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Disordered linkers in multidomain allosteric proteins: Entropic effect to favor the open state or enhanced local concentration to favor the closed state?
Author(s) -
Li Maodong,
Cao Huaiqing,
Lai Luhua,
Liu Zhirong
Publication year - 2018
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.3475
Subject(s) - allosteric regulation , linker , chemistry , molecular dynamics , biophysics , crystallography , stereochemistry , computational chemistry , biochemistry , computer science , biology , receptor , operating system
There are many multidomain allosteric proteins where an allosteric signal at the allosteric domain modifies the activity of the functional domain. Intrinsically disordered regions (linkers) are widely involved in this kind of regulation process, but the essential role they play therein is not well understood. Here, we investigated the effect of linkers in stabilizing the open or the closed states of multidomain proteins using combined thermodynamic deduction and coarse‐grained molecular dynamics simulations. We revealed that the influence of linker can be fully characterized by an effective local concentration [B] 0 . When K d is smaller than [B] 0 , the closed state would be favored; while the open state would be preferred when K d is larger than [B] 0 . We used four protein systems with markedly different domain–domain binding affinity and structural order/disorder as model systems to understand the relationship between [B] 0 and the linker length as well as its flexibility. The linker length is the main practical determinant of [B] 0 . [B] 0 of a flexible linker with 40–60 residues was determined to be in a narrow range of 0.2–0.6 m M , while a too short or too long length would dramatically decrease [B] 0 . With the revealed [B] 0 range, the introduction of a flexible linker makes the regulation of weakly interacting partners possible.