Protein folding: the stepwise assembly of foldon units.

Equilibrium and kinetic hydrogen exchange experiments show that cytochrome c is composed of five foldon units that continually unfold and refold even under native conditions. Folding proceeds by the stepwise assembly of the foldon units rather than one amino acid at a time. The folding pathway is determined by a sequential stabilization process; previously formed foldons guide and stabilize subsequent foldons to progressively build the native protein. Four other proteins have been found to show similar behavior. These results support stepwise protein folding pathways through discrete intermediates.

[1]  Tracy M. Handel,et al.  Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH , 1996, Nature Structural Biology.

[2]  L. Mayne,et al.  Two‐state vs. multistate protein unfolding studied by optical melting and hydrogen exchange , 2000, Protein science : a publication of the Protein Society.

[3]  S. Kennedy,et al.  Thermodynamic and kinetic exploration of the energy landscape of Borrelia burgdorferi OspA by native-state hydrogen exchange. , 2002, Journal of molecular biology.

[4]  K. Dill,et al.  From Levinthal to pathways to funnels , 1997, Nature Structural Biology.

[5]  D. Baker,et al.  Contact order, transition state placement and the refolding rates of single domain proteins. , 1998, Journal of molecular biology.

[6]  C. Pace,et al.  Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding , 1995, Protein science : a publication of the Protein Society.

[7]  B. Zimm,et al.  Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains , 1959 .

[8]  J. Onuchic,et al.  Theory of Protein Folding This Review Comes from a Themed Issue on Folding and Binding Edited Basic Concepts Perfect Funnel Landscapes and Common Features of Folding Mechanisms , 2022 .

[9]  T. Sosnick,et al.  Molecular collapse: The rate‐limiting step in two‐state cytochrome c folding , 1996, Proteins.

[10]  S. Englander,et al.  Cooperative omega loops in cytochrome c: role in folding and function. , 2003, Journal of molecular biology.

[11]  Leland Mayne,et al.  Evidence for an unfolding and refolding pathway in cytochrome c , 1998, Nature Structural Biology.

[12]  J. Onuchic,et al.  Funnels, pathways, and the energy landscape of protein folding: A synthesis , 1994, Proteins.

[13]  S Walter Englander,et al.  Protein hydrogen exchange mechanism: Local fluctuations , 2003, Protein science : a publication of the Protein Society.

[14]  T. Sosnick,et al.  Protein folding intermediates: native-state hydrogen exchange. , 1995, Science.

[15]  L. Mayne,et al.  Intimate view of a kinetic protein folding intermediate: residue-resolved structure, interactions, stability, folding and unfolding rates, homogeneity. , 2003, Journal of molecular biology.

[16]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[17]  S. Marqusee,et al.  Comparison of equilibrium and kinetic approaches for determining protein folding mechanisms. , 2000, Advances in protein chemistry.

[18]  S. Englander,et al.  The N-terminal to C-terminal motif in protein folding and function. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Yawen Bai,et al.  Protein stability parameters measured by hydrogen exchange , 1994, Proteins.

[20]  A. Koide,et al.  Conformational heterogeneity of an equilibrium folding intermediate quantified and mapped by scanning mutagenesis. , 2004, Journal of molecular biology.

[21]  R. Lipsitz,et al.  Specific non-native hydrophobic interactions in a hidden folding intermediate: implications for protein folding. , 2003, Biochemistry.

[22]  S. Englander,et al.  How cytochrome c folds, and why: submolecular foldon units and their stepwise sequential stabilization. , 2004, Journal of molecular biology.

[23]  P. Harbury,et al.  The equilibrium unfolding pathway of a (β/α)8 barrel , 2002 .

[24]  A J Wand,et al.  Local dynamics and stability of apocytochrome b562 examined by hydrogen exchange. , 1998, Biochemistry.

[25]  A J Wand,et al.  Local stability and dynamics of apocytochrome b562 examined by the dependence of hydrogen exchange on hydrostatic pressure. , 1998, Biochemistry.

[26]  J Rumbley,et al.  An amino acid code for protein folding. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[27]  S W Englander,et al.  Isotope effects in peptide group hydrogen exchange , 1993, Proteins.

[28]  A. D. Robertson,et al.  Kinetics of conformational fluctuations by EX1 hydrogen exchange in native proteins. , 2001, Methods in molecular biology.

[29]  S. Englander,et al.  Cytochrome c folding pathway: Kinetic native-state hydrogen exchange , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[30]  V. Hilser,et al.  Ensemble modulation as an origin of denaturant-independent hydrogen exchange in proteins. , 2000, Journal of molecular biology.

[31]  S. Englander,et al.  Recombinant equine cytochrome c in Escherichia coli: high-level expression, characterization, and folding and assembly mutants. , 2002, Biochemistry.

[32]  S. Englander,et al.  Hydrogen exchange methods to study protein folding. , 2004, Methods.

[33]  Yawen Bai,et al.  Relationship between the native-state hydrogen exchange and folding pathways of a four-helix bundle protein. , 2002, Biochemistry.

[34]  L Mayne,et al.  Determinants of protein hydrogen exchange studied in equine cytochrome c , 1998, Protein science : a publication of the Protein Society.

[35]  Yawen Bai,et al.  Primary structure effects on peptide group hydrogen exchange , 1993, Biochemistry.

[36]  Gary J. Pielak,et al.  Entropic Stabilization of Cytochrome c upon Reduction , 1995 .

[37]  S. Englander,et al.  Folding units govern the cytochrome c alkaline transition. , 2003, Journal of molecular biology.

[38]  K. Paul,et al.  On the compounds of ferricytochrome c appearing in acid solution. , 1953, Biochimica et biophysica acta.

[39]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.