Mutation Data Matrix Research Articles

Representation of mutation pressure and selection pressure by PAM matrices

This paper analyses the relationship between the mutation data matrix 1PAM/PET91, representing the effect of both mutation and selection pressures exerted on 16130 homologous proteins of different organisms, and a mutation probability matrix (1PAM/MPM) representing the effect of pure mutation pressure on protein coding of the Borrelia burgdorferi genome. The 1PAM/PMP matrix was derived with the help of computer simulations, which used empirical nucleotide substitution rates found for the B. burgdorferi genome. Here, it is shown that the frequency of amino acid occurrence is strongly related to their effective survival time. We found that the shorter the turnover time of an amino acid under pure mutation pressure, the lower its fraction in the proteins coded by the genome and the more protected by selection pressure is its position in proteins. Results of analyses suggest that during evolution the mutational pressure has been optimised to some extent to the selection requirements.

A mutation data matrix for transmembrane proteins

The widely used Mutation Data Matrix (MDM), is an amino acid comparison matrix calculated from a study of the exchange probabilities (or odds) derived from an analysis of the evolutionary changes seen in groups of very similar proteins. In this work, a mutation data matrix is calculated for membrane spanning segments. This new mutation data matrix is found to be very different from matrices calculated from general sequence sets which are biased towards water-soluble globular proteins, and the differences are discussed in the context of specific structural requirements of membrane spanning segments. This new matrix will help improve the accuracy of integral membrane protein sequence alignments, and could also be of use in the rational design of site directed mutagenesis experiments for this class of proteins.

The rapid generation of mutation data matrices from protein sequences.

An efficient means for generating mutation data matrices from large numbers of protein sequences is presented here. By means of an approximate peptide-based sequence comparison algorithm, the set sequences are clustered at the 85% identity level. The closest relating pairs of sequences are aligned, and observed amino acid exchanges tallied in a matrix. The raw mutation frequency matrix is processed in a similar way to that described by Dayhoff et al. (1978), and so the resulting matrices may be easily used in current sequence analysis applications, in place of the standard mutation data matrices, which have not been updated for 13 years. The method is fast enough to process the entire SWISS-PROT databank in 20 h on a Sun SPARCstation 1, and is fast enough to generate a matrix from a specific family or class of proteins in minutes. Differences observed between our 250 PAM mutation data matrix and the matrix calculated by Dayhoff et al. are briefly discussed.

Primary structure of bacteriophage M2 DNA polymerase: conserved segments within protein-priming DNA polymerases and DNA polymerase I of Escherichia coli

Bacteriophage M2 encodes its own DNA polymerase which catalyses the formation of a primer protein-5'dAMP initiation complex for DNA replication. To understand the relation of structure to function of this ‘protein-priming DNA polymerase’, we have determined the nucleotide sequence of the M2 DNA polymerase-encoding gene (gene G). The deduced 572-amino acid sequence of M2 DNA polymerase shows 82.3% overall homology to that of φ29 DNA polymerase. A homology search with the mutation data matrix revealed that six segments (A-F, from the N terminus) of M2 and φ29 DNA polymerases are homologous with the sequence of Escherichia coli DNA polymerase I (PolI). Segments D and F coincide with the conserved segments of many other DNA polymerases. Therefore, M2 and φ29 DNA polymerases have structural features, at least in the conserved segments, similar to those of PolI and other DNA polymerases. Based on the homology with PolI and the location of the mutations for aphidicolin resistance and nucleoside analog resistance of M2, 029 and herpes simplex virus type-1 DNA polymerases, we propose that segments A-D of the M2 and 029 DNA polymerases constitute a structure which forms the cleft for holding template DNA and that segment D is a region for interacting with dNTP.

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.

Complete amino acid sequence of Shigella toxin B-chain. A novel polypeptide containing 69 amino acids and one disulfide bridge.

The complete amino acid sequence of the B-chain of Shigella toxin has been determined using both liquid- and gas-phase sequenators. It reveals a 69-amino acid peptide with a single disulfide bridge, predicting a subunit molecular weight of 7691. No Asn-X-Ser(Thr) sequence was found, confirming the absence of potential N-glycosylation sites. A computer data bank search using a mutation data matrix did not detect any similarity greater than 30% with known sequences to date, indicating a novel primary structure. However, some distant homology with the 103-residue B-chain of cholera and Escherichia coli enterotoxins was revealed. Hydropathy, fractional exposure, and Chou and Fasman calculations all point to an ordered structure with a hydrophobic core spanning residues 36-52 and a hydrophilic domain between residues 10 and 20, the latter probably representing the most antigenic domain.

Gawk, a novel human pituitary polypeptide: Isolation, immunocytochemical localization and complete amino acid sequence

During the course of reverse-phase high pressure liquid chromatography (RP-HPLC) purification of a postulated big ACTH (1) from human pituitary gland extracts, a highly purified peptide bearing no resemblance to any known polypeptide was isolated. The complete sequence of this 74 amino acid polypeptide, called GAWK, has been determined. Search on a computer data bank on the possible homology to any known protein or fragment, using a mutation data matrix, failed to reveal any homology greater than 30%. An antibody produced against a synthetic fragment allowed us to detect several immunoreactive forms. The antisera also enabled us to localize the polypeptide, by immunocytochemistry, in the anterior lobe of the pituitary gland.

Isolation and NH 2-terminal sequence of a highly conserved human and porcine pituitary protein belonging to a new superfamily : Immunocytochemical localization in pars distalis and pars nervosa of the pituitary and in the supraoptic nucleus of the hypothalamus

The isolation and purification of a 21,000-Da (p I 4.9) novel protein from porcine anterior pituitary and whole human pituitary is described. Comparison of the NH 2-terminal sequence of the first 77 and 81 residues of the human and porcine homologs shows only one conservative substitution at residue 12, namely an Ala for a Thr between these two species. Such high sequence homology is also reflected in their amino acid composition. A computer data-bank search using a mutation data matrix and comparison with 338,327 segments of proteins revealed that this substance should be classified as belonging to a new protein superfamily. Immunocytochemical staining, using an antibody produced against a synthetic fragment, revealed the presence of immunostainable material in the anterior and posterior lobe of the pituitary and in the supraoptic nucleus of the hypothalamus. No staining was observed in the intermediate lobe of the pituitary. Furthermore, purified neurointermediate lobe secretory granule preparations were also shown to contain this novel polypeptide.

Isolation and NH 2-terminal sequence of a novel porcine anterior pituitary polypeptide : Homology to proinsulin, secretin and Rous sarcoma virus transforming protein TVFV60

An M r 21 000 polypeptide, designated APPG, has been purified by reverse-phase, high-performance liquid chromatography (RP-HPLC), from acid extracts of porcine anterior pituitary glands. This acidic protein possesses an isoelectric point of 4.9. Amino acid analysis shows that it is not a glycoprotein and estimates it to contain about 173 amino acids. NH 2-terminal sequence analysis allowed the determination of the first 50 residues unambiguously. A computer data bank search using a mutation data matrix and comparison with 269 012 protein segments indicated that this is a novel polypeptide sequence. However, this search revealed suggestive sequence homologies to a number of peptides of known sequence, including duck proinsulin (30%), Rous sarcoma virus transforming protein TVFV60 (24%) and pig secretin (26%).