Rosettaremodel: A generalized framework for flexible backbone protein design

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  Huang, Po Ssu ^a   Ban, Yih En Andrew ^a,e   Richter, Florian ^a,b   Andre, Ingemar ^c   Vernon, Robert ^d   Schief, William R ^a,f   Baker, David ^a,b  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c LUND UNIVERSITY   (Sweden)

^d HOSPITAL FOR SICK CHILDREN   (Canada)

^e Arzeda Corporation   (United States)

^f SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DISULFIDE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CALCULATION; COMPUTER PROGRAM; COMPUTER SIMULATION; FLEXIBLE BACKBONE PROTEIN DESIGN; MOLECULAR DOCKING; MOLECULAR MODEL; PREDICTION; PROTEIN ASSEMBLY; PROTEIN DEPLETION; PROTEIN DOMAIN; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CLUSTER ANALYSIS; METABOLISM; METHODOLOGY; PROTEIN CONFORMATION; SEQUENCE ANALYSIS;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DISULFIDES; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 80052334922     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0024109     Document Type: Article

References (45)

1. Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ, et al. (2006) Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441: 656-659.
2. Havranek JJ, Baker D, (2009) Motif-directed flexible backbone design of functional interactions. Protein Science 18: 1293-1305.
3. Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, et al. (2009) Exploitation of binding energy for catalysis and design. Nature 461: 1300-1304.
4. Ashworth J, Taylor GK, Havranek JJ, Quadri SA, Stoddard BL, et al. (2010) Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Research 38: 5601-5608.
5. Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, et al. (2005) Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor. Journal of the American Chemical Society 127: 1346-1347.
6. Jiang L, Althoff EA, Clemente FR, Doyle L, Rothlisberger D, et al. (2008) De novo computational design of retro-aldol enzymes. Science 319: 1387-1391.
7. Rothlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, et al. (2008) Kemp elimination catalysts by computational enzyme design. Nature 453: 190-195.
8. Murphy PM, Bolduc JM, Gallaher JL, Stoddard BL, Baker D, (2009) Alteration of enzyme specificity by computational loop remodeling and design. Proceedings of the National Academy of Sciences of the United States of America 106: 9215-9220.
9. Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, et al. (2010) Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction. Science 329: 309-313.
10. Treynor TP, Vizcarra CL, Nedelcu D, Mayo SL, (2007) Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function. Proceedings of the National Academy of Sciences of the United States of America 104: 48-53.
11. Yosef E, Politi R, Choi MH, Shifman JM, (2009) Computational Design of Calmodulin Mutants with up to 900-Fold Increase in Binding Specificity. Journal of Molecular Biology 385: 1470-1480.
12. Grigoryan G, Reinke AW, Keating AE, (2009) Design of protein-interaction specificity gives selective bZIP-binding peptides. Nature 458: 859-864.
13. Shukla UJ, Marino H, Huang PS, Mayo SL, Love JJ, (2004) A designed protein interface that blocks fibril formation. Journal of the American Chemical Society 126: 13914-13915.
14. Huang PS, Love JJ, Mayo SL, (2007) A de novo designed protein-protein interface. Protein Science 16: 2770-2774.
15. Guntas G, Purbeck C, Sammond D, Eletr Z, Jha R, et al. (2009) Computer-based Design of Protein-Protein Interactions. Journal of Biomolecular Structure & Dynamics 26: 854-854.
16. Jha RK, Leaver-Fay A, Yin SY, Wu YB, Butterfoss GL, et al. (2010) Computational Design of a PAK1 Binding Protein. Journal of Molecular Biology 400: 257-270.
17. Fleishman SJ, Whitehead TA, Ekiert DC, Dreyfus C, Corn JE, et al. (2011) Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin. Science 332: 816-821.
18. Shah PS, Hom GK, Ross SA, Lassila JK, Crowhurst KA, et al. (2007) Full-sequence computational design and solution structure of a thermostable protein variant. Journal of Molecular Biology 372: 1-6.
19. Malakauskas SM, Mayo SL, (1998) Design, structure and stability of a hyperthermophilic protein variant. Nature Structural Biology 5: 470-475.
20. Calhoun JR, Kono H, Lahr S, Wang W, DeGrado WF, et al. (2003) Computational design and characterization of a monomeric helical dinuclear metalloprotein. Journal of Molecular Biology 334: 1101-1115.
21. Slovic AM, Kono H, Lear JD, Saven JG, DeGrado WF, (2004) Computational design of water-soluble analogues of the potassium channel KcsA. Proceedings of the National Academy of Sciences of the United States of America 101: 1828-1833.
22. Grigoryan G, Kim YH, Acharya R, Axelrod K, Jain RM, et al. (2011) Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces. Science 332: 1071-1076.
23. Swift J, Wehbi WA, Kelly BD, Stowell XF, Saven JG, et al. (2006) Design of functional ferritin-like proteins with hydrophobic cavities. Journal of the American Chemical Society 128: 6611-6619.
24. Dantas G, Kuhlman B, Callender D, Wong M, Baker D, (2003) A large scale test of computational protein design: Folding and stability of nine completely redesigned globular proteins. Journal of Molecular Biology 332: 449-460.
25. Micklatcher C, Chmielewski J, (1999) Helical peptide and protein design. Current Opinion in Chemical Biology 3: 724-729.
26. Qian B, Raman S, Das R, Bradley P, McCoy AJ, et al. (2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450: 259-264.
27. Hu XZ, Wang HC, Ke HM, Kuhlman B, (2007) High-resolution design of a protein loop. Proceedings of the National Academy of Sciences of the United States of America 104: 17668-17673.
28. Correia BE, Ban YE, Friend DJ, Ellingson K, Xu H, et al. Computational protein design using flexible backbone remodeling and resurfacing: case studies in structure-based antigen design. Journal of Molecular Biology 405: 284-297.
29. Kuhlman B, Sammond DW, Bosch DE, Butterfoss GL, Purbeck C, et al. (2011) Computational Design of the Sequence and Structure of a Protein-Binding Peptide. Journal of the American Chemical Society 133: 4190-4192.
30. 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.
31. Rohl CA, Strauss CEM, Misura KMS, Baker D, (2004) Protein structure prediction using rosetta. Methods Enzymol 383: 66-93.
32. Das R, Baker D, (2008) Macromolecular modeling with Rosetta. Annual Review of Biochemistry 77: 363-382.
33. Canutescu AA, Dunbrack RL, (2003) Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Science 12: 963-972.
34. Mandell DJ, Coutsias EA, Kortemme T, (2009) Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nature Methods 6: 551-552.
35. Smagghe BJ, Huang PS, Ban YEA, Baker D, Springer TA, (2010) Modulation of Integrin Activation by an Entropic Spring in the beta-Knee. Journal of Biological Chemistry 285: 32954-32966.
36. Correia BE, Holmes MA, Huang PS, Strong RK, Schief WR, (2011) High-resolution structure prediction of a circular permutation loop. Protein Science in press.
37. Van Montfort T, Melchers M, Isik G, Menis S, Huang PS, et al. (2011) A Chimeric HIV-1 Envelope Glycoprotein Trimer with an Embedded Granulocyte-Macrophage Colony-stimulating Factor (GM-CSF) Domain Induces Enhanced Antibody and T Cell Responses. Journal of Biological Chemistry 286: 22250-22261.
38. Robbins A, Hannah E, Lamb L, (2008) Learning the vi and vim editors. 7th ed Sebastopol, Calif. O'Reilly Media.
39. Wang C, Bradley P, Baker D, (2007) Protein-protein docking with backbone flexibility. Journal of Molecular Biology 373: 503-519.
40. Rohl CA, Strauss CEM, Chivian D, Baker D, (2004) Modeling structurally variable regions in homologous proteins with rosetta. Proteins-Structure Function and Bioinformatics 55: 656-677.
41. Richter F, Leaver-Fay A, Khare SD, Bjelic S, Baker D, (2011) De Novo Enzyme Design Using Rosetta3. Plos One 6: e19230.
42. Andre I, Bradley P, Wang C, Baker D, (2007) Prediction of the structure of symmetrical protein assemblies. Proceedings of the National Academy of Sciences of the United States of America 104: 17656-17661.
43. Wollacott AM, Zanghellini A, Murphy P, Baker D, (2007) Prediction of structures of multidomain proteins from structures of the individual domains. Protein Science 16: 165-175.
44. Goreshnik I, Maly DJ, (2010) A Small Molecule-Regulated Guanine Nucleotide Exchange Factor. Journal of the American Chemical Society 132: 938-940.
45. Cooper S, Khatib F, Treuille A, Barbero J, Lee J, et al. (2010) Predicting protein structures with a multiplayer online game. Nature 466: 756-760.