Simultaneous prediction of protein folding and docking at high resolution

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 45, 2009, Pages 18978-18983

  Dasa, Rhiju ^a,f   André, Ingemar ^a   Shen, Yang ^b   Wu, Yibing ^c   Lemak, Alexander ^d   Bansal, Sonal ^e   Arrowsmith, Cheryl H ^d   Szyperski, Thomas ^c   Baker, David ^a  

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

^b NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^c UNIVERSITY AT BUFFALO   (United States)

^d UNIVERSITY OF TORONTO   (Canada)

^e WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f STANFORD UNIVERSITY   (United States)

Author keywords

Homo oligomers; Molecular replacement; NMR structure inference; Protein structure prediction; Symmetry

Indexed keywords

HOMO OLIGOMER; LEUCINE; OLIGOMER; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; GOLGI COMPLEX; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN MODIFICATION; PROTEIN MOTIF; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; X RAY CRYSTALLOGRAPHY;

COMPUTER SIMULATION; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN FOLDING; PROTEINS; SOFTWARE;

RUMEX;

EID: 73149111493     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0904407106     Document Type: Article

References (39)

1. Goodsell DS, Olson AJ (2000) Structural symmetry and protein function. Annu Rev Biophys Biomol Struct 29:105-153.
2. Levy ED, Pereira-Leal JB, Chothia C, Teichmann SA (2006) 3D complex: a structural classi-fication of protein complexes. PLoS Comput Biol 2:e155.
3. Andre I, Strauss CE, Kaplan DB, Bradley P, Baker D (2008) Emergence of symmetry in homooligomeric biological assemblies. Proc Natl Acad Sci USA 105:16148-16152.
4. Kuriyan J, Eisenberg D (2007) The origin of protein interactions and allostery in colocalization. Nature 450:983-990.
5. Bradley P, MisuraKM,BakerD(2005)Towardhigh-resolutiondenovostructure prediction for small proteins. Science 309:1868-1871.
6. Das R, et al. (2007) Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins 69:118-128.
7. Jauch R, Yeo HC, Kolatkar PR, ClarkeND(2007) Assessment of CASP7 structure predictions for template free targets. Proteins 69:57-67.
8. LensinkMF,MendezR,WodakSJ (2007)Dockingandscoring proteincomplexes:CAPRI 3rd Edition. Proteins 69:704-718.
9. Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D (2005) Progress in modeling of protein structures and interactions. Science 310:638-642.
10. Das R, BakerD(2008) Macromolecular modeling with Rosetta. Annu Rev Biochem 77:363-382.
11. Simons KT, Kooperberg C, Huang E, BakerD(1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268:209-225.
12. Andre I, Bradley P, Wang C, Baker D (2007) Prediction of the structure of symmetrical protein assemblies. Proc Natl Acad Sci USA 104:17656-17661.
13. Rohl CA, Strauss CE, Misura KM, BakerD(2004) Protein structure prediction using Rosetta. Methods Enzymol 383:66-93.
14. Burguete AS, Fenn TD, Brunger AT, Pfeffer SR (2008) Rab and Arl GTPase family members cooperate in the localization of the golgin GCC185. Cell 132:286-298.
15. Crick FHC (1953) The packing of alpha-helices: simple coiled coils. Acta Crystallogr 6:689-697.
16. O'Shea EK, Klemm JD, Kim PS, Alber T (1991) X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 254:539-544.
17. Nilges M, Brunger AT (1993) Successful prediction of the coiled coil geometry of the GCN4 leucine zipperdomainby simulated annealing: comparison to the X-ray structure. Proteins 15:133-146.
18. Kammerer RA, et al. (2005)Aconserved trimerization motif controls the topology of short coiled coils. Proc Natl Acad Sci USA 102:13891-13896.
19. Qian B, et al. (2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450:259-264.
20. Petsko GA (2000) The grail problem. Genome Biol 1:Comment 002.
21. Strop P, Brzustowicz MR, Brunger AT (2007) Ab initio molecular- replacement phasing for symmetric helical membrane proteins. Acta Crystallogr D 63:188-196.
22. Howard RJ, Clark KA, Holton JM, Minor DL, Jr (2007) Structural insight into KCNQ (Kv7) channel assembly and channelopathy. Neuron 53:663-675.
23. Langer G, Cohen SX, Lamzin VS, Perrakis A (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 3:1171-1179.
24. Cavalli A, Salvatella X, Dobson CM, VendruscoloM(2007) Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci USA 104:9615-9620.
25. ShenY, et al. (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105:4685-4690.
26. Montalvao RW, Cavalli A, Salvatella X, Blundell TL, Vendruscolo M (2008) Structure determination of protein-protein complexes using NMR chemical shifts: Case of an endonuclease colicin-immunity protein complex. J Am Chem Soc 130:15990-15996.
27. Lipsitz RS, Tjandra N (2004) Residual dipolar couplings in NMR structure analysis. Annu Rev Biophys Biomol Struct 33:387-413.
28. Cornilescu G, Marquardt JL, Ottiger M, Bax A (1998) Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc 120:6836-6837.
29. Rohl CA, Baker D (2002) De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. J Am Chem Soc 124:2723-2729.
30. Wu Y, et al., Protocol for NMR-based Structural Genomics, High-quality protein structures solved in high-throughput. Twenty-third International Conference on Magnetic Resonance in Biological Systems, August 24-29, 2008, San Diego, CA.
31. Kuhlman B, Baker D (2000) Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA 97:10383-10388.
32. Thompson MJ, et al. (2006) The 3D profile method for identifying fibril-forming segments of proteins. Proc Natl Acad Sci USA 103:4074-4078.
33. Dunbrack RL, Jr, Cohen FE (1997) Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 6:1661-1681.
34. Simons KT, et al. (1999) Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34:82-95.
35. Morozov AV, Kortemme T, Tsemekhman K, Baker D (2004) Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc Natl Acad Sci USA 101:6946-6951.
36. Kortemme T, Morozov AV, Baker D (2003) An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 326:1239-1259.
37. Lazaridis T, Karplus M (1999) Effective energy function for proteins in solution. Proteins 35:133-152.
38. Kuhlman B, et al. (2003) Design ofanovel globular protein fold with atomic-level accuracy. Science 302:1364-1368.
39. Shen Y,Bax A(2007) Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J Biomol NMR 38:289-302.