How random is a highly denatured protein?

There has been renewed interest in determining the physicochemical properties of denatured states of proteins. In many denatured states there is evidence for the existence of nonrandom configurational distributions. Here we examine the small-angle neutron scattering profile of yeast phosphoglycerate kinase in the native state and in highly denaturing conditions. We show that the denatured protein scattering profile can be interpreted using a model developed for synthetic polymers in which the chain behaves as a random coil in a good solvent, i.e. with excluded volume interactions. The implications of this result for our appreciation of the protein folding process are discussed.

[1]  H. Dyson,et al.  Peptide conformation and protein folding , 1993 .

[2]  T. Bücher.  [63] Phosphoglycerate kinase from Brewer's yeast: d-l,3-Diphosphoglycerate + ADP ⇄ d-3-Phosphoglycerate + ATP , 1955 .

[3]  E. Haas,et al.  Nonlocal interactions stabilize compact folding intermediates in reduced unfolded bovine pancreatic trypsin inhibitor. , 1992, Biochemistry.

[4]  K. Freed,et al.  Static-coherent-scattering function for a single polymer chain: Conformational space renormalization of polymers. V , 1982 .

[5]  P. Gennes.  Scaling Concepts in Polymer Physics , 1979 .

[6]  P. Calmettes,et al.  Structure of nonaqueous electrolyte solutions by small‐angle neutron scattering, hypernetted chain, and Brownian dynamics , 1990 .

[7]  L. Mouawad,et al.  Flexibility and folding of phosphoglycerate kinase. , 1990, Biochimie.

[8]  R. L. Baldwin.  Pulsed H/D-exchange studies of folding intermediates , 1993 .

[9]  M. Kataoka,et al.  Molten globule of cytochrome c studied by small angle X-ray scattering. , 1993, Journal of molecular biology.

[10]  G. Fournet,et al.  Small‐Angle Scattering of X‐Rays , 1956 .

[11]  H. Watson,et al.  Sequence and structure of yeast phosphoglycerate kinase. , 1982, The EMBO journal.

[12]  A. Wada,et al.  ‘Molten‐globule state’: a compact form of globular proteins with mobile side‐chains , 1983, FEBS letters.

[13]  R. Duplessix,et al.  Scattering function of polystyrene , 1987 .

[14]  D. Shortle,et al.  Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea denaturation , 1986, Proteins.

[15]  D. Shortle.  Denatured states of proteins and their roles in folding and stability , 1993 .

[16]  D. Engelman,et al.  Mutations can cause large changes in the conformation of a denatured protein. , 1993, Biochemistry.

[17]  O. Kratky,et al.  Röntgenuntersuchung gelöster Fadenmoleküle , 1949 .

[18]  Bruno H. Zimm,et al.  The Scattering of Light and the Radial Distribution Function of High Polymer Solutions , 1948 .

[19]  A. Fersht,et al.  Principles of protein stability derived from protein engineering experiments , 1993 .

[20]  E. Lattman.  Small angle scattering studies of protein folding , 1994 .

[21]  J. Trewhella,et al.  Denatured states of ribonuclease A have compact dimensions and residual secondary structure. , 1992, Biochemistry.

[22]  G. Porod.  Zusammenhang zwischen mittlerem Endpunktsabstand und Kettenlänge bei Fadenmolekülen , 1949 .

[23]  J. Hermans,et al.  The statistics of stiff chains, with applications to light scattering , 1952 .

[24]  O. Ptitsyn.  Protein folding: Hypotheses and experiments , 1987 .

[25]  C. Dobson,et al.  The folding of hen lysozyme involves partially structured intermediates and multiple pathways , 1992, Nature.

[26]  J. D. Cloizeaux.  Form Factor of an Infinite Kratky-Porod Chain , 1973 .

[27]  Jean Zinn-Justin,et al.  Critical Exponents for the N Vector Model in Three-Dimensions from Field Theory , 1977 .

[28]  O. Glatter,et al.  19 – Small-Angle X-ray Scattering , 1973 .

[29]  Configurational distribution of denatured phosphoglycerate kinase. , 1993, Journal of molecular biology.

[30]  J. R. Huth,et al.  Protein folding and assembly in vitro parallel intracellular folding and assembly. Catalysis of folding and assembly of the human chorionic gonadotropin alpha beta dimer by protein disulfide isomerase. , 1993, The Journal of biological chemistry.

[31]  Thomas E. Creighton,et al.  Stability of folded conformations , 1991 .

[32]  K. Dill.  Dominant forces in protein folding. , 1990, Biochemistry.

[33]  T. Creighton.  Proteins: Structures and Molecular Properties , 1986 .

[34]  L. Mouawad,et al.  Introduction of internal cysteines as conformational probes in yeast phosphoglycerate kinase. , 1990, Protein engineering.

[35]  W. Pfeil,et al.  Cold denaturation-induced conformational changes in phosphoglycerate kinase from yeast. , 1993, Biochemistry.

[36]  P. Flory.  Principles of polymer chemistry , 1953 .

[37]  K. Hirano,et al.  Intestinal-like alkaline phosphatase expressed in normal human adult kidney. , 1989, European journal of biochemistry.

[38]  G. Wider,et al.  NMR determination of residual structure in a urea-denatured protein, the 434-repressor. , 1992, Science.

[39]  T. Witten.  Short‐distance monomer correlations in a self‐repelling polymer chain , 1982 .

[40]  I. Noda,et al.  Particle scattering factor of polymer chains with excluded volumes , 1983 .

[41]  M. Goldberg.  The second translation of the genetic message: protein folding and assembly , 1985 .