A sensitive procedure to compare amino acid sequences.

Methods are discussed that provide sensitive criteria for detection of weak sequence homologies. They are based on the Dayhoff relatedness odds amino acid exchange matrix and certain residue physical characteristics. The search procedure uses several residue probe lengths in comparing all possible segments of two protein sequences, and search plots are shown with peak values displayed over the entire search length. Alignments are automatically effected using the highest search matrix values and without the necessity of gap penalties. Tests for significance are derived from actual protein sequences rather than a random shuffling procedure.

[1]  G. Rose,et al.  Hydrophobicity of amino acid residues in globular proteins. , 1985, Science.

[2]  D. D. Jones,et al.  Amino acid properties and side-chain orientation in proteins: a cross correlation appraoch. , 1975, Journal of theoretical biology.

[3]  R. Poljak,et al.  Three-dimensional structure of immunoglobulins. , 1979, Annual review of biochemistry.

[4]  F. S. Mathews,et al.  On the evolutionary relationship of the 4-alpha-helical heme proteins. The comparison of cytochrome b562 and cytochrome c'. , 1981, The Journal of biological chemistry.

[5]  J. Janin,et al.  Surface and inside volumes in globular proteins , 1979, Nature.

[6]  P. Terpstra,et al.  Prediction of the Occurrence of the ADP-binding βαβ-fold in Proteins, Using an Amino Acid Sequence Fingerprint , 1986 .

[7]  H A Scheraga,et al.  Influence of water on protein structure. An analysis of the preferences of amino acid residues for the inside or outside and for specific conformations in a protein molecule. , 1978, Macromolecules.

[8]  A. Aitken.  Prokaryote-eukaryote relationship and the amino acid sequence of plastocyanin from Anabaena variabilis. , 1975, The Biochemical journal.

[9]  W. Rutter,et al.  Splice junctions: association with variation in protein structure. , 1983, Science.

[10]  K Nishikawa,et al.  Homology in protein sequences expressed by correlation coefficients. , 1981, Journal of theoretical biology.

[11]  B. Matthews,et al.  Comparison of the structures of Cro and λ repressor proteins from bacteriophage λ , 1983 .

[12]  H. Bull,et al.  Surface tension of amino acid solutions: a hydrophobicity scale of the amino acid residues. , 1974, Archives of biochemistry and biophysics.

[13]  H. Saroff.  The uniqueness of protein sequences. Uniqueness diagrams for the Dayhoff file--1984. , 1984, Bulletin of mathematical biology.

[14]  W. Taylor,et al.  Identification of protein sequence homology by consensus template alignment. , 1986, Journal of molecular biology.

[15]  G. Schulz,et al.  Gene duplication in glutathione reductase. , 1980, Journal of molecular biology.

[16]  J. Bishop,et al.  The protein products of the myc and myb oncogenes and adenovirus E1a are structurally related , 1983, Nature.

[17]  G L Gilliland,et al.  Structure of the L-arabinose-binding protein from Escherichia coli at 2.4 A resolution. , 1980, Journal of molecular biology.

[18]  W. Fitch,et al.  An examination of the expected degree of sequence similarity that might arise in proteins that have converged to similar conformational states. The impact of such expectations on the search for homology between the structurally similar domains of rhodanese. , 1981, Journal of molecular biology.

[19]  Graeme Wistow,et al.  X-ray analysis of the eye lens protein γ-II crystallin at 1·9 Å resolution , 1983 .

[20]  G. Schulz,et al.  Structural relationship between glutathione reductase and lipoamide dehydrogenase. , 1984, Journal of molecular biology.

[21]  P M Cullis,et al.  Affinities of amino acid side chains for solvent water. , 1981, Biochemistry.

[22]  P. Argos,et al.  The primary structure of human hemopexin deduced from cDNA sequence: evidence for internal, repeating homology. , 1985, Nucleic acids research.

[23]  A. Mclachlan.  Gene duplications in the structural evolution of chymotrypsin. , 1979, Journal of molecular biology.

[24]  P. Argos,et al.  Primary structural relationships may reflect similar DNA replication strategies. , 1986, Virology.

[25]  K. Stanley.  Homology with hemopexin suggests a possible scavenging function for S‐protein/vitronectin , 1986, FEBS letters.

[26]  P. Argos,et al.  Prediction of secondary structural elements in glycerol-3-phosphate dehydrogenase by comparison with other dehydrogenases. , 1980, European journal of biochemistry.

[27]  P Argos,et al.  Structural comparisons of heme binding proteins. , 1979, Biochemistry.

[28]  P. Argos,et al.  Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. , 1984, Nucleic acids research.

[29]  I. Chaikoff,et al.  Hydrogen transfer in fatty acid synthesis by rat liver and mammarygland cell-free preparations studied with tritum-labeled pyridine nucleotides and glucose. , 1963, Biochimica et biophysica acta.

[30]  B. Strandberg,et al.  Structural comparisons of some small spherical plant viruses. , 1983, Journal of molecular biology.

[31]  C. Chothia.  The nature of the accessible and buried surfaces in proteins. , 1976, Journal of molecular biology.

[32]  R. Huber,et al.  X-ray crystallographic structure of the light-harvesting biliprotein C-phycocyanin from the thermophilic cyanobacterium Mastigocladus laminosus and its resemblance to globin structures. , 1985, Journal of molecular biology.

[33]  P. Ponnuswamy,et al.  Hydrophobic character of amino acid residues in globular proteins , 1978, Nature.

[34]  D. Lipman,et al.  Rapid and sensitive protein similarity searches. , 1985, Science.

[35]  P. Argos,et al.  Human oestrogen receptor cDNA: sequence, expression and homology to v-erb-A , 1986, Nature.

[36]  P. Argos,et al.  Identification of a trpG-related glutamine amide transfer domain in Escherichia coli GMP synthetase. , 1985, The Journal of biological chemistry.

[37]  A. Mclachlan,et al.  Structural repeats and evolution of tobacco mosaic virus coat protein and RNA. , 1980, Journal of molecular biology.

[38]  R Staden,et al.  An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. , 1982, Nucleic acids research.

[39]  P Argos,et al.  Exploring structural homology of proteins. , 1976, Journal of molecular biology.

[40]  P Argos,et al.  The integrase family of site‐specific recombinases: regional similarities and global diversity. , 1986, The EMBO journal.

[41]  A. Lesk,et al.  How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. , 1980, Journal of molecular biology.

[42]  K. B. Ward,et al.  Pseudosymmetry in the structure of myohemerythrin. , 1977, The Journal of biological chemistry.

[43]  A. Mclachlan.  Gene duplication in carp muscle calcium binding protein. , 1972, Nature: New biology.

[44]  A. D. McLachlan,et al.  Solvation energy in protein folding and binding , 1986, Nature.

[45]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[46]  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.

[47]  B. Matthews,et al.  Comparison of the structures of cro and lambda repressor proteins from bacteriophage lambda. , 1989, Journal of molecular biology.

[48]  R D MacElroy,et al.  A simple experimental model for hydrophobic interactions in proteins. , 1984, The Journal of biological chemistry.

[49]  R. Sauer,et al.  Structure of tomato bushy stunt virus. V. Coat protein sequence determination and its structural implications. , 1984, Journal of molecular biology.

[50]  C. Chothia,et al.  Structural patterns in globular proteins , 1976, Nature.

[51]  T. L. Blundell,et al.  Structural evidence for gene duplication in the evolution of the acid proteases , 1978, Nature.

[52]  P. Argos,et al.  A possible nucleotide-binding domain in the tertiary fold of phosphoribosyltransferases. , 1983, The Journal of biological chemistry.

[53]  R. Ambler,et al.  The amino acid sequence of plastocyanin from Chlorella fusca. , 1974, The Biochemical journal.

[54]  W. Turnell,et al.  Relaxin has conformational homology with insulin , 1977, Nature.

[55]  T. L. Blundell,et al.  Hormone families: pancreatic hormones and homologous growth factors , 1980, Nature.

[56]  D J Osguthorpe,et al.  Refined models for computer simulation of protein folding. Applications to the study of conserved secondary structure and flexible hinge points during the folding of pancreatic trypsin inhibitor. , 1979, Journal of molecular biology.

[57]  M. Levitt.  A simplified representation of protein conformations for rapid simulation of protein folding. , 1976, Journal of molecular biology.

[58]  K Nishikawa,et al.  Correspondence of homologies in amino acid sequence and tertiary structure of protein molecules. , 1982, Biochimica et biophysica acta.

[59]  P Argos,et al.  Protein secondary structure. Studies on the limits of prediction accuracy. , 2009, International journal of peptide and protein research.

[60]  M. O. Dayhoff,et al.  Establishing homologies in protein sequences. , 1983, Methods in enzymology.

[61]  T. Blundell,et al.  Four-fold structural repeat in the acid proteases. , 1979, Biochimica et biophysica acta.

[62]  Shneior Lifson,et al.  Antiparallel and parallel β-strands differ in amino acid residue preferences , 1979, Nature.

[63]  M. Sternberg,et al.  An analysis of the structure of triose phosphate isomerase and its comparison with lactate dehydrogenase. , 1978, Journal of molecular biology.

[64]  P Argos,et al.  The taxonomy of protein structure. , 1977, Journal of molecular biology.

[65]  A. Mclachlan,et al.  Confidence limits for homology in protein or gene sequences. The c-myc oncogene and adenovirus E1a protein. , 1985, Journal of molecular biology.

[66]  D C Richardson,et al.  Similarity of three-dimensional structure between the immunoglobulin domain and the copper, zinc superoxide dismutase subunit. , 1976, Journal of molecular biology.