Protein amino acid side chains

Figure 3.1 Principal protein amino acid side-chain metal-ion binding modes (the metal ion represented as a dark filled circle) and (right) the structure of the Ca2+-binding y-carboxyglutamate found in proteins of the blood-clotting cascade.

P2 3-Peptides Bearing Protein Amino Acid Side Chains... 

FIGURE 4.1 Principal protein amino acid side chains involved in metal binding and their metal-ion-binding modes. 

Igumenova TI, Erederick KK, Wand AJ (2006) Qiaracterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. (Them Rev 106 1672-1699... 

Amino acid residues are potential targets of free radical oxidation and nitration. Carbonyl derivatives of proteins may be formed by the interaction of protein amino acid side chains, mainly cysteine, histidine, and lysine residues with reactive aldehydes, such as HNE and ONE generated by peroxidation of PUFAs (polyunsaturated fatty acids). Amino acid and peptide biomarkers of oxidative stress are typically focused on specific proteins related to disease pathology. For instance, the oxidation of histidine and methionine are typically discussed in (3-amyloid plaque formation and HNE-derived histidine adducts are the main focus of modifications on low-density lipoprotein (LDL) (An-nangudi et al., 2008). However, there are several specific examples of general biomarkers of oxidative stress that include endogenous histidine containing dipeptides such as carnosine and anserine as well as the very stable o,o -dityrosine. These will be discussed below. 

Spectrophotometric assays for protein amino acid side chains... 

Mechanistic considerations (Asquith and Otterburn, 1977 Whitaker and Feeney, 1977 Friedman, 1977) suggest that added thiol or sulfite ions can inhibit lysinoalanine formation by at least three distinct mechanisms. The first is by direct competition. The added nucleophile (mercaptide, sulfite, bisulfite, thiocyanate, thiourea, etc.) can trap dehydroalanine residues derived from protein amino acid side chains, forming their respective adducts. In particular, lanthionine side chains (Figure 8)are formed from added cysteine and N-acetyl-cysteine. The second possible mechanism is... 

The comparison of both data sources qualitatively shows a similar picture. Regions of high mobflity are located especially between the secondary structure elements, which are marked on the abscissa of the plot in Figure 7-17. Please remember that the fluctuations plotted in this example also include the amino acid side chains, not only the protein backbone. This is the reason why the side chains of large and flexible amino acids like lysine or arginine can increase the fluctuations dramatically, although the corresponding backbone remains almost immobile. In these cases, it is useful to analyze the fluctuations of the protein backbone and side chains individually. 

Much of protein engineering concerns attempts to explore the relationship between protein stmcture and function. Proteins are polymers of amino acids (qv), which have general stmcture +H3N—CHR—COO , where R, the amino acid side chain, determines the unique identity and hence the stmcture and reactivity of the amino acid (Fig. 1, Table 1). Formation of a polypeptide or protein from the constituent amino acids involves the condensation of the amino-nitrogen of one residue to the carboxylate-carbon of another residue to form an amide, also called peptide, bond and water. The linear order in which amino acids are linked in the protein is called the primary stmcture of the protein or, more commonly, the amino acid sequence. Only 20 amino acid stmctures are used commonly in the cellular biosynthesis of proteins (qv). 

Fig. 2. Protein secondary stmcture (a) the right-handed a-helix, stabilized by intrasegmental hydrogen-bonding between the backbone CO of residue i and the NH of residue t + 4 along the polypeptide chain. Each turn of the helix requires 3.6 residues. Translation along the hehcal axis is 0.15 nm per residue, or 0.54 nm per turn and (b) the -pleated sheet where the polypeptide is in an extended conformation and backbone hydrogen-bonding occurs between residues on adjacent strands. Here, the backbone CO and NH atoms are in the plane of the page and the amino acid side chains extend from C ...

Through combined effects of noncovalent forces, proteins fold into secondary stmctures, and hence a tertiary stmcture that defines the native state or conformation of a protein. The native state is then that three-dimensional arrangement of the polypeptide chain and amino acid side chains that best facihtates the biological activity of a protein, at the same time providing stmctural stabiUty. Through protein engineering subde adjustments in the stmcture of the protein can be made that can dramatically alter its function or stabiUty. 

Fig. 1. The two principal elements of secondary stmcture in proteins, (a) The a-helix stabilized by hydrogen bonds between the backbone of residue i and i + 4. There are 3.6 residues per turn of helix and an axial translation of 150 pm per residue. represents the carbon connected to the amino acid side chain, R. (b) The P sheet showing the hydrogen bonding pattern between neighboring extended -strands. Successive residues along the chain point...

Advantages of chromatography for protein separations include the large number of possible chemical interactions resulting from variations in the frequency and distribution of the amino-acid side chains on the surfaces of the proteins, and the availability of a wide array of different adsorption media. Chromatography has high efficiency and selectivity, and adequate scale-up potential. 

It is interesting to note that the amino acid side chains may be either neutral as in valine, acidic as in glutamic acid or basic as in lysine. The presence of both acidic and basic side chains leads to proteins such as casein acting as amphoteric electrolytes and their physical behaviour will depend on the pH of the environment in which the molecules exist. This is indicated by Figure 30.2, showing a simplified protein molecule with just one acidic and one basic side group. 

The most important aspect of Table 27.1 is that the 20 anino acids that occur in proteins share the common feature of being a-anino acids, and the differences fflnong them are in their side chains. Peptide bonds linking carboxyl and a-anino groups characterize the structure of proteins, but it is the side chains that are mainly responsible for theh properties. The side chains of the 20 commonly occuning amino acids encompass both large and small differences. The major differences between amino acid side chains concern ... 

Proteins are the indispensable agents of biological function, and amino acids are the building blocks of proteins. The stunning diversity of the thousands of proteins found in nature arises from the intrinsic properties of only 20 commonly occurring amino acids. These features include (1) the capacity to polymerize, (2) novel acid-base properties, (3) varied structure and chemical functionality in the amino acid side chains, and (4) chirality. This chapter describes each of these properties, laying a foundation for discussions of protein structure (Chapters 5 and 6), enzyme function (Chapters 14-16), and many other subjects in later chapters. 

Separation methods based on size include size exclusion chromatography, ultra-filtration, and ultracentrifugation (see Chapter Appendix). The ionic properties of peptides and proteins are determined principally by their complement of amino acid side chains. Furthermore, the ionization of these groups is pH-dependent. 

FIGURE 15.2 Enzymes regulated by covalent modification are called interconvertible enzymes. The enzymes protein kinase and protein phosphatase, in the example shown here) catalyzing the conversion of the interconvertible enzyme between its two forms are called converter enzymes. In this example, the free enzyme form is catalytically active, whereas the phosphoryl-enzyme form represents an inactive state. The —OH on the interconvertible enzyme represents an —OH group on a specific amino acid side chain in the protein (for example, a particular Ser residue) capable of accepting the phosphoryl group. 

John.son, L. N., and Barford, D., 1994. Electro.static effects in die control of glycogen pho.sphoryla.se by pho.sphorylation. Protein Science 3 1726-1730. Di.scn.s.sion of die pho.sphate group s ability to deliver two negative charges to a protein, a property that no amino acid side chain can provide. 

Also important for stabilizing a protein s tertiary stmcture are the formation of disulfide bridges between cysteine residues, the formation of hydrogen bonds between nearby amino acid residues, and the presence of ionic attractions, called salt bridges, between positively and negatively charged sites on various amino acid side chains within the protein. 

Evolution has provided the cell with a repertoire of 20 amino acids to build proteins. The diversity of amino acid side chain properties is enormous, yet many additional functional groups have been selectively chosen to be covalently attached to side chains and this further increases the unique properties of proteins. Diese additional groups play a regulatory role allowing the cell to respond to changing cellular conditions and events. Known covalent modifications of proteins now include phosphorylation, methylation, acetylation, ubi-quitylation, hydroxylation, uridylylation and glycosyl-ation, among many others. Intense study in this field has shown the addition of a phosphate moiety to a protein... 

The protein was purified by a dialysis procedure, denatured and analysed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Western blotting indicated that the protein of interest consisted of two components, one of which increased in concentration as the purification proceeded. The authors initially suggested that this could be due to the presence of a number of species produced by modification of the amino acid side-chains, for example, by glyco-sylation, or by modification of the C- or N- terminus. 

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