Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences
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Claudio Luchinat | Vito Calderone | Giacomo Parigi | Garib N. Murshudov | Enrico Ravera | C. Luchinat | G. Murshudov | V. Calderone | E. Ravera | G. Parigi | Mauro Rinaldelli | M. Rinaldelli
[1] R. Huber,et al. Simultaneous refinement of the structure of BPTI against NMR data measured in solution and X-ray diffraction data measured in single crystals. , 1994, Journal of molecular biology.
[2] Jill Trewhella,et al. Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints , 2008, Journal of biomolecular NMR.
[3] Ad Bax,et al. Validation of Protein Structure from Anisotropic Carbonyl Chemical Shifts in a Dilute Liquid Crystalline Phase , 1998 .
[4] J H Prestegard,et al. Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[5] Anastassis Perrakis,et al. Automated protein model building combined with iterative structure refinement , 1999, Nature Structural Biology.
[6] Nico Tjandra,et al. Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR relaxation. , 2005, Journal of magnetic resonance.
[7] G. Clore,et al. Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR , 2007, Nature.
[8] A. Bax,et al. Local and global structure of the monomeric subunit of the potassium channel KcsA probed by NMR. , 2007, Biochimica et biophysica acta.
[9] G. Otting,et al. Paramagnetic labelling of proteins and oligonucleotides for NMR , 2010, Journal of biomolecular NMR.
[10] Oliver F. Lange,et al. Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution , 2008, Science.
[11] C. Luchinat,et al. Solid-state NMR crystallography through paramagnetic restraints. , 2012, Journal of the American Chemical Society.
[12] Charles K. Fisher,et al. Visualizing spatially correlated dynamics that directs RNA conformational transitions , 2007, Nature.
[13] Ad Bax,et al. Simultaneous NMR study of protein structure and dynamics using conservative mutagenesis. , 2008, The journal of physical chemistry. B.
[14] Ad Bax,et al. Modulation of the Alignment Tensor of Macromolecules Dissolved in a Dilute Liquid Crystalline Medium , 1998 .
[15] N. Pannu,et al. REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.
[16] C. D. Barry,et al. Quantitative Determination of Mononucleotide Conformations in Solution using Lanthanide Ion Shift and Broadening NMR Probes , 1971, Nature.
[17] G. G. Stokes. "J." , 1890, The New Yale Book of Quotations.
[18] Harald Schwalbe,et al. Protein alignment by a coexpressed lanthanide-binding tag for the measurement of residual dipolar couplings. , 2003, Journal of the American Chemical Society.
[19] G. Clore,et al. Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein: a unified picture of high probability, fast atomic motions in proteins. , 2006, Journal of molecular biology.
[20] A. Gronenborn,et al. The oligomerization domain of p53: Crystal structure of the trigonal form , 1996, FEBS letters.
[21] L. Kay,et al. What is the average conformation of bacteriophage T4 lysozyme in solution? A domain orientation study using dipolar couplings measured by solution NMR. , 2001, Journal of molecular biology.
[22] J H Prestegard,et al. Determination of protein backbone structures from residual dipolar couplings. , 2005, Methods in enzymology.
[23] P. Keizers,et al. Validation of a lanthanide tag for the analysis of protein dynamics by paramagnetic NMR spectroscopy. , 2010, Journal of the American Chemical Society.
[24] R. Kaptein,et al. Joint refinement as a tool for thorough comparison between NMR and X-ray data and structures of HU protein , 2001, Journal of biomolecular NMR.
[25] J H Prestegard,et al. A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones. , 2001, Journal of the American Chemical Society.
[26] Robin K. Harris,et al. Encyclopedia of nuclear magnetic resonance , 1996 .
[27] M. R. Jensen,et al. On the use of pseudocontact shifts in the structure determination of metalloproteins , 2006, Magnetic resonance in chemistry : MRC.
[28] M. Saraste,et al. FEBS Lett , 2000 .
[29] J. Prestegard,et al. Structure determination of a Galectin‐3–carbohydrate complex using paramagnetism‐based NMR constraints , 2008, Protein science : a publication of the Protein Society.
[30] Wei-Min Liu,et al. Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains , 2011, Journal of biomolecular NMR.
[31] W. Horrocks,et al. Direct evaluation of dipolar nuclear magnetic resonance shifts from single-crystal magnetic measurements. Paramagnetic anisotropy of bis(2,4-pentanedionato)bis(pyridine)cobalt(II) , 1971 .
[32] F. Young. Biochemistry , 1955, The Indian Medical Gazette.
[33] Alexander N. Volkov,et al. Solution structure and dynamics of the complex between cytochrome c and cytochrome c peroxidase determined by paramagnetic NMR , 2006, Proceedings of the National Academy of Sciences.
[34] J. Prestegard,et al. Residual dipolar couplings in structure determination of biomolecules. , 2004, Chemical reviews.
[35] P. Güntert. Automated NMR structure calculation with CYANA. , 2004, Methods in molecular biology.
[36] M. Gochin,et al. Protein structure refinement based on paramagnetic NMR shifts: Applications to wild‐type and mutant forms of cytochrome c , 1995, Protein science : a publication of the Protein Society.
[37] P. Keizers,et al. Design, synthesis, and evaluation of a lanthanide chelating protein probe: CLaNP-5 yields predictable paramagnetic effects independent of environment. , 2008, Journal of the American Chemical Society.
[38] Ad Bax,et al. Solution structure of Ca2+–calmodulin reveals flexible hand-like properties of its domains , 2001, Nature Structural Biology.
[39] M Ikura,et al. Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible. , 1992, Biochemistry.
[40] M. Karplus,et al. Crystallographic R Factor Refinement by Molecular Dynamics , 1987, Science.
[41] V. Gaponenko,et al. Improving the Accuracy of NMR Structures of Large Proteins Using Pseudocontact Shifts as Long-Range Restraints , 2004, Journal of biomolecular NMR.
[42] G L Gilliland,et al. Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. , 1992, Science.
[43] I. Bertini,et al. Paramagnetism-based versus classical constraints: An analysis of the solution structure of Ca Ln calbindin D9k , 2001, Journal of biomolecular NMR.
[44] D. Fushman,et al. A model of interdomain mobility in a multidomain protein. , 2007, Journal of the American Chemical Society.
[45] Ivano Bertini,et al. Magnetic susceptibility in paramagnetic NMR , 2002 .
[46] Kevin Cowtan,et al. The Buccaneer software for automated model building. 1. Tracing protein chains. , 2006, Acta crystallographica. Section D, Biological crystallography.
[47] Ivano Bertini,et al. 13C direct detected NMR increases the detectability of residual dipolar couplings. , 2006, Journal of the American Chemical Society.
[48] D. Svergun,et al. Interdomain Flexibility in Full-length Matrix Metalloproteinase-1 (MMP-1)* , 2009, Journal of Biological Chemistry.
[49] H. Gray,et al. The use of pseudocontact shifts to refine solution structures of paramagnetic metalloproteins: Met80Ala cyano-cytochrome c as an example , 1996, JBIC Journal of Biological Inorganic Chemistry.
[50] N. Tjandra,et al. Analysis of slow interdomain motion of macromolecules using NMR relaxation data. , 2001, Journal of the American Chemical Society.
[51] J H Prestegard,et al. Structural and dynamic analysis of residual dipolar coupling data for proteins. , 2001, Journal of the American Chemical Society.
[52] J. Prestegard,et al. Domain–domain motions in proteins from time-modulated pseudocontact shifts , 2007, Journal of biomolecular NMR.
[53] Ivano Bertini,et al. The catalytic domain of MMP‐1 studied through tagged lanthanides , 2012, FEBS letters.
[54] A. Rosato,et al. MaxOcc: a web portal for maximum occurrence analysis , 2012, Journal of Biomolecular NMR.
[55] I. Bertini,et al. Moving the frontiers in solution and solid-state bioNMR , 2011 .
[56] V. Ramakrishnan,et al. Ribosomal protein L9: a structure determination by the combined use of X-ray crystallography and NMR spectroscopy. , 1996, Journal of molecular biology.
[57] Maxim V. Petoukhov,et al. Conformational space of flexible biological macromolecules from average data. , 2010, Journal of the American Chemical Society.
[58] R. Rosenfeld. Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.
[59] Donata K. Kirchner,et al. Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space , 2012, Journal of Biomolecular NMR.
[60] I. Bertini,et al. Accurate solution structures of proteins from X-ray data and a minimal set of NMR data: calmodulin-peptide complexes as examples. , 2009, Journal of the American Chemical Society.
[61] L. Kay,et al. Orienting domains in proteins using dipolar couplings measured by liquid-state NMR: differences in solution and crystal forms of maltodextrin binding protein loaded with beta-cyclodextrin. , 2000, Journal of molecular biology.
[62] D K Smith,et al. Numerical Optimization , 2001, J. Oper. Res. Soc..
[63] Andrew J. Nieuwkoop,et al. High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data , 2011, Journal of biomolecular NMR.
[64] I. Bertini,et al. Paramagnetic shifts in solid-state NMR of proteins to elicit structural information , 2008, Proceedings of the National Academy of Sciences.
[65] G. Murshudov,et al. Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.
[66] Oliviero Carugo,et al. Systematic Comparison of Crystal and NMR Protein Structures Deposited in the Protein Data Bank , 2010, The open biochemistry journal.
[67] M. Ubbink,et al. Structure of the Complex between Plastocyanin and Cytochrome f from the Cyanobacterium Nostoc sp. PCC 7119 as Determined by Paramagnetic NMR , 2005, Journal of Biological Chemistry.
[68] Randy J. Read,et al. Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.
[69] A. Rosato,et al. Partial Orientation of Oxidized and Reduced Cytochrome b5 at High Magnetic Fields: Magnetic Susceptibility Anisotropy Contributions and Consequences for Protein Solution Structure Determination , 1998 .
[70] F. Walker,et al. Proton magnetic resonance investigation of antiferromagnetic oxo-bridged ferric dimers and related high-spin monomeric ferric complexes , 1973 .
[71] David Baker,et al. Protein structure determination from pseudocontact shifts using ROSETTA. , 2012, Journal of molecular biology.
[72] A. Brunger. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. , 1992 .
[73] J. Williamson,et al. Joint X-ray and NMR refinement of the yeast L30e-mRNA complex. , 2004, Structure.
[74] C. Luchinat,et al. Conformational freedom of metalloproteins revealed by paramagnetism-assisted NMR , 2013 .
[75] Guido Pintacuda,et al. Lanthanide labeling offers fast NMR approach to 3D structure determinations of protein-protein complexes. , 2006, Journal of the American Chemical Society.
[76] C. Griesinger,et al. Paramagnetic tagging of diamagnetic proteins for solution NMR , 2006, Magnetic resonance in chemistry : MRC.
[77] A. Volkov,et al. Visualization of the encounter ensemble of the transient electron transfer complex of cytochrome c and cytochrome c peroxidase. , 2010, Journal of the American Chemical Society.
[78] Ad Bax,et al. Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy. , 2003, Journal of the American Chemical Society.
[79] G. Otting,et al. A dipicolinic acid tag for rigid lanthanide tagging of proteins and paramagnetic NMR spectroscopy. , 2008, Journal of the American Chemical Society.