A novel evaluation of residue and protein volumes by means of laguerre tessellation

Journal of Chemical Information and Modeling

Volumn 50, Issue 5, 2010, Pages 947-960

  Esque, Jeremy ^a   Oguey, Christophe ^a   De Brevern, Alexandre G ^b  

^a UNIVERSITÉ DE CERGY PONTOISE   (France)

^b hôpital Robert Debré et Institut national de la transfusion sanguine   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; GRAIN SIZE AND SHAPE;

DATA BANK; HIGH QUALITY; PROTEIN SIZE; PROTEIN STRUCTURES; PROTEIN SURFACE; PROTEIN VOLUME; SECONDARY STRUCTURES; STANDARD DEVIATION;

PROTEINS;

AMINO ACID; PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN DATABASE; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE;

AMINO ACIDS; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 77952749131     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci9004892     Document Type: Article

References (76)

1. Taylor, W. R. The classification of amino acid conservation J. Theor. Biol. 1986, 119, 205-218
2. Gellatly, B. J.; Finney, J. L. Calculation of protein volumes: an alternative to the Voronoi procedure J. Mol. Biol. 1982, 161, 305-322
3. Harpaz, Y.; Gerstein, M.; Chothia, C. Volume changes on protein folding Structure 1994, 2, 641-649
4. Pontius, J.; Richelle, J.; Wodak, S. J. Deviations from standard atomic volumes as a quality measure for protein crystal structures J. Mol. Biol. 1996, 264, 121-136
5. Richards, F. M. The interpretation of protein structures: total volume, group volume distributions and packing density J. Mol. Biol. 1974, 82, 1-14
6. Tsai, J.; Taylor, R.; Chothia, C.; Gerstein, M. The packing density in proteins: standard radii and volumes J. Mol. Biol. 1999, 290, 253-266
7. Zamyatnin, A. A. Amino acid, peptide, and protein volume in solution Annu. Rev. Biophys. Bioeng. 1984, 13, 145-165
8. Soyer, A.; Chomilier, J.; Mornon, J. P.; Jullien, R.; Sadoc, J. F. Voronoi tessellation reveals the condensed matter character of folded proteins Phys. Rev. Lett. 2000, 85, 3532-3535
9. Goede, A.; Preissner, R.; Frommel, C. Voronoi Cell: new method for allocation of space among atoms: elimination of avoidable errors in calculation of atomic volume and density J. Comput. Chem. 1997, 18, 1113-1123
10. Angelov, B.; Sadoc, J. F.; Jullien, R.; Soyer, A.; Mornon, J. P.; Chomilier, J. Nonatomic solvent-driven Voronoi tessellation of proteins: an open tool to analyze protein folds Proteins 2002, 49, 446-456
11. McConkey, B. J.; Sobolev, V.; Edelman, M. Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure Bioinformatics 2002, 18, 1365-1373
12. Sadoc, J. F.; Jullien, R.; Rivier, N. The Laguerre polyhedral decomposition: application to protein folds Eur. Phys. J. B 2003, 33, 355-363
13. Gerstein, M.; Tsai, J.; Levitt, M. The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra J. Mol. Biol. 1995, 249, 955-966
14. Poupon, A. Voronoi and Voronoi-related tessellations in studies of protein structure and interaction Curr. Opin. Struct. Biol. 2004, 14, 233-241
15. Chothia, C. Structural invariants in protein folding Nature 1975, 254, 304-308
16. Janin, J.; Chothia, C. The structure of protein-protein recognition sites J. Biol. Chem. 1990, 265, 16027-16030
17. Gerstein, M.; Chothia, C. Packing at the protein-water interface Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 10167-10172
18. Liang, J.; Edelsbrunner, H.; Fu, P.; Sudhakar, P. V.; Subramaniam, S. Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape Proteins 1998, 33, 1-17
19. Liang, J.; Edelsbrunner, H.; Fu, P.; Sudhakar, P. V.; Subramaniam, S. Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins Proteins 1998, 33, 18-29
20. Rother, K.; Hildebrand, P. W.; Goede, A.; Gruening, B.; Preissner, R. Voronoia: analyzing packing in protein structures Nucleic Acids Res. 2009, 37, D393-D395
21. Dupuis, F.; Sadoc, J. F.; Mornon, J. P. Protein secondary structure assignment through Voronoi tessellation Proteins 2004, 55, 519-528
22. Birzele, F.; Gewehr, J. E.; Csaba, G.; Zimmer, R. Vorolign - fast structural alignment using Voronoi contacts Bioinformatics 2007, 23, e205-e211
23. Bernauer, J.; Azé, J.; Janin, J.; Poupon, A. A new protein-protein docking scoring function based on interface residue properties Bioinformatics 2007, 23, 555-562
24. Kobayashi, N.; Go, N. A method to search for similar protein local structures at ligand binding sites and its application to adenine recognition Eur. Biophys. J. 1997, 26, 135-144
25. Taylor, W. R. Protein structural domain identification Protein Eng. 1999, 12, 203-216
26. Wako, H.; Yamato, T. Novel method to detect a motif of local structures in different protein conformations Protein Eng. 1998, 11, 981-990
27. Huan, J.; Bandyopadhyay, D.; Wang, W.; Snoeyink, J.; Prins, J.; Tropsha, A. Comparing graph representations of protein structure for mining family-specific residue-based packing motifs J. Comput. Biol. 2005, 12, 657-671
28. Huan, J.; Wang, W.; Washington, A.; Prins, J.; Shah, R.; Tropsha, A. Accurate classification of protein structural families using coherent subgraph analysis Pac. Symp. Biocomput. 2004, 411-422
29. Taylor, T.; Rivera, M.; Wilson, G.; Vaisman, I. I. New method for protein secondary structure assignment based on a simple topological descriptor Proteins 2005, 60, 513-524
30. Deutsch, C.; Krishnamoorthy, B. Four-body scoring function for mutagenesis Bioinformatics 2007, 23, 3009-3015
31. Ilyin, V. A.; Abyzov, A.; Leslin, C. M. Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point Protein Sci. 2004, 13, 1865-1874
32. Roach, J.; Sharma, S.; Kapustina, M.; Carter, C. W., Jr. Structure alignment via Delaunay tetrahedralization Proteins 2005, 60, 66-81
33. Carter, C. W., Jr.; LeFebvre, B. C.; Cammer, S. A.; Tropsha, A.; Edgell, M. H. Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations J. Mol. Biol. 2001, 311, 625-638
34. Gan, H. H.; Tropsha, A.; Schlick, T. Lattice protein folding with two and four-body statistical potentials Proteins 2001, 43, 161-174
35. Krishnamoorthy, B.; Tropsha, A. Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations Bioinformatics 2003, 19, 1540-1548
36. Masso, M.; Vaisman, I. I. Accurate prediction of enzyme mutant activity based on a multibody statistical potential Bioinformatics 2007, 23, 3155-3161
37. Stout, M.; Bacardit, J.; Hirst, J. D.; Smith, R. E.; Krasnogor, N. Prediction of topological contacts in proteins using learning classifier systems Soft. Comput. 2008, 13, 245-258
38. Zimmer, R.; Wohler, M.; Thiele, R. New scoring schemes for protein fold recognition based on Voronoi contacts Bioinformatics 1998, 14, 295-308
39. Fischer, T. B.; Holmes, J. B.; Miller, I. R.; Parsons, J. R.; Tung, L.; Hu, J. C.; Tsai, J. Assessing methods for identifying pair-wise atomic contacts across binding interfaces J. Struct. Biol. 2006, 153, 103-112
40. Hubbard, S. J.; Thornton, J. M. NACCESS, 2.1.1; Dept of Biochemistry and Molecular Biology, University College: London, 1993.
41. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-242
42. Wang, G.; Dunbrack, R. L., Jr. PISCES: a protein sequence culling server Bioinformatics 2003, 19, 1589-1591
43. Wang, G.; Dunbrack, R. L., Jr. PISCES: recent improvements to a PDB sequence culling server Nucleic Acids Res. 2005, 33, W94-W98
44. Lawson, C. L.; Zhang, R. G.; Schevitz, R. W.; Otwinowski, Z.; Joachimiak, A.; Sigler, P. B. Flexibility of the DNA-binding domains of trp repressor Proteins 1988, 3, 18-31
45. Finer-Moore, J. S.; Kossiakoff, A. A.; Hurley, J. H.; Earnest, T.; Stroud, R. M. Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction Proteins 1992, 12, 203-222
46. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. GROMACS: A message-passing parallel molecular dynamics implementation Comput. Phys. Commun. 1995, 91, 43-56
47. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447
48. Lindahl, E.; Hess, B.; van der Spoel, D. GROMACS 3.0: a package for molecular simulation and trajectory analysis J. Mol. Model. 2001, 7, 306-317
49. Van Der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. GROMACS: fast, flexible, and free J. Comput. Chem. 2005, 26 (16) 1701-18
50. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hunenberger, P. H.; Kruger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 manual and user guide; vdf Hochschulverlag AG an der ETH Zürich and BIOMOS b.v.: Zürich, Groningen, 1996.
51. Berendsen, H. J. C.; Postma, P. M.; van Gunsteren, W. F.; Pullman, B. Intermolecular Forces; Reidel: Dordrecht, The Netherlands, 1981.
52. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Dinola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath J. Chem. Phys. 1984, 81, 3684-3690
53. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. LINCS: A linear constraint solver for molecular simulations J. Comput. Chem. 1997, 18, 1463-1472
54. Tironi, I. G.; Sperb, R.; Smith, P. E.; van Gunsteren, W. F. A generalized reaction field method for molecular dynamics simulations J. Chem. Phys. 1995, 102, 5451-5459
55. Kabsch, W.; Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 1983, 22, 2577-2637
56. Delano, W. L. The PyMOL Molecular Graphics System on World Wide Web. http://www.pymol.org (accessed Apr 2010).
57. Singh, R. K.; Tropsha, A.; Vaisman, I. I. Delaunay tessellation of proteins: four body nearest-neighbor propensities of amino acid residues J. Comput. Biol. 1996, 3, 213-221
58. Sugihara, K. Laguerre Voronoi Diagram on the sphere JGG 2002, 6, 69-81
59. Kim, C. H.; Won, C. I.; Cho, Y.; Kim, D.; Lee, S.; Bhak, J. Interaction interfaces in proteins via the Voronoi diagram of atoms C.A.D. 2006, 38, 1192-1204
60. Allaire, M.; Li, Y.; MacKenzie, R. E.; Cygler, M. The 3-D structure of a folate-dependent dehydrogenase/cyclohydrolase bifunctional enzyme at 1.5 A resolution Structure 1998, 6, 173-182
61. Fauchere, J.-L.; Pliska, V. Hydrophobic parameters pi of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides Eur. J. Med. Chem. - Chim. Ther. 1983, 18, 369-375
62. Lobanov, M.; Bogatyreva, N. S.; Galzitskaia, O. V. Radius of gyration is indicator of compactness of protein structure Mol. Biol. (Mosk) 2008, 42, 701-706
63. Galzitskaya, O. V.; Reifsnyder, D. C.; Bogatyreva, N. S.; Ivankov, D. N.; Garbuzynskiy, S. O. More compact protein globules exhibit slower folding rates Proteins 2008, 70, 329-332
64. Ivankov, D. N.; Garbuzynskiy, S. O.; Alm, E.; Plaxco, K. W.; Baker, D.; Finkelstein, A. V. Contact order revisited: influence of protein size on the folding rate Protein Sci. 2003, 12, 2057-2062
65. Fleming, P. J.; Richards, F. M. Protein packing: dependence on protein size, secondary structure and amino acid composition J. Mol. Biol. 2000, 299, 487-498
66. Creighton, T. E. The polymeric nature of proteins. In PROTEINS: Structures and Molecular Properties, 2nd ed.; W. H. Freeman: New York, 1992; p 4.
67. Gekko, K.; Noguchi, H. Compressibility of globular proteins in water at 25.degree.C J. Phys. Chem. 1979, 83, 2706-2714
68. Squire, P. G.; Himmel, M. E. Hydrodynamics and protein hydration Arch. Biochem. Biophys. 1979, 196, 165-177
69. Gelly, J. C.; Etchebest, C.; Hazout, S.; de Brevern, A. G. Protein Peeling 2: a web server to convert protein structures into series of protein units Nucleic Acids Res. 2006, 34, W75-W78
70. Samanta, U.; Bahadur, R. P.; Chakrabarti, P. Quantifying the accessible surface area of protein residues in their local environment Protein Eng. 2002, 15, 659-667
71. Faure, G.; Bornot, A.; de Brevern, A. G. Protein contacts, inter-residue interactions and side-chain modelling Biochimie 2008, 90, 626-639
72. Canutescu, A. A.; Shelenkov, A. A.; Dunbrack, R. L., Jr. A graph-theory algorithm for rapid protein side-chain prediction Protein Sci. 2003, 12, 2001-2014
73. Krivov, G. G.; Shapovalov, M. V.; Dunbrack, R. L., Jr. Improved prediction of protein side-chain conformations with SCWRL4 Proteins 2009, 77, 778-795
74. Eyal, E.; Najmanovich, R.; McConkey, B. J.; Edelman, M.; Sobolev, V. Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins J. Comput. Chem. 2004, 25, 712-724
75. Xu, J.; Jiao, F.; Berger, B. A tree-decomposition approach to protein structure prediction Proc IEEE Comput. Syst. Bioinform. Conf. 2005, 247-256
76. Faure, G.; Bornot, A.; de Brevern, A. G. Analysis of protein contacts into Protein Units Biochimie 2009, 91, 876-887