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Antibody-Like Phosphorylation Sites in Focus of Statistically Based Bilingual Approach


Affiliations
1 Department of Physiology, Charles University, Prague, Czech Republic
2 Laboratory of Cellular Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
3 Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
4 Department of Biochemistry, Charles University, Prague, Czech Republic
 

In accordance with previous reports, the sequences related to phosporylated protein segments occur in conserved variable domains of immunoglobulins including first of all certain N-terminally located segments. Consequently, we look here for the sequences 1) composing human and mouse proteins different from antigen receptors, 2) identical with or highly similar to nucleotide sequence representatives of conserved variable immunoglobulin segments and 3) identical with or closely related to phosphorylation sites. More precisely, we searched for the corresponding actual pairs of DNA and protein sequence segments using five-step bilingual approach employing among others a) different types of BLAST searches, b) two in-principle-different machine-learning methods predicting phosphorylated sites and c) two large databases recording existing phosphorylation sites. The approach identified seven existing phosphorylation sites and thirty-seven related human and mouse segments achieving limits for several predictions or phylogenic parameters. Mostly serines phosporylated with ataxia-telangiectasia-related kinase (involved in regulation of DNA-double-strand-break repair) were indicated or predicted in this study. Hypermutation motifs, located in effective positions of the selected sequence segments, occurred significantly less frequently in transcribed than non-transcribed DNA strands suggesting thus the incidence of mutation events. In addition, marked differences between the numbers and proportions of human and mouse cancer-related sequence items were found in different steps of selection process. The possible role of hypermutation changes within the selected segments and the observed structural relationships are discussed here with respect to DNA damage, carcinogenesis, cancer vaccination, ageing and evolution. Taken together, our data represent additional and sometimes perhaps complementary information to the existing databases of empirically proven phosphorylation sites or pathogenically important spots.

Keywords

Ataxia Telangiectasia-Mutated-Protein (i.e. Kinase ATM, Whose Pathogenic Mutation Is Responsible for Early Death of People), Complementarity Determining Region 1 (of Immunoglobulins, i.e. CDR1 or Hypervariable Region 1), Database (of Functional Structures), Hypermutation (i.e. Mutation of DNA Sequences Mediated by Enzymes), Immunoglobulin (i.e. Ig or Antibody), Phosphorylation (Enzyme Mediated Modification Concerns Here Mostly Protein Sequences).
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  • Antibody-Like Phosphorylation Sites in Focus of Statistically Based Bilingual Approach

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Authors

Jaroslav Kubrycht
Department of Physiology, Charles University, Prague, Czech Republic
Karel Sigler
Laboratory of Cellular Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
Pavel Souček
Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
Jiří Hudeček
Department of Biochemistry, Charles University, Prague, Czech Republic

Abstract


In accordance with previous reports, the sequences related to phosporylated protein segments occur in conserved variable domains of immunoglobulins including first of all certain N-terminally located segments. Consequently, we look here for the sequences 1) composing human and mouse proteins different from antigen receptors, 2) identical with or highly similar to nucleotide sequence representatives of conserved variable immunoglobulin segments and 3) identical with or closely related to phosphorylation sites. More precisely, we searched for the corresponding actual pairs of DNA and protein sequence segments using five-step bilingual approach employing among others a) different types of BLAST searches, b) two in-principle-different machine-learning methods predicting phosphorylated sites and c) two large databases recording existing phosphorylation sites. The approach identified seven existing phosphorylation sites and thirty-seven related human and mouse segments achieving limits for several predictions or phylogenic parameters. Mostly serines phosporylated with ataxia-telangiectasia-related kinase (involved in regulation of DNA-double-strand-break repair) were indicated or predicted in this study. Hypermutation motifs, located in effective positions of the selected sequence segments, occurred significantly less frequently in transcribed than non-transcribed DNA strands suggesting thus the incidence of mutation events. In addition, marked differences between the numbers and proportions of human and mouse cancer-related sequence items were found in different steps of selection process. The possible role of hypermutation changes within the selected segments and the observed structural relationships are discussed here with respect to DNA damage, carcinogenesis, cancer vaccination, ageing and evolution. Taken together, our data represent additional and sometimes perhaps complementary information to the existing databases of empirically proven phosphorylation sites or pathogenically important spots.

Keywords


Ataxia Telangiectasia-Mutated-Protein (i.e. Kinase ATM, Whose Pathogenic Mutation Is Responsible for Early Death of People), Complementarity Determining Region 1 (of Immunoglobulins, i.e. CDR1 or Hypervariable Region 1), Database (of Functional Structures), Hypermutation (i.e. Mutation of DNA Sequences Mediated by Enzymes), Immunoglobulin (i.e. Ig or Antibody), Phosphorylation (Enzyme Mediated Modification Concerns Here Mostly Protein Sequences).