Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry

被引:27
作者
Sharma, Seema [2 ]
Zheng, Haiyan
Huang, Yuanpeng J. [2 ]
Ertekin, Asli [2 ]
Hamuro, Yoshitomo [3 ]
Rossi, Paolo [2 ]
Tejero, Roberto [2 ]
Acton, Thomas B. [2 ]
Xiao, Rong [2 ]
Jiang, Mei [2 ]
Zhao, Li [2 ]
Ma, Li-Chung [2 ]
Swapna, G. V. T. [2 ]
Aramini, James M. [1 ,2 ]
Montelione, Gaetano T. [2 ,4 ]
机构
[1] Rutgers State Univ, CABM, Dept Mol Biol & Biochem, Piscataway, NJ 08854 USA
[2] Rutgers State Univ, NE Struct Genom Consortium, Piscataway, NJ 08854 USA
[3] ExSAR Corp, Monmouth Jct, NJ 08852 USA
[4] Univ Med & Dent New Jersey, Robert Wood Johnson Med Sch, Dept Biochem, Piscataway, NJ 08854 USA
关键词
DXMS; hydrogen-deuterium exchange; mass spectrometry; NMR; partially disordered proteins; protein construct optimization; structural genomics; HYDROGEN-DEUTERIUM EXCHANGE; TORSION ANGLE DYNAMICS; BRAIN-SPECIFIC PROTEIN; ESCHERICHIA-COLI; LIMITED PROTEOLYSIS; TPPP/P25; TUBULIN; GENOMICS; SPECTROSCOPY; ASSEMBLIES;
D O I
10.1002/prot.22394
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Disordered or unstructured regions of proteins, while often very important biologically, can pose significant challenges for resonance assignment and three-dimensional structure determination of the ordered regions of proteins by NMR methods. In this article, we demonstrate the application of H-1/H-2 exchange mass spectrometry (DXMS) for the rapid identification of disordered segments of proteins and design of protein constructs that are more suitable for structural analysis by NMR. In this benchmark study, DXMS is applied to five NMR protein targets chosen from the Northeast Structural Genomics project. These data were then used to design optimized constructs for three partially disordered proteins. Truncated proteins obtained by deletion of disordered N- and C-terminal tails were evaluated using H-1-N-15 HSQC and H-1-N-15 heteronuclear NOE NMR experiments to assess their structural integrity. These constructs provide significantly improved NMR spectra, with minimal structural perturbations to the ordered regions of the protein structure. As a representative example, we compare the solution structures of the full length and DXMS-based truncated construct for a 77-residue partially disordered DUF896 family protein YnzC from Bacillus subtilis, where deletion of the disordered residues (ca. 40% of the protein) does not affect the native structure. In addition, we demonstrate that throughput of the DXMS process' can be increased by analyzing mixtures of up to four proteins without reducing the sequence coverage for each protein. Our results demonstrate that DXMS can serve as a central component of a process for optimizing protein constructs for NMR structure determination.
引用
收藏
页码:882 / 894
页数:13
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