Prediction of protein 13Cα NMR chemical shifts using a combination scheme of statistical modeling and quantum-mechanical analysis

Journal of Molecular Structure

Volumn 995, Issue 1-3, 2011, Pages 163-172

  Liu, Xiuhong ^a   Ren, Yanrong ^b   Zhou, Peng ^a   Shang, Zhicai ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b CHONGQING UNIVERSITY OF EDUCATION   (China)

Author keywords

NMR chemical shift; Protein; Quantum mechanical calculation; Secondary structure

Indexed keywords

DESCRIPTORS; ELECTROSTATIC DESCRIPTORS; ENVIRONMENTAL INFLUENCES; HEURISTIC APPROACH; HIGH QUALITY; MACHINE LEARNING METHODS; MONOMERIC PROTEINS; NMR CHEMICAL SHIFTS; QUANTITATIVE STRUCTURE-PROPERTY RELATIONSHIP; QUANTUM MECHANICAL; QUANTUM-MECHANICAL CALCULATION; SECONDARY STRUCTURE; SIDE-CHAINS; STATISTICAL MODELING; STATISTICAL MODELS; STRUCTURAL EFFECT; STRUCTURAL FEATURE; STRUCTURAL SURVEYS;

BERYLLIUM MINERALS; C (PROGRAMMING LANGUAGE); CHEMICAL SHIFT; HEURISTIC METHODS; LEARNING SYSTEMS; PROTEINS;

CHEMICAL ANALYSIS;

EID: 79957875622     PISSN: 00222860     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molstruc.2011.04.012     Document Type: Article

References (106)

1. K. Wüthrich NMR of Proteins and Nucleic Acids 1986 Wiley New York
2. K. Lindorff-Larsen, R.B. Best, M.A. DePristo, C.M. Dobson, and M. Vendruscolo Nature 433 2005 123 128
3. P. Robustelli, A. Cavalli, and M. Vendruscolo Structure 16 2008 1764 1769
4. P. Luginbühl, T. Szyperski, and K. Wüthrich J. Magn. Reson. Ser. B 109 1995 229 233
5. S. Spera, and A. Bax J. Am. Chem. Soc. 113 1991 5490 5492
6. B. Seavey, E.A. Farr, W.M. Westler, and J.A. Markley J. Biomol. NMR 1 1991 217 236
7. L. Szilágyi Prog. NMR Spectrosc. 27 1995 325 443
8. M. Iwadate, T. Asakura, and M.P. Williamson J. Biomol. NMR 13 1999 199 211
9. K. Ösapay, and D.A. Case J. Am. Chem. Soc. 113 1991 9436 9444
10. D.E. Williams, M.B. Peters, B. Wang, A.E. Roitberg, and K.M. Merz Jr. J. Phys. Chem. A 113 2009 11550 11559
11. E. Oldfield J. Biomol. NMR 5 1995 217 225
12. A.C. de Dios, and E. Oldfield Solid State NMR 6 1996 101 125
13. J.G. Pearson, J.F. Wang, J.L. Markley, H. Le, and E. Oldfield J. Am. Chem. Soc. 117 1995 8823 8829
14. H.B. Le, J.G. Pearson, A.C. de Dios, and E. Oldfield J. Am. Chem. Soc. 117 1995 3800 3807
15. J.A. Vila, M.E. Villegas, H.A. Baldoni, and H.A. Scheraga J. Biomol. NMR 38 2007 221 235
16. J.A. Vila, D.R. Ripoll, and H.A. Scheraga J. Phys. Chem. B 111 2007 6577 6585
17. J.A. Vila, J.M. Aramini, P. Rossi, A. Kuzin, M. Su, J. Seetharaman, R. Xiao, L. Tong, G.T. Montelione, and H.A. Scheraga PNAS 105 2008 14389 14394
18. J.A. Vila, and H.A. Scheraga Proteins 2007 640 654
19. X.P. Xu, and D.A. Case Biopolymers 65 2002 408 423
20. X.P. Xu, and D.A. Case J. Biomol. NMR 21 2001 321 333
21. R.H. Havlin, H. Le, D.D. Laws, A.C. de Dios, and E. Oldfield J. Am. Chem. Soc. 119 1997 11951 11958
22. H. Sun, L.K. Sanders, and E. Oldfield J. Am. Chem. Soc. 124 2002 5486 5495
23. J.G. Pearson, H. Le, L.K. Sanders, N. Godbout, R.H. Havlin, and E. Oldfield J. Am. Chem. Soc. 119 1997 11941 11950
24. M.E. Villegas, J.A. Vila, and H.A. Scheraga J. Biomol. NMR 37 2007 137 146
25. S. Schefzick, C. Kibbey, and M.P. Bradley J. Comb. Chem. 6 2004 916 927
26. R. Bosque, J. Sales, E. Bosch, M. Rosés, M.C. Garcá- Alvarez-Coque, and J.R. Torres-Lapasió J. Chem. Inf. Comput. Sci. 43 2003 1240 1247
27. A.R. Katritzky, U. Maran, V.S. Lobanov, and M. Karelson J. Chem. Inf. Comput. Sci. 40 2000 1 18
28. A.E. Counterman, and D.E. Clemmer J. Am. Chem. Soc. 121 1999 4031 4039
29. X.H. Liu, J. Liang, J.C. Fan, and Z.C. Shang QSAR Comb. Sci. 28 2009 1386 1393
30. D.A. Carlson, U.R. Bernier, and B.D. Sutton J. Chem. Ecol. 24 1998 1845 1865
31. Y.V. Kissin, and G.P. Feulmer J. Chromatogr. Sci. 24 1986 53 59
32. A.R. Katritzky, and K. Chen Anal. Chem. 72 2000 101 109
33. L.S. Anker, and P.C. Jurs Anal. Chem. 64 1992 1157 1164
34. J.W. Ball, and P.C. Jurs Anal. Chem. 65 1993 3615 3621
35. D.L. Clouser, and P.C. Jurs Anal. Chim. Acta 295 1994 221 231
36. D.L. Clouser, and P.C. Jurs Anal. Chim. Acta 321 1996 127 135
37. R. Bosque, and J. Sales J. Chem. Inf. Comput. Sci. 41 2001 225 232
38. C.M. Marian, and M. Gastreich Solid State Nucl. Magn. Reson. 19 2001 29 44
39. P. Zhou, Y. Zhou, H. Mei, F.F. Tian, and Z.L. Li Chin. J. Anal. Chem. 34 2006 200 204
40. A.C. deDios, J.G. Pearson, and E. Oldfield Science 260 1993 1491 1496
41. J. Kuszewski, J.A. Qin, A.M. Gronenborn, and G.M. Clore J. Magn. Reson. Ser. B 106 1995 92 96
42. M. Andrec, D.A. Snyder, Z. Zhou, J. Young, G.T. Montelione, and R.M. Levy Proteins Struct. Funct. Bioinformat. 69 2007 449 465
43. W. Kabsch, and C. Sander Biopolymers 22 1983 2577 2637
44. M. Fujinaga, A.R. Sielecki, R.J. Read, W. Ardelt, M. Laskowski Jr., and M.N. James J. Mol. Biol. 195 1987 397 418
45. E.R. Goedken, J.L. Keck, J.M. Berger, and S. Marqusee Protein Sci. 9 2000 1914 1921
46. S. Napper, L.T. Delbaere, and E.B. Waygood J. Biol. Chem. 274 1999 21776 21782
47. J.M. Guss, H.D. Bartunik, and H.C. Freeman Acta Crystallogr. Sect. B 48 1992 790 811
48. H.J. Park, C. Yang, N. Treff, J.D. Satterlee, and C. Kang Proteins 49 2002 49 60
49. M.J. Maher, Z. Xiao, M.C. Wilce, J.M. Guss, and A.G. Wedd Acta Crystallogr. Sect. D 55 1999 962 968
50. N.M. Glykos, G. Cesareni, and M. Kokkinidis Structure Fold. Des. 7 1999 597 603
51. S. Longhi, M. Czjzek, V. Lamzin, A. Nicolas, and C. Cambillau J. Mol. Biol. 268 1997 779 799
52. R.M. Xu, C. Koch, Y. Liu, J.R. Horton, D. Knapp, K. Nasmyth, and X. Cheng Structure 5 1997 349 358
53. J. Sevcik, L. Urbanikova, Z. Dauter, and K.S. Wilson Acta Crystallogr. Sect. D 54 1998 954 963
54. Y. Takeuchi, Y. Satow, K.T. Nakamura, and Y. Mitsui J. Mol. Biol. 221 1991 309 325
55. M.C. Vaney, S. Maignan, M. Ries-Kautt, and A. Ducriux Acta Crystallogr. Sect. D 52 1996 505 517
56. M. Hennig, A. D'Arcy, I.C. Hampele, M.G. Page, C. Oefner, and G.E. Dale Nat. Struct. Biol. 5 1998 357 362
57. M. Nakasako, H. Takahashi, N. Shimba, I. Shimada, and Y. Arata J. Mol. Biol. 291 1999 117 134
58. M. Konno, M. Ito, T. Hayano, and N. Takahashi J. Mol. Biol. 256 1996 897 908
59. R.C. Durley, and F.S. Mathews Acta Crystallogr. Sect. D 52 1996 65 76
60. I. Zegers, J.C. Martins, R. Willem, and L. Wyns J. Messens. Nat. Struct. Biol. 8 2001 843 847
61. D. Knight, R. Harris, M. Mcalister, J. Phelan, S. Geddes, S. Moss, and P.C. Driscoll J. Biol. Chem. 277 2002 5556 5561
62. K. Harata, M. Muraki, and Y. Jigami J. Mol. Biol. 233 1993 524 535
63. R.D. Smith, J.S. Olson, G.N. Phillips Jr., Correlations between Bound N-alkyl isocyanide Orientations and Pathways for Ligand Binding in Recombinant Myoglobins. Thesis, Rice, 1999.
64. N. Narayana, D.A. Matthews, E.E. Howell, and X. Nguyen-huu Nat. Struct. Biol. 2 1995 1018 1025
65. A.R. Katritzky, V.S. Lobanov, M. Karelson, CODESSA Vers. 2.7, Reference Manual, University of Florida, Gainesville, FL 1995-1997.
66. A.R. Katritzky, V.S. Lobanov, and M. Karelson Chem. Soc. Rev. 24 1995 279 287
67. A.R. Katritzky, V. S. Lobanov, M. Karelson, Comprehensive Descriptors for Structural and Statistical Analysis, Reference Manual, Version 2.0, 1994.
68. J.M. Luco, A.P. Salinas, A.A.J. Torriero, R.N. Vazquez, J. Raba, and E.J. Marchevsky J. Chem. Inf. Comput. Sci. 43 2003 2129 2136
69. J.M. Luco, and E. Marchevsky Curr. Comput. - Aided Drug Des. 2 2006 31 55
70. P. Zhou, Y. Zhou, S. Wu, B. Li, F. Tian, and Z. Li Chin. Sci. Bull. 51 2006 524 529
71. J.A.K. Suykens, and J. Vandewalle Neural Process. Lett. 9 1999 293 300
72. L. Breiman Mach. Learn. 45 2001 5 32
73. V. Svetnik, A. Liaw, C. Tong, J.C. Culberson, R.P. Sheridan, and B.P. Feuston J. Chem. Inf. Comput. Sci. 43 2003 1947 1958
74. V. Svetnik, A. Liaw, and C. Tong T. Lecture Notes Comput. Sci. 3077 2004 334
75. H.A. Chipman, E.I. George, and R.E. McCulloch J. Am. Stat. Assoc. 93 1998 957
76. P. Zhou, F.F. Tian, X. Chen, and Z.C. Shang Biopolymers (Pept. Sci.) 90 2008 772 802
77. P. Zhou, X. Chen, Y. Wu, and Z. Shang Amino Acids 38 2010 199 212
78. O. Obrezanova, G. Csányi, J.M.R. Gola, and M.D. Segall J. Chem. Inf. Model 47 2007 1847 1857
79. C.E. Rasmussen, Evaluation of Gaussian processes and other methods for non-linear regression. PhD thesis, University of Toronto, Canada 1996.
80. P. Wolfe SIAM Rev. 11 1969 226 235
81. M. Baroni, S. Clement, G. Cruciani, N. Kettaneh-Wold, and S. Wold Quant. Struct. Act. Relat. 12 1993 225 231
82. A. Golbraikh, and A. Tropsha J. Mol. Graphics Model. 20 2002 269 276
83. A. Tropsha, P. Gramatica, and V.K. Gombar QSAR Comb. Sci. 22 2003 69 77
84. L. Lorenzo, M.J. González Moa, M. Mandado, and R.A. Mosquera J. Chem. Inf. Model 46 2006 2056 2065
85. A.D. Becke J. Chem. Phys. 98 1993 1372 1377
86. C. Lee, W. Yang, and R.G. Parr Phys. Rev. B 37 1988 785 787
87. R. Ditchfield, W.J. Hehre, and J.A. Pople J. Chem. Phys. 54 1971 724 728
88. W.J. Hehre, R. Ditchfield, and J.A. Pople J. Chem. Phys. 56 1972 2257 2261
89. P.C. Hariharan, and J.A. Pople Theor. Chim. Acta 28 1973 213 222
90. J.A. Vila, H.A. Baldoni, and H.A. Scheraga J. Comput. Chem. 30 2009 884 892
91. P. Zhou, F. Tian, F. Lv, and Z. Shang J. Chromatogr. A 1216 2009 3107 3116
92. ChemoAC Calibration Toolbox, Virtual Institute of Chemometrics and Industrial Metrology, Brussels, Belgium, Matlab code available: < http://www.vicim.com/My%20VICIM%20private%20webbestanden/chemoactbx.zip >.
93. J.A.K. Suykens, T. van Gestel, J. de Brabanter, B. de Moor, J. Vandewalle, Least Squares Support Vector Machines, World Scientific, Singapore, 2002, Matlab code available: < http://www.esat.kuleuven.ac.be/sista/lssvmlab/ downloads/LS-SVMlab1.5aw.tar.gz >.
94. T. Wang, A Matlab Interface of Random Forests, 2003, Matlab code available: < http://lib.stat.cmu.edu/matlab/RandomForest.zip >.
95. C.E. Rasmussen, C.K.I. Williams, Gaussian Processes for Machine Learning, The MIT Press, Massachusetts, 2006, Matlab code available: < http://www.gaussianprocess.org/gpml/code/gpml-matlab.zip >.
96. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, V.G. Zakrzewski, J.A. Jr. Montgomery, R.E. Stratmann, J.C. Burant, S. Dapprich, J.M. Millam, A.D. Daniels, K.N. Kudin, M.C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G.A. Petersson, P.Y. Ayala, Q. Cui, K. Morokuma, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J. Cioslowski, J.V. Ortiz, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R.L. Martin, J. Fox, D. T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P.M. W. Gill, B.G. Johnson, W. Chen, M.W. Wong, J. L. Andres, M. Head-Gordon, E.S. Replogle, J.A. Pople, Gaussian 03, Gaussian, Inc.: Pittsburgh, PA, 2003.
97. R. Aurora, and G.D. Rose Protein Sci. 7 1998 21 38
98. D.T. Stanton, and P.C. Jurs Anal. Chem. 62 1990 2323
99. D.T. Stanton, L.M. Egolf, P.C. Jurs, and M.G. Hicks J. Chem. Inf. Comput. Sci. 32 1992 306 316
100. Handbook of Chemistry and Physics, CRC Press, Cleveland OH, 1974, p. F-112.
101. R.H. Rohrbaugh, and P.C. Jurs Anal. Chim. Acta 199 1987 99 109
102. L.B. Kier Quant. Struct. - Act. Relat. 4 1985 109 116
103. L.B. Kier Computational Chemical Graph Theory D.H. Rouvray, 1990 Nova Science Publishers. New York
104. G. Csizmadia Theory and Practice of MO Calculations on Organic Molecules 1976 Elsevier Amsterdam
105. K. Hébergera, K. Kollár-Hunek. J. Chemometrics, 2010, doi: 10.1002/cem.1320.
106. K. Hébergera Trends Anal. Chem. 29 2010 101 109