Topology representing neural networks reconcile biomolecular shape, structure, and dynamics

Neurocomputing

Volumn 56, Issue 1-4, 2004, Pages 365-379

  Wriggers, Willy ^a,c   Chacón, Pablo ^a   Kovacs, Julio A ^a   Tama, Florence ^a   Birmanns, Stefan ^b  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b FORSCHUNGSZENTRUM JÜLICH   (Germany)

^c University of Texas School of Health Information Sciences at Houston   (United States)

Author keywords

Haptic rendering; Macromolecular assemblies; Multi resolution docking; Normal mode analysis; Volumetric registration

Indexed keywords

DEGREES OF FREEDOM (MECHANICS); MATHEMATICAL MODELS; MOLECULAR DYNAMICS; STEREOCHEMISTRY; TOPOLOGY;

TOPOLOGY-REPRESENTING NETWORKS (TRN);

NEURAL NETWORKS;

ARTICLE; ARTIFICIAL NEURAL NETWORK; CHEMICAL STRUCTURE; COMPLEX FORMATION; COMPUTER MODEL; COMPUTER PROGRAM; DECOMPOSITION; MACROMOLECULE; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR SIZE; MOTION; PREDICTION; PRIORITY JOURNAL; STEREOCHEMISTRY;

EID: 0742306445     PISSN: 09252312     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.neucom.2003.09.007     Document Type: Article

References (47)

1. E.E. Abola, J.L. Sussman, J. Prilusky, N.O. Manning, Protein data bank archives of three-dimensional macromolecular structures, in: C.W. Carter Jr., R.M. Sweet (Eds.), Methods in Enzymology, Vol. 277, Academic Press, San Diego, 1997, pp. 556-571.
2. Alberts B. The cell as a collection of protein machines: preparing the next generation of molecular biologists Cell 92 1998 291-294
3. Bahar I. Atilgan A.R. Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential Fold. Des. 2 1997 173-181
4. Balsera M.A. Wriggers W. Oono Y. Schulten K. Principal component analysis and long time protein dynamics J. Phys. Chem. 100 7 1996 2567-2572
5. ben Avraham D. Tirion M.M. Dynamic and elastic properties of F-actin: a normal-modes analysis Biophys. J. 68 1995 1231-1245
6. Brooks B. Karplus B. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor Biophysics 80 1983 6571-6575
7. Bruant N. Flatters D. Lavery R. Genest D. From atomic to mesoscopic description of the internal dynamics of DNA Biophys. J. 77 1999 2366-2376
8. A.T. Brünger, X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR, The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, 1992.
9. Case D.A. Normal mode analysis of protein dynamics Curr. Opin. Struct. Biol. 4 1994 285-290
10. D.A. Case, Normal mode analysis of biomolecular dynamics, in: W.F. van Gunsteren, P.K.Weiner, A.J. Wilkinson (Eds.), Computer Simulation of Biomolecular Systems, Vol. 3, Kluwer Academic Publishers, Dordrecht, Netherlands, 1997, pp. 284-301.
11. Chacón P. Tama F. Wriggers W. Mega-dalton biomolecular motion captured from electron microscopy reconstructions J. Mol. Biol. 326 2003 485-492
12. Darst S.A. Opalka N. Chacón P. Polyakov A. Richter C. Zhang G. Wriggers W. Conformational flexibility of bacterial RNA polymerase Proc. Natl. Acad. Sci. USA 99 2002 4296-4301
13. Delaunay B. Sur la spère vide Bull. Acad. Sci. USSR VII 1934 793-800
14. DeRosier D.J. Harrison S.C. Macromolecular assemblages: sizing things up Curr. Opin. Struct. Biol. 7 1997 237-238
15. Galkin V.E. Orlova A. Lukoyanova N. Wriggers W. Egelman E.H. ADF stabilizes an existing state of F-actin and can change the tilt of F-actin subunits J. Cell Biol. 153 2001 75-86
16. Gersho A. Gray R.M. Vector quantization and signal compression 1992 Kluwer Academic Publishers Norwell, MA
17. Gerstein M. Krebs W. A database of macromolecular motions Nucl. Acids Res. 26 1998 4280-4290
18. Gerstein M. Lesk A.M. Chothia C. Structural mechanisms for domain movements in proteins Biochemistry 33 1994 6739-6749
19. Gittes F. Mickey B. Nettleton J. Howard J. Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape J. Cell Biol. 120 1993 923-934
20. Goldstein H. Classical Mechanics 1980 Addison-Wesley Reading, MA
21. Hinsen K. Analysis of domain motions by approximate normal mode calculations Proteins: Struct. Funct. Genet. 33 1998 417-429
22. Horiuchi T. Go N. Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme Proteins: Struct. Funct. Genet. 10 1991 106-116
23. Humphrey W.F. Dalke A. Schulten K. VMD-visual molecular dynamics J. Mol. Graphics 14 1996 33-38
24. Kohonen T. Self-Organizing Maps 2nd Edition 1995 Springer Berlin
25. Levitt M. Sander C. Stern P.S. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme J. Mol. Biol. 181 1985 423-447
26. Lin D. Matsumoto A. Go N. Normal mode analysis of a double-stranded DNA dodecamer d(CGCGAATTCGCG) J. Chem. Phys. 107 1997 3684-3690
27. Llorca O. Martin-Benito J. Ritco-Vosonvici M. Grantham J. Hynes G.M. Willison K.R. Carrascosa J.L. Valpuesta J.M. Eukaryotic chaperonin CCT stabilizes actin and tubulin folding intermediates in open quasi-native conformations EMBO J. 19 2000 5971-5979
28. Martinetz T.M. Berkovich S.G. Schulten K. "Neural gas" for vector quantization and its application to time-series prediction IEEE Trans. Neural Networks 4 4 1993 558-569
29. Martinetz T. Schulten K. Topology representing networks Neural Networks 7 1994 507-522
30. Matsumoto A. Go N. Dynamic properties of double-stranded DNA by normal mode analysis J. Chem. Phys. 110 1999 11070-11075
31. McCammon J.A. Harvey S.C. Dynamics of Proteins and Nucleic Acids 1987 Cambridge University Press Cambridge
32. McQuarrie D.A. Statistical Mechanics 1976 Harper and Row New York
33. Nakata K. Prediction of zinc finger DNA binding protein Comput. Appl. Biosci. 11 1995 125-131
34. Ryckaert J.-P. Ciccotti G. Berendsen H.J.C. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 23 1977 327-341
35. Speir J.A. Munshi S. Wang G. Baker T.S. Johnson J.E. Structures of the native and the swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy Structure 3 1995 63-78
36. Stowell M.H.B. Miyazawa A. Unwin N. Macromolecular structure determination by electron microscopy: new advances and recent results Curr. Opin. Struct. Biol. 8 1998 595-600
37. Tama F. Wriggers W. Brooks C.L. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory J. Mol. Biol. 321 2002 297-305
38. Tirion M.M. Large amplitude elastic motions in proteins from a single-parameter atomic analysis Phys. Rev. Lett. 77 1996 1905-1908
39. Wade R.C. Bohr H. Wolynes P.G. Prediction of water binding sites on proteins by neural networks J. Am. Chem. Soc. 114 1992 8284-8285
40. Westcott T.P. Tobias I. Olson W.K. Elasticity theory and numerical analysis of DNA supercoiling: an application to DNA looping J. Phys. Chem. 99 1995 17926-17935
41. Wriggers W. Agrawal R.K. Drew D.L. McCammon J.A. Frank J. Domain motions of EF-G bound to the 70S ribosome: insights from a hand-shaking between multi-resolution structures Biophys. J. 79 2000 1670-1678
42. Wriggers W. Birmanns S. Using Situs for flexible and rigid-body fitting of multi-resolution single molecule data J. Struct. Biol. 133 2001 193-202
43. Wriggers W. Chacón P. Modeling tricks and fitting techniques for multi-resolution structures Structure 9 2001 779-788
44. Wriggers W. Chacón P. Using Situs for the registration of protein structures with low-resolution bead models from X-ray solution scattering J. Appl. Crystallogr. 34 2001 773-776
45. Wriggers W. Milligan R.A. McCammon J.A. Situs: a package for docking crystal structures into low-resolution maps from electron microscopy J. Struct. Biol. 125 1999 185-195
46. Wriggers W. Milligan R.A. Schulten K. McCammon J.A. Self-organizing neural networks bridge the biomolecular resolution gap J. Mol. Biol. 284 1998 1247-1254
47. Wriggers W. Schulten K. Investigating a back door mechanism of actin phosphate release by steered molecular dynamics Proteins: Struct. Funct. Genet. 35 1999 262-273