Supporting Information for: Molecular interpretation of preferential interactions in protein solvation: a solvent-shell perspective by means of minimum-distance distribution functions Leandro Martínez 1 and Seishi Shimizu 2 1 Institute of hemistry and enter for omputational ngineering & Science, University of ampinas. ampinas, SP, razil. leandro@iqm.unicamp.br 2 York Structural iology Laboratory, epartment of hemistry, University of York. Heslington, York, UK. seishi.shimizu@york.ac.uk Table S1: ompositions of the solvents simulated. Urea TMO /mol L 1 N urea N water N T MO N water 26 26.2 - - 9 19671 181 19633 181 19338 361 19183 361 1861 722 1824 - - GN 1,2 K 3 atom ɛ/kcal mol 1 σ/nm q/e q/e O.12.34 8.67 7.4 +.6 +.921 N.2.37.69.693 H 46.449 +.34 +.28 Table S2: Non-bonded parameters for urea for the force-fields used. The charges of the K model were used 3 in combination with the other parameters of the GN model, particularly because σ combination rules are different. The results obtained for the molar volume of urea and preferential interaction parameters were completely satisfactory and supported this adaptation of the force-field. 1
K GN.6.4.2 g(r) 2 4 6 8 1 12 14.6.4.2 g(r) g md (r) g md (r) 2 4 6 8 1 12 14 1 2 3 4 6 7 8 φ u 9 2 4 6 8 1 12 14 1 2 3 4 6 7 8 φ u 9 2 4 6 8 1 12 14 g md (r) and atomic contributions g md (r) and atomic contributions g md (r).6.4.2 g md (r).6.4.2 igure S1: omparison of radial distribution functions (g(r)) and minimum-distance distribution functions (g md (r)) and associated K-integrals for urea models. 1 3 igures and the g(r) (computed between the urea carbon atom and the water atom) and the g md (r) distributions. igures and display the K-integrals computed using the standard integration of the g(r) or the minimum distance count, as described in the main text. igures and show the atomic contributions to the minimum distance distribution of water in each case. The dashed line in igures and indicate the experimental limiting molar volume of urea ( φ u = 44.23 cm 3 mol 1 ), 4 which is slightly underestimated by the GN model and precisely predicted by the K model. 2
GN 1,2 OptKast Osmotic 6 atom ɛ/kcal mol 1 σ/nm q/e ɛ/kcal mol 1 σ/nm q/e ɛ/kcal mol 1 σ/nm q/e O.12.3.37.126.3266.91.126.3266.78 N.2.37 3.2.2926 +.7.2.2926 +28 77.443.3 676.36.26 676.341.312 H 46.14 +.2 18.177 +.11 18.177 +.132 Table S3: Non-bonded parameters for TMO for the force-fields used. The Optimized-Kast and Osmotic 6 models are modifications of the Kast model 7 aiming the improved reproduction of peptide transfer free energies and osmotic pressure measurements, respectively. In both cases, it was found that the Kast model overestimated TMO-TMO interactions. Thus, in particular, the polarity of the NO bond was increased to strengthen the interactions with water. The original Kast model has a partial charges for of.6e and for nitrogen of +.44e. 7 s we show in igure S2, a collateral effect of the increased water-tmo interactions is the underestimated limiting molar volume of TMO. The densitydependence of aqueous TMO solutions pointed to this limitation, as noted in the development of the OptKast model. 3
Osmotic OptKast GN g md (r).6.4.2 g(r) 2 4 6 8 1 12 14 g md (r).6.4.2 g(r) 2 4 6 8 1 12 14 g md (r).6.4.2 g(r) G 2 4 6 8 1 12 14 2 4 6 8 φ u 1 12 2 4 6 8 1 12 14 2 4 6 8 1 φ u 12 2 4 6 8 1 12 14 2 4 6 8 1 φ u H 12 2 4 6 8 1 12 14 g md (r) and atomic contributions g md (r) and atomic contributions g md (r) and atomic contributions g md (r).6.4.2 g md (r).6 g md (r).6.4.2.4.2 I igure S2: omparison of radial distribution functions (g(r)) and minimum-distance distribution functions (g md (r)) and associated K-integrals for TMO models. 1,2,,6 igures,, and G display the g(r) (computed between the central TMO carbon atom and the water atom) and the g md (r) distributions. igures,, and H display the K-integrals computed using the standard integration of the g(r) or the minimum distance count, as described in the main text. igures,, and I show the atomic contributions to the water minimum distance distribution in each case. The dashed line in igures, and H indicate the experimental limiting molar volume of TMO ( φ u = 73.27 cm 3 mol 1 ), 8 which is underestimated by all models. 4
urea - GN g uw md (r) 2.2 g uc md (r) 6 4 3 2 1 TMO - GN g uw md (r) 2.2.2 g uc md (r).2 TMO - OptKast g uw md (r) 2.2.2 g uc md (r).2 igure S3: Minimum-distance distribution functions computed for with the GN force field for urea: () water and () urea. () and (): g md (r) distributions computed for water and TMO using the GN 1,2 model for TMO. () and (): g md (r) distributions computed for water and TMO using the OptKast model for TMO. quivalent plots for the K model 3 of urea and for the Osmotic model 6 of TMO are shown in the main text.
urea - GN TMO - GN TMO - OptKast 4 3 2 1 N/ - total g md (r).2 - total g md (r).2 - total g md (r) (r) and atomic contributions g us md 4 3 2 1 Total 3. 3. Total N/ 2.2 2.4 2.6 2.8 3. Total 2.2 2.4 2.6 2.8 3. igure S4: ecomposition of the g md us (r) into atomic contributions. Plots (), (), and () are insets of (), (), and () focused on the first and second solvation layers. () and () Urea with GN 1,2 model. () and () TMO with GN model. () and () TMO with OptKast model. quivalent plots for the K model 3 of urea and for the Osmotic model 6 of TMO are shown in the main text. 6
Table S4: Kirwood-uff integrals computed from aqueous solutions of urea the simulations with the GN 1,2 and K 3 models in L mol 1. The deviations reported are the standard error of the means of the 34 simulations performed for each system. GN 1,2 K 3 G uw G uc G uw G uc -7.9±1 1.39±.74-7.919±17 -±.68-8.196±19 1.96±.48-8.81±16-3±.38-8.484±29 -.12±.3-8.268±29 -±.31 Table S: Kirwood-uff integrals computed from aqueous solutions of TMO the simulations with the GN 1,2, OptKast and Osmotic 6 models in L mol 1. The deviations reported are the standard error of the means of the 34 simulations performed for each system. GN 1,2 OptKast Osmotic 6 G uw G uc G uw G uc G uw G uc.2-7.744±9-8.2±4-7.746±8-8.87±.62-7.731±8-64±34-7.733±11-8.9±.38-7.74±14-16± -7.683±1-11±.4-7.71±14-8.87±.24-7.688±14-9.68±.3-7.618±13-1±.286 7
urea - GN Guw(r) / L mol 1 1 φ u 1 Guc(r) / L mol 1 1 1 TMO - GN Guw(r) / L mol 1 2 4 6 8 1 12 14 φ u.2 Guc(r) / L mol 1 2 4 6 8 1 12 14.2 TMO - OptKast Guw(r) / L mol 1 2 4 6 8 1 12 14 φ u.2 Guc(r) / L mol 1 2 4 6 8 1 12 14.2 igure S: Kirkwood-uff integrals computed for with the GN force field for urea: () water and () urea. () and (): K integrals computed for water and TMO using the GN 1,2 model for TMO. () and (): K integrals computed for water and TMO using the OptKast model for TMO. The φ u in plots,, and indicate the limiting molar volume of the protein in pure water. 9 quivalent plots for the K model 3 of urea and for the Osmotic model 6 of TMO are shown in the main text. 8
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