Mechanical stability of compact modules of barnase.

Globular proteins are composed of structural elements such as secondary structures and modules. Modules are compact segments consisting of 10-40 contiguous amino acid residues and are often encoded by exons. Therefore, the view that the modular organization of proteins is a result of exon-shuffling or -fusion is given support. Secondary structures such as alpha-helix and beta-sheet are stabilized by hydrogen bonds and are thus considered to be stable, structural elements of a globular domain. Since module boundaries are often located on alpha-helices or beta-sheets, it is not obvious whether the modules are mechanically stable. We carried out molecular dynamics simulations on modules of barnase, a bacterial RNase from Bacillus amyloliquefaciens, for 1 ns in vacuo and 150 ps in water. Five of six modules (M1, 1-24; M2, 25-52; M3, 53-73; M4, 74-88; M5, 89-98) retained native-like conformations during these simulations. Only the C-terminal module (M6, 99-110) was deformed; it is less compact than the other modules. As the modules are mechanically stable they are suitable as parts combined into proteins. Together with RNase activity of the three isolated modules of barnase, M2, M3 and M6, our study supports the view that modules were indeed original building blocks of proteins.