Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding. I. Myohemerythrin.

In an attempt to delineate potential folding initiation sites for different protein structural motifs, we have synthesized series of peptides that span the entire length of the polypeptide chain of two proteins, and examined their conformational preferences in aqueous solution using proton nuclear magnetic resonance and circular dichroism spectroscopy. We describe here the behavior of peptides derived from a simple four-helix bundle protein, myohemerythrin. The peptides correspond to the sequences of the four long helices (the A, B, C and D helices), the N- and C-terminal loops and the connecting sequences between the helices. The peptides corresponding to the helices of the folded protein all exhibit preferences for helix-like conformations in solution. The conformational ensembles of the A- and D-helix peptides contain ordered helical forms, as shown by extensive series of medium-range nuclear Overhauser effect connectivities, while the B- and C-helix peptides exhibit conformational preferences for nascent helix. All four peptides adopt ordered helical conformations in mixtures of trifluoroethanol and water. The terminal and interconnecting loop peptides also appear to contain appreciable populations of conformers with backbone phi and psi angles in the alpha-region and include highly populated hydrophobic cluster and/or turn conformations in some cases. Trifluoroethanol is unable to drive these peptides towards helical conformations. Overall, the peptide fragments of myohemerythrin have a marked preference towards secondary structure formation in aqueous solution. In contrast, peptide fragments derived from the beta-sandwich protein plastocyanin are relatively devoid of secondary structure in aqueous solution (see accompanying paper). These results suggest that the two different protein structural motifs may require different propensities for formation of local elements of secondary structure to initiate folding, and that there is a prepartitioning of conformational space determined by the local amino acid sequence that is different for the helical and beta-sandwich structural motifs.

[1]  J. L. Smith,et al.  Structure of myohemerythrin in the azidomet state at 1.7/1.3 A resolution. , 1987, Journal of molecular biology.

[2]  A Kolinski,et al.  Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics. , 1991, Journal of molecular biology.

[3]  H. Scheraga,et al.  The influence of long-range interactions on the structure of myoglobin. , 1968, Biochemistry.

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

[5]  V. Lim.  Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure. , 1974, Journal of molecular biology.

[6]  S. Suhai,et al.  Secondary structure of the Arg-Gly-Asp recognition site in proteins involved in cell-surface adhesion. Evidence for the occurrence of nested beta-bends in the model hexapeptide GRGDSP. , 1988, European journal of biochemistry.

[7]  J. Schellman,et al.  Optical activity of polypeptides and proteins , 1972, Biopolymers.

[8]  A. Sykes.  Structure and electron transfer reactivity of the blue copper protein plastocyanin , 1985 .

[9]  J. Hermans,et al.  Relative effects of primary and tertiary structure on helix formation in myoglobin and α‐lactalbumin , 1971 .

[10]  J. Skolnick,et al.  Comparison of lattice Monte Carlo dynamics and Brownian dynamics folding pathways of α-helical hairpins , 1991 .

[11]  P. S. Kim,et al.  The C-peptide helix from ribonuclease A considered as an autonomous folding unit. , 1987, Cold Spring Harbor symposia on quantitative biology.

[12]  J. Guss,et al.  Structure of oxidized poplar plastocyanin at 1.6 A resolution. , 1983, Journal of molecular biology.

[13]  C. Brooks,et al.  Nanosecond time scale folding dynamics of a pentapeptide in water. , 1991, Biochemistry.

[14]  K. Wüthrich,et al.  Improved spectral resolution in cosy 1H NMR spectra of proteins via double quantum filtering. , 1983, Biochemical and biophysical research communications.

[15]  Robert L. Baldwin,et al.  NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A , 1988, Nature.

[16]  Timothy F. Havel,et al.  Three-dimensional solution structure of plastocyanin from the green alga Scenedesmus obliquus. , 1988, Science.

[17]  N. Kallenbach,et al.  Persistence of the alpha-helix stop signal in the S-peptide in trifluoroethanol solutions. , 1989, Biochemistry.

[18]  H. Scheraga,et al.  Folding of polypeptide chains in proteins: a proposed mechanism for folding. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[19]  N J Greenfield,et al.  Circular dichroism and optical rotatory dispersion of proteins and polypeptides. , 1973, Methods in Enzymology.

[20]  P. Gooley,et al.  Location of an alpha-helix in fragment 96-133 from bovine somatotropin by 1H NMR spectroscopy. , 1988, Biochemistry.

[21]  M. Williamson,et al.  1H-NMR assignment and secondary structure of a herpes simplex virus glycoprotein D-1 antigenic domain. , 1986, European journal of biochemistry.

[22]  J Skolnick,et al.  Dynamic Monte Carlo simulations of globular protein folding. Model studies of in vivo assembly of four helix bundles and four member beta-barrels. , 1990, Journal of molecular biology.

[23]  R. Lerner,et al.  The immunodominant site of a synthetic immunogen has a conformational preference in water for a type-II reverse turn , 1985, Nature.

[24]  K. Kuwajima,et al.  The molten globule state as a clue for understanding the folding and cooperativity of globular‐protein structure , 1989, Proteins.

[25]  P. Wright,et al.  Complete assignment of the 1H nuclear magnetic resonance spectrum of French bean plastocyanin. Sequential resonance assignments, secondary structure and global fold. , 1988, Journal of molecular biology.

[26]  Andreas Matouschek,et al.  Transient folding intermediates characterized by protein engineering , 1990, Nature.

[27]  H. Scheraga,et al.  Formation of Local Structures in Protein Folding , 1989 .

[28]  F. Schmid,et al.  The mechanism of protein folding. Implications of in vitro refolding models for de novo protein folding and translocation in the cell. , 1990, Biochemistry.

[29]  R. Jaenicke,et al.  Protein folding: local structures, domains, subunits, and assemblies. , 1991, Biochemistry.

[30]  P E Wright,et al.  Defining solution conformations of small linear peptides. , 1991, Annual review of biophysics and biophysical chemistry.

[31]  E. Eyring,et al.  Helix–coil transition kinetics in aqueous poly(α,L‐glutamic acid) , 1975 .

[32]  R. Ambler,et al.  The amino acid sequence of plastocyanin from French bean (Phaseolus vulgaris). , 1974, The Biochemical journal.

[33]  M. Rance.  Improved techniques for homonuclear rotating-frame and isotropic mixing experiments , 1987 .

[34]  L. Regan,et al.  Characterization of a helical protein designed from first principles. , 1988, Science.

[35]  M. Rance,et al.  Obtaining high-fidelity spin-12 powder spectra in anisotropic media: Phase-cycled Hahn echo spectroscopy , 1983 .

[36]  J. Guss,et al.  Crystal structure of plastocyanin from a green alga, Enteromorpha prolifera. , 1990, Journal of molecular biology.

[37]  Structure determination of a tetrasaccharide: transient nuclear Overhauser effects in the rotating frame , 1984 .

[38]  M. Illangasekare,et al.  Circular dichroism studies of distorted α-helices, twisted β-sheets, and β-turns , 1988 .

[39]  L. Gierasch,et al.  Reduced tendency to form a beta turn in peptides from the P22 tailspike protein correlates with a temperature-sensitive folding defect. , 1990, Biochemistry.

[40]  W. D. Phillips,et al.  Sensitive criteria for the critical size for helix formation in oligopeptides. , 1969, Proceedings of the National Academy of Sciences of the United States of America.

[41]  R. Lerner,et al.  The physical basis for induction of protein-reactive antipeptide antibodies. , 1988, Annual review of biophysics and biophysical chemistry.

[42]  M. Karplus,et al.  Diffusion–collision model for protein folding , 1979 .

[43]  H. Dyson,et al.  Solution conformational preferences of immunogenic peptides derived from the principal neutralizing determinant of the HIV-1 envelope glycoprotein gp120. , 1991, Biochemistry.

[44]  R. L. Baldwin,et al.  Early folding intermediate of ribonuclease A. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[45]  J. Berzofsky,et al.  T-cell antigenic peptides from sperm whale myoglobin fold as amphipathic helices: a possible determinant for immunodominance? , 1989, Peptide research.

[46]  R. Woody,et al.  Theoretical study of the contribution of aromatic side chains to the circular dichroism of basic bovine pancreatic trypsin inhibitor. , 1989, Biochemistry.

[47]  R L Stanfield,et al.  Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 A. , 1992, Science.

[48]  R. Jaenicke,et al.  Folding and association of proteins. , 1982, Biophysics of structure and mechanism.

[49]  A. Bellocq,et al.  [Conformation analysis of L-pyroglutamic acid N-methylamide by depolarized Rayleigh diffusion, vibration spectroscopy, and conformational energy calculation]. , 1975, Biopolymers.

[50]  J. Hermans,et al.  Beta poly(L-lysine): a model system for biological self-assembly. , 1974, Journal of molecular biology.

[51]  P S Kim,et al.  Folding of a peptide corresponding to the alpha-helix in bovine pancreatic trypsin inhibitor. , 1989, Biochemistry.

[52]  A. Kolinski,et al.  Simulations of the Folding of a Globular Protein , 1990, Science.

[53]  O B Ptitsyn.  How does protein synthesis give rise to the 3D‐structure? , 1991, FEBS letters.

[54]  J. Skolnick,et al.  Computer simulations of globular protein folding and tertiary structure. , 1989, Annual review of physical chemistry.

[55]  J. King,et al.  Surface amino acids as sites of temperature-sensitive folding mutations in the P22 tailspike protein. , 1988, The Journal of biological chemistry.

[56]  H. Mantsch,et al.  Structural studies with the uveopathogenic peptide M derived from retinal S-antigen. , 1990, Biochemistry.

[57]  P. Wright,et al.  25 – THE H-HELIX OF MYOGLOBIN AS A POTENTIAL INDEPENDENT PROTEIN FOLDING DOMAIN , 1990 .

[58]  F. Blanco,et al.  Tendamistat (12–26) fragment , 1991 .

[59]  C. Dobson,et al.  Hydrophobic clustering in nonnative states of a protein: Interpretation of chemical shifts in NMR spectra of denatured states of lysozyme , 1991, Proteins.

[60]  K Wüthrich,et al.  Sequential resonance assignments in protein 1H nuclear magnetic resonance spectra. Computation of sterically allowed proton-proton distances and statistical analysis of proton-proton distances in single crystal protein conformations. , 1982, Journal of molecular biology.

[61]  D. Case,et al.  Folding of Peptide Fragments of Proteins in Aqueous Solution , 1990 .

[62]  P E Wright,et al.  Folding of immunogenic peptide fragments of proteins in water solution. II. The nascent helix. , 1988, Journal of molecular biology.

[63]  David A. Case,et al.  Unfolding of an α‐helix in water , 1991 .

[64]  B. W. Erickson,et al.  Conformational analysis of COOH-terminal segments of human C3a. Evidence of ordered conformation in an active 21-residue peptide. , 1984, The Journal of biological chemistry.

[65]  M. Goodman,et al.  Mechanisms of protein and polypeptide helix initiation , 1975 .

[66]  P. S. Kim,et al.  A helix stop signal in the isolated S-peptide of ribonuclease A , 1984, Nature.

[67]  M. Sundaralingam,et al.  Water-inserted alpha-helical segments implicate reverse turns as folding intermediates. , 1989, Science.

[68]  A. Fersht,et al.  Detection and characterization of a folding intermediate in barnase by NMR , 1990, Nature.

[69]  C. Brooks,et al.  Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides. , 1991, Biochemistry.

[70]  Theoretical evidence for destabilization of an .alpha.-helix by water insertion: molecular dynamics of hydrated decaalanine , 1990 .

[71]  P. S. Kim,et al.  Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. , 1982, Annual review of biochemistry.

[72]  C B Anfinsen,et al.  An experimental approach to the study of the folding of staphylococcal nuclease. , 1969, The Journal of biological chemistry.

[73]  G. L. Klippenstein,et al.  The primary structure of myohemerythrin. , 1976, Biochemistry.

[74]  H. Edelhoch,et al.  Spectroscopic determination of tryptophan and tyrosine in proteins. , 1967, Biochemistry.

[75]  E. Kaiser,et al.  Design and characterization of peptides with amphiphilic β‐strand structures , 1985 .

[76]  K. Wüthrich,et al.  The X‐Pro peptide bond as an nmr probe for conformational studies of flexible linear peptides , 1976, Biopolymers.

[77]  K Wüthrich,et al.  Polypeptide secondary structure determination by nuclear magnetic resonance observation of short proton-proton distances. , 1984, Journal of molecular biology.

[78]  Christopher M. Dobson,et al.  Demonstration by NMR of folding domains in lysozyme , 1991, Nature.

[79]  T. Creighton,et al.  Experimental studies of protein folding and unfolding. , 1978, Progress in biophysics and molecular biology.

[80]  K Wüthrich,et al.  Conformation of glucagon in a lipid-water interphase by 1H nuclear magnetic resonance. , 1983, Journal of molecular biology.

[81]  C. Tanford,et al.  The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale. , 1971, The Journal of biological chemistry.

[82]  H. Scheraga,et al.  Local interactions in bends of proteins. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[83]  J. Sanders-Loehr,et al.  Structure of the binuclear iron complex in metazidohaemerythrin from Themiste dyscritum at 2.2. Å resolution , 1981, Nature.

[84]  D. Case,et al.  High-resolution solution structure of reduced French bean plastocyanin and comparison with the crystal structure of poplar plastocyanin. , 1991, Journal of molecular biology.

[85]  R. Lerner,et al.  Conformation of a T cell stimulating peptide in aqueous solution , 1989, FEBS letters.

[86]  S. N. Timasheff.  Protein-solvent interactions and protein conformation , 1970 .

[87]  J Tirado-Rives,et al.  Molecular dynamics simulations of the unfolding of an alpha-helical analogue of ribonuclease A S-peptide in water. , 1991, Biochemistry.

[88]  D. E. Parks,et al.  Immunogenic peptides corresponding to the dominant antigenic region alanine-597 to cysteine-619 in the transmembrane protein of simian immunodeficiency virus have a propensity to fold in aqueous solution. , 1992, Biochemistry.

[89]  P. S. Kim,et al.  Intermediates in the folding reactions of small proteins. , 1990, Annual review of biochemistry.

[90]  T. Leist,et al.  Synthesis and physicochemical characterization of major fragments of human leucocyte interferon alpha 1. , 1984, Biochemistry.

[91]  Y. Noda,et al.  Local structures in unfolded lysozyme and correlation with secondary structures in the native conformation: Helix‐forming or ‐breaking propensity of peptide segments , 1991, Biopolymers.

[92]  W. C. Johnson,et al.  Circular dichroism and its empirical application to biopolymers. , 1985, Methods of biochemical analysis.

[93]  R. Lerner,et al.  Conformational preferences of synthetic peptides derived from the immunodominant site of the circumsporozoite protein of Plasmodium falciparum by 1H NMR. , 1990, Biochemistry.

[94]  P E Wright,et al.  1H NMR studies of the solution conformations of an analogue of the C-peptide of ribonuclease A. , 1989, Biochemistry.

[95]  J E Wampler,et al.  Occurrence and role of cis peptide bonds in protein structures. , 1990, Journal of molecular biology.

[96]  P. S. Kim,et al.  27 – Tests Of Isolated β–Sheet Formation In A Cyclic Peptide From BPTI , 1990 .

[97]  K. Wüthrich,et al.  Characterisation of a local structure in the synthetic parathyroid hormone fragment 1--34 by 1H nuclear-magnetic-resonance techniques. , 1978, European journal of biochemistry.

[98]  P. Y. Chou,et al.  Prediction of the secondary structure of proteins from their amino acid sequence. , 2006 .

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

[100]  Ad Bax,et al.  MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy , 1985 .

[101]  R. Lumry,et al.  The dynamics of the helix‐coil transition in poly‐α, L‐glutamic acid , 1964 .

[102]  P E Wright,et al.  Folding of immunogenic peptide fragments of proteins in water solution. I. Sequence requirements for the formation of a reverse turn. , 1988, Journal of molecular biology.

[103]  H. Halvorson,et al.  Consideration of the Possibility that the slow step in protein denaturation reactions is due to cis-trans isomerism of proline residues. , 1975, Biochemistry.

[104]  A. L. V. Geet.  Calibration of the methanol and glycol nuclear magnetic resonance thermometers with a static thermistor probe , 1968 .

[105]  J. E. Brown,et al.  Helix-coil transition of the isolated amino terminus of ribonuclease. , 1971, Biochemistry.

[106]  P. S. Kim,et al.  Nature of the charged-group effect on the stability of the C-peptide helix. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[107]  J Skolnick,et al.  Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. II. Alpha-helical motifs. , 1990, Journal of molecular biology.

[108]  H. Dyson,et al.  Mapping the anatomy of the immunodominant domain of the human immunodeficiency virus gp41 transmembrane protein: peptide conformation analysis using monoclonal antibodies and proton nuclear magnetic resonance spectroscopy , 1991, Journal of virology.

[109]  Kurt Wüthrich,et al.  Origin of τ2 and τ2 ridges in 2D NMR spectra and procedures for suppression , 1986 .

[110]  P E Wright,et al.  Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding. , 1988, Biochemistry.

[111]  Richard R. Ernst,et al.  Investigation of exchange processes by two‐dimensional NMR spectroscopy , 1979 .