Restricted sidechain plasticity in the structures of native proteins and complexes

Protein Science

Volumn 20, Issue 4, 2011, Pages 753-757

  Fleishman, Sarel J ^a   Khare, Sagar D ^a   Koga, Nobuyasu ^a   Baker, David ^a,b  

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

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Aromatic residues; Boltzmann distribution; Entropy of binding; Monomer design; Negative design; Protein design; Rossman fold design; Small molecule binding

Indexed keywords

MONOMER; PROTEIN;

ARTICLE; BINDING KINETICS; COMPARATIVE STUDY; COMPLEX FORMATION; CONTROLLED STUDY; ENERGY TRANSFER; ENTROPY; PLASTICITY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE;

COMPUTER SIMULATION; DATABASES, PROTEIN; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; THERMODYNAMICS;

EID: 79953169868     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.604     Document Type: Article

References (21)

1. Dahiyat BI, Mayo SL (1997) De novo protein design: fully automated sequence selection. Science 278: 82-87. (Pubitemid 27446279)
2. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302: 1364-1368. (Pubitemid 37452172)
3. Shifman JM, Mayo SL (2003) Exploring the origins of binding specificity through the computational redesign of calmodulin. Proc Natl Acad Sci USA 100: 13274-13279. (Pubitemid 37444732)
4. Kortemme T, Joachimiak LA, Bullock AN, Schuler AD, Stoddard BL, Baker D (2004) Computational redesign of protein-protein interaction specificity. Nat Struct Mol Biol 11: 371-379. (Pubitemid 38436803)
5. Rothlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D (2008) Kemp elimination catalysts by computational enzyme design. Nature 453: 190-195. (Pubitemid 351667979)
6. Jiang L, Althoff EA, Clemente FR, Doyle L, Rothlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF III, Hilvert D, Houk KN, Stoddard BL, Baker D (2008) De novo computational design of retro-aldol enzymes. Science 319: 1387-1391. (Pubitemid 351354873)
7. Baker D (2010). An exciting but challenging road ahead for computational enzyme design. Protein Sci 19:1817-1819.
8. Watters AL, Deka P, Corrent C, Callender D, Varani G, Sosnick T, Baker D (2007) The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection. Cell 128: 613-624. (Pubitemid 46198902)
9. Kastritis PL, Bonvin AM (2010) Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. J Proteome Res 9: 2216-2225.
10. Dunbrack RL, Jr, Karplus M (1994) Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Nat Struct Biol 1: 334-340.
11. Das R, Baker D (2008) Macromolecular modeling with rosetta. Annu Rev Biochem 77: 363-382.
12. Bowie JU, Luthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253: 164-170. (Pubitemid 21917131)
13. Havranek JJ, Harbury PB (2003) Automated design of specificity in molecular recognition. Nat Struct Biol 10:45-52. (Pubitemid 36034176)
14. Richardson JS, Richardson DC, Tweedy NB, Gernert KM, Quinn TP, Hecht MH, Erickson BW, Yan Y, McClain RD, Donlan ME, Surles MC (1992) Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992. Biophys J 63: 1185-1209.
15. Zarrinpar A, Park SH, Lim WA (2003) Optimization of specificity in a cellular protein interaction network by negative selection. Nature 426: 676-680. (Pubitemid 38009377)
16. Jha RK, Leaver-Fay A, Yin S, Wu Y, Butterfoss GL, Szyperski T, Dokholyan NV, Kuhlman B (2010) Computational design of a PAK1 binding protein. J Mol Biol 400: 257-270.
17. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ (2005) PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res 33:W363-W367. (Pubitemid 44529944)
18. Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D (2003) Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 331: 281-299. (Pubitemid 36870793)
19. Kortemme T, Kim DE, Baker D (2004) Computational alanine scanning of protein-protein interfaces. Sci STKE2004:pl2.
20. Lawrence MC, Colman PM (1993) Shape complementarity at protein/protein interfaces. J Mol Biol 234: 946-950. (Pubitemid 24027225)
21. Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, Rothlisberger D, Baker D (2006) New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 15: 2785-2794. (Pubitemid 44833759)