title: The solution structure and conformational dynamics of tumor necrosis factor-alpha and a (Cys69----Asp; Cys101----Arg) analog as examined by IR spectroscopy and hydrogen exchange.
abstract: An analog of human tumor necrosis factor-alpha (TNF-alpha) was created with Cys69 and Cys101 replaced with Asp and Arg respectively. We have undertaken a comparative study of the solution conformation and dynamics of the native and analog molecules using a combination of Fourier transform IR spectroscopy and hydrogen-deuterium (H-D) exchange kinetics. IR spectroscopic results indicate that the analog molecule adopts a gross structure similar to that of the native molecule but significant differences in the conformation of the beta-sheets are observed. Increased bandwidths observed for several of the amide I components also suggest a less rigid structure for the analog molecule. Further, by monitoring the frequency shifts of the individual amide I component bands as a function of hydrogen exchange, we have enhanced our ability to assign these components to individual protein secondary structures, particularly the high frequency beta-strand mode. Hydrogen exchange kinetic studies indicate that the Asp-Arg analog adopts a looser, more flexible solution structure relative to the natural sequence molecule.
authors.affiliation: Amgen Inc., Thousand Oaks, CA 91320.
authors.forename: S J
authors.initials: SJ
authors.lastname: Prestrelski
authors.forename: T
authors.initials: T
authors.lastname: Arakawa
mesh_terms: D000818:Animals; D001120:Arginine / Q000737:chemistry; D001224:Aspartic Acid / Q000737:chemistry; D003545:Cysteine / Q000737:chemistry; D003903:Deuterium / Q000737:chemistry; D006859:Hydrogen / Q000737:chemistry; D016297:Mutagenesis, Site-Directed; D011487:Protein Conformation; D013055:Spectrophotometry, Infrared; D014409:Tumor Necrosis Factor-alpha / Q000737:chemistry* / Q000235:genetics*
chemical_list: D014409:Tumor Necrosis Factor-alpha; D001224:Aspartic Acid; D006859:Hydrogen; D001120:Arginine; D003903:Deuterium; D003545:Cysteine