Visualizing the dual space of biological molecules

Computational Biology and Chemistry

Volumn 30, Issue 3, 2006, Pages 219-226

  Eargle, John ^a   Luthey Schulten, Zaida ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Delaunay triangulation; Protein tRNA interface; Tessellation

Indexed keywords

CATALYSTS; ENZYMES; GENETIC ALGORITHMS; GRAPH THEORY; MOLECULAR BIOLOGY; PHOSPHATES; RNA;

DELAUNAY TRIANGULATION; DUAL SPACE; PROTEIN/TRNA INTERFACE; TESSELLATION;

PROTEINS;

ASPARTATE TRANSFER RNA LIGASE; HYDROLASE; IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE; MYOGLOBIN; PROTEIN; RNA;

ALGORITHM; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER GRAPHICS; PROTEIN CONFORMATION;

ALGORITHMS; AMINOHYDROLASES; ASPARTATE-TRNA LIGASE; BINDING SITES; COMPUTER GRAPHICS; MODELS, MOLECULAR; MYOGLOBIN; PROTEIN CONFORMATION; PROTEINS; RNA;

EID: 33744486941     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2006.01.004     Document Type: Article

References (36)

1. Amaro R., Myers R., Davisson V., and Luthey-Schulten Z. Structural elements in IGP synthase exclude water to optimize ammonia transfer. Biophys. J. 89 (2005) 475-487
2. Amaro R., Tajkhorshid E., and Luthey-Schulten Z. Developing an energy landscape for the novel function of a ( β / α)8 barrel: ammonia conduction through HisF. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 7599-7604
3. Cavarelli J., Eriani G., Rees B., Ruff M., Boeglin M., Mitschler A., Martin F., Gangloff J., Thierry J.C., and Moras D. The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction. EMBO J. 13 (1994) 327-337
4. 2 gas transport in CpI [Fe]-hydrogenase and the role of packing defects. Structure 13 (2005) 1321-1329
5. Connolly M.L. Solvent-accessible surfaces of proteins and nucleic acids. Science 221 (1983) 709-713
6. Delaunay, B., 1934. Sur la sphère vide. ivestia akademii nauk SSSR, Otdelenie Matematicheskii i Estestvennyka Nauk 7, 793-800.
7. 8 barrel of imidazole glycerol phosphate synthase bienzyme complex. Structure 10 (2002) 185-193
8. Elber R., and Karplus M. Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin. J. Am. Chem. Soc. 112 (1990) 9161-9175
9. Gerstein M. A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen-combining sites. Acta Cryst. A 48 (1992) 271-276
10. Hebb D. Organization of Behavior (1974), New York
11. Humphrey W., Dalke A., and Schulten K. VMD-visual molecular dynamics. J. Mol. Graph. 14 (1996) 33-38
12. Insight II, 2005. accelrys, San Diego.
13. Lee B., and Richards F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55 (1971) 379-400
14. Li H., Elber R., and Straub J.E. Molecular dynamics simulation of NO recombination to myoglobin mutants. J. Biol. Chem. 268 (1993) 17908-17916
15. Liang J., Edelsbrunner H., Fu P., Sudhakar P.V., and Subramaniam S. Analytical shape computation of macromolecules. I. Molecular area and volume through alpha shape. Protein Struc. Func. Genet. 33 (1998) 1-17
16. Liang J., Edelsbrunner H., Fu P., Sudhakar P.V., and Subramaniam S. Analytical shape computation of macromolecules. II. Inaccessible cavities in proteins. Protein Struc. Func. Genet. 33 (1998) 18-29
17. Martinetz T., and Schulten K. Topology representing networks. Neural Networ. 7 (1994) 507-522
18. MOE, 2005. Molecular Operating Environment. Chemical Computing Group Inc., Montreal.
19. Nicholls A., Sharp K.A., and Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Protein Struc. Func. Genet. 11 (1991) 281-296
20. O'Donoghue P., and Luthey-Schulten Z. Evolution of structure in aminoacyl-tRNA synthetases. Microbiol. Mol. Biol. Rev. 67 (2003) 550
21. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., and Ferrin T.E. Ucsf chimera-a visualization system for exploratory research and analysis. J. Comp. Chem. 25 (2004) 1605
22. Poupon A. Voronoi and Voronoi-related tessellations in studies of protein structure and interaction. Curr. Opin. Struct. Biol. 14 (2004) 233-241
23. Ritter H., Martinetz T., and Schulten K. Neural Computation and Self-Organizing Maps-An Introduction (1992), Addison-Wesley, New York
24. Ruff M., Krishnaswamy S., Boeglin M., Poterszman A., Mitschler A., Podjarny A., Rees B., Thierry J., and Moras D. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science 252 (1991) 1682-1689
25. Sanner M.F., Olson A.J., and Spehner J.C. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38 (1996) 305-320
26. Sayle R.A., and Milner-White E.J. RASMOL: biomolecular graphics for all. Trends Biochem. Sci. 20 (1995) 374
27. Schoenborn B.P. Binding of xenon to horse haemoglobin. Nature 208 (1965) 760-762
28. Schoenborn B.P. Structure of alkaline metmyoglobin-xenon complex. J. Mol. Biol. 45 (1969) 297-303
29. Sethi A., O'Donoghue P., and Luthey-Schulten Z. Evolutionary profiles from the QR factorization of multiple sequence alignments. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 4045-4050
30. Smart O., Goodfellow J., and Wallace B. The Pore Dimensions of Gramicidin A. Biophys. J. 65 (1993) 2455-2460
31. Tilton R.F., and Kuntz Jr. I.D. Nuclear magnetic resonance studies of xenon-129 with myoglobin and hemoglobin. Biochemistry 21 (1982) 6850
32. Ulitsky A., and Elber R. Application of the locally enhanced sampling (LES) and a mean field with a binary collision correction (cLES) to the simulation of Ar diffusion and NO recombination in myoglobin. J. Phys. Chem. 98 (1994) 1034-1043
33. Wang L., Brock A., Herberich B., and Schultz P.G. Expanding the genetic code of Escherichia coli. Science 292 (2001) 498-500
34. Watson H. The stereochemistry of the protein myoglobin. Prog. Stereochem. 4 (1969) 299
35. Woese C.R., Olsen G.J., Ibba M., and Söll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64 (2000) 202-236
36. Wriggers W., Milligan R., Schulten K., and McCammon J. Self-organizing neural networks bridge the biomolecular resolution gap. J. Mol. Biol. 284 (1998) 1247-1254