Torsional Network Model: Normal Modes in Torsion Angle Space Better Correlate with Conformation Changes in Proteins

We introduce the torsional network model (TNM), an elastic network model whose degrees of freedom are the torsion angles of the protein backbone. Normal modes of the TNM displace backbone atoms including C maintaining their covalent geometry. For many proteins, low frequency TNM modes are localized...

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Detalles Bibliográficos
Autores: Méndez, Raúl, Bastolla, Ugo
Tipo de recurso: artículo
Fecha de publicación:2010
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/34092
Acceso en línea:http://hdl.handle.net/10261/34092
Access Level:acceso abierto
Palabra clave:Torsional network model (TNM),
Descripción
Sumario:We introduce the torsional network model (TNM), an elastic network model whose degrees of freedom are the torsion angles of the protein backbone. Normal modes of the TNM displace backbone atoms including C maintaining their covalent geometry. For many proteins, low frequency TNM modes are localized in torsion space yet collective in Cartesian space, reminiscent of hinge motions. A smaller number of TNM modes than anisotropic network model modes are enough to represent experimentally observed conformation changes. We observed significant correlation between the contribution of each normal mode to equilibrium fluctuations and to conformation changes, and defined the excess correlation with respect to a simple neutral model. The stronger this excess correlation, the lower the predicted free energy barrier of the conformation change and the fewer modes contribute to the change.

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