Protein mutant

J. Gao, K. Kuczera, B. Tldor, and M. Karplus. Hidden thermodynamics of mutant proteins A molecular dynamics analysis. Science, 244 1069-1072, 1989. 

IP Boissel, WR Lee, SR Presnell, EE Cohen, HP Bunn. Erythropoietin stiaicture-function relationships. Mutant proteins that test a model of tertiary stiaicture. I Biol Chem 268 15983-15993, 1993. 

C Lee. Testing homology modeling on mutant proteins Pi edictmg stiaictural and thermodynamic effects m the Ala98 Val mutants of T4 lysozyme. Folding Des 1 1-12, 1995. 

WA Lim, A Hodel, RT Sauer, FM Richards. The crystal structure of a mutant protein with altered but improved hydrophobic core packing. Proc Natl Acad Sci USA 91 423-427, 1994. PB Harbury, B Tidor, PS Kim. Repacking proteins cores with backbone freedom Structure prediction for coiled coils. Pi oc Natl Acad Sci USA 92 8408-8412, 1995. 

The quantity kcat/Km is a rate constant that refers to the overall conversion of substrate into product. The ultimate limit to the value of k at/Km is therefore set by the rate constant for the initial formation of the ES complex. This rate cannot be faster than the diffusion-controlled encounter of an enzyme and its substrate, which is between 10 to 10 per mole per second. The quantity kcat/Km is sometimes called the specificity constant because it describes the specificity of an enzyme for competing substrates. As we shall see, it is a useful quantity for kinetic comparison of mutant proteins. 

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. 

The specific role of each amino acid residue for the function of the protein can be tested by making specific mutations of the residue in question and examining the properties of the mutant protein. By combining in this way functional studies in solution, site-directed mutagenesis by recombinant DNA techniques, and three-dimensional structure determination, we are now in a position to gain fresh insights into the way protein molecules work. 

A Mutant Protein That Folds Slowly Can Cause Emphysema and Liver Damage... 

Many diseases are known to be caused by the intracellular retention of mutant proteins or by the impairment of components of the secretory pathway [4]. The disease-causing mechanisms include ... 

Disorders caused by misfolded mutant proteins that fail to pass the quality control system of the ER (e.g., mutations of the cystic fibrosis transmembrane regulator protein (CFTR) causing cystic fibrosis). The mutant proteins are retrotranslocated into the cytosol and finally subjected to proteolysis. In some... 

Most pharmacological strategies for the treatment of protein transport diseases aim to rescue mutant proteins... 

Protein Trafficking and Quality Control. Table 1 Examples of diseases associated with folding-defective, mutant proteins, and pharmacological chaperones used to correct misfolding in vitro... 

Neither chemical nor pharmacological chaperones lead to wild-type expression levels of the mutant proteins at the cell surface. Alternative or additional strategies are needed to improve the intracellular transport of the mutant proteins. In the future, dtugs may also be developed that influence those components of the quality control system that are involed in the retention of misfolded proteins. 

Fig. 10. Comparison between the g values of Cys-to-Ser mutants and wild-type [2Fe-2S] proteins, in cases where the substitution takes place at (A) the reducible site Emd (B) the nom-educible site. The following symbols indicate the various proteins , Anahaena 7120 vegetative ferredoxin , human ferredoxin , Frd B subunit in E. coli fumEirate reductase , Clostridium pasteurianum ferredoxin. Filled and empty symbols indicate the wild-t3ipe and mutant proteins, respectively.

Zahedi R, Bissler J, Davis AR. Andreadis C. Wisnieski J Unique Cl inhibitor dysfunction in a kindred without angioedema. II. Identification of an Ala443 Val substitution and functional analysis 92 of the recombinant mutant protein. J Clin Invest 1995 95 1299-1305. 

The cost of a molecular dynamics (MD) free energy study depends very much on both the system and the goal of the study. If the goal is to reproduce qualitatively an experimental number and interpret it in terms of microscopic interactions, and if the systems of interest (e.g., native and mutant protein) are very similar, then only limited conformational sampling will be needed in most cases, and a few short runs with a small model may suffice. 

M. S. Brown. cDNA cloning of MEV, a mutant protein that facilitates cellular uptake of mevalonate, and identification of the point mutation responsible for its gain of function. J. Biol. Chem. 1992, 267, 23113-23121. 

Changes induced by SNPs (or other mutations) in the protein targets of drugs may result in the medicine being ineffective. In this case, the relevant disease may remain untreated, or else an expensive drug discovery effort will have to be undertaken to identify new molecules that are able to affect the mutant protein. Given that most current small molecule discovery strategies rely on expensive... 

We have employed a more systematic random mutagenesis approach by dividing the BDI into consecutive clusters of 10 amino acid residues (Boxes) that are individually replaced with a string of 10 alanine residues in the full-length Hisg-tagged allele to facilitate affinity purification of the mutant protein (Valasek et ah, 2004). Alternatively, clusters rich in... 

---