Emergence of protein fold families through rational design

PLoS Computational Biology

Volumn 2, Issue 7, 2006, Pages 0725-0733

  Ding, Feng ^a   Dokholyan, Nikolay V ^a  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DESIGN;

DIVERSE PROTEINS; PROTEIN CORE; PROTEIN FAMILY; PROTEIN SEQUENCES; RATIONAL DESIGN; SEQUENCE SIMILARITY; SEQUENCE SPACE; SEQUENCE STRUCTURE; STRUCTURE FACTORS; TIME-SCALES;

PROTEINS;

AMINO ACID SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STOCHASTIC MODEL; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; COMPUTER; COMPUTER PROGRAM; CONFORMATION; ENTROPY; ESCHERICHIA COLI; METABOLISM; METHODOLOGY; MOLECULAR EVOLUTION; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; STATISTICS;

PROTEIN;

COMPUTATIONAL BIOLOGY; COMPUTERS; ENTROPY; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOFTWARE; STOCHASTIC PROCESSES;

EID: 33746639718     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0020085     Document Type: Article

References (55)

1. Levitt M, Chothia C (1976) Structural patterns in globular proteins. Nature 261: 552-558.
2. Govindarajan S, Goldstein RA (1996) Why are some proteins structures so common? Proc Natl Acad Sci U S A 93: 3341-3345.
3. Orengo CA, Jones DT, Thornton JM (1994) Protein superfamilies and domain superfolds. Nature 372: 631-634.
4. Govindarajan S, Goldstein RA (1997) The foldability landscape of model proteins. Biopolymers 42: 427-438.
5. Finkelstein AV, Gutun AM, Badretdinov AY (1993) Why are the same protein folds used to perform different functions? FEBS Lett 325: 23-28.
6. Govindarajan S, Recabarren R, Goldstein RA (1999) Estimating the total number of protein folds. Proteins 35: 408-414.
7. Li H, Helling R, Tang C, Wingreen N (1996) Emergence of preferred structures in a simple model of protein folding. Science 273: 666-669.
8. Chothia C, Gerstein M (1997) Protein evolution. How far can sequences diverge? Nature 385: 579-581.
9. Grishin NV (1997) Estimation of evolutionary distances from protein spatial structures. J Mol Evol 45: 359-369.
10. Murzin AG (1998) How far divergent evolution goes in proteins. Curr Opin Struct Biol 8: 380-387.
11. Holm L (1998) Unification of protein families. Curr Opin Struct Biol 8: 372-379.
12. Rost B (1997) Protein structures sustain evolutionary drift. Fold Des 2: S19-S24.
13. Chothia C (1992) Proteins. One thousand families for the molecular biologist. Nature 357: 543-544.
14. Sander C, Schneider R (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9: 56-68.
15. Flaherty KM, McKay DB, Kabsch W, Holmes KC (1991) Similarity of the three-dimensional structures of actin and the ATPase fragment of a 70-kDa heat shock cognate protein. Proc Natl Acad Sci U S A 88: 5041-5045.
16. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, et al. (1997) CATH-a hierarchic classification of protein domain structures. Structure 5: 1093-1108.
17. Sanchez R, Pieper U, Melo F, Eswar N, Marti-Renom MA, et al. (2000) Protein structure modeling for structural genomics. Nat Struct Biol 7 Suppl: 986-990.
18. Pearl FM, Lee D, Bray JE, Sillitoe I, Todd AE, et al. (2000) Assigning genomic sequences to CATH. Nucleic Acids Res 28: 277-282.
19. Holm L, Sander C (1993) Protein structure comparison by alignment of distance matrices. J Mol Biol 233: 123-138.
20. Holm L, Sander C (1997) An evolutionary treasure: Unification of a broad set of amidohydrolases related to urease. Proteins 28: 72-82.
21. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, et al. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302: 1364-1368.
22. Dokholyan NV, Shakhnovich EI (2001) Understanding hierarchical protein evolution from first principles. J Mol Biol 312: 289-307.
23. Xia Y, Levitt M (2004) Simulating protein evolution in sequence and structure space. Curr Opin Struct Biol 14: 202-207.
24. Dahiyat BI, Mayo SL (1997) De novo protein design: fully automated sequence selection. Science 278: 82-87.
25. Desjarlais JR, Handel TM (1995) De novo design of the hydrophobic cores of proteins. Protein Sci 4: 2006-2018.
26. Desjarlais JR, Handel TM (1995) New strategies in protein design. Curr Opin Biotechnol 6: 460-466.
27. Johnson EC, Lazar GA, Desjarlais JR, Handel TM (1999) Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin. Structure Fold Des 7: 967-976.
28. Kuhlman B, Baker D (2000) Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci U S A 97: 10383-10388.
29. Dwyer MA, Looger LL, Hellinga HW (2004) Computational design of a biologically active enzyme. Science 304: 1967-1971.
30. Larson SM, England JL, Desjarlais JR, Pande VS (2002) Thoroughly sampling sequence space: Large-scale protein design of structural ensembles. Protein Sci 11: 2804-2813.
31. Larson SM, Garg A, Desjarlais JR, Pande VS (2003) Increased detection of structural templates using alignments of designed sequences. Proteins 51: 390-396.
32. Saunders CT, Baker D (2005) Recapitulation of protein family divergence using flexible backbone protein design. J Mol Biol 346: 631-644.
33. Zhou Y, Hall CK, Karplus M (1996) First-order disorder-to-order transition in an isolated homopolymer model. Phys Rev Lett 77: 2822-2825.
34. Zhou Y, Karplus M (1997) Folding thermodynamics of a model three-helix-bundle protein. Proc Natl Acad Sci U S A 94: 14429-14432.
35. Ding F, Dokholyan NV (2005) Simple but predictive protein models. Trends Biotechnol 23: 450-455.
36. Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI (1998) Discrete molecular dynamics studies of the folding of a protein-like model. Fold Des 3: 577-587.
37. Dokholyan NV, Borreguero JM, Buldyrev SV, Ding F, Stanley HE, et al. (2003) Identifying importance of amino acids for protein folding from crystal structures. Methods Enzymol 374: 616-638.
38. Holm L, Ouzounis C, Sander C, Tuparev G, Vriend G (1992) A database of protein structure families with common folding motifs. Protein Sci 1: 1691-1698.
39. Hobohm U, Sander C (1995) A sequence property approach to searching protein databases. J Mol Biol 251: 390-399.
40. Pabo C (1983) Molecular technology. Designing proteins and peptides. Nature 301: 200.
41. Hinds DA, Levitt M (1996) From structure to sequence and back again. J Mol Biol 258: 201-209.
42. Raha K, Wollacott AM, Italia MJ, Desjarlais JR (2000) Prediction of amino acid sequence from structure. Protein Sci 9: 1106-1119.
43. Pokala N, Handel TM (2001) Review: Protein design-where we were, where we are, where we're going. J Struct Biol 134: 269-281.
44. Dunbrack RL Jr., Cohen FE (1997) Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 6: 1661-1681.
45. Dahiyat BI, Mayo SL (1997) Probing the role of packing specificity in protein design. Proc Natl Acad Sci U S A 94: 10172-10177.
46. Jia Z, Quail JW, Waygood EB, Delbaere LT (1993) The 2.0-A resolution structure of Escherichia coli histidine-containing phosphocarrier protein HPr. A redetermination. J Biol Chem 268: 22490-22501.
47. Volz K, Matsumura P (1991) Crystal structure of Escherichia coli CheY refined at 1.7-A resolution. J Biol Chem 266: 15511-15519.
48. Feng S, Kapoor TM, Shirai F, Combs AP, Schreiber SL (1996) Molecular basis for the binding of SH3 ligands with non-peptide elements identified by combinatorial synthesis. Chem Biol 3: 661-670.
49. Larson SM, Davidson AR (2000) The identification of conserved interactions within the SH3 domain by alignment of sequences and structures. Protein Sci 9: 2170-2180.
50. Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI (2002) Direct molecular dynamics observation of protein folding transition state ensemble. Biophys J 83: 3525-3532.
51. Tiana G, Dokholyan NV, Broglia RA, Shakhnovich EI (2004) The evolution dynamics of model proteins. J Chem Phys 121: 2381-2389.
52. Tiana G, Broglia RA, Shakhnovich EI (2000) Hiking in the energy landscape in sequence space: A bumpy road to good folders. Proteins 39: 244-251.
53. Go N (1983) Theoretical studies of protein folding. Annu Rev Biophys Bioeng 12: 183-210.
54. Abe H, Braun W, Noguti T, Go N (1984) Rapid calculation of 1St and 2Nd derivatives of conformational energy with respect to dihedral angles for proteins - general recurrent equations. Computers & Chemistry 8: 239-247.
55. Henikoff S, Henikoff JG (1994) Position-based sequence weights. J Mol Biol 243: 574-578.