Frustration in the energy landscapes of multidomain protein misfolding

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

Volumn 110, Issue 5, 2013, Pages 1680-1685

  Zheng, Weihua ^a   Schafer, Nicholas P ^a   Wolynes, Peter G ^a  

^a RICE UNIVERSITY   (United States)

Author keywords

Aggregation; Funnel

Indexed keywords

AMYLOID; WATER;

AMINO ACID SEQUENCE; ARTICLE; ASSOCIATIVE MEMORY; ENERGY; ENERGY TRANSFER; ENTROPY; HIGH TEMPERATURE; HYDROPHOBICITY; LANDSCAPE; POINT MUTATION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE;

BINDING SITES; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, MOLECULAR; MUSCLE PROTEINS; PROTEIN FOLDING; PROTEIN KINASES; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SRC HOMOLOGY DOMAINS; THERMODYNAMICS;

EID: 84873105668     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1222130110     Document Type: Article

References (30)

1. Wolynes PG (2005) Energy landscapes and solved protein-folding problems.. Philos Trans R Soc A 363:453-467. (Pubitemid 40176985)
2. Selkoe DJ (2003) Folding proteins in fatal ways. Nature 426(6968):900-904. (Pubitemid 38056883)
3. Chiti F, Dobson CM (2006) Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 75:333-366. (Pubitemid 44118036)
4. Silow M, Tan Y-J, Fersht AR, Oliveberg M (1999) Formation of short-lived protein aggregates directly from the coil in two-state folding. Biochemistry 38(40):13006-13012.
5. Yang S, et al. (2004) Domain swapping is a consequence of minimal frustration. Proc Natl Acad Sci USA 101(38):13786-13791. (Pubitemid 39298485)
6. Sambashivan S, Liu Y, Sawaya MR, Gingery M, Eisenberg D (2005) Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native-like structure. Nature 437(7056):266-269. (Pubitemid 41294490)
7. Bennett MJ, Sawaya MR, Eisenberg D (2006) Deposition diseases and 3D domain swapping. Structure 14(5):811-824. (Pubitemid 43674098)
8. Oliveberg M (1998) Alternative explanations for "Multistate" kinetics in protein folding: Transient aggregation and changing transition-state ensembles. Acc Chem Res 31:765-772. (Pubitemid 128474543)
9. Otzen DE, Kristensen O, Oliveberg M (2000) Designed protein tetramer zipped together with a hydrophobic Alzheimer homology: A structural clue to amyloid assembly. Proc Natl Acad Sci USA 97(18):9907-9912.
10. MacPhee CE, Dobson CM (2000) Formation of mixed fibrils demonstrates the generic nature and potential utility of amyloid nanostructures. J Am Chem Soc 122:12707-12713. (Pubitemid 32052199)
11. Fernandez-Escamilla A-M, Rousseau F, Schymkowitz J, Serrano L (2004) Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol 22(10):1302-1306. (Pubitemid 39336784)
12. Tartaglia GG, et al. (2008) Prediction of aggregation-prone regions in structured proteins. J Mol Biol 380(2):425-436.
13. Wright CF, Teichmann SA, Clarke J, Dobson CM (2005) The importance of sequence diversity in the aggregation and evolution of proteins. Nature 438(7069):878-881. (Pubitemid 41753072)
14. Borgia MB, et al. (2011) Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins. Nature 474(7353):662-665.
15. Han J-H, Batey S, Nickson AA, Teichmann SA, Clarke J (2007) The folding and evolution of multidomain proteins. Nat Rev Mol Cell Biol 8(4):319-330. (Pubitemid 46474660)
16. Bryngelson JD, Wolynes PG (1987) Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci USA 84(21):7524-7528.
17. Papoian GA, Ulander J, Eastwood MP, Luthey-Schulten Z, Wolynes PG (2004) Water in protein structure prediction. Proc Natl Acad Sci USA 101(10):3352-3357. (Pubitemid 38338198)
18. Davtyan A, et al. (2012) AWSEM-MD: Protein structure prediction using coarsegrained physical potentials and bioinformatically based local structure biasing. J Phys Chem B 116(29):8494-8503.
19. Zheng W, Schafer NP, Davtyan A, Papoian GA, Wolynes PG (2012) Predictive energy landscapes for protein-protein association. Proc Natl Acad Sci USA 109(47):19244-19249.
20. Frousios KK, Iconomidou VA, Karletidi C-M, Hamodrakas SJ (2009) Amyloidogenic determinants are usually not buried. BMC Struct Biol 9:44.
21. Galzitskaya OV, Garbuzynskiy SO, Lobanov MY (2006) Prediction of amyloidogenic and disordered regions in protein chains. PLoS Comput Biol 2(12):e177.
22. Hamodrakas SJ, Liappa C, Iconomidou VA (2007) Consensus prediction of amyloidogenic determinants in amyloid fibril-forming proteins. Int J Biol Macromol 41(3):295-300. (Pubitemid 46990531)
23. López De La Paz M, Serrano L (2004) Sequence determinants of amyloid fibril formation. Proc Natl Acad Sci USA 101(1):87-92. (Pubitemid 38084208)
24. Zhang Z, Chen H, Lai L (2007) Identification of amyloid fibril-forming segments based on structure and residue-based statistical potential. Bioinformatics 23(17):2218-2225. (Pubitemid 47423858)
25. Sawaya MR, et al. (2007) Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature 447(7143):453-457. (Pubitemid 46816731)
26. Schwartz R, Istrail S, King J (2001) Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues. Protein Sci 10(5):1023-1031. (Pubitemid 32367494)
27. Goldschmidt L, Teng PK, Riek R, Eisenberg D (2010) Identifying the amylome, proteins capable of forming amyloid-like fibrils. Proc Natl Acad Sci USA 107(8):3487-3492.
28. Ferreiro DU, Hegler JA, Komives EA, Wolynes PG (2007) Localizing frustration in native proteins and protein assemblies. Proc Natl Acad Sci USA 104(50):19819-19824.
29. Flory P, et al. (2004) Statistical mechanics of chain molecules. Biopolymers 8:699-700.
30. Wolynes PG, Eaton W (1999) The physics of protein folding. Phys World 12:39-44.