About this Research Topic
The protein sequence-structure-function paradigm was long-time believed to be the foundation of the protein universe. It was assumed that a protein will fold consistently into a native state structure under natural conditions, which means the 3D structure is completely encoded in its amino acid sequence. However, the recognition of intrinsically disordered proteins (IDPs) broke the sequence-structure-function rule. The IDPs or intrinsically disordered regions (IDRs) are highly dynamic and fail to fold into stable, defined structures. Protein disorder is naturally highly abundant. It is estimated that roughly 30% of sequences, 30 residues or longer, drawn randomly from the human proteome, are likely to be IDRs. Approximately 10–30% of prokaryotic and 15–45% of eukaryotic proteins contain intrinsically disordered regions. The highly dynamic nature makes it hard to characterize the structures of these proteins experimentally. Instead, computational simulations provide efficient ways to understand the structure and function of IDPs.
The rapidly developed deep learning methods, such as AlphaFold, provide reliable solutions for the structure inferring of well-defined proteins. However, the structure ensembles, instead of one single structure or several structures, are required to describe the features of the proteins. Due to their dynamic nature, many IDPs can interact with multiple proteins with low affinity but high specificity, enabling them to act as hubs in signaling networks or adapters for multi-protein scaffolds. The low affinity of certain IDPs facilitates fast disengagement from signaling partners, which could be advantageous for rapid shutdown and switching of signaling, allowing better control over the cellular machinery. There is nevertheless much still to learn about how and why the functions are performed in such highly dynamic structures, especially the common structural features in the diverse configurations in the structure ensemble, even across different IDPs. Besides, the function is regulated through a fine balance of alternative splicing, post-translational modifications, expression level, and cell presence duration. The underlying mechanism of how the regulators affect the structural ensembles and further affect the functions of IDPs are eagerly needed.
This Research Topic aims to expand the knowledge on the promising, recent, and novel research trends in the intrinsically disordered proteins field. Specific themes that we would like contributors to address may include, but are not limited to:
• Unveiling new insights or findings about the conformational sampling of important intrinsically disordered proteins.
• Investigating the structural basis of IDP functions, encompassing regulation, drug binding, interactions, and aggregation or phase separations related to IDPs.
• Advancing and expanding force fields, computational methods, or tools for IDP studies.
The rapidly developed deep learning methods, such as AlphaFold, provide reliable solutions for the structure inferring of well-defined proteins. However, the structure ensembles, instead of one single structure or several structures, are required to describe the features of the proteins. Due to their dynamic nature, many IDPs can interact with multiple proteins with low affinity but high specificity, enabling them to act as hubs in signaling networks or adapters for multi-protein scaffolds. The low affinity of certain IDPs facilitates fast disengagement from signaling partners, which could be advantageous for rapid shutdown and switching of signaling, allowing better control over the cellular machinery. There is nevertheless much still to learn about how and why the functions are performed in such highly dynamic structures, especially the common structural features in the diverse configurations in the structure ensemble, even across different IDPs. Besides, the function is regulated through a fine balance of alternative splicing, post-translational modifications, expression level, and cell presence duration. The underlying mechanism of how the regulators affect the structural ensembles and further affect the functions of IDPs are eagerly needed.
This Research Topic aims to expand the knowledge on the promising, recent, and novel research trends in the intrinsically disordered proteins field. Specific themes that we would like contributors to address may include, but are not limited to:
• Unveiling new insights or findings about the conformational sampling of important intrinsically disordered proteins.
• Investigating the structural basis of IDP functions, encompassing regulation, drug binding, interactions, and aggregation or phase separations related to IDPs.
• Advancing and expanding force fields, computational methods, or tools for IDP studies.
Keywords: Intrinsically disordered proteins, Molecular dynamics simulations, Structural ensembles, Regulations, Dynamics
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