Functionally invariant residues

From a comparison of the primary structure of the neurotoxins, Karlsson (11) and Ryden et al. (12) observed that certain invariant amino acid positions in the structural chain are important for the general folding of the molecule, while others are important for the neurotoxic activity. The former are called structurally invariant residues, whereas the later are called functionally invariant residues. 

The electron transport protein, cytochrome c, found in the mitochondria of all eukaryotic organisms, provides the best-studied example of homology. The polypeptide chain of cytochrome c from most species contains slightly more than 100 amino acids and has a molecular weight of about 12.5 kD. Amino acid sequencing of cytochrome c from more than 40 different species has revealed that there are 28 positions in the polypeptide chain where the same amino acid residues are always found (Figure 5.27). These invariant residues apparently serve roles crucial to the biological function of this protein, and thus substitutions of other amino acids at these positions cannot be tolerated. 

Figure 4. Alignment of PelZ and PelC amino acid sequences. The vertical lines indicate identical amino acids and the two points indicate homologous amino acids. The bold letters correspond to the residues probably involved in Ca + binding or catalytic function(s). The two aspartate residues probably involved in Ca binding are indicated with an asterisk. The invariant residues, probably involved in PGA cleavage, are indicated with an open circle. The folding in p-sheets is characterised by the underlined amino acids. Double underlining of PelZ residues is deduced from Chou Fasman and Robson Gamier folding predictions.

Table 5.1 Roles of Invariant Residues with Known Functions in Aspartate Aminotransferase...

In every enzyme family and superfamily, there are invariant residues that are required to maintain structure and/or function. However, for the majority of the residues, considerable variability is tolerated enzymes with <30% sequence identity often have very similar structures and identical functions. Such sequence divergence occurs by neutral drift, a process by which mutations that do not affect the fitness of the organism accumulate over long periods of time. 

The putative catalytic pocket contains five residues two catalytic residues (Asp-537 and Asp-812), which are invariant in all polymerases, and a cluster of three residues (Lys-631, Tyr-639, and Gly-640), which are invariant in all DNA-directed polymerases (126). Lys-631 interacts with the phosphates of NTP substrates. The Y639F mutation results in markedly reduced discrimination against dNTP utilization, without affecting promoter specificity or overall activity of the polymerase (33). Asp-569 and Tyr-571 are also functionally important residues. 

The residues not in the framework region form the loops between the p strands. These loops may vary in length and sequence among immunoglobulin chains of different classes but are constant within each class the sequence of the loops is invariant. The functions of these loops are not known, but they are probably involved in the effector functions of antibodies. When an antibody-antigen complex has been formed, signals are... 

Neurotoxins present in sea snake venoms are summarized. All sea snake venoms are extremely toxic, with low LD5Q values. Most sea snake neurotoxins consist of only 60-62 amino acid residues with 4 disulOde bonds, while some consist of 70 amino acids with 5 disulfide bonds. The origin of toxicity is due to the attachment of 2 neurotoxin molecules to 2 a subunits of an acetylcholine receptor that is composed of a2 6 subunits. The complete structure of several of the sea snake neurotoxins have been worked out. Through chemical modification studies the invariant tryptophan and tyrosine residues of post-synaptic neurotoxins were shown to be of a critical nature to the toxicity function of the molecule. Lysine and arginine are also believed to be important. Other marine vertebrate venoms are not well known. 

From 13 completed amino-acid sequences and 54 partial sequences (>40 residues) of plastocyanins from higher plants it appears that sixty residues are invariant and 7 are conservatively substituted 02,7). With three algal plastocyanins included there are 39 invariant or conservatively substituted groups. It is believed that the same structural features apply to the whole family, and that highly conserved residues are an indication of functional sites on the protein surface. The upper hydrophobic and right-hand-side surfaces are believed to be particularly relevant in this context, the latter including four consecutive... 

In the third model (2, right), the colored residues are those that are located on the surface and occur invariably (red) or almost invariably (orange) in all known insulins. It is assumed that amino acid residues that are not replaced by other residues during the course of evolution are essential for the protein s function. In the case of insulin, almost all of these residues are located on one side of the molecule. They are probably involved in the binding of the hormone to its receptor (see p.224). 

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