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WIREs Comput Mol Sci
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Insights into the binding of intrinsically disordered proteins from molecular dynamics simulation

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Intrinsically disordered proteins (IDPs) are a class of protein that, in the native state, possess no well‐defined secondary or tertiary structure, existing instead as dynamic ensembles of conformations. They are biologically important, with approximately 20% of all eukaryotic proteins disordered, and found at the heart of many biochemical networks. To fulfil their biological roles, many IDPs need to bind to proteins and/or nucleic acids. And although unstructured in solution, IDPs typically fold into a well‐defined three‐dimensional structure upon interaction with a binding partner. The flexibility and structural diversity inherent to IDPs makes this coupled folding and binding difficult to study at atomic resolution by experiment alone, and computer simulation currently offers perhaps the best opportunity to understand this process. But simulation of coupled folding and binding is itself extremely challenging; these molecules are large and highly flexible, and their binding partners, such as DNA or cyclins, are also often large. Therefore, their study requires either simplified representations, advanced enhanced sampling schemes, or both. It is not always clear that existing simulation techniques, optimized for studying folded proteins, are well suited to IDPs. In this article, we examine the progress that has been made in the study of coupled folding and binding using molecular dynamics simulation. We summarize what has been learnt, and examine the state of the art in terms of both methodologies and models. We also consider the lessons to be learnt from advances in other areas of simulation and highlight the issues that remain of be addressed.

The protein Jun is an IDP that undergoes coupled folding and binding to form homo‐ or heterodimeric complexes with DNA. (a) Two Jun monomers, each shown as an ensemble of five conformations taken every 200 nanoseconds from a 1 microsecond Gō model simulation of the isolated protein. (b) The crystal structure of the Jun–Jun homodimer in complex with DNA, from PDB 2H7H.
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Different scales of representation for molecular dynamics simulations of the pKIDKIX system. (a) All‐atom model with explicit water. (b) All‐atom model with implicit water. (c) Coarse‐grained Cα model.
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Possible mechanisms for coupled folding and binding, illustrated using the proteins pKID and KIX. (a) When unbound, an IDP exists as an equilibrium between multiple distinct structures, which may include the fully folded structure. (b) According to the induced fit folding mechanism, the IDP binds to its partner in the unfolded state before (c) folding while attached to its partner. (d) The conformation selection mechanism suggests that the partner protein selects folded structures from the equilibrium ensemble of the IDP, and binds only to them.
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Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods

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