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Prokink: a protocol for numerical evaluation of helix distortions by proline.
Visiers, I; Braunheim, B B; Weinstein, H.
Afiliação
  • Visiers I; Department of Physiology and Biophysics, Mount Sinai School of Medicine, One Gustave Levy Place, New York, NY 10029, USA.
Protein Eng ; 13(9): 603-6, 2000 Sep.
Article em En | MEDLINE | ID: mdl-11054453
Proline residues are known to perturb the structure of helices by introducing a kink between the segments preceding and following the proline residue. The distortion of the helical structure results from the avoided steric clash between the ring of the proline at position (i) and the backbone carbonyl at position (i - 4), as well as the elimination of helix backbone H-bonds for the carbonyls at positions (i - 3) and (i - 4). Both the departure from the ideal helical pattern and the reduction in H-bond stabilization contribute to the observed flexibility of a proline-containing alpha-helix. The special local flexibility of the proline kink can confer an important role on the proline-containing helix in the conformational changes related to the function of the protein. As a useful tool in determining and evaluating the role of proline-induced flexibility and distortions in protein function, we present here a protocol to quantify the geometry of the distortion introduced in helices by prolines both as a time-averaged value and for individual 'snapshots' along a molecular dynamics simulation.
Assuntos
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Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Algoritmos / Prolina / Proteínas / Modelos Moleculares Idioma: En Revista: Protein Eng Assunto da revista: BIOQUIMICA / BIOTECNOLOGIA Ano de publicação: 2000 Tipo de documento: Article País de afiliação: Estados Unidos País de publicação: Reino Unido
Buscar no Google
Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Algoritmos / Prolina / Proteínas / Modelos Moleculares Idioma: En Revista: Protein Eng Assunto da revista: BIOQUIMICA / BIOTECNOLOGIA Ano de publicação: 2000 Tipo de documento: Article País de afiliação: Estados Unidos País de publicação: Reino Unido