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M Kanehisa

Publications and source records attributed to M Kanehisa.

At least 73 records · Page 4Linked to original sources
PubMed1988

A multivariate analysis method for discriminating protein secondary structural segments.

Using discriminant analysis, three types of protein secondary structure segments--helices, beta-strands and coils--are discriminated by amino acid sequence information alone. A variable in the discriminant analysis is defined by the amino acid index used to represent the sequence data and by the calculation method used to extract a feature in this representation. Thus, the three types of secondary structure segments derived from a set of non-homologous proteins from the Protein Data Bank are analyzed by 888 variables, which correspond to the mean, standard deviation, 3.6-residue periodicity and 2-residue periodicity for the numerical profiles determined from 222 published amino acid indices. These variables are combined to obtain best discrimination of the three types of segments. When up to three variables are combined, the best discrimination rate was 75%. The variables selected consist of the mean of alpha propensity (or turn propensity), the mean of beta propensity, and the 3.6-residue periodicity of hydrophobicity. This variable selection procedure can also be applied to other types of discrimination problem, once groups of sequence data are properly organized.

Amino Acid Sequence↗
PubMed1988

Cluster analysis of amino acid indices for prediction of protein structure and function.

The relationship among 222 published indices representing various physicochemical and biochemical properties of amino acid residues has been investigated by hierarchical cluster analysis. The clustering result is illustrated by the minimum spanning tree, which is conveniently divided into four regions: alpha and turn propensities, beta propensity, hydrophobicity and other physicochemical properties including, among others, bulkiness of amino acid residues. In addition, several subclasses of hydrophobicity scales have been identified: preference of inside and outside, accessible surface area, surrounding hydrophobicity and other mostly experimental scales including transfer free energy, partition coefficients, HPLC parameters and polarity. Representative amino acid indices are identified in each of these groups. The collection of amino acid indices is a useful resource for empirical analyses correlating sequence information with structural and functional properties of proteins. As an example, the indices that best reproduce the amino acid mutation data matrix are searched against this collection.

Amino Acids↗
PubMed1987

Detection of weak sequence homology of proteins for tertiary structure prediction.

Multiple measures of similarity were employed to detect weak homologies among protein sequences (e.g., below 30% residue identity). A set of thresholds was empirically determined, by using sample proteins of known structure, so as to select only correct pairs of sequences; correct or incorrect alignment of sequences was judged by direct comparison of corresponding conformations. The empirical criterion thus set up is applicable to the prediction of a protein structure when the structure of the other protein in the pair is known. We searched all the combinations between 84 proteins of known structure and 4610 proteins stored in a sequence database, and found about 4000 pairs of sequences which satisfied the criterion. However, after excluding such pairs of proteins that belong to the same family or superfamily, the number of pairs remaining was reduced to only 19. The reliability of these data for structural prediction is discussed.

Amino Acid Sequence↗
PubMed1986

L-aspartate ammonia-lyase and fumarate hydratase share extensive sequence homology.

Based on our recent determinations of the nucleotide sequences of the L-aspartate ammonia-lyase genes from Escherichia coli and Pseudomonas fluorescens, primary structures of the two L-aspartate ammonia-lyases and fumarate hydratases from Bacillus subtilis and E. coli (N-terminal partial sequence) were compared by computer analysis. These four enzymes exhibited a significant homology of at least 37%, implying that L-aspartate ammonia-lyase and fumarate hydratase share a common evolutionary origin. To authors' knowledge, this feature appears to be the first example showing that two kinds of enzymes catalyzing different types of reactions, albeit similar, share such a high degree of sequence homology.

Amino Acid Sequence↗
PubMed1985

Structure of the human interleukin-2 receptor gene.

The gene encoding the human interleukin-2 (IL-2) receptor consists of 8 exons spanning more than 25 kilobases on chromosome 10. Exons 2 and 4 were derived from a gene duplication event and unexpectedly also are homologous to the recognition domain of human complement factor B. Alternative messenger RNA (mRNA) splicing may delete exon 4 sequences, resulting in a mRNA that does not encode a functional IL-2 receptor. Leukemic T cells infected with HTLV-I and normal activated T cells express IL-2 receptors with identical deduced protein sequences. Receptor gene transcription is initiated at two principal sites in normal activated T cells. Adult T cell leukemia cells infected with HTLV-I show activity at both of these sites, but also at a third transcription initiation site.

Amino Acid Sequence↗
PubMed1985

Prediction of splice junctions in mRNA sequences.

A general method based on the statistical technique of discriminant analysis is developed to distinguish boundaries of coding and non-coding regions in nucleic acid sequences. In particular, the method is applied to the prediction of splicing sites in messenger RNA precursors. Information used for discrimination includes consensus sequence patterns around splice junctions, free energy of snRNA and mRNA base pairing, and statistical differences between coding and non-coding regions such as periodic appearance of specific bases in coding regions reflecting the non-random usage of degenerate codons. Given the reading frame of an exon (but not the exon/intron boundaries), the method will predict the following exon, namely, the intron to be excised out. When applied to human sequences in the GenBank database, the method correctly identified 80% of true splice junctions.

Base Sequence↗
PubMed1985

The detection and classification of membrane-spanning proteins.

Discriminant analysis can be used to precisely classify membrane proteins as integral or peripheral and to estimate the odds that the classification is correct. Specifically, using 102 membrane proteins from the National Biomedical Research Foundation (NBRF) database we find that discrimination between integral and peripheral membrane proteins can be achieved with 99% reliability. Hydrophobic segments of integral membrane proteins can also be distinguished from interior segments of globular soluble proteins with better than 95% reliability. We also propose a procedure for determining boundaries of membrane-spanning segments and apply it to several integral membrane proteins. For the limited data available (such as on transplantation antigens), the residues at the boundaries of a membrane-spanning segment are predictable to within the error inherent in the concept of boundary. As a specific indication of resolution, seven membrane-spanning segments of bacteriorhodopsin are resolved with no information other than sequence, and the predicted boundary residues agree with the experimental data on proteolytic cleavage sites. Several definitive but yet to be tested predictions are also made, and the relation to other predictive methods is briefly discussed. A computer program in FORTRAN for prediction of membrane-spanning segments is available from the authors.

Animals↗
PubMed1985

The GenBank nucleic acid sequence database.

The GenBank nucleic acid sequence database is a computer-based collection of all published DNA and RNA sequences; it contains over five million bases in close to six thousand sequence entries drawn from four thousand five hundred published articles. Each sequence is accompanied by relevant biological annotation. The database is available either on magnetic tape, on floppy diskettes, on-line or in hardcopy form. We discuss the structure of the database, the extent of the data and the implications of the database for research on nucleic acids.

Base Sequence↗
PubMed1984

Prediction of protein function from sequence properties. Discriminant analysis of a data base.

The protein superfamilies in the National Biomedical Research Foundation sequence data base cluster into six groups that can be distinguished on the basis of four variables characterizing amino acid composition and local sequence properties. The variables are average hydrophobicity, net charge, sequence length and periodic variation in hydrophobic residues along the chain. The clusters they distinguish are: globins; chromosomal proteins; contractile system proteins and respiratory proteins other than cytochromes; enzyme inhibitors and toxins; enzymes except hydrolases; and all other proteins. The overall probability of correctly allocating a given protein to one of these functional groups is 0.76, with the allocation reliability being highest for globins (0.97) and for chromosomal proteins (0.93).

Amino Acid Sequence↗
PubMed1984

Use of statistical criteria for screening potential homologies in nucleic acid sequences.

We proposed a simple formula to assess the statistical significance of homologous segments found in comparison of two nucleic acid sequences (Goad and Kanehisa, Nucleic Acids Res. 10, 247-263, 1982). This paper clarifies the basic assumptions of the formula and its reliability is examined by Monte Carlo calculations. The results were satisfactory for random sequences. The formula is a useful measure for screening potentially interesting homologies and it can be implemented in any search algorithms. Examples are given for the screening procedure in the graphic display version of the Goad-Kanehisa algorithm.

Base Sequence↗
PubMed1984

Computer analysis and structure prediction of nucleic acids and proteins.

We have developed an integrated computer system for analysis of nucleic acid and protein sequences, which consists of sequence and structure databases, a relational database, and software for structural analysis. The system is potentially applicable to a number of problems in structural biology including predictive classification of the function and location of oncogene products.

Amino Acid Sequence↗
PubMedDate not supplied

Computation with the KEGG pathway database.

We introduce and discuss a new computational approach towards prediction and inference of biological functions from genomic sequences by making use of the pathway data in KEGG. Due to its piecewise nature, the current approach of predicting each gene function based on sequence similarity searches often fails to reconstruct cellular functions with all necessary components. The pathway diagram in KEGG, which may be considered a wiring diagram of molecules in biological systems, can be utilised as a reference for functional reconstruction. KEGG also contains binary relations that represent molecular interactions and relations and that can be utilised for computing and comparing pathways.

Database Management Systems↗