Transition states in protein folding

Fersht, A.R. Characterizing transition states in protein folding an essential step in the puzzle. Curr. Opin. Struct. Biol 5 79-84, 1994. 

It is pertinent to ask what is the nature of a transition state in protein folding and if there is evidence that transition states do occur.33... 

Banba S, Brooks CL (2000) Energetic frustration and the nature of the transition state in protein folding, J Chem Phys, 113 3423-3433... 

Poso D., Sessions R.B., Lorch M., Clarke A.R. (2000). Progressive stabilization of intermediate and transition states in protein folding reactions by introducing surface hydro-phobic residues. J. Biol. Chem. 275 33723-33726. 

Frustration and the Nature of the Transition State in Protein Folding. 

In mutational T-value analyses of the transition state of protein folding, site-directed mutagenesis is used to introduce nondisruptive mutations at various... 

V. Villegas, J. C. Martinez, F. X. Aviles et al. Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain. Journal of Molecular Biology, 283 (1998), 1027 F. Chiti, N. Taddei, P. M. White et al. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nature Structural Biology, 6 (1999), 1005. 

Friel, CT, Capaldi, AP, and Radford, SE, Structural analysis of the rate-limiting transition states in the folding of Im7 and Im9 Similarities and differences in the folding of homologous proteins./ournaZ of Molecular Biology 326 (2003) 293-305. 

Optimal rates of folding occur when there is not an initial collapse of structure, hydrophobic or otherwise, but when there is a specific and extended nucleus in the transition state model proteins evolve toward nucleation mechanisms with extended nuclei.45,47... 

Proteins are one of the main classes of biopolymers found in living organisms. They can adopt a large variety of structural patterns, which makes them essential cell constituents mostly involved in recognition processes. Their molecular recognition ability is remarkable in catalysis because enzymes have evolved to accommodate transition states in their active site to lower the kinetic barriers of most biochemical reactions. This ability is connected to appropriate primary sequences, and it allows the proteins to fold into well-defined three-dimensional structures. However, the accuracy of the primary sequence, which is ensured by the translation of genomic sequences in... 

Fersht A (2000) 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 1525-1929... 

Prolyl isomerases are enzymes. In protein folding they catalyze cis trans isomerizations in both directions (Miicke and Schmid, 1992) and show equal efficiencies in unfolding and refolding experiments under identical conditions near the midpoint of the unfolding transition. They carry no information about the isomeric states of the prolyl peptide bonds in the protein substrates. The native isomer is selected by the refolding protein itself simply because the molecules... 

Martinez, J. C., Pisabarro, M. T, and Serrano, L. (1998). Obligatory steps in protein folding and the conformational diversity of the transition state. Nat. Struct. Biol. 5, 721-729. 

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