Amino acid variations

Chasman, D. and R.M. Adams, "Predicting the Functional Consequences of Non-Synonymous Single Nucleotide Polymorphisms Structure-Based Assessment of Amino Acid Variation," /. Mol. Biol., 307, 683-706 (2001). 

Several amino acids in AGSl within the nucleotidebinding/hydrolysis motifs differ from their counterparts in Ras, and mutation of these residues in Ras leads to constitutive activity (Barbacid 1987 Feig and Cooper 1988), suggesting that AGSl may be constitutively active. AGS 1 is active in yeast-based assays without any apparent stimuli, and AGS 1 purified from yeast extracts is largely GTP bound (Cismowski et al. 2000). It is presently unclear whether these amino acid variations are sufficient to render AGS 1 constitutively active in mammalian cells or how posttranslational modifications of AGS 1 influence ifs level of basal and stimulated activity. 

Like LAR, ANR is a member of the RED protein family. Full details of the protein structure and reaction mechanism are yet to be published. However, Xie et al. compared the A. thaliana (AtANR) and M. truncatula (MtANR) ANR amino acid sequences and recombinant protein activities, and made suggestions on the possible reaction series. The two recombinant proteins showed significantly different kinetic properties, substrate specificities, and cofactor requirements. Although AtANR and MtANR share only 60% sequence identity, some well-conserved domains are evident, in particular the Rossmann dinucleotidebinding domain (GxxGxxG) near the N-termini. However, two amino acid variations did... 

Daniel Chasman R, Adams M. Predicting the functional consequences of non-synonymous single nucleotide polymorphisms structure-based assessment of amino acid variation. J Mol Biol 1996 307 683-706. 

Various amino acids containing a cyclopropyl residue have been found in members of the Sapindaceae, Hippocastanaceae and Aceraceae. The same plants often contain a range of Q- and Cz-amino acids, with a non-cyclic branched carbon skeleton. The position of branching suggests possible bio-genetic relationships to cyclopropane-containing amino acids. Variation of the basic structures mentioned in Fig. 3.22 is achieved by different chain lengths and by the introduction of double and triple bonds (Fowden, 1981). 

The phenoxazinone ring system of the actinomycins (19 ) is apparently formed from kynurenine and 3-oxykynurenine with methylation taking place at a late stage 73. Reports on amino acid variation and the mechanism of biosynthesis of the D-amino acids present in the side chains continue to appear 71t>75,76 >77>78,... 

Tolerance to Amino Acid Variations in a HLA Class 11 Ligand... 

Tolerance to amino acid variations for binding of undecapeptides to HLA DR1 molecules was determined by calculating the sum of the absolute values of the ln(relC) for all 20 O/Xl0 sublibraries of one sequence position. For sequence positions that allow close contact of the amino acids to the DR1 molecule, low tolerance with respect to biological activity to amino acid variations was expected. In contrast, amino acids variations should be more tolerated in positions projecting away from the binding cleft. The X-ray structure... 

Figure 11.9. Tolerance to amino acid variations in the 11 sequence positions with respect to proliferation of the TCC 5G7. Data were calculated as described from the allele-specific DR2b- Activity Pattern and from the Recognition Pattern of TCC 5G7. Letters indicate amino acids from MBP (85-95).

Udaka K, Wiesmiiller K-H, Kienle S, Jung G, Walden P (1995) Tolerance to amino acid variations in peptides binding to the MHC class I protein H-2Kb, J Biol Chem 720 24130-24136. 

Figure 5 Amino acid variations of BIBP 3226. The receptor affinity has been determined using human neuroblastoma cells (SK-N-MC), which constitutively express the Y1 receptor.

Figure 2. Initial set of 24 amino acid variations to alter substrate specificity and physical properties of proteinase K.

For each of the proteinase K activities tested, we used partial least squares regression (PLSR) to model the relationship between amino acid variation and the variations in proteinase activities (the sequence-activity relationship). The application of these methods to nucleic acids, peptides and proteins has been described previously (7, II, 12, 28-30)... 

We used our PLSR-based sequence activity relationship to assign a regression coefficient to each varied amino acid. We then calculated the predicted activity for a proteinase K variant by summing the regression coefficients for amino acid variations that are present in that variant. In this case we did not include terms to account for interactions between the varied amino acids, though this can also be done 13). Figure 3 shows a good correlation between the predictions of our calculated sequence-activity relationship and the measured ability of heat-treated proteinase K variants to hydrolyze AAPL-p-NA. 

The utility of a sequence-activity model lies in its ability to predict the activity of variants that have not been measured, or to identify amino acid variations that contribute positively to a specific protein property and that can then be experimentally combined. To test our sequence activity model for heat-tolerant hydrolyzers of AAPL-p-NA, we analyzed the regression coefficients from the model, as shown in Figure 4. 

Different Amino Acid Variations are Beneficial for Different Functions... 

The principal component analysis also clusters related functional measures. We selected three representative activities based on the functional clustering shown in Figure 6 for further analysis activity towards AAPL-p-NA at pH 7.0, absolute activity towards AAPL-p-NA following 5 minutes at 65°C and activity towards casein. For each of these activities we constructed PLSR models similar to that shown in Figure 3, and calculated the regression coefficients for each amino acid variation as shown for thermal tolerance in Figure 4. The changes calculated to contribute positively to each property are shown in Table 1. 

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