Barnase stability

There are several examples of application of the FDPB model in theoretical analysis of protein stability. " Fiere we discuss experimental and theoreticaP results for the pFi dependence of barnase stability. Barnase is a ribonuclease from Bacillus amyloliquefaciens, a small (110 residues), monomeric, single-domain enzyme that lacks disulfide bonds and undergoes reversible unfolding by a two-state process. ... 

Prevost, M. Wodak, S. J. Tidor, B. Karplus, M., Contribution of the hydrophobic effect to protein stability — analysis based on simulations of the Ile-96- Ala mutation in barnase, Proc. Natl Acad. Sci. USA 1991, 88,10880-10884. 

Active sites of enzymes and binding sites of proteins are a general source of instability because they contain groups that are exposed to solvent in order to bind substrates and ligands and so are not paired with their normal types of partners. Stability-activity trade-off is also seen with residues in the natural polypeptide inhibitor of barnase, barstar, that has evolved to bind as rapidly as possible to barnase,70 and also in the active site of T4 lysozyme.71... 

Amino acid residues at an internal position. The changes in stability of barnase on making all 19 substitutions of Ala-32 in the second helix38 are in reasonable agreement with equivalent changes in internal positions in model... 

Support for this picture can be found in a study of the two closely related mesophilic proteins barnase and binase. These two extracellular ribonucleases are highly similar in structure, stability, and sequence, differing by only seventeen out of 110 amino acids. Serrano et al. (1993) introduced each mutation present in binase into barnase and measured... 

Hydrogen Bonds to Protein Stability—The Crystal Structure of Two Barnase Mutants. 

Two Buried Salt Bridges in the Stability and Folding Pathway of Barnase. 

Dong F, Vijayakumar M, Zhou HX. Comparison of calcula- 64. tion and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar. Biophys. J. 65. 2354 85 49-60. 

Contribution of the Hydrophobic Effect to Protein Stability. Analysis Based on Simulations of the Ile-96-Ala Mutation in Barnase. 

Figure 9 Stability of barnase versus pH solid circles, experimental data as estimated from the figure in Ref. 133 open squares, computed energies, assuming model compound pKjS for unfolded state, taken from Ref. 34 open diamonds, computed energies, corrected for apparent pK, shifts of carboxylic acids in the denatured state, taken from Ref. 134. The data were brought to one common point for pH 3.

R. Loewenthal, J. Sancho, and A. R. Fersht, /. Mol. Biol., 224, 759 (1992). Histidine-Aromatic Interactions in Barnase. Elevation of Histidine pK and Contribution to Protein Stability. 

M. Prevost and I. Ortmans, Proteins Struct., Funct., Bioinf., 29, 212 (1997). Refolding Simulations of an Isolated Fragment of Barnase into a Native-Like p Hairpin Evidence for Compactness and Hydrogen Bonding as Concurrent Stabilizing Factors. 

The simplest marriage between PB theory and the classical force-field approach is illustrated by the works of Caflisch and Karplus, in which structures from several MD trajectories of barnase were used in PB calculations to determine the electrostatic interaction energy between various groups/ and that of Archontis, Simonson and Karplus, who compared the binding of aspartate and asparagine to aspartyl-tRNA synthetase/ " Other studies are those of Cheatham et ah, on the stability of DNA duplexes/ Srinivasan et ah, on the stability of RNA hairpins/ " Reyes and Kollman, on RNA-protein binding Cubero et al., on triple-stranded DNA formation and Tsui and Case, on trivalent cobalt binding to RNA. 

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