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A Fragment Quantum Mechanical Method for Metalloproteins
Mingyuan Xu1, Xiao He1,2, Tong Zhu1,2
1Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China.
Journal of Chemical Theory and Computation
|January 9, 2019
Summary
A new metal molecular fractionation with conjugate caps (metal-MFCC) method enables efficient quantum calculations for metalloproteins. This approach accurately predicts energies and forces, facilitating ab initio simulations for large protein systems.
Area of Science:
- Computational Chemistry
- Biophysics
- Quantum Mechanics
Background:
- Accurate energy calculations for metalloproteins are vital but theoretically challenging.
- Existing methods struggle with the computational cost of large metalloprotein systems.
Purpose of the Study:
- To develop an efficient linear-scaling quantum calculation method for metalloprotein energy and forces.
- To enable accurate ab initio simulations of metalloproteins.
Main Methods:
- Developed the metal molecular fractionation with conjugate caps (metal-MFCC) approach.
- Calculated protein energy via linear combination of residue, two-body, and metal-binding group interactions.
- Embedded fragment calculations in a point charge field representing the protein environment.
Main Results:
- Metal-MFCC showed excellent agreement with full system calculations (M06-2X/6-31G(d)).
- Achieved efficient ab initio structural optimization for a zinc finger protein using molecular dynamics.
- Demonstrated linear-scaling with a low prefactor and high parallelizability.
Conclusions:
- The metal-MFCC approach provides a highly efficient and accurate method for metalloprotein calculations.
- Enables routine structural optimization and ab initio molecular dynamics for metalloproteins of any size.
- Allows for higher-level quantum chemistry calculations on individual fragments.
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