Chapter 2 Folding and Wrapping Soluble Proteins. Exploring the Molecular Basis of Cooperativity and Aggregation

Progress in Nucleic Acid Research and Molecular Biology

Volumn 83, Issue , 2008, Pages 53-87

  Fernández, Ariel ^a   Zhang, Xi ^a   Chen, Jianping ^a  

^a Rice University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 58749092693     PISSN: 00796603     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0079-6603(08)00602-8     Document Type: Review

References (55)

1. Anfinsen C.B. Principles that govern the folding of protein chains. Science 181 (1973) 223-230
2. Fernández A., Sosnick T.R., and Colubri A. Dynamics of hydrogen-bond desolvation in folding proteins. J. Mol. Biol. 321 (2002) 659-675
3. Cieplack M. Cooperativity and contact order in protein folding. Phys. Rev. E 69 (2004) 031907
4. Jewett A., Pande V.S., and Plaxco K.W. Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates. J. Mol. Biol. 326 (2003) 247-253
5. Scalley-Kim M., and Baker D. Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection. J. Mol. Biol. 338 (2004) 573-583
6. Fernández A., Colubri A., and Berry R.S. Three-body correlations in protein folding: The origin of cooperativity. Physica A 307 (2002) 235-259
7. Fernández A., Kostov K., and Berry R.S. From residue matching patterns to protein folding topographies: General model and bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. USA 96 (1999) 12991-12996
8. Fernández A., Colubri A., and Berry R.S. Topology to geometry in protein folding: Beta-lactoglobulin. Proc. Natl. Acad. Sci. USA 97 (2000) 14062-14066
9. Fernández A., Kardos J., and Goto J. Protein folding: Could hydrophobic collapse be coupled with hydrogen-bond formation. FEBS Lett. 536 (2003) 187-192
10. Fernández A. Conformation-dependent environments in folding proteins. J. Chem. Phys. 114 (2001) 2489-2502
11. Fernández A., Kardos J., Scott R., Goto Y., and Berry R.S. Structural defects and the diagnosis of amyloidogenic propensity. Proc. Natl. Acad. Sci. USA 100 (2003) 6446-6451
12. Fernández A. Keeping dry and crossing membranes. Nat. Biotechnol. 22 (2004) 1081-1084
13. Pietrosemoli N., Crespo A., and Fernández A. Dehydration propensity of order-disorder intermediate regions in soluble proteins. J. Proteome Res. 6 (2007) 3519-3526
14. Fernández A., and Scott R. Dehydron: A structure-encoded signal for protein interactions. Biophys. J. 85 (2003) 1914-1928
15. Avbelj F., and Baldwin R.L. Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: Distributions of phi. Proc. Natl. Acad. Sci. USA 100 (2003) 5742-5747
16. Krantz B.A., Moran L.B., Kentsis A., and Sosnick T.R. D/H amide kinetic isotope effects reveal when hydrogen bonds form during protein folding. Nat. Struct. Biol. 7 (2000) 62-71
17. Fersht A. Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism. Proc. Natl. Acad. Sci. USA 97 (2000) 1525-1929
18. Plaxco K.W., Simmons K.T., and Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277 (1998) 985-994
19. Fernández A., and Scott L.R. Adherence of packing defects in soluble proteins. Phys. Rev. Lett. 91 (2003) 018102
20. Fernández A. What caliber pore is like a pipe? Nanotubes as modulators of ion gradients. J. Chem. Phys. 119 (2003) 5315-5319 Communication**
21. Fernández A., and Scheraga H.A. Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc. Natl. Acad. Sci. USA 100 (2003) 113-118
22. Fernández A., and Berry R.S. Proteins with H-bond packing defects are highly interactive with lipid bilayers: Implications for amyloidogenesis. Proc. Natl. Acad. Sci. USA 100 (2003) 2391-2396
23. Fernández A. Functionality of wrapping defects in soluble proteins: What cannot be kept dry must be conserved. J. Mol. Biol. 337 (2004) 477-483
24. Fernández A., Scott R.L., and Berry R.S. The nonconserved wrapping of conserved folds reveals a trend towards increasing connectivity in proteomic networks. Proc. Natl. Acad. Sci. USA 101 (2004) 2823-2827
25. Fernández A., and Berry R.S. Molecular dimension explored in evolution to promote proteomic complexity. Proc. Natl. Acad. Sci. USA 101 (2004) 13460-13465
26. Fernández A. Molecular basis for evolving modularity in the yeast protein interaction network. PLoS Comp. Biol. 3 (2007) e226
27. Deremble C., and Lavery R. Macromolecular recognition. Curr. Opin. Struc. Biol. 15 (2005) 171-175
28. Ma B., Elkayam T., Wolfson H., and Nussinov R. Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc. Natl. Acad. Sci. USA 100 (2003) 5772-5777
29. Fernández A., Shen M., Colubri A., Sosnick T.R., and Freed K.F. Large-scale context in protein folding: Villin headpiece. Biochemistry 42 (2003) 664-671
30. Duan Y., and Kollman P.A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282 (1998) 740-744
31. Baldwin R.L. Making a network of hydrophobic clusters. Science 295 (2002) 1657-1658
32. Nemethy G., Steinberg I.Z., and Scheraga H.A. The influence of water structure and hydrophobic contacts on the strength of side-chain hydrogen bonds in proteins. Biopolymers 1 (1963) 43-69
33. Fernández A., and Berry R.S. Extent of hydrogen-bond protection in folded proteins: A constraint on packing architectures. Biophys. J. 83 (2002) 2475-2481
34. Novotny J., Bruccoleri R., and Karplus M. Analysis of incorrectly folded protein models. Implications for structure predictions. J. Mol. Biol. 177 (1984) 787-818
35. Daggett V., and Levitt M. A model of the molten globule state from molecular dynamics simulations. Proc. Natl. Acad. Sci. USA 89 (1992) 5142-5146
36. Brooks III C.L., and Case D. Simulations of peptide conformational dynamics and thermodynamics. Chem. Rev. 93 (1993) 2487-2502
37. Fernández A., and Rogale K. Sequence-space selection of cooperative model proteins. J. Phys. A: Math. Gen. 37 (2004) 197-202
38. Kuwata K., Shastry R., Cheng H., Hoshino M., Batt C.A., Goto Y., and Roder H. Structural and kinetic characterization of early folding events in beta-lactoglobulin. Nat. Struct. Biol. 8 (2001) 151-155
39. Fernández A., Appignanesi G., and Colubri A. Finding the collapse-inducing nucleus in a folding protein. J. Chem. Phys. 114 (2001) 8678-8684
40. Nymeyer H., Garcia A.E., and Onuchic J.N. Folding funnels and frustration in off-lattice minimalist protein landscapes. Proc. Natl. Acad. Sci. 95 (1998) 5921-5928
41. Onuchic J.N., Luthey-Schulten Z., and Wolynes P.G. Theory of protein folding: The energy landscape perspective. Annu. Rev. Phys. Chem. 48 (1997) 545-600
42. Chan H.S., and Dill K.A. From levinthal to pathways to funnels. Nat. Struct. Biol. 4 (1997) 10-19
43. Fernández A., Colubri A., and Berry R.S. Topologies to geometries in protein folding: Hierarchical and nonhierarchical scenarios. J. Chem. Phys. 114 (2001) 5871-5888
44. Shi Z., Krantz B.A., Kallenbach N., and Sosnick T.R. Contribution of hydrogen bonding to protein stability estimated from isotope effects. Biochemistry 41 (2002) 2120-2129
45. Fernández A. Time-resolved backbone desolvation and mutational hot spots in folding proteins. Proteins: Struct. Funct. Genet. 47 (2002) 447-457
46. Despa F., Fernández A., and Berry R.S. Dielectric modulation of biological water. Phys. Rev. Lett. 93 (2004) 228104
47. Dobson C.M. Protein misfolding, evolution and disease. Trends Biochem. Sci. 24 (1999) 329-332
48. Dobson C.M. The structural basis of protein folding and its links with human disease. Philos. Trans. R. Soc. Lond. Ser. B 356 (2001) 133-145
49. Fändrich M., and Dobson C.M. The behavior of polyamino acids reveals an inverse side chain effect in amyloid structure formation. EMBO J. 21 (2002) 5682-5690
50. Sunde M., and Blake C.C.F. From the globular to the fibrous state: Protein structure and structural conversion in amyloid formation. Q. Rev. Biophys. 31 (1998) 1-39
51. Dobson C.M. Protein misfolding diseases: Getting out of shape. Nature 418 (2002) 729-730
52. Richardson J.S., and Richardson D.C. Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc. Natl. Acad. Sci. USA 99 (2002) 2754-2759
53. Nelson R., Sawaya M., Balbirnie M., Madsen A., Riekel C., Grothe R., and Eisenberg D. Structure of the cross-beta spine of amyloid-like fibrils. Nature 435 (2005) 773-778
54. Prusiner S.B. Prions. Proc. Natl. Acad. Sci. USA 95 (1998) 13363-13383
55. Krishnan R., and Lindquist S.L. Structural insights into a yeast prion illuminate nucleation and strain diversity. Nature 435 (2005) 765-772