Acidic side-groups

The sequence of amino acids in a peptide can be written using the three-letter code shown in Figure 45.3 or a one-letter code, both in common use. For example, the tripeptide, ala.ala.phe, could be abbreviated further to AAF Although peptides and proteins have chain-like structures, they seldom produce a simple linear system rather, the chains fold and wrap around each other to give complex shapes. The chemical nature of the various amino acid side groups dictates the way in which the chains fold to arrive at a thermodynamically most-favored state. 

We can also incorporate branches by copolymerizing ethylene with vinyl esters and vinyl acids. In addition to their ester or acid side groups, these copolymers also contain the long and short chain branches, which are characteristic of low density polyethylene. 

Figure 42. Synthesis of polyphosphazenes bearing phenyl phosphonic acid side groups.

Ionic strength Salts compete with water for the binding sites on amino acid side groups the amount of water bound to a protein is a function of salt concentration ( ]. The effect of ionic strength on protein functionality has been focused primarily on its effect on solubility ( ). Generally, protein solubility increases at low salt concentrations and decreases at high salt concentrations. 

The structure of proteins determines their function and can be described on four levels, illustrated on page 447. The primary structure is the sequence of amino acids in the polypeptide chain. The secondary structure describes how various short portions of a chain are either wrapped into a coil called an alpha helix or folded into a thin pleated sheet. The tertiary structure is the way in which an entire polypeptide chain may either twist into a long fiber or bend into a globular clump. The quaternary structure describes how separate proteins may join to form one larger complex. Each level of structure is determined by the level before it, which means that ultimately it is the sequence of amino acids that creates the overall protein shape. Fhis final shape is maintained both by chemical bonds and by weaker molecular attractions between amino acid side groups. 

The P-loop structure in crystals of Dictyostelium myosin II is shown in Fig. 5 (Smith and Rayment, 1996). This structure provides an environment where MgATP is coordinated with a large number of the surrounding amino acid side groups. For example, the Mg2+ ion, in addition to interacting with the two terminal phosphates of ATP, is coordinated directly to... 

Among protein oxidation products, formation of protein peroxides should be mentioned. Protein peroxidation occurs as a reaction secondary to free-radical attack on amino acid side groups, effecting a carbon-centered free radical of amino acid formation. Such a radical reacts with the oxygen molecule and produces a hydroperoxide radical ... 

Amino acid analysis for the identification of amino acid side-groups in proteins... 

Acidic Side Groups Aspartic acid Asp 1 1 H -CH2COOH... 

FIGURE 23.19 The structure of silk. The amino acid side groups (shown as R) must be small to fit into a sheet-like structure. Glycine (R=H) and alanine (R=CH3) predominate. The repeating unit is shown as an inset. 

It should be emphasized that the stated resolution of a particular structure determination does not necessarily reflect the clarity of the features present in the electron density map, or the accuracy of the model based on the map. That is, many 3.0 A resolution electron density maps are far more interpretable in terms of protein structure, and the amino acid side groups more recognizable, than are some maps that include higher resolution terms. This is because resolution says nothing about the accuracy of the structure factors used to compute the map. In particular, it gives no indication of the quality of the phase determination, the mean phase error, which is the essential factor that influences contrast between the electron density of the protein and the background noise level in the Fourier map. 

Amino acids Side groups Sericin (% mol) Fibrion (% mol)... 

In other cases, one of the interactions can be so strong that optimal contact with other binding sites cannot materialize. Examples for this have been discussed above, e.g., with the porphyrin-based host, which cannot differentiate between nucleotides and nucleosides due to fhe dominating stacking effects. Even adverse, anti-cooperative effects between selectivity and affinity sites can be tolerated, in particular if fhe aim is stereoselectivity. In the chiral crown ether (Fig. 2.16), which is the basis of Crarris chiral resolution machine [69], stereoselection is due to interactions between amino acid side groups and the crown ether... 

By means of x-ray diffraction of crystalline protein and of NMR spectroscopy of the molecules in solution, the complete three-dimensional structure of a protein can be established. Many proteins show an intricate, tightly folded structure, which includes secondary structure elements. Generally, hydrophilic amino acid side groups are predominantly at the surface, and hydrophobic ones in the core of the structure. The driving forces for folding are discussed in Section 7.2.1. The role of water is essential and it may be stated that... 

Figure 10 Possible oxidative mechanisms for the production of acidic side groups from basic amino acid residues. Asterisk indicates site of oxidative attack...

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