Improved technologies now routinely provide protein NMR structures useful for molecular replacement.

Molecular replacement (MR) is widely used for addressing the phase problem in X-ray crystallography. Historically, crystallographers have had limited success using NMR structures as MR search models. Here, we report a comprehensive investigation of the utility of protein NMR ensembles as MR search models, using data for 25 pairs of X-ray and NMR structures solved and refined using modern NMR methods. Starting from NMR ensembles prepared by an improved protocol, FindCore, correct MR solutions were obtained for 22 targets. Based on these solutions, automatic model rebuilding could be done successfully. Rosetta refinement of NMR structures provided MR solutions for another two proteins. We also demonstrate that such properly prepared NMR ensembles and X-ray crystal structures have similar performance when used as MR search models for homologous structures, particularly for targets with sequence identity >40%.

[1]  Yang Zhang,et al.  Template‐based modeling and free modeling by I‐TASSER in CASP7 , 2007, Proteins.

[2]  Ian W. Davis,et al.  Structure validation by Cα geometry: ϕ,ψ and Cβ deviation , 2003, Proteins.

[3]  A. Gronenborn,et al.  Crystal structure of interleukin 8: symbiosis of NMR and crystallography. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Roland L Dunbrack,et al.  Outcome of a workshop on applications of protein models in biomedical research. , 2009, Structure.

[5]  Yang Zhang,et al.  Scoring function for automated assessment of protein structure template quality , 2004, Proteins.

[6]  Adam Zemla,et al.  LGA: a method for finding 3D similarities in protein structures , 2003, Nucleic Acids Res..

[7]  M M Woolfson,et al.  Direct methods in crystallography , 1961 .

[8]  M. Rossmann,et al.  Patterson and molecular‐replacement techniques , 2006 .

[9]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[10]  John E. Johnson,et al.  Synergy of NMR, computation, and X-ray crystallography for structural biology. , 2009, Structure.

[11]  M. F. Perutz,et al.  Isomorphous replacement and phase determination in non‐centrosymmetric space groups , 1956 .

[12]  C R Kissinger,et al.  Rapid automated molecular replacement by evolutionary search. , 1999, Acta crystallographica. Section D, Biological crystallography.

[13]  E. Saff,et al.  Distributing many points on a sphere , 1997 .

[14]  T. A. Jones,et al.  Crystal structures of cellular retinoic acid binding proteins I and II in complex with all-trans-retinoic acid and a synthetic retinoid. , 1995, Structure.

[15]  M Wilmanns,et al.  Molecular replacement with NMR models using distance-derived pseudo B factors. , 1996, Acta crystallographica. Section D, Biological crystallography.

[16]  David Baker,et al.  proteins STRUCTURE O FUNCTION O BIOINFORMATICS Improving NMR protein structure quality by Rosetta refinement: A molecular , 2022 .

[17]  George N Phillips,et al.  SOMoRe: a multi-dimensional search and optimization approach to molecular replacement. , 2003, Acta crystallographica. Section D, Biological crystallography.

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

[19]  P. Bradley,et al.  High-resolution structure prediction and the crystallographic phase problem , 2007, Nature.

[20]  J. Thornton,et al.  AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR , 1996, Journal of biomolecular NMR.

[21]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[22]  Lars Malmström,et al.  Automated prediction of CASP‐5 structures using the Robetta server , 2003, Proteins.

[23]  Anna Tramontano,et al.  Evaluating the usefulness of protein structure models for molecular replacement , 2005, ECCB/JBI.

[24]  David E. Kim,et al.  Free modeling with Rosetta in CASP6 , 2005, Proteins.

[25]  Y. W. Chen.  Solution solution: using NMR models for molecular replacement. , 2001, Acta crystallographica. Section D, Biological crystallography.

[26]  E J Dodson,et al.  Does NMR mean "not for molecular replacement"? Using NMR-based search models to solve protein crystal structures. , 2000, Structure.

[27]  David Baker,et al.  Protein structure prediction and analysis using the Robetta server , 2004, Nucleic Acids Res..

[28]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[29]  Burkhard Rost,et al.  Structural genomics is the largest contributor of novel structural leverage , 2009, Journal of Structural and Functional Genomics.

[30]  Jinfeng Liu,et al.  Novel leverage of structural genomics , 2007, Nature Biotechnology.

[31]  Michael G. Rossmann,et al.  The single isomorphous replacement method , 1961 .

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

[33]  M. Perutz,et al.  The structure of haemoglobin. II , 1954, Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences.

[34]  Fei Long,et al.  ARP/wARP and molecular replacement: the next generation , 2007, Acta crystallographica. Section D, Biological crystallography.

[35]  Randy J Read,et al.  The application of multivariate statistical techniques improves single-wavelength anomalous diffraction phasing. , 2004, Acta crystallographica. Section D, Biological crystallography.

[36]  M. Perutz,et al.  The structure of haemoglobin - IV. Sign determination by the isomorphous replacement method , 1954, Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences.

[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]  K. Misura,et al.  PROTEINS: Structure, Function, and Bioinformatics 59:15–29 (2005) Progress and Challenges in High-Resolution Refinement of Protein Structure Models , 2022 .

[39]  D. Blow,et al.  The detection of sub‐units within the crystallographic asymmetric unit , 1962 .

[40]  Randy J. Read,et al.  Dauter Iterative model building , structure refinement and density modification with the PHENIX AutoBuild wizard , 2007 .

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

[42]  M. Karplus,et al.  Solution of a Protein Crystal Structure with a Model Obtained from NMR Interproton Distance Restraints , 1987, Science.

[43]  D. Eisenberg,et al.  A challenging case for protein crystal structure determination: the mating pheromone Er-1 from Euplotes raikovi. , 1996, Acta crystallographica. Section D, Biological crystallography.

[44]  J Navaza,et al.  Implementation of molecular replacement in AMoRe. , 2001, Acta crystallographica. Section D, Biological crystallography.

[45]  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.

[46]  M Kokkinidis,et al.  A stochastic approach to molecular replacement. , 2000, Acta crystallographica. Section D, Biological crystallography.

[47]  V S Lamzin,et al.  ARP/wARP and molecular replacement. , 2001, Acta crystallographica. Section D, Biological crystallography.

[48]  W. Hendrickson.  Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. , 1991, Science.

[49]  G. Montelione,et al.  Structural basis for suppression of a host antiviral response by influenza A virus , 2008, Proceedings of the National Academy of Sciences.

[50]  Randy J. Read,et al.  Pushing the boundaries of molecular replacement with maximum likelihood. , 2001, Acta crystallographica. Section D, Biological crystallography.

[51]  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.

[52]  G. Montelione,et al.  Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI Production Centers. , 2008, Structure.

[53]  Richard Axel,et al.  Crystal structure of a soluble form of the human T cell coreceptor CD8 at 2.6 Å resolution , 1992, Cell.

[54]  Martyn D. Winn,et al.  MrBUMP: an automated pipeline for molecular replacement , 2007, Acta crystallographica. Section D, Biological crystallography.

[55]  L. Kelley,et al.  An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures. , 1997, Protein engineering.

[56]  A Vagin,et al.  An approach to multi-copy search in molecular replacement. , 2000, Acta crystallographica. Section D, Biological crystallography.

[57]  G. Clore,et al.  A systematic case study on using NMR models for molecular replacement: p53 tetramerization domain revisited. , 2000, Acta crystallographica. Section D, Biological crystallography.

[58]  T F Havel,et al.  The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X‐ray structures , 1992, Protein science : a publication of the Protein Society.

[59]  G Jogl,et al.  COMO: a program for combined molecular replacement. , 2001, Acta crystallographica. Section D, Biological crystallography.

[60]  J. L. Smith,et al.  A probability representation for phase information from multiwavelength anomalous dispersion. , 1990, Acta crystallographica. Section A, Foundations of crystallography.

[61]  M G Rossmann,et al.  The molecular replacement method. , 1990, Acta crystallographica. Section A, Foundations of crystallography.

[62]  Philip Evans,et al.  An introduction to molecular replacement , 2007, Acta crystallographica. Section D, Biological crystallography.

[63]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using Modeller , 2006, Current protocols in bioinformatics.

[64]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[65]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2007, Current protocols in protein science.

[66]  M. Buehner,et al.  Human interleukin-4 and variant R88Q: phasing X-ray diffraction data by molecular replacement using X-ray and nuclear magnetic resonance models. , 1995, Journal of molecular biology.