Side chains amino acid structure

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. 

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. 

FIGURE 2.6 The procarcinogen benzo[a]pyrene oriented in the CYPlAl active site (stereo view) via n- n stacking between aromatic rings on the substrate and those of the complementary amino acid side chains, such that 7,8-epoxidation can occur. The substrate is shown with pale lines in the upper structures. The position of metabolism is indicated by an arrow in the lower structure (after Lewis 1996). 

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,... 

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... 

Higher orders of protein structure are stabilized primarily—and often exclusively—by noncovalent interactions. Principal among these are hydrophobic interactions that drive most hydrophobic amino acid side chains into the interior of the protein, shielding them... 

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. 

The structure is reasonable if the peptide backbone is correct and if the four amino acid side chains match the structures shown in Figure 13-32. 

Imately 65 X 55 X 50 It Is composed of four polypeptide chains each resembling quite closely the myoglobin chain The three dimensional structure of the subunits Is held together by weak noncovalent bonds The polar amino acid side chains are In contact with the solvent, and the nonpolar residues are located In the Interior of the molecule or In regions which form the contacts between chains The heme group Is located In a pocket In each chain residues In contact with heme are Invariable ( e are the same In different mammalian hemoglobins) and the bonds between heme and chain are hydrophobic Interactions Contacts between like chains (a-a are... 

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. 

Once an electron density map has become available, atoms may be fitted into the map by means of computer graphics to give an initial structural model of the protein. The quality of the electron density map and structural model may be improved through iterative structural refinement but will ultimately be limited by the resolution of the diffraction data. At low resolution, electron density maps have very few detailed features (Fig. 6), and tracing the protein chain can be rather difficult without some knowledge of the protein structure. At better than 3.0 A resolution, amino acid side chains can be recognized with the help of protein sequence information, while at better than 2.5 A resolution solvent molecules can be observed and added to the structural model with some confidence. As the resolution improves to better than 2.0 A resolution, fitting of individual atoms may be possible, and most of the... 

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 crystallographic structure of rubredoxin from Clostridium pasteurianum at 2.5 A, a resolution sufficient to reveal the sequence of several of the bulky amino acid side chains, shows the iron coordinated to two pairs of cysteine residues located rather near the termini of the polypeptide chain (Fig. 1). A related rubredoxin, with a three times larger molecular weight, from Pseudomonas oleovorans is believed to bind iron in a similar fashion. This conclusion is based on physical probes, especially electron paramagnetic resonance spectroscopy, all of which indicate that the iron is in each case situated in a highly similar environment however, the proteins display some specificity in catalytic function. 

The modification of amino acids in proteins and peptides by oxidative processes plays a major role in the development of disease and in aging (Halliwell and Gutteridge, 1989, 1990 Kim et al., 1985 Tabor and Richardson, 1987 Stadtman, 1992). Tissue damage through free radical oxidation is known to cause various cancers, neurological degenerative conditions, pulmonary problems, inflammation, cardiovascular disease, and a host of other problems. Oxidation of protein structures can alter activity, inhibit normal protein interactions, modify amino acid side chains, cleave peptide bonds, and even cause crosslinks to form between proteins. 

The effect of the amino acid spacer on iron(III) affinity was investigated using a series of enterobactin-mimic TRENCAM-based siderophores (82). While TRENCAM (17) has structural similarities to enterobactin, in that it is a tripodal tris-catechol iron-binding molecule, the addition of amino acid spacers to the TRENCAM frame (Fig. 10) increases the stability of the iron(III) complexes of the analogs in the order ofbAla (19)complex stability is attributed to the intramolecular interactions of the additional amino acid side chains that stabilize the iron-siderophore complex slightly. 

The description of protein structure as presented thus far may lead to the conclusion that proteins are static, rigid structures. This is not the case. A protein s constituent atoms are constantly in motion, and groups ranging from individual amino acid side chains to entire domains can be displaced via random motion by anything up to approximately 0.2 nm. A protein s conformation, therefore, displays a limited degree of flexibility, and such movement is termed breathing . 

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