Mechanical stability of compact modules of barnase. 1997

K Takahashi, and M Oohashi, and T Noguti, and M Go
Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Japan.

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.

UI MeSH Term Description Entries
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D003198 Computer Simulation Computer-based representation of physical systems and phenomena such as chemical processes. Computational Modeling,Computational Modelling,Computer Models,In silico Modeling,In silico Models,In silico Simulation,Models, Computer,Computerized Models,Computer Model,Computer Simulations,Computerized Model,In silico Model,Model, Computer,Model, Computerized,Model, In silico,Modeling, Computational,Modeling, In silico,Modelling, Computational,Simulation, Computer,Simulation, In silico,Simulations, Computer
D004795 Enzyme Stability The extent to which an enzyme retains its structural conformation or its activity when subjected to storage, isolation, and purification or various other physical or chemical manipulations, including proteolytic enzymes and heat. Enzyme Stabilities,Stabilities, Enzyme,Stability, Enzyme
D001426 Bacterial Proteins Proteins found in any species of bacterium. Bacterial Gene Products,Bacterial Gene Proteins,Gene Products, Bacterial,Bacterial Gene Product,Bacterial Gene Protein,Bacterial Protein,Gene Product, Bacterial,Gene Protein, Bacterial,Gene Proteins, Bacterial,Protein, Bacterial,Proteins, Bacterial
D012260 Ribonucleases Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-. Nucleases, RNA,RNase,Acid Ribonuclease,Alkaline Ribonuclease,Ribonuclease,RNA Nucleases,Ribonuclease, Acid,Ribonuclease, Alkaline
D014618 Vacuum A space in which the pressure is far below atmospheric pressure so that the remaining gases do not affect processes being carried on in the space. Vacuums
D014867 Water A clear, odorless, tasteless liquid that is essential for most animal and plant life and is an excellent solvent for many substances. The chemical formula is hydrogen oxide (H2O). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) Hydrogen Oxide
D017433 Protein Structure, Secondary The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to ALPHA-HELICES; BETA-STRANDS (which align to form BETA-SHEETS), or other types of coils. This is the first folding level of protein conformation. Secondary Protein Structure,Protein Structures, Secondary,Secondary Protein Structures,Structure, Secondary Protein,Structures, Secondary Protein

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