Publicação
Parametrization of synthetic amino acids
| Resumo: | C(alpha)-C(alpha)dialkylglycines, sarcosine, O-methyltyrosine and beta-(imidazol-1-yl)-alanine are noncoded amino acids with a large pharmaceutical potential. We have developed a set of parameters for these amino acids, consistent with the AMBER force field. Several dipeptide and tripeptide models were built to simulate the different possibilities for insertion of the noncoded amino acids in a peptide backbone. Bonding parameters were obtained from both existing force fields and quantum calculations. The Coulombic parameters have been determined using a multiconformational weighted approach and a restricted electrostatic potential fitting, at a 6-31G* ab initio level. Molecular dynamics simulations have been carried out on the model peptides to validate the parameters obtained. The characteristic geometry features such as the planarity of peptide bonds have been conserved on these models. The peptide models, which included monosubstituted residues, have revealed considerable backbone flexibility. The conformational flexibility of the peptides containing disubstituted residues has been significantly restricted by the length and volume of their side chains. |
|---|---|
| Autores principais: | Preto, Marco A. C. |
| Outros Autores: | Melo, André; Costa, Susana P. G.; Maia, Hernâni Lopes Silva; Ramos, Maria J. |
| Assunto: | Ciências Naturais::Ciências Químicas |
| Ano: | 2003 |
| País: | Portugal |
| Tipo de documento: | artigo |
| Tipo de acesso: | acesso restrito |
| Instituição associada: | Universidade do Minho |
| Idioma: | inglês |
| Origem: | RepositóriUM - Universidade do Minho |
| _version_ | 1867438992769679360 |
|---|---|
| author | Preto, Marco A. C. |
| author2 | Melo, André Costa, Susana P. G. Maia, Hernâni Lopes Silva Ramos, Maria J. |
| author2_role | author author author author |
| author_facet | Preto, Marco A. C. Melo, André Costa, Susana P. G. Maia, Hernâni Lopes Silva Ramos, Maria J. |
| author_role | author |
| contributor_name_str_mv | RepositóriUM - Universidade do Minho |
| country_str | PT |
| creators_json_txt | [{\"Person.name\":\"Preto, Marco A. C.\"},{\"Person.name\":\"Melo, André\"},{\"Person.name\":\"Costa, Susana P. G.\"},{\"Person.name\":\"Maia, Hernâni Lopes Silva\"},{\"Person.name\":\"Ramos, Maria J.\"}] |
| datacite.contributors.contributor.contributorName.fl_str_mv | RepositóriUM - Universidade do Minho |
| datacite.creators.creator.creatorName.fl_str_mv | Preto, Marco A. C. Melo, André Costa, Susana P. G. Maia, Hernâni Lopes Silva Ramos, Maria J. |
| datacite.date.Accepted.fl_str_mv | 2003-01-01T00:00:00Z |
| datacite.date.embargoed.fl_str_mv | 10000-01-01T00:00:00Z |
| datacite.rights.fl_str_mv | http://purl.org/coar/access_right/c_16ec |
| datacite.subjects.subject.fl_str_mv | Ciências Naturais::Ciências Químicas |
| datacite.titles.title.fl_str_mv | Parametrization of synthetic amino acids |
| dc.contributor.none.fl_str_mv | RepositóriUM - Universidade do Minho |
| dc.creator.none.fl_str_mv | Preto, Marco A. C. Melo, André Costa, Susana P. G. Maia, Hernâni Lopes Silva Ramos, Maria J. |
| dc.date.Accepted.fl_str_mv | 2003-01-01T00:00:00Z |
| dc.date.embargoed.fl_str_mv | 10000-01-01T00:00:00Z |
| dc.format.none.fl_str_mv | application/pdf application/pdf |
| dc.identifier.none.fl_str_mv | https://hdl.handle.net/1822/86454 |
| dc.language.none.fl_str_mv | eng |
| dc.publisher.none.fl_str_mv | American Chemical Society |
| dc.rights.none.fl_str_mv | http://purl.org/coar/access_right/c_16ec |
| dc.subject.none.fl_str_mv | Ciências Naturais::Ciências Químicas |
| dc.title.fl_str_mv | Parametrization of synthetic amino acids |
| dc.type.none.fl_str_mv | http://purl.org/coar/resource_type/c_6501 |
| description | C(alpha)-C(alpha)dialkylglycines, sarcosine, O-methyltyrosine and beta-(imidazol-1-yl)-alanine are noncoded amino acids with a large pharmaceutical potential. We have developed a set of parameters for these amino acids, consistent with the AMBER force field. Several dipeptide and tripeptide models were built to simulate the different possibilities for insertion of the noncoded amino acids in a peptide backbone. Bonding parameters were obtained from both existing force fields and quantum calculations. The Coulombic parameters have been determined using a multiconformational weighted approach and a restricted electrostatic potential fitting, at a 6-31G* ab initio level. Molecular dynamics simulations have been carried out on the model peptides to validate the parameters obtained. The characteristic geometry features such as the planarity of peptide bonds have been conserved on these models. The peptide models, which included monosubstituted residues, have revealed considerable backbone flexibility. The conformational flexibility of the peptides containing disubstituted residues has been significantly restricted by the length and volume of their side chains. |
| dirty | 0 |
| eu_rights_str_mv | restrictedAccess |
| format | article |
| fulltext.url.fl_str_mv | https://repositorium.uminho.pt/bitstreams/e4f4eef2-7a2e-4dd7-909f-eb5e06dddddf/download |
| id | rum_a2c5bd32ac8cf188a7e71fb4b94a2d8a |
| identifier.url.fl_str_mv | https://hdl.handle.net/1822/86454 |
| instacron_str | repositorium |
| institution | Universidade do Minho |
| instname_str | Universidade do Minho |
| language | eng |
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| network_name_str | RepositóriUM - Universidade do Minho |
| oai_identifier_str | oai:repositorium.uminho.pt:1822/86454 |
| organization_str_mv | urn:organizationAcronym:repositorium |
| person_str_mv | Preto, Marco A. C. Melo, André Costa, Susana P. G. Maia, Hernâni Lopes Silva Ramos, Maria J. |
| publishDate | 2003 |
| publisher.none.fl_str_mv | American Chemical Society |
| reponame_str | RepositóriUM - Universidade do Minho |
| repository_id_str | urn:repositoryAcronym:rum |
| service_str_mv | urn:repositoryAcronym:rum |
| spelling | engAmerican Chemical SocietyporC(alpha)-C(alpha)dialkylglycines, sarcosine, O-methyltyrosine and beta-(imidazol-1-yl)-alanine are noncoded amino acids with a large pharmaceutical potential. We have developed a set of parameters for these amino acids, consistent with the AMBER force field. Several dipeptide and tripeptide models were built to simulate the different possibilities for insertion of the noncoded amino acids in a peptide backbone. Bonding parameters were obtained from both existing force fields and quantum calculations. The Coulombic parameters have been determined using a multiconformational weighted approach and a restricted electrostatic potential fitting, at a 6-31G* ab initio level. Molecular dynamics simulations have been carried out on the model peptides to validate the parameters obtained. The characteristic geometry features such as the planarity of peptide bonds have been conserved on these models. The peptide models, which included monosubstituted residues, have revealed considerable backbone flexibility. The conformational flexibility of the peptides containing disubstituted residues has been significantly restricted by the length and volume of their side chains.application/pdfapplication/pdfporParametrization of synthetic amino acidsPreto, Marco A. C.Melo, AndréCosta, Susana P. G.Maia, Hernâni Lopes SilvaRamos, Maria J.HostingInstitutionOrganizationalRepositóriUM - Universidade do Minhoe-mailmailto:repositorium@usdb.uminho.ptrepositorium@usdb.uminho.ptCITATIONPreto, M. A. C., Melo, A., Costa, S. P. G., Maia, H. L. S., & Ramos, M. J. (2003, November 27). Parametrization of Synthetic Amino Acids. The Journal of Physical Chemistry B. American Chemical Society (ACS). http://doi.org/10.1021/jp030544yISSNIsPartOf1520-6106DOIIsPartOf10.1021/jp030544y20032023-08-20T15:52:47Z10000-01-01T00:00:00Z2003-01-01T00:00:00ZHandlehttps://hdl.handle.net/1822/86454http://purl.org/coar/access_right/c_16ecrestricted accesshttp://www.oecd.org/science/inno/38235147.pdfFields of Science and Technology (FOS)Ciências Naturais::Ciências Químicas288680 bytes391450 bytesliteraturehttp://purl.org/coar/resource_type/c_6501journal articlehttp://purl.org/coar/access_right/c_f1cfapplication/pdffulltexthttps://repositorium.uminho.pt/bitstreams/e4f4eef2-7a2e-4dd7-909f-eb5e06dddddf/downloadhttp://purl.org/coar/access_right/c_f1cfapplication/pdffulltexthttps://repositorium.uminho.pt/bitstreams/47609df9-e761-485a-920f-8e99b10621bc/download |
| spellingShingle | Parametrization of synthetic amino acids Preto, Marco A. C. Ciências Naturais::Ciências Químicas |
| status | SINGLETON |
| subject.other.fl_str_mv | Ciências Naturais::Ciências Químicas |
| title | Parametrization of synthetic amino acids |
| title_full | Parametrization of synthetic amino acids |
| title_fullStr | Parametrization of synthetic amino acids |
| title_full_unstemmed | Parametrization of synthetic amino acids |
| title_short | Parametrization of synthetic amino acids |
| title_sort | Parametrization of synthetic amino acids |
| topic | Ciências Naturais::Ciências Químicas |
| topic_facet | Ciências Naturais::Ciências Químicas |
| url | https://hdl.handle.net/1822/86454 |
| visible | 1 |