Prediction of Stable Globular Proteins Using Negative Design with Non-native Backbone Ensembles

Structure

Volumn 23, Issue 11, 2015, Pages 2011-2021

  Davey, James A ^a   Damry, Adam M ^a   Euler, Christian K ^a   Goto, Natalie K ^a   Chica, Roberto A ^a  

^a UNIVERSITY OF OTTAWA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CHYMOTRYPSIN INHIBITOR; GLOBULAR PROTEIN; LYSOZYME; PROTEIN VARIANT; VIRUS PROTEIN V; BACTERIAL PROTEIN; IGG FC-BINDING PROTEIN, STREPTOCOCCUS; SERINE PROTEINASE INHIBITOR; VEGETABLE PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; CIRCULAR DICHROISM; CRYSTAL STRUCTURE; ENTEROBACTERIA PHAGE F1; ENTEROBACTERIA PHAGE T4; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STABILITY; CHEMISTRY; MOLECULAR DYNAMICS; MOLECULAR GENETICS; PROTEIN FOLDING;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PLANT PROTEINS; PROTEIN FOLDING; PROTEIN STABILITY; SERINE PROTEINASE INHIBITORS;

EID: 84946127965     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2015.07.021     Document Type: Article

References (47)

1. M.H. Ali, C.M. Taylor, G. Grigoryan, K.N. Allen, B. Imperiali, and A.E. Keating Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed alpha/beta structure Structure 13 2005 225 234
2. B.D. Allen, and S.L. Mayo Dramatic performance enhancements for the FASTER optimization algorithm J. Comput. Chem. 27 2006 1071 1075
3. B.D. Allen, and S.L. Mayo An efficient algorithm for multistate protein design based on FASTER J. Comput. Chem. 31 2010 904 916
4. B.D. Allen, A. Nisthal, and S.L. Mayo Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles Proc. Natl. Acad. Sci. USA 107 2010 19838 19843
5. F.E. Boas, and P.B. Harbury Potential energy functions for protein design Curr. Opin. Struct. Biol. 17 2007 199 204
6. D.N. Bolon, R.A. Grant, T.A. Baker, and R.T. Sauer Specificity versus stability in computational protein design Proc. Natl. Acad. Sci. USA 102 2005 12724 12729
7. S.D. Bond, B.J. Leimkuhler, and B.B. Laird The Nosé-Poincaré method for constant temperature molecular dynamics J. Comput. Phys. 151 1999 114 134
8. M.S.A. Busch, A. Lopes, D. Mignon, and T. Simonson Computational protein design: software implementation, parameter optimization, and performance of a simple model J. Comput. Chem. 29 2008 1092 1102
9. Chemical Computing Group Molecular Operating Environment (MOE) 2012 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7
10. R.A. Chica, M.M. Moore, B.D. Allen, and S.L. Mayo Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries Proc. Natl. Acad. Sci. USA 107 2010 20257 20262
11. B.I. Dahiyat, and S.L. Mayo Probing the role of packing specificity in protein design Proc. Natl. Acad. Sci. USA 94 1997 10172 10177
12. J.A. Davey, and R.A. Chica Multistate approaches in computational protein design Protein Sci. 21 2012 1241 1252
13. J.A. Davey, and R.A. Chica Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles Proteins 82 2014 771 784
14. I.W. Davis, W.B. Arendall 3rd, D.C. Richardson, and J.S. Richardson The backrub motion: how protein backbone shrugs when a sidechain dances Structure 14 2006 265 274
15. L. Ding, K. Chen, P.A. Santini, Z. Shi, and N.R. Kallenbach The pentapeptide GGAGG has PII conformation J. Am. Chem. Soc. 125 2003 8092 8093
16. R.L. Dunbrack, and F.E. Cohen Bayesian statistical analysis of protein side-chain rotamer preferences Protein Sci. 6 1997 1661 1681
17. T. Gallagher, P. Alexander, P. Bryan, and G.L. Gilliland Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR Biochemistry 33 1994 4721 4729
18. D.B. Gordon, S.A. Marshall, and S.L. Mayo Energy functions for protein design Curr. Opin. Struct. Biol. 9 1999 509 513
19. G. Grigoryan Absolute free energies of biomolecules from unperturbed ensembles J. Comput. Chem. 34 2013 2726 2741
20. G. Grigoryan, A.W. Reinke, and A.E. Keating Design of protein-interaction specificity gives selective bZIP-binding peptides Nature 458 2009 859 864
21. S.C. Howell, K.K. Inampudi, D.P. Bean, and C.J. Wilson Understanding thermal adaptation of enzymes through the multistate rational design and stability prediction of 100 adenylate kinases Structure 22 2014 218 229
22. T.R. Hynes, and R.O. Fox The crystal structure of staphylococcal nuclease refined at 1.7 A resolution Proteins 10 1991 92 105
23. L. Jiang, E.A. Althoff, F.R. Clemente, L. Doyle, D. Rothlisberger, A. Zanghellini, J.L. Gallaher, J.L. Betker, F. Tanaka, C.F. Barbas 3rd, and et al. De novo computational design of retro-aldol enzymes Science 319 2008 1387 1391
24. G.T. Kapp, S. Liu, A. Stein, D.T. Wong, A. Remenyi, B.J. Yeh, J.S. Fraser, J. Taunton, W.A. Lim, and T. Kortemme Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair Proc. Natl. Acad. Sci. USA 109 2012 5277 5282
25. E.H. Kellogg, A. Leaver-Fay, and D. Baker Role of conformational sampling in computing mutation-induced changes in protein structure and stability Proteins 79 2011 830 838
26. N. Koga, R. Tatsumi-Koga, G. Liu, R. Xiao, T.B. Acton, G.T. Montelione, and D. Baker Principles for designing ideal protein structures Nature 491 2012 222 227
27. B. Kuhlman, G. Dantas, G.C. Ireton, G. Varani, B.L. Stoddard, and D. Baker Design of a novel globular protein fold with atomic-level accuracy Science 302 2003 1364 1368
28. P. Labute Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures Proteins 75 2009 187 205
29. F. Lauck, C.A. Smith, G.F. Friedland, E.L. Humphris, and T. Kortemme RosettaBackrub - a web server for flexible backbone protein structure modeling and design Nucleic Acids Res. 38 2010 W569 W575
30. T. Lazaridis, and M. Karplus Effective energy function for proteins in solution Proteins 35 1999 133 152
31. S.L. Mayo, B.D. Olafson, and W.A. Goddard Dreiding - a generic force-field for molecular simulations J. Phys. Chem. 94 1990 8897 8909
32. C.A. McPhalen, and M.N. James Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds Biochemistry 26 1987 261 269
33. W. Meng, N. Lyle, B. Luan, D.P. Raleigh, and R.V. Pappu Experiments and simulations show how long-range contacts can form in expanded unfolded proteins with negligible secondary structure Proc. Natl. Acad. Sci. USA 110 2013 2123 2128
34. T. Mittag, and J.D. Forman-Kay Atomic-level characterization of disordered protein ensembles Curr. Opin. Struct. Biol. 17 2007 3 14
35. S.G. Nash A survey of truncated-Newton methods J. Comput. Appl. Math. 124 2000 45 59
36. N. Pokala, and T.M. Handel Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity J. Mol. Biol. 347 2005 203 227
37. H.K. Privett, G. Kiss, T.M. Lee, R. Blomberg, R.A. Chica, L.M. Thomas, D. Hilvert, K.N. Houk, and S.L. Mayo Iterative approach to computational enzyme design Proc. Natl. Acad. Sci. USA 109 2012 3790 3795
38. P.D. Renfrew, E.J. Choi, R. Bonneau, and B. Kuhlman Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design PLoS One 7 2012 e32637
39. D. Rothlisberger, O. Khersonsky, A.M. Wollacott, L. Jiang, J. DeChancie, J. Betker, J.L. Gallaher, E.A. Althoff, A. Zanghellini, O. Dym, and et al. Kemp elimination catalysts by computational enzyme design Nature 453 2008 190 195
40. J.B. Siegel, A. Zanghellini, H.M. Lovick, G. Kiss, A.R. Lambert, J.L. St Clair, J.L. Gallaher, D. Hilvert, M.H. Gelb, B.L. Stoddard, and et al. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction Science 329 2010 309 313
41. M.M. Skinner, H. Zhang, D.H. Leschnitzer, Y. Guan, H. Bellamy, R.M. Sweet, C.W. Gray, R.N. Konings, A.H. Wang, and T.C. Terwilliger Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein Proc. Natl. Acad. Sci. USA 91 1994 2071 2075
42. P.B. Stranges, and B. Kuhlman A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds Protein Sci. 22 2013 74 82
43. A.G. Street, and S.L. Mayo Pairwise calculation of protein solvent-accessible surface areas Fold Des. 3 1998 253 258
44. J.B. Sturgeon, and B.B. Laird Symplectic algorithm for constant-pressure molecular dynamics using a Nosé-Poincaré thermostat J. Chem. Phys. 112 2000 3474 3482
45. J. Wang, P. Cieplak, and P.A. Kollman How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21 2000 1049 1074
46. L.H. Weaver, and B.W. Matthews Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution J. Mol. Biol. 193 1987 189 199
47. S. Yin, F. Ding, and N.V. Dokholyan Modeling backbone flexibility improves protein stability estimation Structure 15 2007 1567 1576