a preformed binding interface in the unbound ensemble of an intrinsically disordered protein evidence from molecular simulations预制绑定接口的系综的内在无序蛋白质分子模拟的证据.pdfVIP
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a preformed binding interface in the unbound ensemble of an intrinsically disordered protein evidence from molecular simulations预制绑定接口的系综的内在无序蛋白质分子模拟的证据
A Preformed Binding Interface in the Unbound Ensemble
of an Intrinsically Disordered Protein: Evidence from
Molecular Simulations
Michael Knott, Robert B. Best*
University of Cambridge, Department of Chemistry, Cambridge, United Kingdom
Abstract
Intrinsically disordered proteins play an important role in cellular signalling, mediated by their interactions with other
biomolecules. A key question concerns the nature of their binding mechanism, and whether the bound structure is induced
only by proximity to the binding partner. This is difficult to answer through experiment alone because of the very
heterogeneous nature of the unbound ensemble, and the probable rapid interconversion of the various unbound
structures. Here we report the most extensive set of simulations on NCBD to date: we use large-scale replica exchange
molecular dynamics to explore the unbound state. An important feature of the study is the use of an atomistic force field
that has been parametrised against experimental data for weakly structured peptides, together with an accurate explicit
water model. Neither the force field nor the starting conformations are biased towards a particular structure. The regions of
NCBD that have high helical propensity in the simulations correspond closely to helices in the ‘core’ unbound conformation
determined by NMR, although no single member of the simulated unbound ensemble closely resembles the core
conformation, or either of the two known bound conformations. We have validated the results against NMR spectroscopy
and SAXS measurements, obtaining reasonable agreement. The two helices which most stabilise the binding of NCBD with
ACTR are formed readily; the third helix,
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