacyl-tRNAs is crucially important for two reasons. First each amino acid must be covalently linked to a tRNA molecule in order to take part in protein synthesis, which depends upon the adaptor function of tRNA to ensure that the correct amino acids are incorporated. Second, the covalent bond that is formed between the amino acid and the tRNA is a high energy bond that enables the amino acid to react with the end of the growing polypeptide chain to form a new peptide bond. For this reason, the synthesis of aminoacyl-tRNA is also referred to as amino acid activation. Amino acids that are not linked to tRNAs cannot be added to the growing polypeptide. 

Super glue is a polymer of methyl cyanoacrylate. Because both the cyano and carbonyl groups of the monomer help stabilize carbanions, this compound is sensitive to polymerization by the anionic mechanism. The tube of glue contains very pure monomer, which does not polymerize until it contacts an initiator. However, contact with any nucleophile causes rapid polymerization. Therefore, when the tube is opened, polymerization is initiated by water in the air, by SiOH groups on a glass surface, by FeOH groups on an iron surface, or by various nucleophiles that are part of the proteins in skin. The adhesion between the polymer and the surface to which it is applied is very strong because the polymer chains are covalently linked to the nucleophiles that are part of the surface ... 

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