Solution NMR in structural genomics.

Structural genomics (also known as structural proteomics) aims to generate accurate three-dimensional models for all folded, globular proteins and domains in the protein universe to understand the relationship between protein sequence, structure and function. NMR spectroscopy of small (<20 kDa) proteins has been used successfully within several large-scale structural genomics projects for more than six years now. Recent advances coming from traditional NMR structural biology laboratories as well as large scale centers and consortia using NMR for structural genomics promise to facilitate NMR analysis making it even a more efficient and increasingly automated procedure.

[1]  J H Prestegard,et al.  Determination of protein backbone structures from residual dipolar couplings. , 2005, Methods in enzymology.

[2]  A. Grishaev,et al.  ABACUS, a direct method for protein NMR structure computation via assembly of fragments , 2005, Proteins.

[3]  Ian Hunt,et al.  From gene to protein: a review of new and enabling technologies for multi-parallel protein expression. , 2005, Protein expression and purification.

[4]  Gaetano T Montelione,et al.  Assessing precision and accuracy of protein structures derived from NMR data , 2005, Proteins.

[5]  Alexander Grishaev,et al.  Protein structure elucidation from minimal NMR data: the CLOUDS approach. , 2005, Methods in enzymology.

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

[7]  Arash Bahrami,et al.  High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection. , 2005, Journal of the American Chemical Society.

[8]  Alan S. Stern,et al.  NMR Data Processing , 1996 .

[9]  Martin Hammarström,et al.  Rapid screening for improved solubility of small human proteins produced as fusion proteins in Escherichia coli , 2002, Protein science : a publication of the Protein Society.

[10]  Charles D Schwieters,et al.  Completely automated, highly error-tolerant macromolecular structure determination from multidimensional nuclear overhauser enhancement spectra and chemical shift assignments. , 2004, Journal of the American Chemical Society.

[11]  Gaohua Liu,et al.  NMR data collection and analysis protocol for high-throughput protein structure determination. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[12]  M Nilges,et al.  Automated assignment of ambiguous nuclear overhauser effects with ARIA. , 2001, Methods in enzymology.

[13]  Qin Zhao,et al.  Prevention of aggregation after refolding by balanced stabilization-destabilization: production of the Arabidopsis thaliana protein APG8a (At4g21980) for NMR structure determination. , 2004, Protein expression and purification.

[14]  Peter Güntert,et al.  Automated NMR protein structure calculation , 2003 .

[15]  A. Stern,et al.  Accelerated acquisition of high resolution triple-resonance spectra using non-uniform sampling and maximum entropy reconstruction. , 2004, Journal of magnetic resonance.

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

[17]  Michael Nilges,et al.  NOE assignment with ARIA 2.0: the nuts and bolts. , 2004, Methods in molecular biology.

[18]  Mark Gerstein,et al.  Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium. , 2005, Methods in enzymology.

[19]  M. Nilges,et al.  Refinement of protein structures in explicit solvent , 2003, Proteins.

[20]  Ray Freeman,et al.  Fast multi-dimensional NMR of proteins , 2003, Journal of biomolecular NMR.

[21]  K. Wüthrich,et al.  NMR screening and crystal quality of bacterially expressed prokaryotic and eukaryotic proteins in a structural genomics pipeline. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

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

[23]  M. Billeter,et al.  Accurate relaxation parameters for large proteins. , 2004, Journal of magnetic resonance.

[24]  Thomas Szyperski,et al.  Rapid NMR data collection. , 2005, Methods in enzymology.

[25]  Ad Bax,et al.  Weak alignment NMR: a hawk-eyed view of biomolecular structure. , 2005, Current opinion in structural biology.

[26]  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.

[27]  F. Studier,et al.  Protein production by auto-induction in high density shaking cultures. , 2005, Protein expression and purification.

[28]  K. Wüthrich,et al.  Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling. , 1989, Biochemistry.

[29]  Martin Hammarström,et al.  His tag effect on solubility of human proteins produced in Escherichia coli: a comparison between four expression vectors , 2004, Journal of Structural and Functional Genomics.

[30]  Gerhard Wagner,et al.  Non-uniformly sampled double-TROSY hNcaNH experiments for NMR sequential assignments of large proteins. , 2006, Journal of the American Chemical Society.

[31]  Gert Vriend,et al.  Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors , 2005, PLoS Comput. Biol..

[32]  Takanori Kigawa,et al.  Preparation of Escherichia coli cell extract for highly productive cell-free protein expression , 2004, Journal of Structural and Functional Genomics.

[33]  Torsten Herrmann,et al.  Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. , 2002, Journal of molecular biology.

[34]  Alexander Grishaev,et al.  BACUS: A Bayesian protocol for the identification of protein NOESY spectra via unassigned spin systems* , 2004, Journal of biomolecular NMR.

[35]  Torsten Herrmann,et al.  NMR for structural proteomics of Thermotoga maritima: Screening and structure determination , 2004, Journal of Structural and Functional Genomics.

[36]  J. Hoch,et al.  High-resolution aliphatic side-chain assignments in 3D HCcoNH experiments with joint H–C evolution and non-uniform sampling , 2005, Journal of biomolecular NMR.

[37]  G. Vriend,et al.  Definition of a New Information-Based Per-Residue Quality Parameter , 2005, Journal of biomolecular NMR.

[38]  John L Markley,et al.  High–throughput automated platform for nuclear magnetic resonance–based structural proteomics , 2005, Expert review of proteomics.

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

[40]  Gaetano T Montelione,et al.  Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles , 2005, Proteins.

[41]  Thomas Szyperski,et al.  A generalized approach to automated NMR peak list editing: application to reduced dimensionality triple resonance spectra. , 2004, Journal of magnetic resonance.

[42]  Ray Freeman,et al.  Hyperdimensional NMR spectroscopy. , 2006, Journal of the American Chemical Society.

[43]  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.

[44]  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.

[45]  Brian E. Coggins,et al.  (4,2)D Projection--reconstruction experiments for protein backbone assignment: application to human carbonic anhydrase II and calbindin D(28K). , 2005, Journal of the American Chemical Society.

[46]  T. Sawasaki,et al.  High-throughput, genome-scale protein production method based on the wheat germ cell-free expression system. , 2003, Biotechnology advances.

[47]  G. Phillips,et al.  Comparison of cell‐based and cell‐free protocols for producing target proteins from the Arabidopsis thaliana genome for structural studies , 2005, Proteins.

[48]  D. Wishart,et al.  An NMR approach to structural proteomics , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[49]  T. Szyperski,et al.  Principles and applications of GFT projection NMR spectroscopy , 2006, Magnetic resonance in chemistry : MRC.

[50]  T. Torizawa,et al.  Efficient production of isotopically labeled proteins by cell-free synthesis: A practical protocol , 2004, Journal of biomolecular NMR.

[51]  K. Wüthrich,et al.  Letter to the Editor: NMR Structure Determination of the Hypothetical Protein TM1290 from Thermotoga Maritima using Automated NOESY Analysis , 2004, Journal of biomolecular NMR.

[52]  K. Wüthrich,et al.  Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS , 2002, Journal of biomolecular NMR.

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

[54]  K. Gardner,et al.  Identification and optimization of protein domains for NMR studies. , 2005, Methods in enzymology.

[55]  D. Ejima,et al.  Is arginine a protein-denaturant? , 2005, Protein expression and purification.

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

[57]  Thomas Szyperski,et al.  G-matrix Fourier transform NOESY-based protocol for high-quality protein structure determination. , 2005, Journal of the American Chemical Society.

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