title: Evolutionally conserved intermediates between ubiquitin and NEDD8.
abstract: The investigation of common structural motifs provides additional information on why proteins conserve similar topologies yet may have non-conserved amino acid sequences. Proteins containing the ubiquitin superfold have similar topologies, although the sequence conservation is rather poor. Here, we present novel similarities and differences between the proteins ubiquitin and NEDD8. They have 57% identical sequence, almost identical backbone topology and similar functional strategy, although their physiological functions are mutually different. Using variable pressure NMR spectroscopy, we found that the two proteins have similar conformational fluctuation in the evolutionary conserved enzyme-binding region and contain a structurally similar locally disordered conformer (I) in equilibrium with the basic folded conformer (N). A notable difference between the two proteins is that the equilibrium population of I is far greater for NEDD8 (DeltaG(0)(NI)<5 kJ/mol) than for ubiquitin (DeltaG(0)(NI)=15.2(+/-1.0) kJ/mol), and that the tendency for overall unfolding (U) is also far higher for NEDD8 (DeltaG(0)(NU)=11.0(+/-1.5) kJ/mol) than for ubiquitin (DeltaG(0)(NU)=31.3(+/-4.7) kJ/mol). These results suggest that the marked differences in thermodynamic stabilities of the locally disordered conformer (I) and the overall unfolding species (U) are a key to determine the functional differences of the two structurally similar proteins in physiology.
authors.affiliation: RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-chou, Sayo-gun, Hyogo, 679-5148, Japan.
authors.forename: Ryo
authors.initials: R
authors.lastname: Kitahara
authors.forename: Yoshiki
authors.initials: Y
authors.lastname: Yamaguchi
authors.forename: Eri
authors.initials: E
authors.lastname: Sakata
authors.forename: Takeshi
authors.initials: T
authors.lastname: Kasuya
authors.forename: Keiji
authors.initials: K
authors.lastname: Tanaka
authors.forename: Koichi
authors.initials: K
authors.lastname: Kato
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Yokoyama
authors.forename: Kazuyuki
authors.initials: K
authors.lastname: Akasaka
mesh_terms: D000595:Amino Acid Sequence; D019143:Evolution, Molecular; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D000075687:NEDD8 Protein; D019906:Nuclear Magnetic Resonance, Biomolecular; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics; D025801:Ubiquitin / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D014452:Ubiquitins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism
chemical_list: D000075687:NEDD8 Protein; C082860:NEDD8 protein, human; D025801:Ubiquitin; D014452:Ubiquitins