Maximum entropy: A complement to Tikhonov regularization for determination of pair distance distributions by pulsed ESR

Journal of Magnetic Resonance

Volumn 177, Issue 2, 2005, Pages 184-196

  Chiang, Yun Wei ^a   Borbat, Peter P ^a   Freed, Jack H ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

Cytochrome c; Double electron electron resonance; Double quantum coherence ESR; Maximum entropy; T4 lysozyme

Indexed keywords

CONVERGENCE OF NUMERICAL METHODS; INFORMATION ANALYSIS; ITERATIVE METHODS; MATHEMATICAL MODELS; PARAMAGNETIC RESONANCE; PROBABILITY; PROBLEM SOLVING;

CYTOCHROME C; DOUBLE ELECTRON-ELECTRON RESONANCE; DOUBLE-QUANTUM COHERENCE ESR; MAXIMUM ENTROPY; T4 LYSOZYME;

ENTROPY;

CYTOCHROME C; LYSOZYME; PEPTIDE FRAGMENT; T4 LYSOZYME (11 36); T4 LYSOZYME (11-36);

ARTICLE; CHEMISTRY; ELECTRON SPIN RESONANCE; ENTROPY; METHODOLOGY; PROBABILITY; PROTEIN CONFORMATION; SPIN LABELING; STATISTICAL MODEL;

CYTOCHROMES C; ELECTRON SPIN RESONANCE SPECTROSCOPY; ENTROPY; LINEAR MODELS; MURAMIDASE; PEPTIDE FRAGMENTS; PROBABILITY; PROTEIN CONFORMATION; SPIN LABELS;

EID: 28044472953     PISSN: 10907807     EISSN: 10960856     Source Type: Journal    
DOI: 10.1016/j.jmr.2005.07.021     Document Type: Article

References (44)

1. C.W. Groetsch The theory of Tikhonov regularization for Fredholm equations of the first kind 1984 Pitman Advanced Pub. Program Boston
2. Y.W. Chiang, P.P. Borbat, and J.H. Freed The determination of pair distance distributions by pulsed ESR using Tikhonov regularization J. Mag. Reson. 172 2005 279 295
3. G. Jeschke, G. Panek, A. Godt, A. Bender, and H. Paulsen Data analysis procedures for pulse ELDOR measurements of broad distance distributions Appl. Magn. Reson. 26 2004 223 244
4. M.K. Bowman, A.G. Maryasov, N. Kim, and V.J. DeRose Visualization of distance distribution from pulsed double electron-electron resonance data Appl. Magn. Reson. 26 2004 23 39
5. L.J. Berliner, G.R. Eaton, and S.S. Eaton Biological magnetic resonance: distance measurements in biological systems by EPR 2000 Kluwer Academic/Plenum Publishers New York
6. P.P. Borbat, J.H. Davis, S.E. Butcher, and J.H. Freed Measurement of large distances in biomolecules using double-quantum filtered refocused electron spin-echoes J. Am. Chem. Soc. 126 2004 7746 7747
7. P.P. Borbat, H.S. Mchaourab, and J.H. Freed Protein structure determination using long-distance constraints from double-quantum coherence ESR: study of T4 lysozyme J. Am. Chem. Soc. 124 2002 5304 5314
8. B.G. Dzikovski, P.P. Borbat, and J.H. Freed Spin-labeled gramicidin A: channel formation and dissociation Biophys. J. 87 2004 3504 3517
9. G. Jeschke, C. Wegener, M. Nietschke, H. Jung, and H.-J. Steinhoff Interresidual distance determination by four-pulse double electron-electron resonance in an integral membrane protein: the Na+/proline transporter PutP of Escherichia coli Biophys. J. 86 2004 2551 2557
10. V.M. Grigoryants, K.A. DeWeerd, and C.P. Scholes Method of rapid mix EPR applied to the folding of bi-spin-labeled protein as a probe for the dynamic onset of interaction between sequentially distant side chains J. Phys. Chem. B. 108 2004 9463 9468
11. K. DeWeerd, V. Grigoryants, Y. Sun, J.S. Fetrow, and C.P. Scholes EPR-detected folding kinetics of externally located cysteine-directed spin-labeled mutants of iso-1-cytochrome c Biochemistry 40 2001 15846 15855
12. P.C. Hansen Rank-deficient and discrete ill-posed problems : numerical aspects of linear inversion 1997 SIAM Philadelphia
13. J. Weese A reliable and fast method for the solution of Fredholm integral-equations of the 1st kind based on Tikhonov regularization Comput. Phys. Commun. 69 1992 99 111
14. T. Roths, M. Marth, J. Weese, and J. Honerkamp A generalized regularization method for nonlinear ill-posed problems enhanced for nonlinear regularization terms Comput. Phys. Commun. 139 2001 279 296
15. U. Amato, and W. Hughes Maximum-entropy regularization of fredholm integral-equations of the 1st kind Inverse Probl. 7 1991 793 808
16. J. Skilling, and R.K. Bryan Maximum-entropy image-reconstruction-general algorithm Monthly Notices R. Astron. Soc. 211 1984 111 124
17. A.K. Livesey, and J.C. Brochon Analyzing the distribution of decay constants in pulse-fluorometry using the maximum-entropy method Biophys. J. 52 1987 693 706
18. E.T. Jaynes Information theory and statistical mechanics Phys. Rev. 106 1957 620 630
19. E.T. Jaynes Information theory and statistical mechanics. 2 Phys. Rev. 108 1957 171 190
20. B.R. Frieden Restoring with maximum likelihood and maximum entropy J. Opt. Soc. Am. 62 1972 511 518
21. A.K. Livesey, and J. Skilling Maximum-entropy theory Acta Crystallogr. A 41 1985 113 122
22. S.F. Gull, and G.J. Daniell Image-reconstruction from incomplete and noisy data Nature 272 1978 686 690
23. E.D. Laue, J. Skilling, J. Staunton, S. Sibisi, and R.G. Brereton Maximum-entropy method in nuclear magnetic-resonance spectroscopy J. Mag. Reson. 62 1985 437 452
24. E.D. Laue, J. Skilling, and J. Staunton Maximum-entropy reconstruction of spectra containing antiphase peaks J. Mag. Reson. 63 1985 418 424
25. P.P.B. Eggermont Maximum-entropy regularization for fredholm integral-equations of the 1st kind SIAM J. Math. Anal. 24 1993 1557 1576
26. H.W. Engl, and G. Landl Convergence-rates for maximum-entropy regularization SIAM J. Numer. Anal. 30 1993 1509 1536
27. G. Jeschke, A. Koch, U. Jonas, and A. Godt Direct conversion of EPR dipolar time evolution data to distance distributions J. Magn. Reson. 155 2002 72 82
28. A.D. Milov, Y.D. Tsvetkov, F. Formaggio, S. Oancea, C. Toniolo, and J. Raap Solvent effect on the distance distribution between spin labels in aggregated spin labeled trichogin GA IV dimer peptides as studied by pulsed electron-electron double resonance Phys. Chem. Chem. Phys. 6 2004 3596 3603
29. A.D. Milov, A.G. Maryasov, and Y.D. Tsvetkov Pulsed electron double resonance (PELDOR) and its applications in free-radicals research Appl. Magn. Reson. 15 1998 107 143
30. M. Klaus, and R.T. Smith A hilbert-space approach to maximum-entropy reconstruction Math. Methods Appl. Sci. 10 1988 397 406
31. G. Landl, and R.S. Anderssen Non-negative differentially constrained entropy-like regularization Inverse Probl. 12 1996 35 53
32. T. Elfving An algorithm for maximum entropy image reconstruction from noisy data Math. Comput. Model. 12 1989 729 745
33. H.W. Engl, M. Hanke, and A. Neubauer Regularization of Inverse Problems 1996 Kluwer Academic Publishers Dordrecht; Boston
34. G. Landl, T. Langthaler, H.W. Englt, and H.F. Kauffmann Distribution of event times in time-resolved fluorescence: the exponential series approach-algorithm, regularization, analysis J. Computat. Phys. 95 1991 1 28
35. R. Fletcher Practical methods of optimization 1987 Wiley Chichester; New York
36. P.C. Hansen Regularization tools Version 3.0 for Matlab 5.2 Numer. Algorithms 20 1999 195 196
37. P.C. Hansen, and D.P. Oleary The use of the l-curve in the regularization of discrete Ill-posed problems SIAM J. Sci. Comput. 14 1993 1487 1503
38. P.C. Hansen P. Johnston Computational Inverse Problems in Electrocardiology 2000 WIT Press 119 142
39. A.A. Istratov, and O.F. Vyvenko Exponential analysis in physical phenomena Rev. Sci. Instrum. 70 1999 1233 1257
40. T. Reginska A regularization parameter in discrete ill-posed problems SIAM J. Sci. Comput. 17 1996 740 749
41. G. Wahba Practical approximate solutions to linear operator equations when data are noisy SIAM J. Numer. Anal. 14 1977 651 667
42. A. Isayama, N. Iwama, T. Showa, Y. Hosoda, N. Isei, S. Ishida, and M. Sato Maximum entropy estimation of electron cyclotron emission spectra from incomplete interferograms in ELMy H-mode tokamak experiment Jpn. J. Appl. Phys. Part 1 42 2003 5787 5796
43. J.G. Lyubovitsky, H.B. Gray, and J.R. Winkler Mapping the cytochrome c folding landscape J. Am. Chem. Soc. 124 2002 5481 5485
44. E.V. Pletneva, H.B. Gray, and J.R. Winkler Many faces of the unfolded state: conformational heterogeneity in denatured yeast cytochrome c J. Mol. Biol. 345 2005 855 867