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On the role of residue phosphorylation in 14-3-3 partners: AANAT as a case study

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ABSTRACT

Twenty years ago, a novel concept in protein structural biology was discovered: the intrinsically disordered regions (IDRs). These regions remain largely unstructured under native conditions and the more are studied, more properties are attributed to them. Possibly, one of the most important is their ability to conform a new type of protein-protein interaction. Besides the classical domain-to-domain interactions, IDRs follow a ‘fly-casting’ model including ‘induced folding’. Unfortunately, it is only possible to experimentally explore initial and final states. However, the complete movie of conformational changes of protein regions and their characterization can be addressed by in silico experiments. Here, we simulate the binding of two proteins to describe how the phosphorylation of a single residue modulates the entire process. 14-3-3 protein family is considered a master regulator of phosphorylated proteins and from a modern point-of-view, protein phosphorylation is a three component system, with writers (kinases), erasers (phosphatases) and readers. This later biological role is attributed to the 14-3-3 protein family. Our molecular dynamics results show that phosphorylation of the key residue Thr31 in a partner of 14-3-3, the aralkylamine N-acetyltransferase, releases the fly-casting mechanism during binding. On the other hand, the non-phosphorylation of the same residue traps the proteins, systematically and repeatedly driving the simulations into wrong protein-protein conformations.

No MeSH data available.


Molecular recognition.(a) RMSF for phosphorylated Thr31 in AANAT and non-phosphorylated Thr31 in AANAT during 10 ns ≤ t ≤ 100 ns. (b) H-bond count between proteins using a 0.35 nm cutoff for the full protein-protein system and only residues belonging to αhelix 9 (positions from 200 to 228 in 14-3-3ζ).
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f6: Molecular recognition.(a) RMSF for phosphorylated Thr31 in AANAT and non-phosphorylated Thr31 in AANAT during 10 ns ≤ t ≤ 100 ns. (b) H-bond count between proteins using a 0.35 nm cutoff for the full protein-protein system and only residues belonging to αhelix 9 (positions from 200 to 228 in 14-3-3ζ).

Mentions: 14-3-3 protein family is considered a master regulator of phosphorylated proteins, binding more than 2000 different clients in a many-to-one, disordered-to-structured fashion. Figure 6 shows the fluctuation of 14-3-3ζ during both simulations (AANAT, AANAT*). Our results indicate that the binding pocket is the most mobile region of 14-3-3. The proposed auto-inhibitory C-terminal of 14-3-3 that contains the α-helix 9 is flexible, however, its importance is more clearly observed when we analyzed H-bonds. Remarkably, the phosphorylation of Thr31 in AANAT* produced an increase in the number of H-bonds towards α-helix 9 comparable to the numbers of H-bonds between AANAT and the entire 14-3-3ζ protein. Although the total number of H-bonds in region II (unrestrained simulation) are independent of the phosphoryl group in Thr31 (comparing the black line with the red one in Fig. 6b), the phosphorylation causes a high increase in region III. Also, almost all H-bonds of phosphorylated Thr31 are formed towards α-helix 9 in 14-3-3ζ (comparing the yellow line with the red one in the Fig. 6b). Taken together, this information could suggest that α-helix 9 is the main driving force to promote the right conformation and location of phosphorylated Thr31 in the major binding groove of 14-3-3ζ.


On the role of residue phosphorylation in 14-3-3 partners: AANAT as a case study
Molecular recognition.(a) RMSF for phosphorylated Thr31 in AANAT and non-phosphorylated Thr31 in AANAT during 10 ns ≤ t ≤ 100 ns. (b) H-bond count between proteins using a 0.35 nm cutoff for the full protein-protein system and only residues belonging to αhelix 9 (positions from 200 to 228 in 14-3-3ζ).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5384239&req=5

f6: Molecular recognition.(a) RMSF for phosphorylated Thr31 in AANAT and non-phosphorylated Thr31 in AANAT during 10 ns ≤ t ≤ 100 ns. (b) H-bond count between proteins using a 0.35 nm cutoff for the full protein-protein system and only residues belonging to αhelix 9 (positions from 200 to 228 in 14-3-3ζ).
Mentions: 14-3-3 protein family is considered a master regulator of phosphorylated proteins, binding more than 2000 different clients in a many-to-one, disordered-to-structured fashion. Figure 6 shows the fluctuation of 14-3-3ζ during both simulations (AANAT, AANAT*). Our results indicate that the binding pocket is the most mobile region of 14-3-3. The proposed auto-inhibitory C-terminal of 14-3-3 that contains the α-helix 9 is flexible, however, its importance is more clearly observed when we analyzed H-bonds. Remarkably, the phosphorylation of Thr31 in AANAT* produced an increase in the number of H-bonds towards α-helix 9 comparable to the numbers of H-bonds between AANAT and the entire 14-3-3ζ protein. Although the total number of H-bonds in region II (unrestrained simulation) are independent of the phosphoryl group in Thr31 (comparing the black line with the red one in Fig. 6b), the phosphorylation causes a high increase in region III. Also, almost all H-bonds of phosphorylated Thr31 are formed towards α-helix 9 in 14-3-3ζ (comparing the yellow line with the red one in the Fig. 6b). Taken together, this information could suggest that α-helix 9 is the main driving force to promote the right conformation and location of phosphorylated Thr31 in the major binding groove of 14-3-3ζ.

View Article: PubMed Central - PubMed

ABSTRACT

Twenty years ago, a novel concept in protein structural biology was discovered: the intrinsically disordered regions (IDRs). These regions remain largely unstructured under native conditions and the more are studied, more properties are attributed to them. Possibly, one of the most important is their ability to conform a new type of protein-protein interaction. Besides the classical domain-to-domain interactions, IDRs follow a ‘fly-casting’ model including ‘induced folding’. Unfortunately, it is only possible to experimentally explore initial and final states. However, the complete movie of conformational changes of protein regions and their characterization can be addressed by in silico experiments. Here, we simulate the binding of two proteins to describe how the phosphorylation of a single residue modulates the entire process. 14-3-3 protein family is considered a master regulator of phosphorylated proteins and from a modern point-of-view, protein phosphorylation is a three component system, with writers (kinases), erasers (phosphatases) and readers. This later biological role is attributed to the 14-3-3 protein family. Our molecular dynamics results show that phosphorylation of the key residue Thr31 in a partner of 14-3-3, the aralkylamine N-acetyltransferase, releases the fly-casting mechanism during binding. On the other hand, the non-phosphorylation of the same residue traps the proteins, systematically and repeatedly driving the simulations into wrong protein-protein conformations.

No MeSH data available.