Using peptides to study RNA-protein recognition

Abstract In biology, as in other sciences, the study of a particular system often is made simpler if the system is first reduced to small components. In structural biology, studies of large macromolecules can be hampered if, for example a molecule has too many flexible segments that prevent it from crystallizing or if it exceeds the practical size limit for nuclear magnetic resonance (NMR), currently -20-30 kDa. To overcome these problems, structural biologists often try to identify small, stable subdomains that retain the essential characteristics of the larger system but behave well under NMR conditions or crystallize. Some types of proteins, such as transcription factors, seem particularly well-suited to this approach because many are constructed from small structural and functional domains that can be studied as isolated modules (1). The structures of several DNA-binding domains were solved only after the domains were localized to short polypeptides, typically <100 amino acids, that bound to DNA with the same specificity as the intact proteins.