2020 Fiscal Year Research-status Report
Computational investigation of the role of disordered regions in enzymatic reactions
| Project/Area Number |
20K15737
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| Research Institution | Institute of Physical and Chemical Research |
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Principal Investigator |
Dokainish Hisham 国立研究開発法人理化学研究所, 開拓研究本部, 特別研究員 (20825575)
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| Project Period (FY) |
2020-04-01 – 2022-03-31
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| Keywords | Enzyme catalysis / IDR / Enhance sampling |
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| Outline of Annual Research Achievements |
In the first year:
I explored the role of intrinsic disordered region (IDR) in an engineered chrosimate mutase with an IDR. Both classical and enhanced sampling (gREST) molecular dynamics (MD) simulations were used to sample protein conformations in the presence of IDR. Also classical MD simulation with rmsd restraints was performed to limit IDR motion and compare the results.
Notably, IDR motion was found to be crucial for the enzyme catalysis. As IDR motion was found to allow for a breathing-like motion in the active site that affect the substrate conformation, allowing for reactive complex formation with carbo-carbon distances of 2.5 angstrom; that allow for reaction to occur. In the absence of active site QM optimization of the substrate show that the carbon-carbon distance is 3.8 angstrom; and it is more stable by 19 Kcal/Mol in comparison to reactive conformation. Indeed, restricting IDR motion hinder the formation of reactive complex and larger carbon-carbon distance were observed. In gREST simulation, all atoms in the IDR were included using all energy terms.
Since the application of gREST method in larger proteins would be computationally expensive, I propose a new method to enhance protein motion by selectively choose Lennard Jonnes and charge of surface charged residues which drastically reduce the number of atoms in the solute region and reduce computational cost. I applied the method to enhance domain motion in ribose binding protein and were able to explore open to close conformational landscape and study ligand binding in detail, two paper were published.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
In the Original proposal, I proposed to use chrosimate mutase as a model system to find a proper method that can account for IDR effect on chemical reaction. I anticipated that IDR would affect the reaction barriers which would require the extensive use of QM/MM calculations starting from long/enhanced MD simulations. However, I was able to observe the role of IDR at the level of MD simulation and simple QM calculation of the substrate. So extensive QM/MM calculations has not been needed as proposed. As IDR play a role in stabilizing reactive complex. Secondly, to be able to carry out simulations of larger protein, I already established a method that can enhance protein motion using selective residues.
So in summary, despite the slight change of plans based on simulation results, the progress is smooth and I can now work on more complex targets as proposed.
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| Strategy for Future Research Activity |
In the second year:
1) I plan to finalize Chrosimate mutase study and publish the results.
2) I plan to study IDR role in Sporosarcina pasteurii UreG (SpUreG). First I will test if IDR would have similar role as in chrosimate mutase by using my enhanced sampling method (gREST-SSCR) and compare active site organization to IDR restrained simulation. Carry out QM/MM calculation to obtain reaction energetics and confirm the effect of IDR.
3) I also plan to explore IDR motion correlation to active site arrangment in Human Glucokinases.
The two new systems might confirm current conclusion based on chrosimate mutase, or might shed the light on new roles of IDR in enzyme catalysis.
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| Causes of Carryover |
Due to Covid-19, there 's no travel or conferences expenses in the last year.
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Research Products
(2 results)
