Understanding the role of the topology in protein folding by computational inverse folding experiments

Computational Biology and Chemistry

Volumn 32, Issue 4, 2008, Pages 233-239

  Mucherino, Antonio ^a   Costantini, Susan ^a,b   di Serafino, Daniela ^a   D'Apuzzo, Marco ^a   Facchiano, Angelo ^a,b   Colonna, Giovanni ^a  

^a SECOND UNIVERSITY OF NAPLES   (Italy)

^b CNR   (Italy)

Author keywords

All alpha proteins; Computational method; Global optimization model; Protein fold; Protein folding; Topology

Indexed keywords

ABSTRACTING; AMINES; AMINO ACIDS; BIOMOLECULES; COMPUTATIONAL GEOMETRY; COMPUTATIONAL METHODS; COMPUTER NETWORKS; DATA STRUCTURES; ERROR ANALYSIS; GEOMETRY; HEALTH; MATHEMATICAL MODELS; MODEL STRUCTURES; NUMERICAL METHODS; ORGANIC ACIDS; PROTEINS; STRUCTURAL PROPERTIES; TOPOLOGY;

AMINO-ACID SEQUENCES; COMPLEX SYSTEMS; COMPUTATIONAL APPROACH; CONFORMATIONAL STATES; CRYSTALLOGRAPHIC STRUCTURES; ELSEVIER (CO); EMERGENT PROPERTY; ENERGETIC PROPERTIES; FOLDING PROCESSES; GEOMETRICAL PROPERTIES; HELICAL PROTEINS; INVERSE FOLDING; LARGE DATA; NATIVE TOPOLOGY; PROTEIN SEQUENCING; SIDE CHAINS; TERTIARY STRUCTURES; TOPOLOGICAL FEATURES;

PROTEIN FOLDING;

AMINO ACID; PROTEIN;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; HYDROGEN BOND; METABOLISM; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; THERMODYNAMICS;

AMINO ACIDS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; HYDROGEN BONDING; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; THERMODYNAMICS;

EID: 45549083443     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2008.03.015     Document Type: Article

References (40)

1. Aurora R., Creamer T.P., Srinivasan R., and Rose G.D. Local interactions in protein folding: lessons from the α-helix. J. Biol. Chem. 272 (1997) 1413-1416
2. Baker D. A surprising simplicity to protein folding. Nature 405 (2000) 39-42
3. Banavar J.R., Maritan A., Micheletti C., and Trovato A. Geometry and physics of proteins. Proteins 47 (2002) 315-322
4. Banavar J.R., Hoang T.X., Maritan A., Seno F., and Trovato A. Unified perspective on proteins: a physics approach. Phys. Rev. E 70 (2004) 041905
5. Camazine S., Deneubourg J.L., and Franks N. Self-Organization in Biological Systems (2001), Princeton University Press, Princeton, NJ
6. Ceci G., Mucherino A., D'Apuzzo M., di Serafino D., Costantini S., Facchiano A., and Colonna G. Computational methods for protein fold prediction: an ab-initio topological approach. Data Mining Biomed., Spring. Optim. Appl. Ser. 7 (2006) 391-430
7. Chou K.C. A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins 21 (1995) 319-344
8. Costantini S., Facchiano A.M., and Colonna G. Evaluation of the structural quality of modeled proteins by using globularity criteria. BMC Struct. Biol. 7 (2007) 9
9. Cuff A.L., and Martin A.C.R. Analysis of void volumes in proteins and application to stability of the p53 tumour suppressor protein. J. Mol. Biol. 344 (2004) 1199-1209
10. Denton M., and Marshall C. Protein folds: laws of form revisited. Nature 410 (2001) 417
11. Fleming P.J., Gong H., and Rose G. Secondary structure determines protein topology. Protein Sci. 15 (2006) 1829-1834
12. Frauenfelder H. Proteins: paradigm of the complexity. PNAS USA 99 (2002) 2479-2490
13. Galloway J.W. Reflections on the ambivalent helix. Experientia 45 (1989) 859-872
14. Galloway J.W. Helical Imperative: Paradigm of Form and Function. Encyclopedia of Life Sciences (2001), Macillan Publishers Ltd., Nature Publishing Group
15. Gonzalez O., and Maddocks J.H. Global curvature, thickness, and the ideal shapes of knots. PNAS USA 96 (1999) 4769-4773
16. Hoang T.X., Trovato A., Seno F., Banavar J.R., and Maritan A. Geometry and symmetry presculpt the free-energy landscape of proteins. PNAS USA 101 (2004) 7960-7964
17. Hobohm U., Scharf M., Schneider R., and Sander C. Selection of representative protein data sets. Protein Sci. 1 (1992) 409-417
18. Holm L., and Sander C. Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace, application to model building and detection of co-ordinate errors. J. Mol. Biol. 218 (1991) 183-194
19. Huang C., Getahun Z., Zhu Y., Klemke J., De Grado W.F., and Gai F. Helix formation diffusion search. PNAS USA 99 (2002) 2788-2793
20. Hubbard S.J., Campbell S.F., and Thornton J.M. Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors. J. Mol. Biol. 220 (1991) 507-530
21. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
22. Kirkpatrick S., Gelatt, and Vecchi M.P. Optimization by simulated annealing. Science 220 (1983) 671-680
23. Kolodny R., Koehl P., Guibas L., and Levitt M. Small libraries of protein fragments model native protein structures accurately. J. Mol. Biol. 323 (2002) 297-307
24. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK-a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26 (1993) 283-291
25. Lezon T.R., Banavar J.R., Lesk A.M., and Maritan A. What determines the spectrum of protein native state structures?. Proteins 63 (2006) 273-277
26. Maritan A., Micheletti C., Trovato A., and Banavar J.R. Optimal shapes of compact strings. Nature 406 (2000) 287-290
27. Martin A.C. The ups and downs of protein topology; rapid comparison of protein structure. Protein Eng. 13 (2000) 829-837
28. McDonald I.K., and Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238 (1994) 777-793
29. McLachlan A.D. Rapid comparison of protein structures. Acta Cryst. A38 (1982) 871-873
30. Moult J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr. Opin. Struct. Biol. 15 (2005) 285-289
31. Orengo C.A., Michie A.D., Jones S., Jones D.T., Swindells M.B., and Thornton J.M. CATH-a hierarchic classification of protein domain structures. Structure 5 (1997) 1093-1108
32. Park B.H., and Levitt M. The complexity and accuracy of discrete state models of protein structure. J. Mol. Biol. 249 2 (1995) 493-507
33. Pettitt C.S., McGuffin L.J., and Jones D.T. Improving sequence-based fold recognition by using 3D model quality assessment. Bioinformatics 21 (2005) 3509-3515
34. Rose G.D., Fleming P.J., Banavar J., and Maritan A. A backbone-based theory of protein folding. PNAS USA 103 (2006) 16623-16633
35. Shir Y., and Kamien R.D. Entropically driven helix formation. Science 307 (2005) 1067
36. Tosatto S.C. The victor/FRST function for model quality estimation. J. Comp. Biol. 12 (2005) 1316-1327
37. Vincent J.J., Tai C.-H., Sathyanarayana B.K., and Lee B. Assessment of CASP6 predictions for new and nearly new fold targets. Proteins 61 7 (2005) 67-83
38. Yee D.P., Cha H.S., Havel T.F., and Dill K.A. Does compactness induce secondary structure in proteins? Study of poly-alanine chains computed by distance geometry. J. Mol. Biol. 241 (1994) 557-573
39. Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res. 31 (2003) 3370-3374
40. Zhang Y., Hubner I.A., Arakaki A.K., Shakhnovich E., and Skolnich J. On the origin and highly likely completeness of single-domain protein structures. PNAS USA 103 8 (2006) 2605-2610