Secondary structure prediction from multiple sequence data: blood clotting factor XIII and Yersinia protein-tyrosine phosphatase.

Predictions of protein structure are best tested without prior knowledge of the protein three-dimensional structure. Three-dimensional atomic models will soon be determined by X-ray crystallography for the alpha-subunit of human blood clotting factor XIII and members of the family of protein tyrosine specific phosphatases. Accordingly, we here present secondary structure predictions for each of these proteins. The secondary structure predictions were generated from aligned sets of protein sequences. This technique has previously provided reliable predictions for the Annexins and the SH2 domains. The factor XIII alpha prediction contains 39 regions predicted in strand conformation (34% of the protein) with only 3 helices (4%). The protein tyrosine phosphatases have 12 predicted strands and 5 helices (30 and 17%, respectively). We expect greater reliability from regions of alignments that show clear patterns of residue conservation (61% of factor XIII alpha and 57% of the protein tyrosine phosphatases). The aligned protein tyrosine phosphatases show two regions (L39-L80 and I138-E253) with clear patterns of residue conservation separated by a region of variable amino acid composition. We suggest this indicates that the tyrosine phosphatase fold comprises two domains separated by an exposed linker. Potential phosphate binding sites are identified in the protein tyrosine phosphatases.

[1]  R. Rice,et al.  Transglutaminases: multifunctional cross‐linking enzymes that stabilize tissues , 1991, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[2]  Human placenta protein-tyrosine-phosphatase: amino acid sequence and relationship to a family of receptor-like proteins , 1989 .

[3]  G. Barton,et al.  Conservation analysis and structure prediction of the SH2 family of phosphotyrosine binding domains , 1992, FEBS letters.

[4]  W R Taylor,et al.  Predicted structure for the calcium-dependent membrane-binding proteins p35, p36, and p32. , 1987, Protein engineering.

[5]  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.

[6]  E. Davie.  Introduction to the blood coagulation cascade and cloning of blood coagulation factors , 1986 .

[7]  G. Barton,et al.  The limits of protein secondary structure prediction accuracy from multiple sequence alignment. , 1993, Journal of molecular biology.

[8]  B. Rost,et al.  Prediction of protein secondary structure at better than 70% accuracy. , 1993, Journal of molecular biology.

[9]  Y. Takahashi,et al.  Primary structure of blood coagulation factor XIIIa (fibrinoligase, transglutaminase) from human placenta. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[10]  J. Dixon,et al.  Protein tyrosine phosphatase activity of an essential virulence determinant in Yersinia. , 1990, Science.

[11]  G. Barton.  Protein multiple sequence alignment and flexible pattern matching. , 1990, Methods in enzymology.

[12]  C Sander,et al.  Progress in protein structure prediction? , 1993, Trends in biochemical sciences.

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

[14]  S. Benner,et al.  Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: a prediction of the structure of the catalytic domain of protein kinases. , 1991, Advances in enzyme regulation.

[15]  D. Barford,et al.  Crystal structure of human protein tyrosine phosphatase 1B. , 1994, Science.

[16]  George D. Rose,et al.  Prediction of chain turns in globular proteins on a hydrophobic basis , 1978, Nature.

[17]  M. Sternberg,et al.  Prediction of protein secondary structure and active sites using the alignment of homologous sequences. , 1987, Journal of molecular biology.

[18]  M. Karplus,et al.  Protein secondary structure prediction with a neural network. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[19]  D. Teller,et al.  Expression, purification, and characterization of human factor XIII in Saccharomyces cerevisiae. , 1990, Biochemistry.

[20]  C. Croce,et al.  Cloning of three human tyrosine phosphatases reveals a multigene family of receptor-linked protein-tyrosine-phosphatases expressed in brain. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[21]  J. Thornton,et al.  Analysis and prediction of the different types of β-turn in proteins , 1988 .

[22]  Robert B. Russell,et al.  Protein structure prediction , 1993, Nature.

[23]  I. Crawford,et al.  Prediction of secondary structure by evolutionary comparison: Application to the α subunit of tryptophan synthase , 1987, Proteins.

[24]  G. Barton,et al.  Amino acid sequence analysis of the annexin super-gene family of proteins. , 1991, European journal of biochemistry.

[25]  N. Tonks,et al.  Protein tyrosine phosphatases: a diverse family of intracellular and transmembrane enzymes. , 1991, Science.