Optimal identification of semi-rigid domains in macromolecules from molecular dynamics Simulation

PLoS ONE

Volumn 5, Issue 5, 2010, Pages

  Bernhard, Stefan ^a   Noé, Frank ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONE; PEPTIDE DERIVATIVE; PREALBUMIN; CHAPERONIN;

ARTICLE; CONFORMATIONAL TRANSITION; MACROMOLECULE; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; MOLECULAR MODEL; MUTATION; PROTEIN DOMAIN; PROTEIN STRUCTURE; RELIABILITY; SIMULATION; CHEMISTRY; CLUSTER ANALYSIS; METABOLISM; TIME;

CHAPERONIN 10; CHAPERONIN 60; CLUSTER ANALYSIS; MACROMOLECULAR SUBSTANCES; MOLECULAR DYNAMICS SIMULATION; PREALBUMIN; TIME FACTORS;

EID: 77956285109     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010491     Document Type: Article

References (66)

1. Bao G (2002) Mechanics of biomolecules. J Mech Phys Solid 50: 2237-2274.
2. Bustamante C, Smith S, Liphardt J, Smith D (2000) Single-molecule studies of DNA mechanics. Curr Opin Struct Biol 10: 279-285.
3. Gardel ML, Nakamura F, Hartwig JH, Crocker JC, Stossel TP, et al. (2006) Prestressed F-actin networks cross-linked by hinged filamins replicate mechanical properties of cells. Proc Natl Acad Sci Unit States Am 103: 1762-7.
4. Lavery R, Lebrun A, Allemand J, Bensimon D (2002) Structure and mechanics of single biomolecules: experiment and simulation. J Phys Condens Matter 14: 383-414.
5. Micheletti C, Lattanzi G, Maritan A (2007) Elastic properties of proteins: insight on the folding process and the evolutionary selection of native structures. J Mol Biol 321: 909-21.
6. Splettstoesser T, Noe F, Oda T, Smith J (2008) Nucleotide-dependence of Gactin conformation from multiple molecular dynamics simulations and observation of a putatively polymerization-competent superclosed state. Proteins: Structure, Functions, and Bioinformatics.
7. Ahmed A, Gohlke H (2006) Multiscale Modeling of Macromolecular Conformational Changes Combining Concepts From Rigidity and Elastic Network Theory. Proteins: Structure, Functions, and Bioinformatics 63: 1038-1051.
8. Ayton GS, Noid WG, Voth GA (2007) Multiscale modeling of biomolecular systems: in serial and in parallel. Curr Opin Struct Biol 17: 192-8.
9. Izvekov S, Voth G (2005) A multiscale coarse-graining method for biomolecular systems. J Phys Chem B 109: 2469-2473.
10. Atilgan A, Akan P, Baysal C (2004) Small-World Communication of Residues and Significance for Protein Dynamics. Biophys J 86: 85-91.
11. Bagci Z, Jernigan R, Bahar I (2002) Residue packing in proteins: Uniform distribution on a coarse-grained scale. J Chem Phys 116: 2269-2276.
12. Anselmi C, Bocchinfuso G, Scipioni A, Santis P (2001) Identification of protein domains on topological basis. Biopolymers 58: 218-229.
13. Nicolas WL, Rose G, Eyck L, Zimm B (1995) Rigid domains in proteins: an algorithmic approach to their identification. Proteins: Structure, Functions, and Bioinformatics 23: 38-48.
14. Liljas A, Rossman M (1974) X-ray studies of protein interactions. Annu Rev Biochem 43: 475-507.
15. Wodak SJ, Janin J (1981) Location of structural domains in proteins. Biochemistry 20: 6544-6552.
16. Lesk AM, Rose GD (1981) Folding units in globular proteins. Proc Natl Acad Sci Unit States Am 78: 4304-4308.
17. Zehfus MH (1987) Continuous compact protein domains. Proteins: Structure, Functions, and Bioinformatics 16: 90-110.
18. Xuan Z, Ling L, Chen R (2000) A new method for protein domain recognition. Eur Biophys J 29: 7-16.
19. Wriggers W, Schulten K (1997) Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins: Structure, Functions, and Bioinformatics 29: 1-14.
20. Taylor WR (1999) Protein structural domain identification. Protein Eng 12: 203-216.
21. Balsera MA, Wriggers W, Oono Y, Schulten K (1996) Principal Component Analysis and Long Time Protein Dynamics. J Phys Chem 100: 2567-2572.
22. Ma J (2005) Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure 13: 373-80.
23. Bahar I, Rader AJ (2005) Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 15: 586-92.
24. Hinsen K (1998) Analysis of domain motions by approximate normal mode calculations. Proteins: Structure, Functions, and Bioinformatics 33: 417-429.
25. Zhang Z, Lu L, Noid W, Krishna V (2008) A systematic methodology for defining coarse-grained sites in large biomolecules. Biophys J 95: 5073-5083.
26. Héry S, Genest D, Smith J (1998) X-ray Diffuse Scattering and Rigid-Body Motion in Crystalline Lysozyme Probed by Molecular Dynamics Simulation. J Mol Biol 279: 303-319.
27. Yesylevskyy SO, Kharkyanen VN, Demchenko AP (2006) Hierarchical clustering of the correlation patterns: new method of domain identification in proteins. Biophys Chem 119: 84-93.
28. Shibuya T (2008) Fast Hinge Detection Algorithms for Flexible Protein Structures. IEEE ACM Trans Comput Biol Bioinformatics PP: 1.
29. Potestio R, Pontiggia F, Micheletti C (2009) Coarse-Grained Description of Protein Internal Dynamics: An Optimal Strategy for Decomposing Proteins in Rigid Subunits. Biophys J 96: 4993-5002.
30. Hayward S (2004) Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements. J Mol Biol 339: 1001.
31. Carlson H, McCammon J (2000) Accommodating protein flexibility in computational drug design. Mol Pharmacol 57: 213-218.
32. Mustard D, Ritchie D (2005) Docking essential dynamics eigenstructures. Proteins: Structure, Functions, and Bioinformatics 60: 269-274.
33. Navizet I, Lavery R, Jernigan R (2004) Myosin flexibility: structural domains and collective vibrations. Proteins: Structure Function and Bioinformatics 54: 384-393.
34. Menor S, de Graff A, Thorpe M (2009) Hierarchical plasticity from pair distance fluctuations. Phys Biol 6: 036017.
35. Jünger M, Reinelt G (2004) Combinatorial Optimization and Integer Programming. In: Optimization and Operations Research Encyclopedia of Life Support Systems EOLSS. pp 321-327.
36. Yesylevskyy S, Kharkyanen V (2009) Fuzzy domains: New way of describing flexibility and interdependence of the protein domains. Proteins: Structure, Functions, and Bioinformatics 74: 980-995.
37. Gill P, Murray W, Saunders M (1995) User's guide for QPOPT 1.0: A Fortran package for Quadratic programming Dept of Operations Research, Stanford University.
38. Noé F, Daidone I, Smith J, di Nola A, Amadei A (2008) Solvent Electrostriction- Driven Peptide Folding Revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation. J Phys Chem B 112: 11155-11163.
39. Klabunde T, Petrassi HM, Oza VB, Raman P, Kelly JW, et al. (2000) Rational design of potent human transthyretin amyloid disease inhibitors. Nature Structural Biology 7: 312-21.
40. Sali A, Blundell T (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234: 779-815.
41. Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7: 306-317.
42. Hess B, Bekker H, Berendsen H, Fraaije J (1997) LINCS: A Linear Constraint Solver for molecular simulations. J Comput Chem 18: 1463-1472.
43. Blake CF, Geisow M, Swan I, Rerat C, Rerat B (1974) Structure of human plasma prealbumin at 2.5 Angstrom resolution. A preliminary report on the polypeptide chain conformation, quaternary structure and thyroxine binding. J Mol Biol 88: 1-12.
44. Sunde M, Blake C (1997) The structure of amyloid fibrils by electron microscopy and X-ray diffraction. Adv Protein Chem 50: 123-159.
45. Tan SY, Pepys M (1995) Amyloidosis. Histopathology 25: 403-414.
46. Damas A, Saraiva M (2000) Review: TTR Amyloidosis-Structural Features Leading to Protein Aggregation and Their Implications on Therapeutic Strategies. J Struct Biol 130: 290-299.
47. Rochet J, Lansbury P (2000) Amyloid fibrillogenesis: themes and variations. Curr Opin Struct Biol 10: 60-68.
48. Jaroniec C, MacPhee C, Astrof N, Dobson C, Griffin R (2002) Molecular conformation of a peptide fragment of transthyretin in an amyloid fibril. Proc Natl Acad Sci Unit States Am 99: 16748-16753.
49. Cendron L, Trovato A, Seno F, Folli C, Alfieri B, et al. (2009) Amyloidogenic Potential of Transthyretin Variants. J Biol Chem 284: 25832.
50. Altland K, Winter P, Sauerborn M (1999) Electrically neutral microheterogeneity of human plasma transthyretin (prealbumin) detected by isoelectric focusing in urea gradients. Electrophoresis 20: 1349-1364.
51. Takeuchi M, Mizuguchi M, Kouno T, Shinohara Y, Aizawa T, et al. (2006) Destabilization of transthyretin by pathogenic mutations in the DE loop. Proteins: Structure, Function, and Bioinformatics 66: 716-725.
52. Jenne D, Denzel K, Blatzinger P, Winter P (1996) A new isoleucine substitution of Val-20 in transthyretin tetramers selectively impairs dimer- dimer contacts and causes systemic amyloidosis. Proc Natl Acad Sci Unit States Am 93: 6302-6307.
53. Altland K, Benson M, Costello C, Ferlini A (2007) Genetic microheterogeneity of human transthyretin detected by IEF. Electrophoresis 28: 2053-2064.
54. Foss T, Wiseman R, Kelly J (2005) The Pathway by Which the Tetrameric Protein Transthyretin Dissociates. Biochemistry 44: 15525-33.
55. Serag AA, Altenbach C, Gingery M, Hubbell W, Yates TO (2002) Arrangement of subunits and ordering of ß-strands in an amyloid sheet. Nat Struct Biol 9: 734-739.
56. Sørensen J, Hamelberg D, Schiøtt B, McCammon JA (2007) Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism. Peptide Science 86: 73-82.
57. Saraiva M (2001) Transthyretin mutations in hyperthyroxinemia and amyloid diseases. Hum Mutat 17: 493-503.
58. Motozaki Y, Sugiyama Y, Ishida C, Komai K, Matsubara S, et al. (2007) Phenotypic heterogeneity in a family with FAP due to a TTR Leu58Arg mutation: A clinicopathologic study. J Neurol Sci 260: 236-239.
59. Mayhew M, Silva A, Martin J, Erdjument-Bromage H, Tempst P, et al. (1996) Protein folding in the central cavity of the GroEL-GroES chaperonin complex. Nature 379: 420-426.
60. Ma J, Sigler P, Xu Z, Karplus M (2000) A dynamic model for the allosteric mechanism of GroEL. J Mol Biol 302: 303-313.
61. Walter S (2002) Structure and function of the GroE chaperone. Cell Mol Life Sci 59: 1589-97.
62. Keskin O, Bahar I, Flatow D, Covell D, Jernigan R (2002) Molecular Mechanisms of Chaperonin GroEL- GroES Function. Biochemistry 41: 491-501.
63. Kim M, Jernigan R, Chirikjian G (2005) Rigid-Cluster Models of Conformational Transitions in Macromolecular Machines and Assemblies. Biophys J 89: 43-55.
64. Chennubhotla C, Bahar I (2006) Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES. Mol Syst Biol 36: 1-13.
65. Arkhipov A, Larson S, McPherson A, Schulten K (2006) Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure 14: 437-449.
66. Arkhipov A, Freddolino P, Schulten K (2006) Stability and dynamics of virus capsids described by coarse-grained modeling. Structure 14: 1767-1777.