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Dynamics comparison of two myoglobins with a distinct heme active site.
Lin, Ying-Wu; Wu, Yi-Mou; Liao, Li-Fu.
Afiliação
  • Lin YW; School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. linlinying@hotmail.com
J Mol Model ; 18(4): 1591-6, 2012 Apr.
Article em En | MEDLINE | ID: mdl-21805122
Sperm whale myoglobin (swMb) is a well-studied heme protein, both experimentally and theoretically. Comparatively, little attention has been paid to another member of Mb family, Aplysia limacina myoglobin (apMb). swMb and apMb have the same overall structure and perform the same biological function, i.e., O(2) carrier, while using a distinct heme active site. To provide insights into the structure-function relationship for these two Mbs, we herein made a comparison in terms of their dynamics properties using molecular dynamics simulation. We analyzed the overall structure and protein motions, as well as the intramolecular contacts, namely salt-bridges and hydrogen bonds, especially the interactions between the heme propionate groups and the polypeptide chain. The internal cavities in apMb were also compared to the well-known xenon and other cavities in swMb. Based on current simulations, we propose a unique "arginine gate" for apMb, which has a similar function to the histidine gate observed for swMb in previous studies. This study provides valuable information for understanding the homology of heme proteins, and also aids in rational design of structural and functional heme proteins by alternating the heme active site.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Heme / Hemeproteínas / Mioglobina Limite: Animals Idioma: En Revista: J Mol Model Assunto da revista: BIOLOGIA MOLECULAR Ano de publicação: 2012 Tipo de documento: Article País de afiliação: China País de publicação: Alemanha

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Heme / Hemeproteínas / Mioglobina Limite: Animals Idioma: En Revista: J Mol Model Assunto da revista: BIOLOGIA MOLECULAR Ano de publicação: 2012 Tipo de documento: Article País de afiliação: China País de publicação: Alemanha