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He P , Zhang BW , Arasteh S , Wang L , Abel R , Levy RM
Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates
J Phys Chem Lett. 2018 Aug 2;9(15) :4428-4435
PMID: 30024165    PMCID: PMC6092130    URL: https://www.ncbi.nlm.nih.gov/pubmed/30024165
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Abstract
We introduce a novel method called restrain-free energy perturbation-release (R-FEP-R) to estimate conformational free energy changes via an alchemical path, which for some conformational landscapes like those associated with cellular signaling proteins in the kinase family is more direct and readily converged than the corresponding free energy changes along the physical path. The R-FEP-R method was developed from the dual topology free energy perturbation method that is widely applied to estimate the binding free energy difference between two ligands. In R-FEP-R, the free energy change between two conformational basins is calculated by free energy perturbations that remove those atoms involved in the conformational change from their initial conformational basin while simultaneously growing them back according to the final conformational basin. Both the initial and final dual topology states are unphysical, but they are designed in a way such that the unphysical contributions to the initial and final partition functions cancel. Compared with other advanced sampling algorithms such as umbrella sampling and metadynamics, the R-FEP-R method does not require predetermined transition pathways or reaction coordinates that connect the two conformational states. As a first illustration, the R-FEP-R method was applied to calculate the free energy change between conformational basins for alanine dipeptide in solution and for a side chain in the binding pocket of T4 lysozyme. The results obtained by R-FEP-R agree with the benchmarks very well.
Notes
1948-7185 He, Peng Zhang, Bin W ORCID: http://orcid.org/0000-0003-3007-4900 Arasteh, Shima Wang, Lingle ORCID: http://orcid.org/0000-0002-8170-6798 Abel, Robert Levy, Ronald M ORCID: http://orcid.org/0000-0001-8696-5177 R01 GM030580/GM/NIGMS NIH HHS/United States S10 OD020095/OD/NIH HHS/United States Journal Article United States J Phys Chem Lett. 2018 Jul 24:4428-4435. doi: 10.1021/acs.jpclett.8b01851.