title: Proton nuclear magnetic resonance study of an active pentapeptide fragment of ubiquitin.
abstract: The aqueous solution conformation of Tyr-Asn-Ile-Gln-Lys (UB5) corresponding to positions 59-63 of the polypeptide, ubiquitin, has been investigated by proton NMR. Like the parent protein, UB5 induces nonspecifically both T and B lymphocyte differentiation. The various NH and CH resonances of this pentapeptide have been assigned, and its solution conformation has been probed through a study of chemical shift variations with pH, temperature dependence of amide hydrogen chemical shifts, vicinal NH--C alpha H and C alpha H--C beta H2 coupling constant data, and amide hydrogen-exchange rates. The latter were measured in H2O by using a combination of transfer of solvent saturation and saturation recovery NMR experiments. The data are compatible with the assumption of a highly motile dynamic equilibrium among different conformations for this peptide. The various secondary amide hydrogens remain essentially exposed to the solvent. The temperature-dependence study of the amide hydrogen chemical shifts also did not reveal any strong internal hydrogen bonds. A rotamer population analysis of tyrosine and asparagine side chains suggests that two of the rotomers are predominantly populated for each of these residues. From these results, a picture emerges of the dynamic conformation of UB5 in aqueous solution.
mesh_terms: D002868:Chromosomal Proteins, Non-Histone / Q000032:analysis*; D006859:Hydrogen / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy; D009698:Nucleoproteins / Q000032:analysis*; D009842:Oligopeptides / Q000032:analysis*; D010446:Peptide Fragments / Q000032:analysis*; D011487:Protein Conformation; D011522:Protons; D013696:Temperature; D014452:Ubiquitins
chemical_list: D002868:Chromosomal Proteins, Non-Histone; D009698:Nucleoproteins; D009842:Oligopeptides; D010446:Peptide Fragments; D011522:Protons; D014452:Ubiquitins; D006859:Hydrogen