Charged residues

The amino acids are usually divided into three different classes defined hy the chemical nature of the side chain. The first class comprises those with strictly hydrophobic side chains Ala (A), Val (V), Leu (L), He (1), Phe (F), Pro (P), and Met (M). The four charged residues, Asp (D), Glu (E), Lys (K), and Arg (R), form the second class. The third class comprises those with polar side chains Ser (S), Thr (T), Cys (C), Asn (N), Gin (Q), His (H), Tyr (Y), and Trp (W). The amino acid glycine (G), which has only a hydrogen atom as a side chain and so is the simplest of the 20 amino acids, has special properties and is usually considered either to form a fourth class or to belong to the first class. 

The first sequence is from the enzyme citrate synthase, residues 260-270, which form a buried helix the second sequence is from the enzyme alcohol dehydrogenase, residues 355-365, which form a partially exposed helix and the third sequence is from troponin-C, residues 87-97, which form a completely exposed helix. Charged residues are colored red, polar residues ate blue, and hydrophobic residues are green. 

Asp 189 at the bottom of the substrate specificity pocket interacts with Lys and Arg side chains of the substrate, and this is the basis for the preferred cleavage sites of trypsin (see Figures 11.11 and 11.12). It is almost trivial to infer, from these observations, that a replacement of Asp 189 with Lys would produce a mutant that would prefer to cleave substrates adjacent to negatively charged residues, especially Asp. On a computer display, similar Asp-Lys interactions between enzyme and substrate can be modeled within the substrate specificity pocket but reversed compared with the wild-type enzyme. 

The helices are aligned according to approximate positions within the membrane and with respect to the photosynthetic pigments. LA is the first helix of subunit L, ME is the last helix of subunit M, HA is the only transmembrane helix of subunit H. Charged residues are eol-ored red, polar residues are blue, hydrophobic residues are green, and glycine is yellow. (From T.O. Yeates et al., Proc. Natl. Acad. Sci. USA 84 6438-6442, 1987.)... 

Figure 13.26 Schematic diagram of the SH2 domain from the Src tyrosine kinase with bound peptide. The SH2 domain (blue) comprises a central p sheet surrounded by two a helices. Three positively charged residues (green) are involved in binding the phosphotyrosine moiety of the bound peptide (red). (Adapted from G. Waksman et al.. Cell 72 779-790, 1993.)...

FIGURE 6.24 (a) The alpha helix consisting of residues 153-166 (red) in flavodoxin from Anahaena is a surface helix and is amphipathic. (b) The two helices (yellow and blue) in the interior of the citrate synthase dimer (residues 260-270 in each monomer) are mostly hydrophobic, (c) The exposed helix (residues 74-87—red) of calmodulin is entirely accessible to solvent and consists mainly of polar and charged residues. 

In globular protein structures, it is common for one face of an a-helix to be exposed to the water solvent, with the other face toward the hydrophobic interior of the protein. The outward face of such an amphiphilic helix consists mainly of polar and charged residues, whereas the inward face contains mostly nonpolar, hydrophobic residues. A good example of such a surface helix is that of residues 153 to 166 of flavodoxin from Anabaena (Figure 6.24). Note that the helical wheel presentation of this helix readily shows that one face contains four hydrophobic residues and that the other is almost entirely polar and charged. 

Less commonly, an a-helix can be completely buried in the protein interior or completely exposed to solvent. Citrate synthase is a dimeric protein in which a-helical segments form part of the subunit-subunit interface. As shown in Figure 6.24, one of these helices (residues 260 to 270) is highly hydrophobic and contains only two polar residues, as would befit a helix in the protein core. On the other hand. Figure 6.24 also shows the solvent-exposed helix (residues 74 to 87) of cahnodulln, which consists of 10 charged residues, 2 polar residues, and only 2 nonpolar residues. 

If certain quanta suitable for the excitation of a line are absorbed without photon emission, a radiationless transition is likely. This transition is known as the Auger effect,39 and it may be thought to involve an absorption by the atom of the photon produced when the hole in the K shell is filled by an electron from one of the external shells such as the L shell. The absorption of this photon results in the ejection of a second electron from one of the shells to leave a doubly charged residue of what had been a normal atom. The atom in this condition is described by naming the two states in which the electron holes are to be found e.g., the atom is in the LL or LM or LN state. An atom in such a state is, of course, vastly different from the usual divalent cation. 

Sequence of amino acids that determine the transport of proteins into the nucleus. Although there is no clear consensus, nuclear localization signals tend to be rich in positively charged residues, which allow interaction with proteins from the nuclear import machinery (i.e., importins). 

The maturation of the precursor protein involves their proteolytic cleavage. There are two proteins important in this cleavage, so-called processing protease and protease enhancing peptide. These are now believed to be nonidentical subunits of the same enzyme. The structural requirements for recognition of the cleavage site are not fully understood and except for a positively charged residue at position (-2) there is no consensus sequence around this site. 

There are alternative explanations for the actual mechanism by which these ions are produced, e.g. the ion-evaporation [11] and charge-residue models [12], and these have been debated for some time. 

According to the ion-evaporation model, the droplets become smaller until a point is reached at which the surface charge is sufficiently high for direct ion evaporation into the gas phase to occur. In the case of the charge-residue model, repeated Coulombic explosions take place until droplets are formed that contain a single ion. Evaporation of the solvent continues until an ion is formed in the vapour phase. 

Charge-residue mechanism One of the two mechanisms used to account for the production of ions by electrospray ionization. 

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