Quantum mechanical NMR simulation algorithm for protein-size spin systems

Journal of Magnetic Resonance

Volumn 243, Issue , 2014, Pages 107-113

  Edwards, Luke J ^a,b   Savostyanov, D V ^b   Welderufael, Z T ^b   Lee, Donghan ^c   Kuprov, Ilya ^b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^c MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

Nuclear magnetic resonance; Protein; Simulation

Indexed keywords

LATTICE THEORY; NUCLEAR MAGNETIC RESONANCE; PHYSICAL CHEMISTRY; PROTEINS; QUANTUM THEORY; SPIN DYNAMICS;

DECOHERENCE PROPERTIES; DENSITY OPERATORS; ISOTOPICALLY ENRICHED; NUCLEAR SPIN STATE; QUANTUM MECHANICAL; QUANTUM MECHANICAL SIMULATIONS; SIMULATION; SIMULATION ALGORITHMS;

NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

SPIN LABELING; UBIQUITIN;

ALGORITHM; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; HUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROCEDURES; QUANTUM THEORY; SPIN LABELING;

ALGORITHMS; COMPUTER SIMULATION; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; QUANTUM THEORY; SPIN LABELS; UBIQUITIN;

EID: 84899849667     PISSN: 10907807     EISSN: 10960856     Source Type: Journal    
DOI: 10.1016/j.jmr.2014.04.002     Document Type: Article

References (41)

1. R.R. Ernst, G. Bodenhausen, and A. Wokaun Principles of nuclear magnetic resonance in one and two dimensions Clarendon 1987
2. P. Hodgkinson, and L. Emsley Numerical simulation of solid-state NMR experiments Progr. NMR Spec. 36 2000 201 239
3. J. Cavanagh, W.J. Fairbrother, A.G. Palmer, M. Rance, and N.J. Skelton Protein NMR Spectroscopy 2007 Academic Press
4. A.G. Palmer NMR characterization of the dynamics of biomacromolecules Chem. Rev. 104 2004 3623 3640
5. U. Schollwöck The density-matrix renormalization group in the age of matrix product states Ann. Phys. 326 2011 96 192
6. G.K.-L. Chan, and S. Sharma The density matrix renormalization group in quantum chemistry Annu. Rev. Phys. Chem. 62 2011 465 481
7. 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)
8. I. Kuprov Polynomially scaling spin dynamics II: further state-space compression using Krylov subspace techniques and zero track elimination J. Magn. Reson. 195 2008 45 51
9. L.J. Edwards, D.V. Savostyanov, A.A. Nevzorov, M. Concistrè, G. Pileio, and I. Kuprov Grid-free powder averages: on the applications of the Fokker-Planck equation to solid state NMR J. Magn. Reson. 235 2013 121 129
10. M.E. Halse, J.N. Dumez, and L. Emsley Quasi-equilibria in reduced Liouville spaces J. Chem. Phys. 136 2012
11. M. Krzystyniak, L.J. Edwards, and I. Kuprov Destination state screening of active spaces in spin dynamics simulations J. Magn. Reson. 210 2011 228 232
12. A. Karabanov, I. Kuprov, G.T.P. Charnock, A. van der Drift, L.J. Edwards, and W. Kockenberger On the accuracy of the state space restriction approximation for spin dynamics simulations J. Chem. Phys. 135 2011 084106 084108
13. H.J. Hogben, P.J. Hore, and I. Kuprov Strategies for state space restriction in densely coupled spin systems with applications to spin chemistry J. Chem. Phys. 132 2010 174101
14. J.N. Dumez, M.C. Butler, and L. Emsley Numerical simulation of free evolution in solid-state nuclear magnetic resonance using low-order correlations in Liouville space J. Chem. Phys. 133 2010
15. M.C. Butler, J.N. Dumez, and L. Emsley Dynamics of large nuclear-spin systems from low-order correlations in Liouville space Chem. Phys. Lett. 477 2009 377 381
16. I. Kuprov Diagonalization-free implementation of spin relaxation theory for large spin systems J. Magn. Reson. 209 2011 31 38
17. S. Even Graph Algorithms 2012 Cambridge University Press
18. 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
19. L.J. Edwards, and I. Kuprov Parallel density matrix propagation in spin dynamics simulations J. Chem. Phys. 136 2012
20. R.S. Dumont, S. Jain, and A. Bain Simulation of many-spin system dynamics via sparse matrix methodology J. Chem. Phys. 106 1997 5928 5936 (Pubitemid 127580693)
21. S. Macura, and R.R. Ernst Elucidation of cross relaxation in liquids by two-dimensional NMR-spectroscopy Mol. Phys. 41 1980 95 117
22. L.E. Kay, M. Ikura, R. Tschudin, and A. Bax Three-dimensional triple-resonance NMR spectroscopy of isotopically enriched proteins J. Magn. Reson. 89 1990 496 514
23. J. Schleucher, M. Schwendinger, M. Sattler, P. Schmidt, O. Schedletzky, S.J. Glaser, O.W. Sørensen, and C. Griesinger A general enhancement scheme in heteronuclear multidimensional NMR employing pulsed field gradients J. Biomol. NMR 4 1994 301 306
24. F.C. Bernstein, T.F. Koetzle, G.J.B. Williams, E.F. Meyer, M.D. Brice, J.R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi Protein data bank - computer-based archival file for macromolecular structures J. Mol. Biol. 112 1977 535 542 (Pubitemid 8109216)
25. E.L. Ulrich, H. Akutsu, J.F. Doreleijers, Y. Harano, Y.E. Ioannidis, J. Lin, M. Livny, S. Mading, D. Maziuk, Z. Miller, E. Nakatani, C.F. Schulte, D.E. Tolmie, R.K. Wenger, H.Y. Yao, and J.L. Markley BioMagResBank Nucl. Acids Res. 36 2008 402 408
26. T.G. Oas, C.J. Hartzell, F.W. Dahlquist, and G.P. Drobny The amide N-15 chemical-shift tensors of 4 peptides determined from C-13 dipole-coupled chemical-shift powder patterns J. Am. Chem. Soc. 109 1987 5962 5966 (Pubitemid 17150186)
27. T.G. Oas, C.J. Hartzell, T.J. Mcmahon, G.P. Drobny, and F.W. Dahlquist The carbonyl C-13 chemical-shift tensors of 5 peptides determined from N-15 dipole-coupled chemical-shift powder patterns J. Am. Chem. Soc. 109 1987 5956 5962
28. R. Burton, and N. Tjandra Determination of the residue-specific 15N CSA tensor principal components using multiple alignment media J. Biomol. NMR 35 2006 249 259 (Pubitemid 44288743)
29. M. Kaupp, M. Bühl, and V.G. Malkin Calculation of NMR and EPR Parameters: Theory and Applications 2004 Wiley
30. M. Karplus Vicinal proton coupling in nuclear magnetic resonance J. Am. Chem. Soc. 85 1963 2870 2871
31. A.B. Sahakyan, A.A. Shahkhatuni, A.G. Shahkhatuni, and H.A. Panosyan Dielectric permittivity and temperature effects on spin-spin couplings studied on acetonitrile Magn. Reson. Chem. 46 2008 63 68
32. D. Zaccari, V. Barone, J. Peralta, R. Contreras, O. Taurian, E. Díez, and A. Esteban Solvent effects on nuclear magnetic resonance 2J(C, Hf) and 1J(C, Hf) spin-spin coupling constants in acetaldehyde Int. J. Mol. Sci. 4 2003 93 106 (Pubitemid 38957252)
33. Y.E. Shapiro, E. Kahana, and E. Meirovitch Domain mobility in proteins from NMR/SRLS J. Phys. Chem. B 113 2009 12050 12060
34. J.J. Prompers, and R. Brüschweiler General framework for studying the dynamics of folded and nonfolded proteins by NMR relaxation spectroscopy and MD simulation J. Am. Chem. Soc. 124 2002 4522 4534 (Pubitemid 34441586)
35. R.K. Wangsness, and F. Bloch The dynamical theory of nuclear induction Phys. Rev. 89 1953 728 739
36. A.G. Redfield The Theory of Relaxation Processes Advance Magnetic Resonance 1965 Academic Press 1 30
37. M. Goldman Formal theory of spin-lattice relaxation J. Magn. Reson. 149 2001 160 187
38. R.R.P. Senthamarai, I. Kuprov, and K. Pervushin Benchmarking NMR experiments: a relational database of protein pulse sequences J. Magn. Reson. 203 2010 129 137
39. P. de Fouquieres, S.G. Schirmer, S.J. Glaser, and I. Kuprov Second order gradient ascent pulse engineering J. Magn. Reson. 212 2011 412 417
40. I. Kuprov Spin system trajectory analysis under optimal control pulses J. Magn. Reson. 233 2013 107 112
41. G.T.P. Charnock, M. Krzystyniak, and I. Kuprov Molecular structure refinement by direct fitting of atomic coordinates to experimental ESR spectra J. Magn. Reson. 216 2012 62 68