Molecular structure refinement by direct fitting of atomic coordinates to experimental ESR spectra

Journal of Magnetic Resonance

Volumn 216, Issue , 2012, Pages 62-68

  Charnock, G T P ^a   Krzystyniak, M ^a   Kuprov, Ilya ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Direct fitting; ESR; Structure

Indexed keywords

ATOMIC COORDINATE; DIRECT FITTING; DYNAMICS SIMULATION; EQUILIBRIUM GEOMETRIES; ESR SPECTRA; HYPERFINE COUPLING; INTERNAL COORDINATES; LOCAL MINIMUM PROBLEM; QUANTUM-MECHANICAL CALCULATION; SOLID-STATE ELECTRON; SPECTRAL FITTING; SPIN INTERACTION; STRUCTURE REFINEMENTS;

PARAMAGNETIC RESONANCE; SPECTRUM ANALYSIS; STRUCTURE (COMPOSITION);

ELECTRON SPIN RESONANCE SPECTROSCOPY;

PROTEIN; RIBONUCLEOTIDE REDUCTASE; TYROSINE;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER; COMPUTER SIMULATION; CONFORMATION; ECONOMICS; ELECTRON SPIN RESONANCE; ENZYMOLOGY; ESCHERICHIA COLI; METHODOLOGY; NORMAL DISTRIBUTION; SALMONELLA TYPHIMURIUM; X RAY DIFFRACTION;

ALGORITHMS; COMPUTER SIMULATION; COMPUTERS; ELECTRON SPIN RESONANCE SPECTROSCOPY; ESCHERICHIA COLI; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NORMAL DISTRIBUTION; PROTEINS; RIBONUCLEOTIDE REDUCTASES; SALMONELLA TYPHIMURIUM; TYROSINE; X-RAY DIFFRACTION;

EID: 84858337473     PISSN: 10907807     EISSN: 10960856     Source Type: Journal    
DOI: 10.1016/j.jmr.2012.01.003     Document Type: Article

References (48)

1. G.M. Clore, and A.M. Gronenborn Determining the structures of large proteins and protein complexes by NMR Trend. Biotechnol. 16 1998 22 34 (Pubitemid 28064815)
2. M. Helgstrand, P. Kraulis, P. Allard, and T. Härd Ansig for windows: an interactive computer program for semiautomatic assignment of protein NMR spectra J. Biomol. NMR 18 2000 329 336 (Pubitemid 32065087)
3. C.D. Schwieters, J.J. Kuszewski, and G. Marius Clore Using Xplor-NIH for NMR molecular structure determination Progr. NMR Spectr. 48 2006 47 62
4. Y. Shen, O. Lange, F. Delaglio, P. Rossi, J.M. Aramini, G.H. Liu, A. Eletsky, Y.B. Wu, K.K. Singarapu, A. Lemak, A. Ignatchenko, C.H. Arrowsmith, T. Szyperski, G.T. Montelione, D. Baker, and A. Bax Consistent blind protein structure generation from NMR chemical shift data Proc. Natl. Acad. Sci. USA 105 2008 4685 4690 (Pubitemid 351753807)
5. W.F. Vranken, W. Boucher, T.J. Stevens, R.H. Fogh, A. Pajon, M. Llinas, E.L. Ulrich, J.L. Markley, J. Ionides, and E.D. Laue The CCPN data model for NMR spectroscopy: development of a software pipeline Protein Struct. Funct. Bioinform. 59 2005 687 696 (Pubitemid 40695845)
6. P.P. Borbat, and J.H. Freed Multiple-quantum ESR and distance measurements Chem. Phys. Lett. 313 1999 145 154 (Pubitemid 129556635)
7. E. De Alba, and N. Tjandra NMR dipolar couplings for the structure determination of biopolymers in solution Progr. NMR Spectr. 40 2002 175 197 (Pubitemid 34100263)
8. T. Herrmann, P. Güntert, and K. Wüthrich Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS J. Biomol. NMR 24 2002 171 189 (Pubitemid 36113646)
9. G. Jeschke, and Y. Polyhach Distance measurements on spin-labelled biomacromolecules by pulsed electron paramagnetic resonance Phys. Chem. Chem. Phys. 9 2007 1895 1910
10. P. Güntert, C. Mumenthaler, and K. Wüthrich Torsion angle dynamics for NMR structure calculation with the new program DYANA J. Mol. Biol. 273 1997 283 298 (Pubitemid 27460230)
11. S.J. Clark, M.D. Segall, C.J. Pickard, P.J. Hasnip, M.J. Probert, K. Refson, and M.C. Payne First principles methods using CASTEP Z. Kristall. 220 2005 567 570 (Pubitemid 40778242)
12. F. Neese Configuration interaction calculation of electronic g tensors in transition metal complexes Int. J. Quant. Chem. 83 2001 104 114 (Pubitemid 32517560)
13. F. Neese Quantum chemical calculations of spectroscopic properties of metalloproteins and model compounds: EPR and Mössbauer properties Curr. Opin. Chem. Biol. 7 2003 125 135 (Pubitemid 36126503)
14. F. Neese Efficient and accurate approximations to the molecular spin-orbit coupling operator and their use in molecular g-tensor calculations J. Chem. Phys. 122 2005 1 13 (Pubitemid 41047650)
15. R.K. Harris NMR crystallography: the use of chemical shifts Solid State Sci. 6 2004 1025 1037
16. R.K. Harris, P. Hodgkinson, C.J. Pickard, J.R. Yates, and V. Zorin Chemical shift computations on a crystallographic basis: some reflections and comments Magn. Reson. Chem. 45 2007 S174 S186
17. R. Improta, and V. Barone Interplay of electronic, environmental, and vibrational effects in determining the hyperfine coupling constants of organic free radicals Chem. Rev. 104 2004 1231 1253
18. N. Rega, M. Cossi, and V. Barone Development and validation of reliable quantum mechanical approaches for the study of free radicals in solution J. Chem. Phys. 105 1996 11060 11067 (Pubitemid 126748047)
19. D.A. Svistunenko, and C.E. Cooper A new method of identifying the site of tyrosyl radicals in proteins Biophys. J. 87 2004 582 595 (Pubitemid 38880111)
20. D.A. Svistunenko, and G.A. Jones Tyrosyl radicals in proteins: a comparison of empirical and density functional calculated EPR parameters Phys. Chem. Chem. Phys. 11 2009 6600 6613
21. V. Barone, and P. Cimino Validation of the B3LYP/N07D and PBE0/N07D computational models for the calculation of electronic g-tensors J. Chem. Theory Comput. 5 2009 192 199
22. H.J. Hogben, M. Krzystyniak, G.T.P. Charnock, P.J. Hore, and I. Kuprov Spinach - a software library for simulation of spin dynamics in large spin systems J. Magn. Reson. 208 2011 179 194
23. I. Kuprov Diagonalization-free implementation of spin relaxation theory for large spin systems J. Magn. Reson. 209 2011 31 38
24. I. Kuprov, N. Wagner-Rundell, and P.J. Hore Polynomially scaling spin dynamics simulation algorithm based on adaptive state-space restriction J. Magn. Reson. 189 2007 241 250 (Pubitemid 350051985)
25. R.A. Atkinson, and V. Saudek Direct fitting of structure and chemical shift to NMR spectra J. Chem. Soc. Faraday. Trans. 93 1997 3319 3323 (Pubitemid 127781972)
26. D.H. Brouwer A structure refinement strategy for NMR crystallography: an improved crystal structure of silica-ZSM-12 zeolite from (29)Si chemical shift tensors J. Magn. Reson. 194 2008 136 146
27. J.H. Freed, P.P. Borbat, and H.S. Mchaourab Protein structure determination using long-distance constraints from double-quantum coherence ESR: study of T4 lysozyme J. Am. Chem. Soc. 124 2002 5304 5314 (Pubitemid 34506927)
28. L. Hermosilla, C. Sieiro, P. Calle, M. Zerbetto, and A. Polimeno Modeling of cw-EPR spectra of propagating radicals in methacrylic polymerization at different temperatures J. Phys. Chem. B 112 2008 11202 11208
29. A. Soleilhavoup, M.R. Hampson, S.J. Clark, J.S.O. Evans, and P. Hodgkinson Using O-17 solid-state NMR and first principles calculation to characterise structure and dynamics in inorganic framework materials Magn. Reson. Chem. 45 2007 S144 S155
30. D.C. Liu, and J. Nocedal On the limited memory BFGS method for large scale optimization Math. Progr. 45 1989 503 528 (Pubitemid 20660315)
31. P. Pulay, G. Fogarasi, F. Pang, and J.E. Boggs Systematic abinitio gradient calculation of molecular geometries, force constants, and dipole-moment derivatives J. Am. Chem. Soc. 101 1979 2550 2560
32. I. Kuprov, and C.T. Rodgers Derivatives of spin dynamics simulations J. Chem. Phys. 131 2009 11
33. J.N. Dumez, and C.J. Pickard Calculation of NMR chemical shifts in organic solids: accounting for motional effects J. Chem. Phys. 130 2009
34. K. Ruud, P.O. strand, and P.R. Taylor Zero-point vibrational effects on proton shieldings: functional-group contributions from ab initio calculations J. Am. Chem. Soc. 123 2001 4826 4833 (Pubitemid 32895780)
35. H. Husein Mor, H. Weihe, and J. Bendix Fitting of EPR spectra: the importance of a flexible bandwidth J. Magn. Reson. 207 2010 283 286
36. Y.V. Rakitin, G.M. Larin, V.V. Minin, Interpretation of ESR Spectra of Coordination Compounds, Nauka, 1993.
37. H.B. Schlegel A comparison of geometry optimization with internal, Cartesian, and mixed coordinates Int. J. Quant. Chem. 1992 243 252
38. Y.W. Chiang, P.P. Borbat, and J.H. Freed The determination of pair distance distributions by pulsed ESR using Tikhonov regularization J. Magn. Reson. 172 2005 279 295 (Pubitemid 40072533)
39. P.C. Hansen, T.K. Jensen, and G. Rodriguez An adaptive pruning algorithm for the discrete L-curve criterion J. Comput. Appl. Math. 198 2007 483 492 (Pubitemid 44402949)
40. T.K. Jensen, and P.C. Hansen Iterative regularization with minimum-residual methods BIT Numer. Math. 47 2007 103 120
41. G.A. Shultz, R.B. Schnabel, and R.H. Byrd A family of trust-region-based algorithms for unconstrained minimization with strong global convergence properties SIAM J. Numer. Anal. 22 1985 47 67
42. H.B. Schlegel Analytical 2nd derivatives of 2 electron integrals over s and p cartesian gaussians J. Chem. Phys. 90 1989 5630 5634
43. A.D. Becke A new mixing of hartree-fock and local density-functional theories J. Chem. Phys. 98 1993 1372 1377
44. K. Ruud, T. Helgaker, K.L. Bak, P. Jorgensen, and H.J.A. Jensen Hartree-Fock limit magnetizabilities from London orbitals J. Chem. Phys. 99 1993 3847 3859
45. V. Barone, Recent Advances in Density Functional Methods, World Scientific, 1996.
46. M. Eriksson, A. Jordan, and H. Eklund Structure of Salmonella typhimurium nrdF ribonucleotide reductase in its oxidized and reduced forms Biochemistry 37 1998 13359 13369 (Pubitemid 28449581)
47. P. Nordlund, and H. Eklund Structure and function of the Escherichia coli ribonucleotide reductase protein R2 J. Mol. Biol. 232 1993 123 164 (Pubitemid 23245406)
48. W.T. Dixon, and D. Murphy Determination of acidity constants of some phenol radical cations by means of electron-spin resonance J. Chem. Soc. Faraday Trans. 72 1976 1221 1230