A general method for the unbiased improvement of solution NMR structures by the use of related X-Ray data, the AUREMOL-ISIC algorithm

BMC Structural Biology

Volumn 6, Issue , 2006, Pages

  Brunner, Konrad ^a   Gronwald, Wolfram ^a   Trenner, Jochen M ^a   Neidig, Klaus Peter ^b   Kalbitzer, Hans Robert ^a  

^a UNIVERSITY OF REGENSBURG   (Germany)

^b BRUKER BIOSPIN GMBH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN; PROTEIN G; RAS PROTEIN;

ALGORITHM; ARTICLE; BAYES THEOREM; COMPUTER PROGRAM; DATA BASE; DIMERIZATION; MACROMOLECULE; NUCLEAR MAGNETIC RESONANCE; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE; STREPTOCOCCUS; STRUCTURE ANALYSIS; X RAY ANALYSIS;

ALGORITHMS; BACTERIAL PROTEINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MAP KINASE KINASE KINASES; NERVE TISSUE PROTEINS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN STRUCTURE, TERTIARY; RAL GUANINE NUCLEOTIDE EXCHANGE FACTOR; RAS PROTEINS; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE PROTEINS; SOFTWARE; STREPTOCOCCUS;

SCHIZOSACCHAROMYCES POMBE; STREPTOCOCCUS;

EID: 33748441391     PISSN: 14726807     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-6-14     Document Type: Article

References (40)

1. Annila A, Aito H, Thulin E, Drakenberg T: Recognition of protein folds via dipolar couplings. J Biomol NMR 1999, 14:223-230.
2. Bowers PM, Strauss CEM, Baker D: De novo protein structure determination using sparse NMR data. J Biomol NMR 2000, 18:311-318.
3. Simons KT, Kooperberg C, Huang E, Baker D: Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions. J Mol Biol 1997, 268:209-225.
4. Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D: Improved Recognition of Native-Like protein Structures Using a Combination of Sequence-Dependent and Sequence-Independent Features of Proteins. Proteins 1999, 34:82-95.
5. Delagio F, Kontaxis G, Bax A: Protein Structure Determination Using Molecular Fragment Replacement and NMR Dipolar Couplings. J Am Chem Soc 2000, 122:2142-2143.
6. Andrec M, Harano Y, Jacobson MP, Friesner RA, Levy RM: Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction. J Struct Funct Genomics 2002, 2:103-111.
7. Haliloglu T, Kolinski A, Skolnick J: Use of Residual Dipolar Couplings as Restraints in Ab Initio Protein Structure Prediction. Biopolymers 2003, 70:548-562.
8. Albrecht M, Hanisch D, Zimmer R, Lengauer T: Improving fold recognition of protein threading by experimental distance constraints. In Silico Biology 2002, 2:1-12.
9. Li W, Zhang Y, Kihara D, Huang YJ, Zheng D, Montelione G, Kolinski A, Skolnick J: TOUCHSTONEX: Protein Structure Prediction With Sparse NMR Data. Proteins 2003, 53:290-306.
10. Shaanan B, Gronenborn AM, Cohen GH, Gilliland GL, Veerapandian B, Davies DR, Clore GM: Combining Experimental Information from Crystal and Solution Studies: Joint X-ray and NMR refinement. Science 1992, 257:961-964.
11. Schiffer CA, Huber R, Wüthrich K, Gunsteren WF: Simultaneous Refinement of the Structure of BPTI Against NMR Data Measured in Solution and X-ray Diffraction Data Measured in Single Crystals. J Mol Biol 1994, 241:588-599.
12. Hoffman DW, Cameron CS, Davies C, White SW, Ramakrishnan V: Ribosomal Protein L9: A Structure Determination by the Combined Use of X-ray Crystallography and NMR Spectroscopy. J Mol Biol 1996, 264:1058-1071.
13. Miller M, Lubkowski J, Rao KKM, Danishefsky AT, Omichinski JG, Sakaguchi K, Sakamoto H, Apella E, Gronenborn AM, Clore GM: The Oligomerization Domain of p53: Crystal Structure of the Trigonal Form. FEBS Lett 1996, 399:166-170.
14. Raves ML, Doreleijers JF, Vis H, Vorgias CE, Wilson KS, Kaptein R: Joint refinement as a tool for thorough comparison between NMR and X-ray data and structures of HU protein. J Biomol NMR 2001, 21:235-248.
15. Chao J, Williamson JR: Joint X-Ray and NMR Refinement of the Yeast L30e-mRNA Complex. Structure 2004, 12:1165-1176.
16. Gronwald W, Huber F, Grünewald P, Spörner M, Wohlgemuth S, Herrmann C, Kalbitzer HR: Solution Structure of the Ras binding Domain of the Protein Kinase Byr2 from Schizosaccharomyces pombe. Structure 2001, 9:1029-1041.
17. Scheffzek K, Grünewald P, Wohlgemuth S, Kabsch W, Tu H, Wigler M, Wittinghofer A, Herrmann C: The Ras-Byr2RBD Complex: Structural Basis for Ras Effector Recognition in Yeast. Structure 2001, 9:1043-1050.
18. Geyer M, Herrmann C, Wohlgemuth S, Wittinghofer A, Kalbitzer HR: Structure of the Ras-binding domain of RalGEF and implications for Ras binding and signalling. Nat Struc Biol 1997, 4:694-699.
19. Vetter IR, Linnemann T, Wohlgemuth S, Geyer M, Kalbitzer HR, Herrmann C, Wittinghofer A: Structural and Biochemical Analysis of Ras-Effector signaling via RalGDS. FEBS Lett 1999, 451:175-180.
20. Byeon IL, Louis JM, Gronenborn AM: A protein Contortionist: Core mutations of GB1 that Induce Dimerization and Domain Swapping. J Mol Biol 2003, 333:141-152.
21. Achari A, Hale SP, Howard AJ, Clore GM, Gronenborn AM, Hardman KD, Whitlow M: 1.67-Å X-ray Structure of the B2 Immunoglobulin-Binding Domain of Strptococcal Protein G and Comparison to the NMR Structure of the B1 Domain. Biochemistry 1992, 31:10449-10457.
22. Kirkpatrick S, Gelatt CD, Vecchi MP: Optimization by Simulated Annealing. Science 1983, 220:671-680.
23. Möglich A, Weinfurtner D, Maurer T, Gronwald W, Kalbitzer HR: A Restraint Molecular Dynamics and Simulated Annealing Approach for Protein Homology Modeling Utilizig Mean angles. BMC-Bioinformatics 2005, 6:91.
24. Möglich A, Weinfurtner D, Gronwald W, Maurer T, Kalbitzer HR: PERMOL: Restraint-Based Protein Homology Modeling Using DYANA or CNS. Bioinformatics 2005, 21:2110-2111.
25. Nabuurs SB, Nederveen AJ, Vranken W, Doreleijers JF, Bonvin AMJJ, Vuister GW, Vriend G, Spronk CAEM: DRESS: a Database of REfined Solution NMR Structures. Proteins 2004, 55:483-486.
26. Linge JP, Williams MA, Spronk CAEM, Bonvin AMJJ, Nilges M: Refinement of protein structures in explicit solvent. Proteins 2003, 50:496-506.
27. Gronwald W, Kirchhofer R, Gorler A, Kremer W, Ganslmeier B, Neidig KP, Kalbitzer HR: RFAC, a program for automated NMR R-factor estimation. J Biomol NMR 2000, 17:137-151.
28. Rieping W, Habeck M, Nilges M: Inferential Structure Determination. Science 2005, 309:303-306.
29. Gronwald W, Kalbitzer HR: Automated structure determination of proteins by NMR spectroscopy. Prog NMR Spectrosc 2004, 44:33-96.
30. Holton J, Alber T: Automated Protein Crystal Structure Determination using ELVES. Proc Natl Acad Sci USA 2004, 101:1537-1542.
31. Cruickshank DWJ: Remarks About Protein Structure Precision. Acta Cryst D 1999, 55:583-601.
32. Güntert P, Mumenthaler C, Wüthrich K: Torsion Angle Dynamics for NMR Structure Calculation with the New Program DYANA. J Mol Biol 1997, 273:283-298.
33. Schwieters CD, Kuszewski J, Tjandra NL, Clore GM: The Xplor-NIH NMR molecular structure determination package. J Magn Reson 2003, 160:65-73.
34. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grossekunstleve RW, Jiang J-S, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL: Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination. Acta Cryst 1998, D54:905-921.
35. Sachs L: Angewandte Statistik Berlin: Springer Verlag; 1997.
36. Freund J: University of Heidelberg; 1994.
37. Huber F, Gronwald W, Wohlgemuth S, Herrmann C, Geyer M, Wittinghofer A, Kalbitzer HR: Letter to the Editor: Sequential NMR Assignment of the Ras-Binding Domain of Byr2. J Biomol NMR 2000, 16:355-356.
38. Döker R, Maurer T, Kremer W, Neidig K-P, Kalbitzer HR: Determination of Mean and Standard Deviation of Dihedral Angles. BBRC 1999, 257:348-350.
39. Laskowski RA, Rullmann JAC, MacArthur MW, Kaptein R, Thornton JM: AQUA and PROCHECK-NMR Programs for checking the quality of protein structures solved by NMR. J Biomol NMR 1996, 8:477-486.
40. Koradi R, Billeter M, Wüthrich K: MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graphics 1996, 14:51-55.