Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo

Overview

Journal J Chem Theory Comput

Publisher American Chemical Society

Specialties Biochemistry
Chemistry

Date 2017 Nov 2

PMID 29091438

Citations 28

Authors

Gregory A Ross

Hannah E Bruce Macdonald

Christopher Cave-Ayland

Ana I Cabedo Martinez

Jonathan W Essex

Affiliations

Soon will be listed here.

Abstract

The ability of grand canonical Monte Carlo (GCMC) to create and annihilate molecules in a given region greatly aids the identification of water sites and water binding free energies in protein cavities. However, acceptance rates without the application of biased moves can be low, resulting in large variations in the observed water occupancies. Here, we show that replica-exchange of the chemical potential significantly reduces the variance of the GCMC data. This improvement comes at a negligible increase in computational expense when simulations comprise of runs at different chemical potentials. Replica-exchange GCMC is also found to substantially increase the precision of water binding free energies as calculated with grand canonical integration, which has allowed us to address a missing standard state correction.

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References

Gathiaka S, Liu S, Chiu M, Yang H, Stuckey J, Kang Y . D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. J Comput Aided Mol Des. 2016; 30(9):651-668. PMC: 5562487. DOI: 10.1007/s10822-016-9946-8. View

Yin J, Henriksen N, Slochower D, Shirts M, Chiu M, Mobley D . Overview of the SAMPL5 host-guest challenge: Are we doing better?. J Comput Aided Mol Des. 2016; 31(1):1-19. PMC: 5241188. DOI: 10.1007/s10822-016-9974-4. View

Steinbrecher T, Joung I, Case D . Soft-core potentials in thermodynamic integration: comparing one- and two-step transformations. J Comput Chem. 2011; 32(15):3253-63. PMC: 3187911. DOI: 10.1002/jcc.21909. View

Mikol V, Papageorgiou C, Borer X . The role of water molecules in the structure-based design of (5-hydroxynorvaline)-2-cyclosporin: synthesis, biological activity, and crystallographic analysis with cyclophilin A. J Med Chem. 1995; 38(17):3361-7. DOI: 10.1021/jm00017a020. View

Ernst J, Clubb R, Zhou H, Gronenborn A, Clore G . Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR. Science. 1995; 267(5205):1813-7. DOI: 10.1126/science.7892604. View

Stone J, Hardy D, Ufimtsev I, Schulten K . GPU-accelerated molecular modeling coming of age. J Mol Graph Model. 2010; 29(2):116-25. PMC: 2934899. DOI: 10.1016/j.jmgm.2010.06.010. View

Michel J, Foloppe N, Essex J . Rigorous Free Energy Calculations in Structure-Based Drug Design. Mol Inform. 2016; 29(8-9):570-8. DOI: 10.1002/minf.201000051. View

Steinbrecher T, Mobley D, Case D . Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations. J Chem Phys. 2007; 127(21):214108. DOI: 10.1063/1.2799191. View

Huggins D, Sherman W, Tidor B . Rational approaches to improving selectivity in drug design. J Med Chem. 2012; 55(4):1424-44. PMC: 3285144. DOI: 10.1021/jm2010332. View

10.

Earl D, Deem M . Parallel tempering: theory, applications, and new perspectives. Phys Chem Chem Phys. 2009; 7(23):3910-6. DOI: 10.1039/b509983h. View

11.

Kadirvelraj R, Foley B, Dyekjaer J, Woods R . Involvement of water in carbohydrate-protein binding: concanavalin A revisited. J Am Chem Soc. 2008; 130(50):16933-42. PMC: 2626182. DOI: 10.1021/ja8039663. View

12.

Moucka F, Lisal M, Skvor J, Jirsak J, Nezbeda I, Smith W . Molecular simulation of aqueous electrolyte solubility. 2. Osmotic ensemble Monte Carlo methodology for free energy and solubility calculations and application to NaCl. J Phys Chem B. 2011; 115(24):7849-61. DOI: 10.1021/jp202054d. View

13.

Nasief N, Tan H, Kong J, Hangauer D . Water mediated ligand functional group cooperativity: the contribution of a methyl group to binding affinity is enhanced by a COO(-) group through changes in the structure and thermodynamics of the hydration waters of ligand-thermolysin complexes. J Med Chem. 2012; 55(19):8283-302. PMC: 3495596. DOI: 10.1021/jm300472k. View

14.

Woo H, Dinner A, Roux B . Grand canonical Monte Carlo simulations of water in protein environments. J Chem Phys. 2004; 121(13):6392-400. DOI: 10.1063/1.1784436. View

15.

Shirts M, Chodera J . Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys. 2008; 129(12):124105. PMC: 2671659. DOI: 10.1063/1.2978177. View

16.

Lakkaraju S, Raman E, Yu W, MacKerell Jr A . Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations. J Chem Theory Comput. 2014; 10(6):2281-2290. PMC: 4053307. DOI: 10.1021/ct500201y. View

17.

Vollmuth F, Geyer M . Interaction of propionylated and butyrylated histone H3 lysine marks with Brd4 bromodomains. Angew Chem Int Ed Engl. 2010; 49(38):6768-72. DOI: 10.1002/anie.201002724. View

18.

Aldeghi M, Heifetz A, Bodkin M, Knapp S, Biggin P . Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations. J Am Chem Soc. 2016; 139(2):946-957. PMC: 5253712. DOI: 10.1021/jacs.6b11467. View

19.

Davis A, Teague S, Kleywegt G . Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angew Chem Int Ed Engl. 2003; 42(24):2718-36. DOI: 10.1002/anie.200200539. View

20.

Nucci N, Pometun M, Wand A . Site-resolved measurement of water-protein interactions by solution NMR. Nat Struct Mol Biol. 2011; 18(2):245-9. PMC: 3058360. DOI: 10.1038/nsmb.1955. View