title: Automated protein fold determination using a minimal NMR constraint strategy.
abstract: Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium-accuracy fold information can often provide key clues about protein evolution and biochemical function(s). In this article we describe a largely automatic strategy for rapid determination of medium-accuracy protein backbone structures. Our strategy derives from ideas originally introduced by other groups for determining medium-accuracy NMR structures of large proteins using deuterated, (13)C-, (15)N-enriched protein samples with selective protonation of side-chain methyl groups ((13)CH(3)). Data collection includes acquiring NMR spectra for automatically determining assignments of backbone and side-chain (15)N, H(N) resonances, and side-chain (13)CH(3) methyl resonances. These assignments are determined automatically by the program AutoAssign using backbone triple resonance NMR data, together with Spin System Type Assignment Constraints (STACs) derived from side-chain triple-resonance experiments. The program AutoStructure then derives conformational constraints using these chemical shifts, amide (1)H/(2)H exchange, nuclear Overhauser effect spectroscopy (NOESY), and residual dipolar coupling data. The total time required for collecting such NMR data can potentially be as short as a few days. Here we demonstrate an integrated set of NMR software which can process these NMR spectra, carry out resonance assignments, interpret NOESY data, and generate medium-accuracy structures within a few days. The feasibility of this combined data collection and analysis strategy starting from raw NMR time domain data was illustrated by automatic analysis of a medium accuracy structure of the Z domain of Staphylococcal protein A.
authors.affiliation: Center for Advanced Biotechnology and Medicine (CABM), Northeast Structural Genomics Consortium, and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA.
authors.forename: Deyou
authors.initials: D
authors.lastname: Zheng
authors.forename: Yuanpeng J
authors.initials: YJ
authors.lastname: Huang
authors.forename: Hunter N B
authors.initials: HN
authors.lastname: Moseley
authors.forename: Rong
authors.initials: R
authors.lastname: Xiao
authors.forename: James
authors.initials: J
authors.lastname: Aramini
authors.forename: G V T
authors.initials: GV
authors.lastname: Swapna
authors.forename: Gaetano T
authors.initials: GT
authors.lastname: Montelione
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D004578:Electron Spin Resonance Spectroscopy; D023281:Genomics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013205:Staphylococcal Protein A / Q000737:chemistry; D013997:Time Factors
chemical_list: D011506:Proteins; D013205:Staphylococcal Protein A