Branching in the sequential folding pathway of cytochrome c

Previous results indicate that the folding pathways of cytochrome c and other proteins progressively build the target native protein in a predetermined stepwise manner by the sequential formation and association of native‐like foldon units. The present work used native state hydrogen exchange methods to investigate a structural anomaly in cytochrome c results that suggested the concerted folding of two segments that have little structural relationship in the native protein. The results show that the two segments, an 18‐residue omega loop and a 10‐residue helix, are able to unfold and refold independently, which allows a branch point in the folding pathway. The pathway that emerges assembles native‐like foldon units in a linear sequential manner when prior native‐like structure can template a single subsequent foldon, and optional pathway branching is seen when prior structure is able to support the folding of two different foldons.

[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]  G. Brayer,et al.  High-resolution three-dimensional structure of horse heart cytochrome c. , 1990, Journal of molecular biology.

[3]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[4]  M. Karplus,et al.  Protein Folding: A Perspective from Theory and Experiment. , 1998, Angewandte Chemie.

[5]  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.

[6]  J. Onuchic,et al.  Understanding protein folding with energy landscape theory Part I: Basic concepts , 2002, Quarterly Reviews of Biophysics.

[7]  R. Zwanzig,et al.  Levinthal's paradox. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Virgil L. Woods,et al.  Structure and properties of α-synuclein and other amyloids determined at the amino acid level , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[9]  A R Panchenko,et al.  Foldons, protein structural modules, and exons. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[10]  S. Walter Englander,et al.  Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR , 1988, Nature.

[11]  A. Schechter,et al.  Nuclear magnetic resonance titration curves of histidine ring protons. 3. Ribonuclease. , 1972, Journal of molecular biology.

[12]  G. Rose,et al.  Loops in globular proteins: a novel category of secondary structure. , 1986, Science.

[13]  T. Kiefhaber,et al.  Three-state model for lysozyme folding: triangular folding mechanism with an energetically trapped intermediate. , 1997, Journal of molecular biology.

[14]  Virgil L. Woods,et al.  Structure and properties of alpha-synuclein and other amyloids determined at the amino acid level. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Yawen Bai,et al.  A protein folding pathway with multiple folding intermediates at atomic resolution. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

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

[17]  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.

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

[19]  P. Harbury,et al.  The equilibrium unfolding pathway of a (beta/alpha)8 barrel. , 2002, Journal of molecular biology.

[20]  S Walter Englander,et al.  Order of steps in the cytochrome C folding pathway: evidence for a sequential stabilization mechanism. , 2006, Journal of molecular biology.

[21]  C. Matthews,et al.  Sequential vs. parallel protein-folding mechanisms: experimental tests for complex folding reactions. , 2002, Biophysical chemistry.

[22]  S W Englander,et al.  Stable submolecular folding units in a non-compact form of cytochrome c. , 1991, Journal of molecular biology.

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

[24]  J. Onuchic,et al.  Navigating the folding routes , 1995, Science.

[25]  S. Englander,et al.  Functional role of a protein foldon—An Ω‐loop foldon controls the alkaline transition in ferricytochrome c , 2005, Proteins.

[26]  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.

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

[28]  J. Yewdell.  Serendipity strikes twice: the discovery and rediscovery of defective ribosomal products (DRiPS). , 2005, Cellular and molecular biology.

[29]  S W Englander,et al.  Experimental study of the protein folding landscape: unfolding reactions in cytochrome c. , 1999, Journal of molecular biology.

[30]  C L Brooks,et al.  Simulations of protein folding and unfolding. , 1998, Current opinion in structural biology.

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

[32]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1974, Nature.

[33]  S. Marqusee,et al.  Folding of an isolated ribonuclease H core fragment , 2008, Protein science : a publication of the Protein Society.

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

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

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

[37]  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.

[38]  L. Mayne,et al.  Submolecular cooperativity produces multi-state protein unfolding and refolding. , 2002, Biophysical chemistry.

[39]  S. Englander,et al.  Protein misfolding: optional barriers, misfolded intermediates, and pathway heterogeneity. , 2004, Journal of molecular biology.

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

[41]  J. S. Cohen,et al.  Nuclear Magnetic Resonance Titration Curves of Histidine Ring Protons , 2002 .

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

[43]  Ma˚rten Wickstro¨m.  Cytochromes c: evolutionary structural and physicochemical aspects , 1991 .

[44]  S. Marqusee,et al.  A rapid test for identification of autonomous folding units in proteins. , 2000, Journal of molecular biology.

[45]  P. Wolynes,et al.  A funneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[46]  T. Kiefhaber,et al.  A salt-induced kinetic intermediate is on a new parallel pathway of lysozyme folding. , 1999, Biochemistry.

[47]  R. L. Baldwin.  The nature of protein folding pathways: The classical versus the new view , 1995, Journal of biomolecular NMR.

[48]  T. Oas,et al.  A statistical thermodynamic model of the protein ensemble. , 2006, Chemical reviews.

[49]  Carlos Bustamante,et al.  Direct Observation of the Three-State Folding of a Single Protein Molecule , 2005, Science.

[50]  Christopher J. Oldfield,et al.  Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling , 2005, Journal of molecular recognition : JMR.

[51]  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.

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

[53]  J. Cohen,et al.  Nuclear magnetic resonance titration curves of histidine ring protons. V. Comparative study of cytochrome c from three species and the assignment of individual proton resonances. , 1974, The Journal of biological chemistry.

[54]  F. Crick,et al.  Molecular structure of nucleic acids , 2004, JAMA.

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

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

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

[58]  S Walter Englander,et al.  Protein folding: the stepwise assembly of foldon units. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

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

[60]  H. Hamm,et al.  Potent Peptide Analogues of a G Protein Receptor-binding Region Obtained with a Combinatorial Library (*) , 1996, The Journal of Biological Chemistry.

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

[62]  John F. Carpenter,et al.  Physical Stability of Proteins in Aqueous Solution: Mechanism and Driving Forces in Nonnative Protein Aggregation , 2003, Pharmaceutical Research.

[63]  C. Tanford.  Protein denaturation. , 1968, Advances in protein chemistry.

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

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

[66]  J. Onuchic,et al.  Understanding protein folding with energy landscape theory Part II: Quantitative aspects , 2002, Quarterly Reviews of Biophysics.

[67]  S. Englander,et al.  A unified mechanism for protein folding: Predetermined pathways with optional errors , 2007, Protein science : a publication of the Protein Society.

[68]  S W Englander,et al.  Future directions in folding: The multi‐state nature of protein structure , 1996, Proteins.

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

[70]  C. Matthews,et al.  Barriers in protein folding reactions. , 2000, Advances in protein chemistry.

[71]  S. Lifson,et al.  On the Theory of Helix—Coil Transition in Polypeptides , 1961 .

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