Comparison of mode analyses at different resolutions applied to nucleic acid systems

Biophysical Journal

Volumn 89, Issue 5, 2005, Pages 2939-2949

  Van Wynsberghe, Adam W ^a   Cui, Qiang ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEIC ACID; RIBOZYME; RNA;

ANALYTIC METHOD; ARTICLE; CALCULATION; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; NUCLEIC ACID STRUCTURE; PARAMETER; PROTEIN CONFORMATION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; TECHNIQUE; VALIDATION PROCESS;

EID: 25844441847     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.065664     Document Type: Article

References (89)

1. Feig, M., and C. L. Brooks. 2004. Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr. Opin. Struct. Biol. 14:217-224.
2. Schlitter, J., M. Engels, and P. Kruger. 1994. Targeted molecular-dynamics-a new approach for searching pathways of conformational transitions. J. Mol. Graph. 12:84-89.
3. Im, W., S. Bemeche, and B. Roux. 2001. Generalized solvent boundary potential for computer simulations. J. Chem. Phys. 114:2924-2937.
4. Shurki, A., and A. Warshel. 2003. Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress. Adv. Protein Chem. 66:249-313.
5. Gao, J. L. 1996. Hybrid quantum and molecular mechanical simulations: an alternative avenue to solvent effects in organic chemistry. Acct. Chem. Res. 29:298-305.
6. Field, M. J., P. A. Bash, and M. Karplus. 1990. A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations. J. Comput. Chem. 11:700-733.
7. Rodriguez-Gomez, D., E. Darve, and A. Pohorille. 2004. Assessing the efficiency of free energy calculation methods. J. Chem. Phys. 120: 3563-3578.
8. Park, S., and K. Schulten. 2004. Calculating potentials of mean force from steered molecular dynamics simulations. J. Chem. Phys. 120: 5946-5961.
9. Jensen, M. O., S. Park, E. Tajkhorshid, and K. Schulten. 2002. Energetics of glycerol conduction through aquaglyceroporin GlpF. Proc. Natl. Acad. Sci. USA. 99:6731-6736.
10. Jarzynski, C. 1997. Nonequilibrium equality for free energy differences. Phys. Rev. Lett. 78:2690-2693.
11. Brooks, B., and M. Karplus. 1983. Harmonic dynamics of proteins-normal modes and fluctuations in bovine pancreatic trypsin-inhibitor. Proc. Natl. Acad. Sci. USA. 80:6571-6575.
12. Go, N., T. Noguti, and T. Nishikawa. 1983. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. USA. 80:3696-3700.
13. Hayward, S. 2001. Normal mode analysis of biological molecules. In Computational Biochemistry and Biophysics. O.M. Becker, A.D. MacKerell Jr., B. Roux, and M. Watanabe, editors. Marcel Dekker, New York.
14. Levitt, M., C. Sander, and P. S. Stem. 1983. The normal modes of a protein-native bovine pancreatic trypsin inhibitor. Int. J. Quantum Chem. 10:181-199.
15. Ma, J. P. 2005. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure. 13:373-380.
16. Cui, Q., G. H. Li, J. P. Ma, and M. Karplus. 2004. A normal mode analysis of structural plasticity in the biomolecular motor F-1-ATPase. J. Mol. Biol. 340:345-372.
17. 2+-ATPase. Biophys. J. 83:2457-2474.
18. Krebs, W. G., V. Alexandrov, C. A. Wilson, N. Echols, H. Y. Yu, and M. Gerstein. 2002. Normal-mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins. 48:682-695.
19. Thomas, A., K. Hinsen, M. J. Field, and D. Perahia. 1999. Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study. Proteins. 34:96-112.
20. Seno, Y., and N. Go. 1990. Deoxymyoglobin studied by the conformational normal mode analysis. I. Dynamics of globin and the hemoglobin interaction. J. Mol. Biol. 216:95-109.
21. Tama, F., F. X. Gadea, O. Marques, and Y. H. Sanejouand. 2000. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins. 41:1-7.
22. Mouawad, L., and D. Perahia. 1993. Diagonalization in a mixed basis-a method to compute low-frequency normal modes for large macromolecules. Biopolymers. 33:599-611.
23. Tirion, M. M. 1996. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1905-1908.
24. Doruker, P., R. L. Jemigan, and I. Bahar. 2002. Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 23:119-127.
25. Haliloglu, T., I. Bahar, and B. Erman. 1997. Gaussian dynamics of folded proteins. Phys. Rev. Lett. 79:3090-3093.
26. Bahar, I., A. R. Atilgan, and B. Erman. 1997. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2:173-181.
27. Tama, F., and Y. H. Sanejouand. 2001. Conformational change of proteins arising from normal mode calculations. Protein Eng. 14:1-6.
28. Atilgan, A. R., S. R. Durell, R. L. Jemigan, M. C. Demirel, O. Keskin, and I. Bahar. 2001. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80:505-515.
29. Doruker, P., A. R. Atilgan, and I. Bahar. 2000. Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to α-amylase inhibitor. Proteins. 40:512-524.
30. Delarue, M., and Y. H. Sanejouand. 2002. Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. J. Mol. Biol. 320:1011-1024.
31. Tama, F., M. Valle, J. Frank, and C. L. Brooks. 2003. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl. Acad. Sci. USA. 100:9319-9323.
32. Wang, Y. M., A. J. Rader, I. Bahar, and R. L. Jemigan. 2004. Global ribosome motions revealed with elastic network model. J. Struct. Biol. 147:302-314.
33. Cech, T. R. 2002. Ribozymes, the first 20 years. Biochem. Soc. Trans. 30:1162-1166.
34. Guerriertakada, C., K. Gardiner, T. Marsh, N. Pace, and S. Altman. 1983. The RNA moiety of ribonuclease-P is the catalytic subunit of the enzyme. Cell. 35:849-857.
35. Cech, T. R., A. J. Zaug, and P. J. Grabowski. 1981. In vitro splicing of the ribosomal-RNA precursor of Tetrahymena-involvement of a guanosine nucleotide in the excision of the intervening sequence. Cell. 27:487-496.
36. Winkler, W., A. Nahvi, and R. R. Breaker. 2002. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature. 419:952-956.
37. Scott, W. G., J. B. Murray, J. R. P. Arnold, B. L. Stoddard, and A. Klug. 1996. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science. 274:2065-2069.
38. Serganov, A., Y. R. Yuan, O. Pikovskaya, A. Polonskaia, L. Malinina, A. T. Phan, C. Hobartner, R. Micura, R. R. Breaker, and D. J. Patel. 2004. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem. Biol. 11:1729-1741.
39. Egli, M. 2004. Nucleic acid crystallography: current progress. Curr. Opin. Chem. Biol. 8:580-591.
40. Batey, R. T., S. D. Gilbert, and R. K. Montange. 2004. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature. 432:411-415.
41. Adams, P. L., M. R. Stahley, A. B. Kosek, J. M. Wang, and S. A. Strobel. 2004. Crystal structure of a self-splicing group I intron with both exons. Nature. 430:45-50.
42. Ke, A. L., K. H. Zhou, F. Ding, J. H. D. Gate, and J. A. Doudna. 2004. A conformational switch controls hepatitis δ-virus ribozyme catalysis. Nature. 429:201-205.
43. Krasilnikov, A. S., X. J. Yang, T. Pan, and A. Mondragon. 2003. Crystal structure of the specificity domain of ribonuclease P. Nature. 421:760-764.
44. Rupert, P. B., A. P. Massey, S. T. Sigurdsson, and A. R. Ferre-D'Amare. 2002. Transition state stabilization by a catalytic RNA. Science. 298:1421-1424.
45. Zhang, L., and J. A. Doudna. 2002. Structural insights into group II intron catalysis and branch-site selection. Science. 295:2084-2088.
46. Ando, T., T. Tanaka, and Y. Kikuchi. 2003. Substrate shape specificity of E. coli RNase P ribozyme is dependent on the concentration of magnesium ion. J. Biochem. (Tokyo). 133:445-451.
47. Reiter, N. J., H. Blad, F. Abildgaard, and S. E. Butcher. 2004, Dynamics in the U6 RNA intramolecular stem-loop: a base-flipping conformational change. Biochemistry. 43:13739-13747.
48. Hampel, K. J., and J. M. Burke. 2003. Solvent protection of the hammerhead ribozyme in the ground state: evidence for a cation-assisted conformational change leading to catalysis. Biochemistry. 42: 4421-4429.
49. Shan, S. O., and D. Herschlag. 2002. Dissection of a metal-ion-mediated conformational change in Tetrahymena ribozyme catalysis. RNA. 8:861-872.
50. Pereira, M. J. B., D. A. Harris, D. Rueda, and N. G. Walter. 2002. Reaction pathway of the irans-acting hepatitis δ-virus ribozyme: a conformational change accompanies catalysis. Biochemistry. 41:730-740.
51. Peracchi, A., L. Beigelman, E. C. Scott, O. C. Uhlenbeck, and D. Herschlag. 1997. Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation. J. Biol. Chem. 272:26822-26826.
52. 2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules. Proc. Natl. Acad. Sci. USA. 99:4284-4289.
53. Pinard, R., K. J. Hampel, J. E. Heckman, D. Lambert, P. A. Chan, F. Major, and J. M. Burke. 2001. Functional involvement of G8 in the hairpin ribozyme cleavage mechanism. EMBO J. 20:6434-6442.
54. Peracchi, A., A. Karpeisky, L. Maloney, L. Beigelman, and D. Herschlag. 1998. A core-folding model for catalysis by the hammer-head ribozyme accounts for its extraordinary sensitivity to basic mutations. Biochemistry. 37:14765-14775.
55. Zhuang, X. W., H. Kim, M. J. B. Pereira, H. P. Babcock, N. G. Walter, and S. Chu. 2002. Correlating structural dynamics and function in single ribozyme molecules. Science. 296:1473-1476.
56. Viduna, D., K. Hinsen, and G. Kneller. 2000. Influence of molecular flexibility on DNA radiosensitivity: a simulation study. Phys. Rev. E. 62:3986-3990.
57. Zacharias, M. 2000. Comparison of molecular dynamics and harmonic mode calculations on RNA. Biopolymers. 54:547-560.
58. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM-a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
59. Cornell, W. D., P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman. 1996. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197.
60. Pearlman, D. A., D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham, S. Debolt, D. Ferguson, G. Seibel, and P. Kollman. 1995. AMBER, a package of computer programs for applying molecular mechanics, normal-mode analysis, molecular dynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun. 91:1-41.
61. Foloppe, N., and A. D. MacKerell. 2000. All-atom empirical force field for nucleic acids. I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem. 21:86-104.
62. Aqvist, J. 1990. Ion-water interaction potentials derived from free-energy perturbation simulations. J. Phys. Chem. 94:8021-8024.
63. Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald-an N-Log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
64. Steinbach, P. J., and B. R. Brooks. 1994. New spherical cutoff methods for long-range forces in macromolecular simulation. J. Comput. Chem. 15:667-683.
65. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
66. Grabmüller, H. 1996, SOLVATE 1.0: a program to create atomic solvent models, http://www.mpibpc.mpg.de/groups/grubmueller/solvate. html.
67. Hermann, T., P. Auffinger, and E. Westhof. 1998. Molecular dynamics investigations of hammerhead ribozyme RNA. Eur. Biophys. J. Biophys. Lett. 27:153-165.
68. Pley, H. W., K. M. Flaherty, and D. B. McKay. 1994. Three-dimensional structure of a hammerhead ribozyme. Nature. 372:68-74.
69. Jolliffe, I. T. 2002. Principal Component Analysis. Springer-Verlag, New York.
70. Hayward, S., A. Kitao, and N, Go. 1994. Harmonic and anharmonic aspects in the dynamics of BPTI-a normal-mode analysis and principal component analysis. Protein Sci. 3:936-943.
71. Baisera, M. A., W. Wriggers, Y. Oono, and K. Schulten. 1996. Principal component analysis and long-time protein dynamics. J. Phys. Chem. 100:2567-2572.
72. Becker, O. 2001. Conformational analysis. In Computational Biochemistry and Biophysics. O.M. Becker, A.D. MacKerell Jr., B. Roux, and M. Watanabe, editors. Marcel Dekker, New York.
73. Li, G. H., A. Van Wynsberghe, O. N. A. Demerdash, and Q. Cui. 2005. Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems. Q. Cui and I. Bahar, editors. CRC Press, Boca Raton, FL.
74. Hinsen, K. 1998. Analysis of domain motions by approximate normal mode calculations. Proteins. 33:417-429.
75. Blount, K. F., and O. C. Uhlenbeck. 2005. The structure-function dilemma of the hammerhead ribozyme. Annu. Rev. Biophys. Biomol. Struct. 34:415-440.
76. Scott, W. G., J. T. Finch, and A. Klug. 1995. The crystal-structure of an all-RNA hammerhead ribozyme-a proposed mechanism for RNA catalytic cleavage. Cell. 81:991-1002.
77. 2+ ions slightly reorient stems I and II of the hammerhead ribozyme to increase the probability of formation of the catalytic core. Biochemistry. 42:9924-9936.
78. Suzumura, K., Y. Takagi, M. Orita, and K. Taira. 2004. NMR-based reappraisal of the coordination of a metal ion at the pro-Rp oxygen of the A9/G10.1 site in a hammerhead ribozyme. J. Am. Chem. Soc. 126:15504-15511.
79. Heckman, J. E., D. Lambert, and J. M. Burke. 2005. Photocrosslinking detects a compact, active structure of the hammerhead ribozyme. Biochemistry. 44:4148-4156.
80. Van Wynsberghe, A., G. H. Li, and Q. Cui. 2004. Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle. Biochemistry. 43:13083-13096.
81. Tozzini, V. 2005. Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 15:144-150.
82. Tama, F., W. Wriggers, and C. L. Brooks. 2002. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J. Mol. Biol. 321:297-305.
83. Ming, D., Y. F. Kong, M. A. Lambert, Z. Huang, and J. P. Ma. 2002. How to describe protein motion without amino acid sequence and atomic coordinates. Proc. Natl. Acad. Sci. USA. 99:8620-8625.
84. Liang, J., and K. A. Dill. 2001. Are proteins well-packed? Biophys. J. 81:751-766.
85. Sasaki, N., R. Ohkura, and K. Sutoh. 2003. Dictyostelium myosin II mutations that uncouple the converter swing and ATP hydrolysis cycle. Biochemistry. 42:90-95.
86. Ito, K., T. Q. P. Uyeda, Y. Suzuki, K. Sutoh, and K. Yamamoto. 2003. Requirement of domain-domain interaction for conformational change and functional ATP hydrolysis in myosin. J. Biol. Chem. 278:31049-31057.
87. Zheng, W. J., B. R. Brooks, S. Doniach, and D. Thirumalai. 2005. Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. Structure. 13:565-577.
88. Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD: visual molecular dynamics. J. Mol. Graph. 14:33-38.
89. Kraulis, P. J. 1991. MOLSCRIPT-a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950.