Sticky salts: overbinding of monovalent cations to phosphorylations in all-atom forcefields

This repository contains the files and data associated to the article :Sticky salts: overbinding of monovalent cations to phosphorylations in all-atom forcefields by Jules Marien, Julie Puyo-Fourtine, Chantal Prévost, Sophie Sacquin-Mora and Elise Duboué-DijonUniversité Paris Cité, CNRS, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, 75005, Paris, France ABSTRACT : Phosphorylation is a major post-translational modification, which is involved in the regulation of the dynamics and function of Intrinsically Disordered Proteins (IDPs). We recently characterized a phenomenon, which we termed $n$-Phosphate collaborations ($n$P-collabs), where bulk cations form stable bridges between several phosphoresidues in all-atom molecular dynamic simulations. $n$P-collabs were found to be sensitive to the combination of forcefields and cation types. Here, we attempt to assess the physical relevance of these $n$P-collabs by evaluating the strength of the cation/phosphate interaction through osmotic coefficient ($\phi$) calculations on the model $\mathrm{2Na^{+}HPO_4^{2-}}$ and $\mathrm{2K^{+}HPO_4^{2-}}$ salts, using different classical forcefields for phosphorylations. All forcefields were found to overestimate the strength of the interaction to various degrees. We thus designed new parameters for CHARMM36m and AmberFF99SB-ILDN using the Electronic Continuum Correction (ECC) approach, which provide remarkable agreement for $\phi$ values for both cation types and over a range of concentrations. We provide a preliminary test of these ECC parameters for phosphorylations by simulating the sevenfold-phosphorylated rhodopsin peptide 7PP and comparing secondary chemical shifts to experimental data. Conformational ensembles resulting from the ECC-derived phosphorylated forcefields display both qualitative and quantitative improvements with regards to full-charge forcefields. We thus conclude that long-lasting $n$P-collabs are artifacts for classical forcefields born from the lack of explicit polarization, and propose a possible computational strategy for the extensive parameterization of phosphorylations. The presence of long-lived $n$P-collabs in simulations produced using classical forcefields is therefore a serious concern for the accurate modelling of multiphosphorylated peptides and IDPs, which are at the center of research questions regarding neurodegenerative diseases such as Alzheimer's or Parkinson's. TECHNICAL ACKNOWLEDGMENTS : The implementation for the TIP4P-D water model used in combination with the CHARMM36m forcefield [1] in this paper was kindly provided by Dr. Josef Hritz and Dr. Vojtech Zapletal as rapported in their work [2]. DESCRIPTION: - DeltaG_calculations : contains the files necessary to run the calculation of the binding free energy between a cation (Na+ or K+) and a phosphate group HPO_4^{2-}. It is organized into four subdirectories, corresponding to the four force fields used: A99, A99-ECC, C36, and C36-ECC. Within each force field folder, there are two subdirectories, one for each ion (K or Na). In each ion-specific folder, the contributions from different interaction modes were computed: contact and solvent-shared (SSHIP). To close the thermodynamic cycle, it was also necessary to evaluate the solvation free energy of the ion, stored in the ion_seul folder. Each simulation folder contains: 0-eq – the initial equilibration phase ; 1-TA – the alchemical transformation phase. In the 1-TA directory, the transformation is divided into 15 λ-windows, stored in folders L-X (with X ranging from 1 to 15). The common folder contains files shared by all λ-windows. The analyse folder contains copies of the .xvg output files from the different λ-windows, which were used as input for gmx bar. Complete simulation trajectories and all related files have been preserved. However, in order to maintain a low data volumetry, only one replicate of each calculation is provided. In the published work, three independent replicates were performed for each condition in order to evaluate the error bars. - Osmotic_coefficient_HPO4 : contains the files necessary to run the calculation of the osmotic coefficient for solutions of $\mathrm{2Na^{+}HPO_4^{2-}}$ or $\mathrm{2K^{+}HPO_4^{2-}}$ with the different forcefields mentioned in the manuscript. In each folder of production (2_Production_concentration_???), only the output file of the first replica (without the .xtc trajectory file) was kept in order to maintain a low data volumetry. Replicas can be easily rerun by duplicating the Replica1 folder and changing the seed of the simulation in the .mdp file. Results of the osmotic calculations are available in the Analyse_osmotic folders. - Simulations_7PP_peptide : contains the files necessary to run the simulations of the hyperphosphorylated peptide 7PP [3]. Although the complete .xtc trajectory files with water were removed to maintain a low data volumetry, the simulations of the peptide with the cations are available in the folders Replica?/0_Postproduction REFERENCES : [1] Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmüller H, MacKerell AD Jr. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat Methods. 2017 Jan;14(1):71-73. doi: 10.1038/nmeth.4067. [2] Zapletal V, Mládek A, Melková K, Louša P, Nomilner E, Jaseňáková Z, Kubáň V, Makovická M, Laníková A, Žídek L, Hritz J. Choice of Force Field for Proteins Containing Structured and Intrinsically Disordered Regions. Biophys J. 2020 Apr 7;118(7):1621-1633. doi: 10.1016/j.bpj.2020.02.019. [3] Kisselev OG, McDowell JH, Hargrave PA. The arrestin-bound conformation and dynamics of the phosphorylated carboxy-terminal region of rhodopsin. FEBS Lett. 2004 Apr 30;564(3):307-11. doi: 10.1016/S0014-5793(04)00226-1.