Mutant stability

BLR BL21 reck mutant BL21 recA mutant stabilizes tandem repeats... 

Protein stability is the free energy difference (AG) between the folded and unfolded states at physiological conditions, and it is in the range of 5-25 kcal/mol. Site-directed mutagenesis experiments provided a wealth of data for understanding the importance of chemical interactions for the stability of proteins during amino acid substitutions. Protein stability is experimentally measured with differential scanning calorimetry, circular dichroism, fluorescence spectroscopy, and so forth. The availability of such data in an electronically accessible database would be a valuable resource for the analysis and prediction of protein mutant stability. 

For the mutations on the surface of the protein, the classifications based on the chemical nature of amino acids, such as hydrophobic amino acids (Ala, Cys, Phe, Gly, He, Leu, Met, Val, Trp, and Tyr), amino acid side chains that can form hydrogen bonds (Asp, Cys, Glu, His, Lys, Met, Asn, Gin, Arg, Ser, Thr, Trp, and Tyr), and so forth, improved the correlation between amino acid properties and protein mutant stability. Furthermore, the inclusion of neighboring and surrounding residues remarkably improved the correlation in all the subgroups of mutations. This result indicates that the information from nearby polar/charged amino acid residues and/or the aliphatic and aromatic residues that are close in space is important for the stability of exposed mutations. 

Gilis D, Rooman M, PoPMuSiC, an algorithm for predicting protein mutant stability changes application to prion proteins. Protein Eng. 2000 13 849-856. 

In Figure 7b, the data are plotted as AG yielding a linear function. Extrapolation to 2ero denaturant provides a quantitative estimate of the intrinsic stability of the protein, AG, which in principle is the free energy of unfolding for the protein in the absence of denaturant. Comparison of the AG values between mutant and wild-type proteins provides a quantitative means of assessing the effects of point mutations on the stability of a protein. 

Y-Y Shi, AE Mark, C Wang, F Fluang, FIJC Berendsen, WF Van Gunsteren. Can the stability of protein mutants be predicted by free energy calculations Protein Eng 6 289-295,... 

Subtilisins are a group of serine proteinases that are produced by different species of bacilli. These enzymes are of considerable commercial interest because they are added to the detergents in washing powder to facilitate removal of proteinaceous stains. Numerous attempts have therefore recently been made to change by protein engineering such properties of the subtilisin molecule as its thermal stability, pH optimum, and specificity. In fact, in 1988 subtilisin mutants were the subject of the first US patent granted for an engineered protein. 

The single mutation Asp 32-Ala reduces the catalytic reaction rate by a factor of about lO compared with wild type. This rate reduction reflects the role of Asp 32 in stabilizing the positive charge that His 64 acquires in the transition state. A similar reduction of kcat and kcat/ m (2.5 x 10 ) is obtained for the single mutant Asn 155-Thr. Asn 155 provides one of the two hydrogen bonds to the substrate transition state in the oxyanion hole of subtilisin. 

Model building shows that the OH group of Thr in the mutant is too far away to provide such a hydrogen bond. The loss of this feature of the stabilization of the transition state thus reduces the rate by more than a thousandfold. 

Lysozyme from bacteriophage T4 is a 164 amino acid polypeptide chain that folds into two domains (Figure 17.3) There are no disulfide bridges the two cysteine residues in the amino acid sequence, Cys 54 and Cys 97, are far apart in the folded structure. The stability of both the wild-type and mutant proteins is expressed as the melting temperature, Tm, which is the temperature at which 50% of the enzyme is inactivated during reversible beat denat-uration. For the wild-type T4 lysozyme the Tm is 41.9 °C. 

Both types of mutations have been made in T4 lysozyme. The chosen mutations were Gly 77-Ala, which caused an increase in Tm of 1 °C, and Ala 82-Pro, which increased Tm by 2 °C. The three-dimensional structures of these mutant enzymes were also determined the Ala 82-Pro mutant had a structure essentially identical to the wild type except for the side chain of residue 82 this strongly indicates that the effect on Tm of Ala 82-Pro is indeed due to entropy changes. Such effects are expected to be additive, so even though each mutation makes only a small contribution to increased stability, the combined effect of a number of such mutations should significantly increase a protein s stability. 

Mutants that fill cavities in hydrophobic cores do not stabilize T4 lysozyme... 

These results indicate that is it possible to change the fold of a protein by changing a restricted set of residues. They also confirm the validity of the rules for stability of helical folds that have been obtained by analysis of experimentally determined protein structures. One obvious impliction of this work is that it might be possible, by just changing a few residues in Janus, to design a mutant that flip-flops between a helical and p sheet structures. Such a polypeptide would be a very interesting model system for prions and other amyloid proteins. 

Protein engineering is now routinely used to modify protein molecules either via site-directed mutagenesis or by combinatorial methods. Factors that are Important for the stability of proteins have been studied, such as stabilization of a helices and reducing the number of conformations in the unfolded state. Combinatorial methods produce a large number of random mutants from which those with the desired properties are selected in vitro using phage display. Specific enzyme inhibitors, increased enzymatic activity and agonists of receptor molecules are examples of successful use of this method. 

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