An analysis of the helix‐to‐strand transition between peptides with identical sequence

An analysis of peptide segments with identical sequence but that differ significantly in structure was performed over non‐redundant databases of protein structures. We focus on those peptides, which fold into an α‐helix in one protein but a β‐strand in another. While the study shows that many such structurally ambivalent peptides contain amino acids with a strong helical preference collocated with amino acids with a strong strand preference, the results overwhelmingly indicate that the peptide's environment ultimately dictates its structure. Furthermore, the first naturally occurring structurally ambivalent nonapeptide from evolutionary unrelated proteins is described, highlighting the intrinsic plasticity of peptide sequences. We even find seven proteins that show structural ambivalence under different conditions. Finally, a computer algorithm has been implemented to identify regions in a given sequence where secondary structure prediction programs are likely to make serious mispredictions. Proteins 2000;41:248–256. © 2000 Wiley‐Liss, Inc.

[1]  Gaston H. Gonnet,et al.  Darwin v. 2.0: an interpreted computer language for the biosciences , 2000, Bioinform..

[2]  S. Ramaswamy,et al.  Crystal structure of NAD(P)H:flavin oxidoreductase from Escherichia coli. , 1999, Biochemistry.

[3]  R. Sauer,et al.  Evolution of a protein fold in vitro. , 1999, Science.

[4]  B. Kobe.  Autoinhibition by an internal nuclear localization signal revealed by the crystal structure of mammalian importin α , 1999, Nature Structural Biology.

[5]  Jaime Prilusky,et al.  Automated analysis of interatomic contacts in proteins , 1999, Bioinform..

[6]  L. Johnson,et al.  Effects of Phosphorylation of Threonine 160 on Cyclin-dependent Kinase 2 Structure and Activity* , 1999, The Journal of Biological Chemistry.

[7]  Malin M. Young,et al.  Predicting conformational switches in proteins , 1999, Protein science : a publication of the Protein Society.

[8]  Malin M. Young,et al.  Predicting allosteric switches in myosins , 1999, Protein science : a publication of the Protein Society.

[9]  D. Baker,et al.  Improved recognition of native‐like protein structures using a combination of sequence‐dependent and sequence‐independent features of proteins , 1999, Proteins.

[10]  G. Rose,et al.  Is protein folding hierarchic? I. Local structure and peptide folding. , 1999, Trends in biochemical sciences.

[11]  J. Abrahams,et al.  Implications for function and therapy of a 2.9 A structure of binary-complexed antithrombin. , 1998, Journal of molecular biology.

[12]  J. Kastrup,et al.  Structure of the C-type lectin carbohydrate recognition domain of human tetranectin. , 1998, Acta crystallographica. Section D, Biological crystallography.

[13]  S. Jacchieri.  Study of α-helix to β-strand to β-sheet transitions in amyloid: the role of segregated hydrophobic β-strands , 1998 .

[14]  A. Gronenborn,et al.  Solution structure of cyanovirin-N, a potent HIV-inactivating protein , 1998, Nature Structural Biology.

[15]  S. Sudarsanam,et al.  Structural diversity of sequentially identical subsequences of proteins: Identical octapeptides can have different conformations , 1998, Proteins.

[16]  S. Jacchieri.  Study of alpha-helix to beta-strand to beta-sheet transitions in amyloid: the role of segregated hydrophobic beta-strands. , 1998, Biophysical chemistry.

[17]  Tim J. P. Hubbard,et al.  SCOP: a structural classification of proteins database , 1998, Nucleic Acids Res..

[18]  J. Abrahams,et al.  The anticoagulant activation of antithrombin by heparin. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[19]  R A Houghten,et al.  Secondary structure induction in aqueous vs membrane‐like environments , 1997, Biopolymers.

[20]  F E Cohen,et al.  Solution structure of a 142-residue recombinant prion protein corresponding to the infectious fragment of the scrapie isoform. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[21]  J. Kastrup,et al.  Crystal structure of tetranectin, a trimeric plasminogen‐binding protein with an α‐helical coiled coil , 1997, FEBS letters.

[22]  J. M. Levin,et al.  Exploring the limits of nearest neighbour secondary structure prediction. , 1997, Protein engineering.

[23]  M. Hennig,et al.  Crystal structure at 2.0 A resolution of phosphoribosyl anthranilate isomerase from the hyperthermophile Thermotoga maritima: possible determinants of protein stability. , 1997, Biochemistry.

[24]  E A Merritt,et al.  Raster3D: photorealistic molecular graphics. , 1997, Methods in enzymology.

[25]  B Rost,et al.  Better 1D predictions by experts with machines , 1997, Proteins.

[26]  S Thirup,et al.  Helix unwinding in the effector region of elongation factor EF-Tu-GDP. , 1996, Structure.

[27]  D Baker,et al.  Global properties of the mapping between local amino acid sequence and local structure in proteins. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[28]  P. S. Kim,et al.  Context-dependent secondary structure formation of a designed protein sequence , 1996, Nature.

[29]  D. Butler.  Slow release of data adds to BSE confusion , 1996, Nature.

[30]  P. Argos,et al.  Knowledge‐based protein secondary structure assignment , 1995, Proteins.

[31]  Kornelia Polyak,et al.  Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex , 1995, Nature.

[32]  M. Bolognesi,et al.  Crystal structure of Escherichia coli pyruvate kinase type I: molecular basis of the allosteric transition. , 1995, Structure.

[33]  R A Houghten,et al.  Induced conformational states of amphipathic peptides in aqueous/lipid environments. , 1995, Biophysical journal.

[34]  J. Springer,et al.  Structural studies of metal binding by inositol monophosphatase: evidence for two-metal ion catalysis. , 1995, Biochemistry.

[35]  V. Muñoz,et al.  Intrinsic secondary structure propensities of the amino acids, using statistical ϕ–ψ matrices: Comparison with experimental scales , 1994 .

[36]  T. J. Stillman,et al.  The three-dimensional structure of PNGase F, a glycosyl asparaginase from Flavobacterium meningosepticum , 1994 .

[37]  J. Skehel,et al.  Structure of influenza haemagglutinin at the pH of membrane fusion , 1994, Nature.

[38]  B. Matthews,et al.  Three-dimensional structure of β-galactosidase from E. coli. , 1994, Nature.

[39]  G. Rose,et al.  α‐Helix‐forming propensities in peptides and proteins , 1994 .

[40]  K. Wüthrich,et al.  The NMR structure of the pulmonary surfactant-associated polypeptide SP-C in an apolar solvent contains a valyl-rich alpha-helix. , 1994, Biochemistry.

[41]  L Regan,et al.  A thermodynamic scale for the beta-sheet forming tendencies of the amino acids. , 1994, Biochemistry.

[42]  Johnson Wc,et al.  Importance of environment in determining secondary structure in proteins. , 1994 .

[43]  P. S. Kim,et al.  Measurement of the β-sheet-forming propensities of amino acids , 1994, Nature.

[44]  B. Matthews,et al.  Three-dimensional structure of beta-galactosidase from E. coli. , 1994, Nature.

[45]  D. V. Waterhous,et al.  Importance of environment in determining secondary structure in proteins. , 1994, Biochemistry.

[46]  H. Baker,et al.  Crystallographic studies on metal and anion substituted human lactoferrin. , 1994, Advances in experimental medicine and biology.

[47]  V. Muñoz,et al.  Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales. , 1994, Proteins.

[48]  T. J. Stillman,et al.  The three-dimensional structure of PNGase F, a glycosylasparaginase from Flavobacterium meningosepticum. , 1994, Structure.

[49]  Scott R. Presnell,et al.  Origins of structural diversity within sequentially identical hexapeptides , 1993, Protein science : a publication of the Protein Society.

[50]  J. Nyborg,et al.  The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation. , 1993, Structure.

[51]  E. Baker,et al.  Structure of the recombinant N-terminal lobe of human lactoferrin at 2.0 A resolution. , 1993, Journal of molecular biology.

[52]  B. Matthews,et al.  Structural basis of amino acid alpha helix propensity. , 1993, Science.

[53]  Jeremy M. Berg,et al.  Thermodynamic β -sheet propensities measured using a zinc-finger host peptide , 1993, Nature.

[54]  B. Matthews,et al.  How amino-acid insertions are allowed in an alpha-helix of T4 lysozyme. , 1993, Nature.

[55]  Lynne Regan,et al.  A Thermodynamic Scale for the , & Sheet Forming Tendencies of the Amino Acids , 1993 .

[56]  J. Skehel,et al.  Binding of influenza virus hemagglutinin to analogs of its cell-surface receptor, sialic acid: analysis by proton nuclear magnetic resonance spectroscopy and X-ray crystallography. , 1994, Biochemistry.

[57]  R. Huber,et al.  Crystal structure of cleaved equine leucocyte elastase inhibitor determined at 1.95 A resolution. , 1992, Journal of molecular biology.

[58]  M. Levitt.  Accurate modeling of protein conformation by automatic segment matching. , 1992, Journal of molecular biology.

[59]  W. C. Johnson,et al.  Environment affects amino acid preference for secondary structure. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[60]  P. Argos,et al.  Analysis of insertions/deletions in protein structures. , 1992, Journal of molecular biology.

[61]  U. Hobohm,et al.  Selection of representative protein data sets , 1992, Protein science : a publication of the Protein Society.

[62]  G. Schulz,et al.  Structure of cyclodextrin glycosyltransferase refined at 2.0 A resolution. , 1991, Journal of molecular biology.

[63]  N R Kallenbach,et al.  Side chain contributions to the stability of alpha-helical structure in peptides. , 1990, Science.

[64]  W. DeGrado,et al.  A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. , 1990, Science.

[65]  Robert L. Baldwin,et al.  Relative helix-forming tendencies of nonpolar amino acids , 1990, Nature.

[66]  S. Wodak,et al.  Modelling the polypeptide backbone with 'spare parts' from known protein structures. , 1989, Protein engineering.

[67]  P Argos,et al.  Analysis of sequence-similar pentapeptides in unrelated protein tertiary structures. Strategies for protein folding and a guide for site-directed mutagenesis. , 1987, Journal of molecular biology.

[68]  R. Lerner,et al.  Identical short peptide sequences in unrelated proteins can have different conformations: a testing ground for theories of immune recognition. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[69]  C Sander,et al.  On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

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

[71]  J. Garnier,et al.  Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. , 1978, Journal of molecular biology.

[72]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1978, Archives of biochemistry and biophysics.

[73]  V. Lim.  Algorithms for prediction of α-helical and β-structural regions in globular proteins , 1974 .