Synthetic, structural and biological studies of the ubiquitin system: chemically synthesized and native ubiquitin fold into identical three-dimensional structures

• Published in: Biochemical journal 1994-04, Vol.299 (1), p.159-163
• Main Authors: Alexeev, D, Bury, S.M, Turner, M.A, Ogunjobi, O.M, Muir, T.W, Ramage, R, Sawyer, L
• Format: Article
• Language: English
• Subjects: Biological and medical sciences; Chemistry; comparisons; Crystalline structure; crystallography; Crystallography, X-Ray; Exact sciences and technology; Fundamental and applied biological sciences. Psychology; Molecular biophysics; Organic chemistry; Peptides; Preparations and properties; Protein Conformation; Protein Folding; protein structure; structure; Structure in molecular biology; ubiquitin; Ubiquitins - chemical synthesis; Ubiquitins - chemistry; X-ray diffraction
• ISSN: 0264-6021; 1470-8728
• DOI: 10.1042/bj2990159

The solid-phase chemical synthesis of ubiquitin produced a molecule with physicochemical properties similar to those of the natural protein. We have grown crystals of this synthetic ubiquitin and performed an X-ray analysis at 1.8 angstrom resolution in order to compare the synthetic protein with the known natural structure. The crystals were isomorphous with those of the natural protein, the R-factor between them being 7.1%. Difference Fourier analysis shows that the synthetic and natural structures are indistinguishable. The co-ordinates of the natural ubiquitin (IUBQ) were used as the starting point for restrained least-squares refinement (TNT program) against the synthetic X-ray data. The refinement converged to R = 16.5% and the resulting model did not change when refined against natural ubiquitin X-ray data (R = 18.7%). From both the refinement and featureless difference Fourier synthesis, we conclude that the synthetic and natural protein structures are identical. A short discussion about the uses of proteins with 'non-standard' amino acid residues is included.