Recognition of protein folds via dipolar couplings

Abstract

Alignment of proteins in dilute liquid crystalline medium gives rise to residual dipolar couplings which provide orientational information of vectors connecting the interacting nuclei. Considering that proteins are mainly composed of regular secondary structures in a finite number of different mutual orientations, main chain dipolar couplings appear sufficient to reveal structural resemblance. Similarity between dipolar couplings measured from a protein and corresponding values computed from a known structure imply homologous structures. For dissimilar structures the agreement between experimental and calculated dipolar couplings remains poor. In this way protein folds can be readily recognized prior to a comprehensive structure determination. This approach has been demonstrated by showing the similarity in fold between the hitherto unknown structure of calerythrin and sarcoplasmic calcium-binding proteins from Nereis diversicolorand Branchiostoma lanceolatumwith known crystal structures. Abbreviations:CSA, chemical shift anisotropy; D6PC, dihexanoyl phosphatidylcholine; D7PC, diheptanoyl phosphatidylcholine; DMPC, dimyristoyl phosphatidylcholine; INEPT, insensitive nuclei enhancement by polarization transfer; NOE, nuclear Overhauser enhancement; PDB, Protein Data Bank entries 1cll: calmodulin, 1rec: recoverin, 1tco: serine-threonine phosphatase B2, 2bbm: calmodulin complexed with myosin light chain kinase, 2sas: sarcoplasmic calcium-binding protein from an amphioxus Branchiostoma lanceolatum , 2scp: sarcoplasmic calcium-binding protein from a sandworm Nereis diversicolor; TROSY, transverse relaxation optimized spectroscopy.