Protein, amino acid substitutions

Henikoff S and J G Henikoff 1992. Amino Acid Substitution Matrices from Protein Blocks. Proceedir Hie National Academy of Sciences LISA 89 10915-10919. 

Klapper 1, R Hagstrom, RFine, K Sharp and B Honig 1986. Focusing of Electric Fields in tire Actir e Sit of CuZn Superoxide Dismutase Effects of Ionic Strength and Amino-Acid Substitution. Proteins Structure, Function and Genetics 1 47-59. 

Although FeMo-cofactor is clearly knpHcated in substrate reduction cataly2ed by the Mo-nitrogenase, efforts to reduce substrates using the isolated FeMo-cofactor have been mosdy equivocal. Thus the FeMo-cofactor s polypeptide environment must play a critical role in substrate binding and reduction. Also, the different spectroscopic features of protein-bound vs isolated FeMo-cofactor clearly indicate a role for the polypeptide in electronically fine-tuning the substrate-reduction site. Site-directed amino acid substitution studies have been used to probe the possible effects of FeMo-cofactor s polypeptide environment on substrate reduction (163—169). Catalytic and spectroscopic consequences of such substitutions should provide information concerning the specific functions of individual amino acids located within the FeMo-cofactor environment (95,122,149). 

The elegant genetic studies by the group of Charles Yanofsky at Stanford University, conducted before the crystal structure was known, confirm this mechanism. The side chain of Ala 77, which is in the loop region of the helix-turn-helix motif, faces the cavity where tryptophan binds. When this side chain is replaced by the bulkier side chain of Val, the mutant repressor does not require tryptophan to be able to bind specifically to the operator DNA. The presence of a bulkier valine side chain at position 77 maintains the heads in an active conformation even in the absence of bound tryptophan. The crystal structure of this mutant repressor, in the absence of tryptophan, is basically the same as that of the wild-type repressor with tryptophan. This is an excellent example of how ligand-induced conformational changes can be mimicked by amino acid substitutions in the protein. 

Bowie, J.U. Deciphering the message in protein sequences tolerance to amino acid substitutions. Science 247 1306-1310, 1990. 

Given a large population of individuals, a considerable number of sequence variants can be found for a protein. These variants are a consequence of mutations in a gene (base substitutions in DNA) that have arisen naturally within the population. Gene mutations lead to mutant forms of the protein in which the amino acid sequence is altered at one or more positions. Many of these mutant forms are neutral in that the functional properties of the protein are unaffected by the amino acid substitution. Others may be nonfunctional (if loss of function is not lethal to the individual), and still others may display a range of aberrations between these two extremes. The severity of the effects on function depends on the nature of the amino acid substitution and its role in the protein. These conclusions are exemplified by the more than 300 human... 

Mutations in two genes directly lead to a disease. Mutations in the AQPO gene lead to dominantly inherited cataract. Single amino acid substitution in the AQPO gene in both mice and humans result in proteins with impaired trafficking to the plasma membrane and cataract formation, due to loss of the integrity of the lens. 

Although the second Cys of the three groups of cysteine residues expected to coordinate the [4Fe-4S] centers of E. coli nitrate reductase were systematically mutated to induce their conversion into [3Fe-4S] centers, this conversion was achieved only in the case of the C247D mutation affecting the lowest potential [4Fe-4S] center (E. Valay, B. Guigliarelli, M. Asso, P. Bertrand, and F. Blasco, unpublished results, 1998). This result, which confirms the proposed coordination scheme (174), shows once again that the coordination capacity of the various Cys motifs of a protein can be differently affected by amino acid substitutions. 

Amino acid substitutions on the native y52 8sKIpeptide, coiled-coil domain of human fibrin were able to stabilize the coiled-coil formation. These substitutions were targeted to the positions that compose the interface between coiled-coil strands while the solvent-exposed residues were left unperturbed. This strategy aimed at reducing the likelihood of immunogenicity for future in vivo apphcafion of these materials. In contrast to PEG block copolymers with end blocks that are not used for directed assembly, PEG copolymers with coiled-coil protein motives aim to enhance intermolecular interactions and control over the assembly conditions [85, 173]. 

The most frequent application of SPOT-synthesis has been in the preparation of peptide arrays for the identification of linear B-cell epitopes. If the protein antigen is known, a set of overlapping peptides that encompass the entire sequence can be readily synthesized and assayed for binding of antibody (Reineke et al., 1999). The individual residues critical for binding can then be determined by SPOT-synthesis of peptides containing amino acid substitutions. 

Fig. 4. Substitution matrix based on disordered protein families. Below the diagonal are the scores for each amino acid substitution. Above the diagonal are the differences between BLOSUM 62 and the disorder matrix. On the diagonal are the scores/differences. (From Radivojac et al., 2002, PSB 2002 7, 589-600, with permission of World Scientific Publishing Co. Pte Ltd.)...

Reverse-phase HPLC (RP-HPLC) separates proteins on the basis of differences in their surface hydophobicity. The stationary phase in the HPLC column normally consists of silica or a polymeric support to which hydrophobic arms (usually alkyl chains, such as butyl, octyl or octadecyl groups) have been attached. Reverse-phase systems have proven themselves to be a particularly powerful analytical technique, capable of separating very similar molecules displaying only minor differences in hydrophobicity. In some instances a single amino acid substitution or the removal of a single amino acid from the end of a polypeptide chain can be detected by RP-HPLC. In most instances, modifications such as deamidation will also cause peak shifts. Such systems, therefore, may be used to detect impurities, be they related or unrelated to the protein product. RP-HPLC finds extensive application in, for example, the analysis of insulin preparations. Modified forms, or insulin polymers, are easily distinguishable from native insulin on reverse-phase columns. 

Henikoff, S., and Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A. 89, 10915-10919. 

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