NMR-based automated protein structure determination.

NMR spectra analysis for protein structure determination can now in many cases be performed by automated computational methods. This overview of the computational methods for NMR protein structure analysis presents recent automated methods for signal identification in multidimensional NMR spectra, sequence-specific resonance assignment, collection of conformational restraints, and structure calculation, as implemented in the CYANA software package. These algorithms are sufficiently reliable and integrated into one software package to enable the fully automated structure determination of proteins starting from NMR spectra without manual interventions or corrections at intermediate steps, with an accuracy of 1-2 Å backbone RMSD in comparison with manually solved reference structures.

[1]  Kurt Wüthrich,et al.  Sequence-specific NMR assignment of proteins by global fragment mapping with the program Mapper , 2000, Journal of biomolecular NMR.

[2]  Matthias Huber,et al.  Automated solid-state NMR resonance assignment of protein microcrystals and amyloids , 2013, Journal of biomolecular NMR.

[3]  Kurt Wüthrich,et al.  The program ASNO for computer-supported collection of NOE upper distance constraints as input for protein structure determination , 1993 .

[4]  Bin Wu,et al.  The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013 , 2015, Journal of biomolecular NMR.

[5]  Bruce A. Johnson,et al.  NMR View: A computer program for the visualization and analysis of NMR data , 1994, Journal of biomolecular NMR.

[6]  M Nilges,et al.  Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. , 1995, Journal of molecular biology.

[7]  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.

[8]  M. Billeter,et al.  MUNIN: A new approach to multi-dimensional NMR spectra interpretation , 2001, Journal of biomolecular NMR.

[9]  Piotr Klukowski,et al.  Computer vision-based automated peak picking applied to protein NMR spectra , 2015, Bioinform..

[10]  Wayne Boucher,et al.  The CCPN data model for NMR spectroscopy: Development of a software pipeline , 2005, Proteins.

[11]  Oliver F Lange,et al.  Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta , 2014, Journal of biomolecular NMR.

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

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

[14]  Peter Güntert,et al.  Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins , 2013, Journal of biomolecular NMR.

[15]  Kazuo Shinozaki,et al.  Letter to the Editor: NMR assignment of the hypothetical ENTH-VHS domain At3g16270 from Arabidopsis thaliana , 2004, Journal of biomolecular NMR.

[16]  Peter Güntert,et al.  SAIL – stereo-array isotope labeling , 2009, Quarterly Reviews of Biophysics.

[17]  P. Güntert,et al.  Combined automated NOE assignment and structure calculation with CYANA , 2015, Journal of Biomolecular NMR.

[18]  Harald Schwalbe,et al.  Blind testing of routine, fully automated determination of protein structures from NMR data. , 2012, Structure.

[19]  Wayne Boucher,et al.  CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis , 2016, Journal of Biomolecular NMR.

[20]  J. Cavanagh.  Protein NMR Spectroscopy: Principles and Practice , 1995 .

[21]  T. Herrmann,et al.  Advances in automated NMR protein structure determination , 2011, Quarterly Reviews of Biophysics.

[22]  Mark J Howard,et al.  Protein NMR spectroscopy , 1998, Current Biology.

[23]  Peter Güntert,et al.  Automated assignment of NMR chemical shifts using peak-particle dynamics simulation with the DYNASSIGN algorithm , 2009, Journal of biomolecular NMR.

[24]  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.

[25]  H Oschkinat,et al.  Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. , 1997, Journal of molecular biology.

[26]  P. Güntert,et al.  Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK , 2017, Journal of biomolecular NMR.

[27]  Peter Güntert,et al.  Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment , 2004, Journal of Structural and Functional Genomics.

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

[29]  Peter Güntert,et al.  Automated protein structure determination from NMR spectra. , 2006, Journal of the American Chemical Society.

[30]  Werner Braun,et al.  Automated combined assignment of NOESY spectra and three-dimensional protein structure determination , 1997, Journal of biomolecular NMR.

[31]  Xin Gao,et al.  PICKY: a novel SVD-based NMR spectra peak picking method , 2009, Bioinform..

[32]  Zhi Liu,et al.  WaVPeak: picking NMR peaks through wavelet-based smoothing and volume-based filtering , 2012, Bioinform..

[33]  K Wüthrich,et al.  Automated sequence-specific NMR assignment of homologous proteins using the program GARANT , 1996, Journal of biomolecular NMR.

[34]  Kurt Wüthrich,et al.  Processing of multi-dimensional NMR data with the new software PROSA , 1992 .

[35]  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.

[36]  W. Gronwald,et al.  Automated structure determination of proteins by NMR spectroscopy , 2004 .

[37]  J. Keeler.  Understanding NMR Spectroscopy , 2005 .

[38]  K Wüthrich,et al.  Sequential resonance assignments as a basis for determination of spatial protein structures by high resolution proton nuclear magnetic resonance. , 1982, Journal of molecular biology.

[39]  Robert Powers,et al.  A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams , 1991 .

[40]  Antonio Rosato,et al.  CASD-NMR: critical assessment of automated structure determination by NMR , 2009, Nature Methods.

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

[42]  G. Marius Clore,et al.  Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm , 2008, Journal of biomolecular NMR.

[43]  Tim J. Stevens,et al.  Structure calculation, refinement and validation using CcpNmr Analysis , 2015, Acta crystallographica. Section D, Biological crystallography.

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

[45]  Peter Güntert,et al.  Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA , 2015, Journal of biomolecular NMR.

[46]  K. Wüthrich,et al.  Torsion angle dynamics for NMR structure calculation with the new program DYANA. , 1997, Journal of molecular biology.

[47]  H N Moseley,et al.  Automated analysis of NMR assignments and structures for proteins. , 1999, Current opinion in structural biology.

[48]  W. Braun,et al.  Automated assignment of simulated and experimental NOESY spectra of proteins by feedback filtering and self-correcting distance geometry. , 1995, Journal of molecular biology.

[49]  Michael Nilges,et al.  ARIA2: Automated NOE assignment and data integration in NMR structure calculation , 2007, Bioinform..

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

[51]  M. Zweckstetter,et al.  Mars - robust automatic backbone assignment of proteins , 2004, Journal of biomolecular NMR.

[52]  K Wüthrich,et al.  The program XEASY for computer-supported NMR spectral analysis of biological macromolecules , 1995, Journal of biomolecular NMR.

[53]  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..

[54]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[55]  Kurt Wüthrich,et al.  GARANT‐a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra , 1997 .

[56]  Peter Güntert,et al.  Automated and assisted RNA resonance assignment using NMR chemical shift statistics , 2013, Nucleic acids research.

[57]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[58]  Peter Güntert,et al.  Automated structure determination from NMR spectra , 2009, European Biophysics Journal.

[59]  Peter Güntert,et al.  Increased reliability of nuclear magnetic resonance protein structures by consensus structure bundles. , 2015, Structure.

[60]  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.

[61]  Torsten Herrmann,et al.  Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH , 2008, Journal of biomolecular NMR.

[62]  Peter Güntert,et al.  Peakmatch: a simple and robust method for peak list matching , 2013, Journal of biomolecular NMR.

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

[64]  Martin Billeter,et al.  Fully automated sequence-specific resonance assignments of hetero- nuclear protein spectra , 2003, Journal of biomolecular NMR.

[65]  Peter Güntert,et al.  Spatial elucidation of motion in proteins by ensemble-based structure calculation using exact NOEs , 2012, Nature Structural &Molecular Biology.

[66]  Peter Güntert,et al.  A new algorithm for reliable and general NMR resonance assignment. , 2012, Journal of the American Chemical Society.