The Amino Acid Side Chains

The general categories of side chains include those with acidic, basic, sulfur-containing, and neutral aliphatic residues, respectively. We shall discuss each in turn. 

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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. 

Similar ligand-ligand interactions have been reported for a large number of ternary -amino acid complexes, built up of two different amino acid.s. A compilation of 72 examples is presented in reference 39. The extra stabilisation due to ligand-ligand interactions in these complexes depends on the character of the amino-acid side chains and amounts to 0.34 - 0.57 kJ/mole for combinations of aromatic and aliphatic side chains and 0.11 - 6.3 kJ/mole when arene - arene interactions are possible. ... 

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 ...

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. 

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. 

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. 

Fig. 2.14 Formulae of /5-peptides 81 and 82 forming stable 3,4-helical structures in aqueous solution and schematic representation of the position of the amino acid side-chains looking down the 3,4-helix axis [128, 165]...

The structural versatility of pseudopoly (amino acids) can be increased further by considering dipeptides as monomeric starting materials as well. In this case polymerizations can be designed that involve one of the amino acid side chains and the C terminus, one of the amino acid side chains and the N terminus, or both of the amino acid side chains as reactive groups. The use of dipeptides as monomers in the manner described above results in the formation of copolymers in which amide bonds and nonamide linkages strictly alternate (Fig. 3). It is noteworthy that these polymers have both an amino function and a carboxylic acid function as pendant chains. This feature should facilitate the attachment of drug molecules or crosslinkers,... 

FIGURE 3 Schematic representation of a pseudopoly (amino acid) derived from the side chain polymerization of a dipeptide carrying protecting groups X and Y. The wavy line symbolizes a nonamide bond. In this polymer, the amino acid side chains are an integral part of the polymer backbone while the termini have become pendant chains. In the backbone, amide and nonamide bonds strictly alternate. 

To be successful in these applications, it is important that materials can self-assemble into precisely defined structures. Peptide-based polymers have many advantages over conventional synthetic polymers since they are able to hierarchically assemble into stable, ordered conformations [4]. Depending on the substituents of the amino acid side chain, polypeptides are able to adopt a multitude of... 

An alternative to modifying the functional group attached to fibrils is to utilise the chemistry present in the amino acid side chains. Furthermore, as peptides often undergo specific modification by enzymes in vivo, these could be harnessed for synthetic purposes. Qll (Ac-QQKFQFQFEQQ-Am, a fibril-forming peptide based on Pi 1-2), was coupled to lysine-based molecules by treatment with an enzyme (tissue transglutaminase, TGase) which results in a reaction between lysine and glutamine side chains [72] (Fig. 32). 

The DQFCOSY spectrum of RpII in D O is shown in Figure 2. Each cross peak in this spectrum identifies a pair of coupled spins of the amino acid side chains. Since couplings are not propagated efficiently across amide bonds, all groups of coupled spins occur within individual amino acids. The chemical structure of an amino acid side chain is reflected in the characteristic coupling network and chemical shifts (13). Valine spin system (CH-CH-(CH3)2) explicitly shown in Figure 2 as an example. 

Interaction with a lipid bilayer driven by a potential difference and by polar and/or hydrophobic forces between the amino acid side chains of the pardaxin tetramers and the polar membrane lipid head group triggers insertion from a "raft" like structure. 

Solid state 13C CPMAS NMR spectra of Wheat High Molecular Weight (W.HMW) subunits show well resolved resonances identical with spectra of dry protein and peptide samples [24], Most of the amino acids side-chain resonances are found in the 0-35 ppm region followed by the alpha resonances of the most abundant amino acids glycine, glutamine and proline at chemical shifts of 42, 52 and 60 ppm, respectively, and the carbonyl carbons show a broad peak in 172-177 ppm region. The CPMAS spectra of hydrated whole HMW provides important information on the structural characteristics. 

Figure 21 Space-filling model of the structure with the lowest overall energy showing the amino acid side chains hindering axial approach to Nin. Color code C, light blue H, white N, dark blue O, red Ni11,...

The amino acid side chains and enzymes cofactors provide functional groups that are used to make the reaction go faster by providing new pathways and by making existing pathways faster. 

The result is the electron density map of the protein crystal. The final task for the crystallographer is to build the appropriate protein model, i. e., putting amino acid for amino acid into the electron density. Routinely the theoretical amplitudes and phases are calculated from the model and compared to the experimental data in order to check the correctness of model building. The positions of the protein backbone and the amino acid side chains are well defined by X-ray structures at a... 

Although the stabilizing interactions between the amino acid side chains of PLC/j, and the choline headgroup are readily apparent in the PLC fc-phosphonate inhibitor complex, it is more difficult to identify contacts between the protein and the acyl chains of the inhibitor [45]. In part this is because thermal motion in the acyl side chains, especially the sn-1 chain, renders them somewhat disordered. Consequently, the measured distances between the side chain carbons... 

One of the questions that is commonly addressed in mechanistic proposals is how is the active site water activated for nucleophilic attack on the phosphodi-ester bond Numerous combinations of amino acid side chains and zinc ions have been proposed for this role, but there has been little consensus. Critical to all the general base hypotheses is a quite reasonable assumption about catalysis by PLC5c The nucleophilic attack on the phosphodiester moiety proceeds via an in-line mechanism resulting in stereochemical inversion of configuration at phosphorus [86]. While this assumption is consistent with the position of the active site water molecules in the PLCBc-phosphonate inhibitor complex [45], it has not yet been established experimentally. This structure provides a detailed picture of how the amino acid side chains of Glul46, Glu4, Asp55, and the zinc ions interact with the phosphonate inhibitor (Fig. 12), so mechanistic hypotheses now have a structural basis. 

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