Stanford
The Martínez Group Bridging the gap between Molecular Dynamics and Quantum Chemistry Bridging the gap between Molecular Dynamics and Quantum Chemistry
Bridging the gap between Molecular Dynamics and Quantum Chemistry

Quantum Calculations on Proteins

Due to the computational efficiency of GPUs, it is now possible to perform quantum computations on protein systems. The computations compare favorably to both molecular mechanics simulations as well as experiment, especially for relatively disordered systems.

 

 

 

We aim to unravel the excited-state dynamics of photoactive proteins such as Green Fluorescent Protein (GFP), Photoactive Yellow Protein (PYP), rhodopsins and carotenoid proteins using a two-pronged approach. First, static explorations of excited-state properties and potential-energy surfaces are achieved, for example, by characterizing the Franck-Condon region of the relevant excited states and by locating excited-state equilibrium geometries as well as minimal-energy conical intersections (MECIs). Second, we perform nonadiabatic dynamics simulations using the ab initio multiple spawning (AIMS) method. To tackle these large protein systems, we use the QM/MM approach, where for the QM part we mostly use multiconfigurational methods such as SA-CASSCF, FOMO-CASCI and alpha-CASSCF.

Related Publications

  • Christine M. Isborn, Andreas W. Goetz, Matthew A. Clark, Ross C. Walker, and Todd J. Martínez, Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein, Journal of Chemical Theory and Computation, 8, 5092-5106, 2012. [link]
  • Heather J. Kulik, Nathan Luehr, Ivan S. Ufimtsev, and Todd J. Martínez, Ab Initio Quantum Chemistry for Protein Structures, Journal of Physical Chemistry B, 116, 12501-12509, 2012. [link]
  • Ivan S. Ufimtsev, Nathan Luehr, and Todd J. Martínez, Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics, Journal of Physical Chemistry Letters, 2, 1789-1793, 2011. [link]
  • Lee-Ping Wang, Keri A. McKiernan, Joseph Gomes, Kyle A. Beauchamp, Teresa Head-Gordon, Julia E. Rice, William C. Swope, Todd J. Martínez, and Vijay S. Pande, Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15, Journal of Physical Chemistry B, 121, 4023-4039, 2017. [link]
  • Johan H. Both, Robert M. Parrish, Todd J. Martínez, and Steven G. Boxer, Rational Protein Design via Structure-Energetics-Function Relationships in the Photoactive Yellow Protein (PYP) Model System, Biophysical Journal, 114, 410a, 2018. [link]
  • Lina J. Nåbo, Jógvan Magnus Haugaard Olsen, Todd J. Martínez, and Jacob Kongsted, The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein, Journal of Chemical Theory and Computation, 13, 6230-6236, 2017. [link]