Amino acids distance methods

Four pairs of structures with identical descriptors merge at a distance of zero. From the chemist s point of view clustering appears more satisfying than the linear projection method PCA (with only 47.6% of the total variance preserved by the first two PCA scores). A number of different clustering algorithms have been applied to the 20 standard amino acids by Willet (1987). 

Another useful type of representation for protein structures is the diagonal plot. It is a matrix with the amino acid sequence number along both axes, in which either distance between the respective a-carbons or contact between the respective residues is plotted for each possible pair of residues (see Fig. 10). The diagonal plot is probably the most successful method yet devised of quantitatively mapping the... 

The use of autoradiographic methods confirmed bidirectional replication. Strains of amino acid aux-otrophs with small nucleoside triphosphate pools were used. The addition of amino acids after starvation led to initiation of replication with only a 6-min lag. The cells were labeled with [3H]thymidine, and after the replication forks had moved a short distance from the origin of replication the cells were given a pulse of "super-hot" [3H]thymidine. Using autoradiography it was possible to observe the clearly bidirectional replication forks378 (Fig. 27-17). Replication in other bacteria is also bidirectional. 

The results of these efforts show that no method of tRNA recognition is universal.2443 In some cases, e.g., for methionine- or valine-specific tRNAs, the synthetase does not aminoacylate a modified tRNA if the anticodon structure is incorrect. Although the anticodon is 7.5 ran away from the CCA end of the tRNA, the synthetases are large enzymes. Many of them are able to accommodate this large distance between a recognition site and the active site (Fig. 29-9A). For some other tRNAs the anticodon is not involved in recognition 245 For yeast tRNAphe residues in the stem of the dihydrouridine loop and at the upper end of the amino acid acceptor stem seem to be critical.241... 

A more sophisticated method involves the combination of metal-substituted proteins with electron acceptors covalently attached to the amino acid residue located at the protein surface. The [Ru(NH3)5]3+ complex attached to the histidine residue had been used in Zn-substituted myoglobin [71,72] or cytochrome b562 [73] as an electron acceptor. This design allows the distance between donor and acceptor to be fixed and is very useful for experimental analysis of intramolecular electron transfer in proteins. 

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