Quaternionic representation of the genetic code.
Identifieur interne : 000864 ( Ncbi/Merge ); précédent : 000863; suivant : 000865Quaternionic representation of the genetic code.
Auteurs : C Manuel Carlevaro [Argentine] ; Ramiro M. Irastorza [Argentine] ; Fernando Vericat [Argentine]Source :
- Bio Systems ; 2016.
Abstract
A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order of appearance of the amino acids along the evolution as inferred from work that mixtures known experimental results with theoretical speculations. Suggested by the diagram we propose a Hamilton quaternions based mathematical representation of the code as it stands now-a-days. The central object in the description is a codon function that assigns to each amino acid an integer quaternion in such a way that the observed code degeneration is preserved. We emphasize the advantages of a quaternionic representation of amino acids taking as an example the folding of proteins. With this aim we propose an algorithm to go from the quaternions sequence to the protein three dimensional structure which can be compared with the corresponding experimental one stored at the Protein Data Bank. In our criterion the mathematical representation of the genetic code in terms of quaternions merits to be taken into account because it describes not only most of the known properties of the genetic code but also opens new perspectives that are mainly derived from the close relationship between quaternions and rotations.
DOI: 10.1016/j.biosystems.2015.12.009
PubMed: 26751396
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Electronic address: manuel@iflysib.unlp.edu.ar.</nlm:affiliation><country xml:lang="fr">Argentine</country><wicri:regionArea>Instituto de Física de Líquidos y Sistemas Biológicos, 59 Nro. 789, 1900 La Plata, Argentina; Universidad Tecnológica Nacional, Facultad Regional Buenos Aires, Mozart Nro. 2300, C14071VT Buenos Aires</wicri:regionArea><wicri:noRegion>C14071VT Buenos Aires</wicri:noRegion></affiliation></author><author><name sortKey="Irastorza, Ramiro M" sort="Irastorza, Ramiro M" uniqKey="Irastorza R" first="Ramiro M" last="Irastorza">Ramiro M. Irastorza</name><affiliation wicri:level="1"><nlm:affiliation>Instituto de Física de Líquidos y Sistemas Biológicos, 59 Nro. 789, 1900 La Plata, Argentina; Instituto de Ingeniería y Agronomía, Universidad Nacional Arturo Jauretche, 1888 Florencio Varela, Buenos Aires, Argentina. 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Electronic address: manuel@iflysib.unlp.edu.ar.</nlm:affiliation><country xml:lang="fr">Argentine</country><wicri:regionArea>Instituto de Física de Líquidos y Sistemas Biológicos, 59 Nro. 789, 1900 La Plata, Argentina; Universidad Tecnológica Nacional, Facultad Regional Buenos Aires, Mozart Nro. 2300, C14071VT Buenos Aires</wicri:regionArea><wicri:noRegion>C14071VT Buenos Aires</wicri:noRegion></affiliation></author><author><name sortKey="Irastorza, Ramiro M" sort="Irastorza, Ramiro M" uniqKey="Irastorza R" first="Ramiro M" last="Irastorza">Ramiro M. Irastorza</name><affiliation wicri:level="1"><nlm:affiliation>Instituto de Física de Líquidos y Sistemas Biológicos, 59 Nro. 789, 1900 La Plata, Argentina; Instituto de Ingeniería y Agronomía, Universidad Nacional Arturo Jauretche, 1888 Florencio Varela, Buenos Aires, Argentina. Electronic address: rirastorza@iflysib.unlp.edu.ar.</nlm:affiliation><country xml:lang="fr">Argentine</country><wicri:regionArea>Instituto de Física de Líquidos y Sistemas Biológicos, 59 Nro. 789, 1900 La Plata, Argentina; Instituto de Ingeniería y Agronomía, Universidad Nacional Arturo Jauretche, 1888 Florencio Varela, Buenos Aires</wicri:regionArea><wicri:noRegion>Buenos Aires</wicri:noRegion></affiliation></author><author><name sortKey="Vericat, Fernando" sort="Vericat, Fernando" uniqKey="Vericat F" first="Fernando" last="Vericat">Fernando Vericat</name><affiliation wicri:level="1"><nlm:affiliation>Instituto de Física de Líquidos y Sistemas Biológicos, 59 Nro. 789, 1900 La Plata, Argentina; Grupo de Aplicaciones Matemáticas y Estadísticas de la Facultad de Ingeniería (GAMEFI), Universidad Nacional de La Plata, Calle 115 y 48, 1900 La Plata, Argentina. Electronic address: vericat@iflysib.unlp.edu.ar.</nlm:affiliation><country xml:lang="fr">Argentine</country><wicri:regionArea>Instituto de Física de Líquidos y Sistemas Biológicos, 59 Nro. 789, 1900 La Plata, Argentina; Grupo de Aplicaciones Matemáticas y Estadísticas de la Facultad de Ingeniería (GAMEFI), Universidad Nacional de La Plata, Calle 115 y 48, 1900 La Plata</wicri:regionArea><wicri:noRegion>1900 La Plata</wicri:noRegion></affiliation></author></analytic><series><title level="j">Bio Systems</title><idno type="e-ISSN">1872-8324</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order of appearance of the amino acids along the evolution as inferred from work that mixtures known experimental results with theoretical speculations. Suggested by the diagram we propose a Hamilton quaternions based mathematical representation of the code as it stands now-a-days. The central object in the description is a codon function that assigns to each amino acid an integer quaternion in such a way that the observed code degeneration is preserved. We emphasize the advantages of a quaternionic representation of amino acids taking as an example the folding of proteins. With this aim we propose an algorithm to go from the quaternions sequence to the protein three dimensional structure which can be compared with the corresponding experimental one stored at the Protein Data Bank. In our criterion the mathematical representation of the genetic code in terms of quaternions merits to be taken into account because it describes not only most of the known properties of the genetic code but also opens new perspectives that are mainly derived from the close relationship between quaternions and rotations.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">26751396</PMID><DateCreated><Year>2016</Year><Month>1</Month><Day>25</Day></DateCreated><DateRevised><Year>2016</Year><Month>1</Month><Day>25</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1872-8324</ISSN><JournalIssue CitedMedium="Internet"><Volume>141</Volume><PubDate><Year>2016</Year><Month>Jan</Month><Day>2</Day></PubDate></JournalIssue><Title>Bio Systems</Title><ISOAbbreviation>BioSystems</ISOAbbreviation></Journal><ArticleTitle>Quaternionic representation of the genetic code.</ArticleTitle><Pagination><MedlinePgn>10-19</MedlinePgn></Pagination><ELocationID EIdType="pii">S0303-2647(15)00208-7</ELocationID><ELocationID EIdType="doi">10.1016/j.biosystems.2015.12.009</ELocationID><Abstract><AbstractText NlmCategory="UNASSIGNED">A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order of appearance of the amino acids along the evolution as inferred from work that mixtures known experimental results with theoretical speculations. Suggested by the diagram we propose a Hamilton quaternions based mathematical representation of the code as it stands now-a-days. The central object in the description is a codon function that assigns to each amino acid an integer quaternion in such a way that the observed code degeneration is preserved. We emphasize the advantages of a quaternionic representation of amino acids taking as an example the folding of proteins. With this aim we propose an algorithm to go from the quaternions sequence to the protein three dimensional structure which can be compared with the corresponding experimental one stored at the Protein Data Bank. In our criterion the mathematical representation of the genetic code in terms of quaternions merits to be taken into account because it describes not only most of the known properties of the genetic code but also opens new perspectives that are mainly derived from the close relationship between quaternions and rotations.</AbstractText><CopyrightInformation>Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.</CopyrightInformation></Abstract><AuthorList><Author><LastName>Carlevaro</LastName><ForeName>C Manuel</ForeName><Initials>CM</Initials><AffiliationInfo><Affiliation>Instituto de Física de Líquidos y Sistemas Biológicos, 59 Nro. 789, 1900 La Plata, Argentina; Universidad Tecnológica Nacional, Facultad Regional Buenos Aires, Mozart Nro. 2300, C14071VT Buenos Aires, Argentina. Electronic address: manuel@iflysib.unlp.edu.ar.</Affiliation></AffiliationInfo></Author><Author><LastName>Irastorza</LastName><ForeName>Ramiro M</ForeName><Initials>RM</Initials><AffiliationInfo><Affiliation>Instituto de Física de Líquidos y Sistemas Biológicos, 59 Nro. 789, 1900 La Plata, Argentina; Instituto de Ingeniería y Agronomía, Universidad Nacional Arturo Jauretche, 1888 Florencio Varela, Buenos Aires, Argentina. Electronic address: rirastorza@iflysib.unlp.edu.ar.</Affiliation></AffiliationInfo></Author><Author><LastName>Vericat</LastName><ForeName>Fernando</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Instituto de Física de Líquidos y Sistemas Biológicos, 59 Nro. 789, 1900 La Plata, Argentina; Grupo de Aplicaciones Matemáticas y Estadísticas de la Facultad de Ingeniería (GAMEFI), Universidad Nacional de La Plata, Calle 115 y 48, 1900 La Plata, Argentina. Electronic address: vericat@iflysib.unlp.edu.ar.</Affiliation></AffiliationInfo></Author></AuthorList><Language>ENG</Language><PublicationTypeList><PublicationType UI="">JOURNAL ARTICLE</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>1</Month><Day>2</Day></ArticleDate></Article><MedlineJournalInfo><MedlineTA>Biosystems</MedlineTA><NlmUniqueID>0430773</NlmUniqueID><ISSNLinking>0303-2647</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Broken symmetry</Keyword><Keyword MajorTopicYN="N">Genetic code evolution</Keyword><Keyword MajorTopicYN="N">Hamilton quaternions</Keyword><Keyword MajorTopicYN="N">Protein folding</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>9</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2015</Year><Month>12</Month><Day>4</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>12</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>1</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>1</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>1</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26751396</ArticleId><ArticleId IdType="pii">S0303-2647(15)00208-7</ArticleId><ArticleId IdType="doi">10.1016/j.biosystems.2015.12.009</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Argentine</li></country></list><tree><country name="Argentine"><noRegion><name sortKey="Carlevaro, C Manuel" sort="Carlevaro, C Manuel" uniqKey="Carlevaro C" first="C Manuel" last="Carlevaro">C Manuel Carlevaro</name></noRegion><name sortKey="Irastorza, Ramiro M" sort="Irastorza, Ramiro M" uniqKey="Irastorza R" first="Ramiro M" last="Irastorza">Ramiro M. Irastorza</name><name sortKey="Vericat, Fernando" sort="Vericat, Fernando" uniqKey="Vericat F" first="Fernando" last="Vericat">Fernando Vericat</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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