Proteopedia entry: Bovine pancreatic ribonuclease a

Abstract

This Proteopedia article presents a structural analysis of the well-studied, model enzyme, bovine pancreatic ribonuclease A (RNase A; Fig. 1). RNase A serves as a common discussion point in introductory biochemistry courses, where RNase A is used to illustrate diverse topics ranging from protein structure, function, folding, and enzymatic activity to total protein synthesis. RNase A is standardly depicted in its simple, monomeric state oriented with the active site cleft of its kidney bean structure in the center of the picture (Figs. 1 a and 1 c). This simplistic depiction of the structure and biology of RNase A, based solely on its secondary structure of a four-strand antiparallel β-sheet and three α-helices, undervalues the wealth of additional structural, biological, and chemical advances that RNase A has facilitated. In an interconnected series of five Proteopedia pages, undergraduate students from a second semester biochemistry course used interactive structural applets and integrated descriptions of RNase A to illustrate its historical significance, enzymology, folding, synthesis, solution structure, oligomeric assemblies, and therapeutic applications. Specific focal points from the pages include illustrating the difference between NMR and X-ray crystallography structures with comparisons between flexible and rigid portions of the RNase A structure (Fig. 1 a). RNase A also forms domain-swapped multimers in solution, and experimenting with the oligomerization state of RNase A has served as a model for understanding oligomerization diseases like Alzheimer's disease (Fig. 1 b). Total chemical synthesis of proteins was also developed using RNase A, and newer semisynthetic methods of protein synthesis continue to be refined using RNase A (Fig. 1 c). The five Proteopedia pages are presented together as a resource for biochemistry courses where students can explore protein structure through the easily accessible package of RNase A and as an illustration of hands-on experiences in protein structure, protein visualization, and multimedia design using Proteopedia. Unusual structural features of RNase A. (a) NMR structure of RNase A (PDB code: 2AAS). Top 32 solution structures shown to highlight the flexibility in the loops and termini of RNase A. (b) Domain-swapped dimer of RNase A (PDB code: 1A2W). Dimer formed by swapping of the N-terminal helix between two RNase A monomers (blue and green). (c) Semisynthetic RNase A (PDB code: 1SRN). A noncovalent complex between residues 1 and 118 of RNase A (blue) and a synthetic peptide comprising residues 111–124 (yellow). The synthetic peptide is colored to indicate the hydrophobicity of the peptide: yellow = hydrophobic; red = acidic; brown = basic.