Abstract
Bacteria Deinococcus radiodurans strain R1 was extremely resistant to ionizing radiation, UV light, hydrogen peroxide, and numerous other agents that damage DNA as well as being highly resistant to desiccation. It is clear that the D. radiodurans strain R1 whole genome which carries 3,195 predicted genes, consists of two chromosomes, one megaplasmid, and one plasmid. This combination of factors has positioned D. radiodurans as a promising candidate for the study of mechanisms of DNA damage and repair, as well as its exploitation for practical purposes such as cleanup and stabilization of radioactive waste sites. Radiation resistance of D. radiodurans seems very complex and is determined collectively by some features revealed by genome analysis, as well as by many more subtle structural peculiarities of proteins and DNA that are not readily inferred from the comparative sequences analysis. The fundamental questions underlying the extreme resistance phenotype of D. radiodurans remain unanswered. In this study, two protein databases including Deinococcus radiodurans R1 and E. coli K-12, were applied to whole protein sequences comparative analysis. Several computational tools developed from RDBMS (Relation Database Management System), were applied to this study. From the protein database comparison results, our target is to find the possible mechanisms by which proteins can become radiation resistant, either by a special 3-dimensional structure or by using a set of stable amino acids in the sequence.
| Original language | English |
|---|---|
| Title of host publication | Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04 |
| Editors | F. Valafar, H. Valafar |
| Pages | 314-321 |
| Number of pages | 8 |
| Publication status | Published - Dec 1 2004 |
| Externally published | Yes |
| Event | Proceedings of the International Conference on Mathematics and Engineering Techniques in medicine and Biological Sciences, METMBS'04 - Las Vegas, NV, United States Duration: Jun 21 2004 → Jun 24 2004 |
Conference
| Conference | Proceedings of the International Conference on Mathematics and Engineering Techniques in medicine and Biological Sciences, METMBS'04 |
|---|---|
| Country | United States |
| City | Las Vegas, NV |
| Period | 6/21/04 → 6/24/04 |
Fingerprint
Keywords
- Amino Acid Compositions
- Database
- Deinococcus radiodurans R1
- Protein sequences
ASJC Scopus subject areas
- Engineering(all)
Cite this
Exploring of radiation resistance from bacterium Deinococcus radiodurans R1 by amino acid compositions of proteins : View from comparative whole protein sequences. / Chang, Chia Wen; Chang, Wen Chang; Chen, Mao Yen; Kao, Cheng Yan.
Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04. ed. / F. Valafar; H. Valafar. 2004. p. 314-321.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
}
TY - GEN
T1 - Exploring of radiation resistance from bacterium Deinococcus radiodurans R1 by amino acid compositions of proteins
T2 - View from comparative whole protein sequences
AU - Chang, Chia Wen
AU - Chang, Wen Chang
AU - Chen, Mao Yen
AU - Kao, Cheng Yan
PY - 2004/12/1
Y1 - 2004/12/1
N2 - Bacteria Deinococcus radiodurans strain R1 was extremely resistant to ionizing radiation, UV light, hydrogen peroxide, and numerous other agents that damage DNA as well as being highly resistant to desiccation. It is clear that the D. radiodurans strain R1 whole genome which carries 3,195 predicted genes, consists of two chromosomes, one megaplasmid, and one plasmid. This combination of factors has positioned D. radiodurans as a promising candidate for the study of mechanisms of DNA damage and repair, as well as its exploitation for practical purposes such as cleanup and stabilization of radioactive waste sites. Radiation resistance of D. radiodurans seems very complex and is determined collectively by some features revealed by genome analysis, as well as by many more subtle structural peculiarities of proteins and DNA that are not readily inferred from the comparative sequences analysis. The fundamental questions underlying the extreme resistance phenotype of D. radiodurans remain unanswered. In this study, two protein databases including Deinococcus radiodurans R1 and E. coli K-12, were applied to whole protein sequences comparative analysis. Several computational tools developed from RDBMS (Relation Database Management System), were applied to this study. From the protein database comparison results, our target is to find the possible mechanisms by which proteins can become radiation resistant, either by a special 3-dimensional structure or by using a set of stable amino acids in the sequence.
AB - Bacteria Deinococcus radiodurans strain R1 was extremely resistant to ionizing radiation, UV light, hydrogen peroxide, and numerous other agents that damage DNA as well as being highly resistant to desiccation. It is clear that the D. radiodurans strain R1 whole genome which carries 3,195 predicted genes, consists of two chromosomes, one megaplasmid, and one plasmid. This combination of factors has positioned D. radiodurans as a promising candidate for the study of mechanisms of DNA damage and repair, as well as its exploitation for practical purposes such as cleanup and stabilization of radioactive waste sites. Radiation resistance of D. radiodurans seems very complex and is determined collectively by some features revealed by genome analysis, as well as by many more subtle structural peculiarities of proteins and DNA that are not readily inferred from the comparative sequences analysis. The fundamental questions underlying the extreme resistance phenotype of D. radiodurans remain unanswered. In this study, two protein databases including Deinococcus radiodurans R1 and E. coli K-12, were applied to whole protein sequences comparative analysis. Several computational tools developed from RDBMS (Relation Database Management System), were applied to this study. From the protein database comparison results, our target is to find the possible mechanisms by which proteins can become radiation resistant, either by a special 3-dimensional structure or by using a set of stable amino acids in the sequence.
KW - Amino Acid Compositions
KW - Database
KW - Deinococcus radiodurans R1
KW - Protein sequences
UR - http://www.scopus.com/inward/record.url?scp=11144294190&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=11144294190&partnerID=8YFLogxK
M3 - Conference contribution
AN - SCOPUS:11144294190
SN - 1932415432
SN - 9781932415438
SP - 314
EP - 321
BT - Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04
A2 - Valafar, F.
A2 - Valafar, H.
ER -