Barnase

Bond C ], K-B Wong, ] Clarke, A R Ferscht and V Daggett 1997. Characterisation of Residual Structure in the Tliermally Denatured State of Barnase by Simulation and Experiment Description of the Folding Pathway. Proceedings of the National Academy of Sciences USA 94 13409-13413. 

The details of many all-atom unfolding simulation studies have been summarized in several reviews [17,46,47]. These studies include unfolding simulations of a-lactalbumin, lysozyme, bovine pancreatic trypsin inhibitor (BPTI), barnase, apomyoglobin, [3-lacta-mase, and more. The advantage of these simulations is that they provide much more detailed information than is available from experiment. However, it should be stressed that there is still only limited evidence that the pathways and intermediates observed in the nanosecond unfolding simulations correlate with the intermediates observed in the actual experiments. 

Figure 6.4 Schematic diagram of the structure of the enzyme barnase which is foided into a five stranded antiparallel p sheet (blue) and two a helices (red).

Figure 6.5 (a) Some proteins such as barnase fold through one major pathway whereas others fold through multiple pathways. 

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. 

Various bacterial ribonucleases as well as the fungal ribonucleases Ty Uj, and U2 (see also Fig. 5-43) have amino acid sequences related to that of RNase A763 764 764a but with distinctly different three-dimensional structures. The active sites contain Glu, His, and Arg side chains. For RNase Ty Glu 58 and His 92 appear to provide acid-base catalysis with assistance from Tyr 38, Arg 77, and His 40.763 765 A glutamate carboxylate also appears to be the catalytic base in the related RNase, called barnase, from Bacillus amyloliquefaciens.766... 

Figure 1.5 A right-handed a helix of the ribonuclease, barnase (residues 6-18).

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... 

Consolidation of 2° and 3° more concerted for barstar than barnase... 

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