A novel strategy for NMR resonance assignment and protein structure determination

The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution – especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.

[1]  K. Wüthrich.  NMR of proteins and nucleic acids , 1988 .

[2]  A M Gronenborn,et al.  Four-dimensional heteronuclear triple-resonance NMR spectroscopy of interleukin-1 beta in solution. , 1990, Science.

[3]  Ad Bax,et al.  Correlating Backbone Amide and Side-Chain Resonances in Larger Proteins By Multiple Relayed Triple Resonance NMR , 1992 .

[4]  Vladislav Orekhov,et al.  Automatic assignment of protein backbone resonances by direct spectrum inspection in targeted acquisition of NMR data , 2008, Journal of biomolecular NMR.

[5]  Peter Güntert,et al.  KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies , 2007, Journal of biomolecular NMR.

[6]  Oliver F. Lange,et al.  Consistent blind protein structure generation from NMR chemical shift data , 2008, Proceedings of the National Academy of Sciences.

[7]  Gaetano T Montelione,et al.  Evaluating protein structures determined by structural genomics consortia , 2006, Proteins.

[8]  G. Montelione,et al.  Automated analysis of protein NMR assignments using methods from artificial intelligence. , 1997, Journal of molecular biology.

[9]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[10]  A. Bax,et al.  Resolution enhancement and spectral editing of uniformly 13C-enriched proteins by homonuclear broadband 13C decoupling , 1992 .

[11]  Robert Powers,et al.  A topology‐constrained distance network algorithm for protein structure determination from NOESY data , 2005, Proteins.

[12]  Cheryl H Arrowsmith,et al.  NMR and X-ray crystallography, complementary tools in structural proteomics of small proteins. , 2005, Journal of the American Chemical Society.

[13]  Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach , 2008, Journal of biomolecular NMR.

[14]  P. Kraulis,et al.  Ansig for Windows: An interactive computer program for semiautomatic assignment of protein NMR spectra , 2000, Journal of biomolecular NMR.

[15]  Cheryl H. Arrowsmith,et al.  NleG Type 3 Effectors from Enterohaemorrhagic Escherichia coli Are U-Box E3 Ubiquitin Ligases , 2010, PLoS pathogens.

[16]  R. Freeman,et al.  New methods for fast multidimensional NMR , 2003, Journal of biomolecular NMR.

[17]  M. Billeter,et al.  Three-way decomposition of a complete 3D 15N-NOESY-HSQC , 2002, Journal of biomolecular NMR.

[18]  Thomas Szyperski,et al.  Protein NMR spectroscopy in structural genomics , 2000, Nature Structural Biology.

[19]  M Ikura,et al.  Improved three-dimensional1H−13C−1H correlation spectroscopy of a13C-labeled protein using constant-time evolution , 1991, Journal of biomolecular NMR.

[20]  Mark C. W. van Rossum,et al.  State Based Model of Long-Term Potentiation and Synaptic Tagging and Capture , 2009, PLoS Comput. Biol..

[21]  A. Bax,et al.  TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts , 2009, Journal of biomolecular NMR.

[22]  Michael Nilges,et al.  ARIA: automated NOE assignment and NMR structure calculation , 2003, Bioinform..

[23]  E. Laue,et al.  Conventional and exponential sampling for 2D NMR experiments with application to a 2D NMR spectrum of a protein , 1987 .

[24]  Gaetano T Montelione,et al.  Automated protein fold determination using a minimal NMR constraint strategy , 2003, Protein science : a publication of the Protein Society.

[25]  Kurt Wüthrich,et al.  Solution NMR structure determination of proteins revisited , 2008, Journal of biomolecular NMR.

[26]  Ad Bax,et al.  Amino acid type determination in the sequential assignment procedure of uniformly 13C/15N-enriched proteins , 1993, Journal of biomolecular NMR.

[27]  V. Orekhov,et al.  Optimization of resolution and sensitivity of 4D NOESY using Multi-dimensional Decomposition , 2005, Journal of biomolecular NMR.

[28]  James M Aramini,et al.  Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination. , 2005, Journal of the American Chemical Society.

[29]  E. Zuiderweg,et al.  Mapping protein-protein interactions in solution by NMR spectroscopy. , 2002, Biochemistry.

[30]  T. Logan,et al.  Side chain and backbone assignments in isotopically labeled proteins from two heteronuclear triple resonance experiments , 1992, FEBS letters.

[31]  Michael Nilges,et al.  Structural bioinformatics ARIA 2 : Automated NOE assignment and data integration in NMR structure calculation , 2007 .

[32]  L. Overman,et al.  Stereocontrolled construction of carbocyclic rings by sequential cationic cyclization-pinacol rearrangements , 1989 .

[33]  S. Grzesiek,et al.  Improved 3D triple-resonance NMR techniques applied to a 31 kDa protein , 1992 .

[34]  Vladislav Yu Orekhov,et al.  Optimizing resolution in multidimensional NMR by three-way decomposition , 2003, Journal of biomolecular NMR.

[35]  L. Kay,et al.  Heteronuclear 3D NMR and isotopic labeling of calmodulin. Towards the complete assignment of the 1H NMR spectrum. , 1990, Biochemical pharmacology.

[36]  L. Kay,et al.  A novel approach for sequential assignment of proton, carbon-13, and nitrogen-15 spectra of larger proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin , 1990 .

[37]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[38]  L. Kay,et al.  A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. , 1990, Biochemistry.

[39]  L. Kay,et al.  Secondary structure and side-chain 1H and 13C resonance assignments of calmodulin in solution by heteronuclear multidimensional NMR spectroscopy. , 1991, Biochemistry.

[40]  L. Kay,et al.  Triple-resonance multidimensional NMR study of calmodulin complexed with the binding domain of skeletal muscle myosin light-chain kinase: indication of a conformational change in the central helix. , 1991, Biochemistry.

[41]  P. Güntert.  Automated NMR structure calculation with CYANA. , 2004, Methods in molecular biology.

[42]  Mark Gerstein,et al.  Structural proteomics of an archaeon , 2000, Nature Structural Biology.

[43]  G. Marius Clore,et al.  Use of dipolar 1H–15N and 1H–13C couplings in the structure determination of magnetically oriented macromolecules in solution , 1997, Nature Structural Biology.

[44]  Brian D Sykes,et al.  Smartnotebook: A semi-automated approach to protein sequential NMR resonance assignments , 2003, Journal of biomolecular NMR.

[45]  H. Valafar,et al.  Backbone solution structures of proteins using residual dipolar couplings: Application to a novel structural genomics target , 2005, Journal of Structural and Functional Genomics.

[46]  Robert Powers,et al.  Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. , 2005, Journal of the American Chemical Society.

[47]  Arash Bahrami,et al.  Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy , 2009, PLoS Comput. Biol..

[48]  D. Baker,et al.  De novo protein structure generation from incomplete chemical shift assignments , 2009, Journal of biomolecular NMR.

[49]  T. Szyperski,et al.  GFT NMR, a new approach to rapidly obtain precise high-dimensional NMR spectral information. , 2003, Journal of the American Chemical Society.

[50]  L. Kay,et al.  Overcoming the overlap problem in the assignment of 1H NMR spectra of larger proteins by use of three-dimensional heteronuclear 1H-15N Hartmann-Hahn-multiple quantum coherence and nuclear Overhauser-multiple quantum coherence spectroscopy: application to interleukin 1 beta. , 1989, Biochemistry.

[51]  H. Atreya,et al.  A tracked approach for automated NMR assignments in proteins (TATAPRO) , 2000, Journal of biomolecular NMR.

[52]  Ad Bax,et al.  Three-dimensional triple-resonance NMR Spectroscopy of isotopically enriched proteins. 1990. , 1990, Journal of magnetic resonance.

[53]  Woonghee Lee,et al.  PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy , 2009, Bioinform..

[54]  L. Kay,et al.  Gradient-Enhanced Triple-Resonance Three-Dimensional NMR Experiments with Improved Sensitivity , 1994 .

[55]  Ad Bax,et al.  An efficient experiment for sequential backbone assignment of medium-sized isotopically enriched proteins , 1992 .

[56]  G. Marius Clore,et al.  1H1H correlation via isotropic mixing of 13C magnetization, a new three-dimensional approach for assigning 1H and 13C spectra of 13C-enriched proteins , 1990 .

[57]  A. Bax,et al.  An efficient NMR approach for obtaining sequence‐specific resonance assignments of larger proteins based on multiple isotopic labeling , 1990, FEBS Letters.

[58]  Ad Bax,et al.  Three-dimensional heteronuclear NMR of nitrogen-15 labeled proteins , 1989 .