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Intrinsically disordered regions (IDRs) are important components of protein functionality, with their charge distribution serving as a key factor in determining their roles. Notably, many proteins possess IDRs that are highly negatively charged, characterized by sequences rich in aspartate (D) or glutamate (E) residues. Bioinformatic analyses indicate that negatively charged low-complexity IDRs are significantly more common than their positively charged counterparts rich in arginine (R) or lysine (K). For instance, sequences of 10 or more consecutive negatively charged residues (D or E) are present in 268 human proteins. In contrast, corresponding sequences of 10 or more consecutive positively charged residues (K or R) are present in only 12 human proteins. Interestingly, about 50% of proteins containing D/E tracts function as DNA-binding or RNA-binding proteins. Negatively charged IDRs can electrostatically mimic nucleic acids and dynamically compete with them for the DNA-binding domains (DBDs) or RNA-binding domains (RBDs) that are positively charged. This leads to a phenomenon known as autoinhibition, in which the negatively charged IDRs inhibit binding to nucleic acids by occupying the binding interfaces within the proteins through intramolecular interactions. Rather than merely reducing binding activity, negatively charged IDRs offer significant advantages for the functions of DNA/RNA-binding proteins. The dynamic competition between negatively charged IDRs and nucleic acids can accelerate the target search processes for these proteins. When a protein encounters DNA or RNA, the electrostatic repulsion force between the nucleic acids and the negatively charged IDRs can trigger conformational changes that allow the nucleic acids to access DBDs or RBDs. Additionally, when proteins are trapped at high-affinity non-target sites on DNA or RNA ("decoys"), the electrostatic repulsion from the negatively charged IDRs can rescue the proteins from these traps. Negatively charged IDRs act as gatekeepers, rejecting nonspecific ligands while allowing the target to access the molecular interfaces of DBDs or RBDs, which increases binding specificity. These IDRs can also promote proper protein folding, facilitate chromatin remodeling by displacing other proteins bound to DNA, and influence phase separation, affecting local pH. The functions of negatively charged IDRs can be regulated through protein-protein interactions, post-translational modifications, and proteolytic processing. These characteristics can be harnessed as tools for protein engineering. Some frame-shift mutations that convert negatively charged IDRs into positively charged ones are linked to human diseases. Therefore, it is crucial to understand the physicochemical properties and functional roles of negatively charged IDRs that compete with nucleic acids.
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Modeling protein–nucleic acid complexes with extremely large conformational changes using Flex‐LZerD
Abstract Proteins and nucleic acids are key components in many processes in living cells, and interactions between proteins and nucleic acids are often crucial pathway components. In many cases, large flexibility of proteins as they interact with nucleic acids is key to their function. To understand the mechanisms of these processes, it is necessary to consider the 3D atomic structures of such protein–nucleic acid complexes. When such structures are not yet experimentally determined, protein docking can be used to computationally generate useful structure models. However, such docking has long had the limitation that the consideration of flexibility is usually limited to small movements or to small structures. We previously developed a method of flexible protein docking which could model ordered proteins which undergo large‐scale conformational changes, which we also showed was compatible with nucleic acids. Here, we elaborate on the ability of that pipeline, Flex‐LZerD, to model specifically interactions between proteins and nucleic acids, and demonstrate that Flex‐LZerD can model more interactions and types of conformational change than previously shown.
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- Award ID(s):
- 2146026
- PAR ID:
- 10418663
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- PROTEOMICS
- Volume:
- 23
- Issue:
- 17
- ISSN:
- 1615-9853
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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