Secondary structural features of modules M2 and M3 of barnase in solution by NMR experiment and distance geometry calculation

Proteins consist of structural units such as globular domains, secondary structures, and modules. Modules were originally defined by partitioning a globular domain into compact regions, each of which is a contiguous polypeptide segment having a compact conformation. Since modules show close correlations with the intron positions of genes, they are regarded as primordial polypeptide pieces encoded by exons and shuffled, leading to yield new combination of them in early biological evolution. Do modules maintain their native conformations in solution when they are excised at their boundaries? In order to find answers to this question, we have synthesized modules of barnase, one of the bacterial RNases, and studied the solution structures of modules M2 (amino acid residues 24–52) and M3 (52–73) by 2D NMR studies. Some local secondary structures, α‐helix, and β‐turns in M2 and β‐turns in M3, were observed in the modules at the similar positions to those in the intact barnase but the overall state seems to be in a mixture of random and native conformations. The present result shows that the excised modules have propensity to form similar secondary structures to those of the intact barnase. © 1993 Wiley‐Liss, Inc.

[1]  T. Noguti,et al.  Localization of hydrogen‐bonds within modules in barnase , 1993, Proteins.

[2]  P E Wright,et al.  Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding. I. Myohemerythrin. , 1992, Journal of molecular biology.

[3]  A. Fersht,et al.  An N-terminal fragment of barnase has residual helical structure similar to that in a refolding intermediate. , 1992, Journal of molecular biology.

[4]  Alan R. Fersht,et al.  Determination of the three-dimensional solution structure of barnase using nuclear magnetic resonance spectroscopy , 1991 .

[5]  J. Janin,et al.  Crystal structure of a barnase-d(GpC) complex at 1.9 A resolution. , 1991, Journal of molecular biology.

[6]  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.

[7]  J. Palmer,et al.  An ancient group I intron shared by eubacteria and chloroplasts , 1990, Science.

[8]  Ming-Qun Xu,et al.  Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in cyanobacteria , 1990, Science.

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

[10]  O. Jardetzky,et al.  α-Proton chemical shifts and secondary structure in proteins , 1989 .

[11]  Terrence G. Oas,et al.  A peptide model of a protein folding intermediate , 1988, Nature.

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

[13]  E. Olejniczak,et al.  Improvement of 2D NOE spectra of biomacromolecules in H2O solution by coherent suppression of the solvent resonance , 1986 .

[14]  Walter Gilbert,et al.  On the antiquity of introns , 1986, Cell.

[15]  J E Darnell,et al.  Speculations on the early course of evolution. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[16]  N Go,et al.  Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. , 1985, Journal of molecular biology.

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

[18]  L. Patthy.  Evolution of the proteases of blood coagulation and fibrinolysis by assembly from modules , 1985, Cell.

[19]  W Gilbert,et al.  Genes-in-pieces revisited. , 1985, Science.

[20]  T. Südhof,et al.  Cassette of eight exons shared by genes for LDL receptor and EGF precursor. , 1985, Science.

[21]  Rachel E. Klevit,et al.  Improving two-dimensional NMR spectra by t1 ridge subtraction , 1985 .

[22]  H. Eklund,et al.  Correlation of exons with structural domains in alcohol dehydrogenase. , 1984, The EMBO journal.

[23]  M. Belfort,et al.  Intervening sequence in the thymidylate synthase gene of bacteriophage T4. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

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

[25]  M Go,et al.  Modular structural units, exons, and function in chicken lysozyme. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[26]  D. States,et al.  A two-dimensional nuclear overhauser experiment with pure absorption phase in four quadrants☆ , 1982 .

[27]  Cyrus Chothia,et al.  Molecular structure of a new family of ribonucleases , 1982, Nature.

[28]  K Wüthrich,et al.  Sequential resonance assignments as a basis for determination of spatial protein structures by high resolution proton nuclear magnetic resonance. , 1982, Journal of molecular biology.

[29]  M. Go.  Correlation of DNA exonic regions with protein structural units in haemoglobin , 1981, Nature.

[30]  Dieter Suter,et al.  Two-dimensional chemical exchange and cross-relaxation spectroscopy of coupled nuclear spins , 1981 .

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

[32]  Kurt Wüthrich,et al.  1H‐nmr parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H‐Gly‐Gly‐X‐L‐Ala‐OH , 1979 .

[33]  W. Gilbert.  Why genes in pieces? , 1978, Nature.

[34]  R. Hartley,et al.  Amino-acid sequence of extracellular ribonuclease (barnase) of Bacillus amyloliquefaciens. , 1972, Nature: New biology.

[35]  M. Nomura,et al.  Ribonuclease of Bacillus subtilis. , 1958, Biochimica et biophysica acta.

[36]  P E Wright,et al.  Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding. II. Plastocyanin. , 1992, Journal of molecular biology.

[37]  L. Hood,et al.  Diversity of the immunoglobulin gene superfamily. , 1989, Advances in immunology.

[38]  M Go,et al.  Protein architecture and the origin of introns. , 1987, Cold Spring Harbor symposia on quantitative biology.

[39]  C. Blake.  Exons and the evolution of proteins. , 1985, International review of cytology.

[40]  N. Isaacs,et al.  Three-dimensional structure of goose-type lysozyme from the egg white of the Australian black swan, Cygnus atratus. , 1985, Australian journal of biological sciences.

[41]  M. Go.  Protein structures and split genes. , 1985, Advances in biophysics.