An intrinsically disordered protein (IDP) does not have a definite 3D structure, and because of its highly flexible nature it evolves dynamically in very large and diverse regions of the phase space. A standard molecular dynamics run can sample only a limited region of the latter; even though this kind of simulation may be effective in sampling local temporary secondary structures, it is not sufficient to highlight properties that require a larger sampling of the space to be detected, like transient tertiary structures. But if the structure of an IDP is dynamically evolved using metadynamics (an algorithm that keeps track of the regions of the phase space already sampled), the system can be forced to wander in a much larger region of the phase space. We have applied this procedure to the simulation of tau, one of the largest totally disordered proteins. Combining the results of the simulation with small-angle X-ray scattering yields a significant improvement in the sampling of the phase space in comparison with standard molecular dynamics, and hints at the persistence of an extended hairpin tertiary structure encompassing the N terminal, the proline-rich domain, and the repeats domain.

Transient tertiary structures in tau, an intrinsically disordered protein

BATTISTI, Anna;
2013

Abstract

An intrinsically disordered protein (IDP) does not have a definite 3D structure, and because of its highly flexible nature it evolves dynamically in very large and diverse regions of the phase space. A standard molecular dynamics run can sample only a limited region of the latter; even though this kind of simulation may be effective in sampling local temporary secondary structures, it is not sufficient to highlight properties that require a larger sampling of the space to be detected, like transient tertiary structures. But if the structure of an IDP is dynamically evolved using metadynamics (an algorithm that keeps track of the regions of the phase space already sampled), the system can be forced to wander in a much larger region of the phase space. We have applied this procedure to the simulation of tau, one of the largest totally disordered proteins. Combining the results of the simulation with small-angle X-ray scattering yields a significant improvement in the sampling of the phase space in comparison with standard molecular dynamics, and hints at the persistence of an extended hairpin tertiary structure encompassing the N terminal, the proline-rich domain, and the repeats domain.
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Battisti, Anna; Gabriele, Ciasca; Alexander, Tenenbaum
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/20.500.11767/32746
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