Uncovering Differences in Hydration Free Energies and Structures for Model Compound Mimics of Charged Side Chains of Amino Acids

Abstract

Free energies of hydration are of fundamental interest for modeling and understanding conformational and phase equilibria of macromolecular solutes in aqueous phases. Of particular relevance to systems such as intrinsically disordered proteins are the free energies of hydration and hydration structures of model compounds that mimic charged side chains of Arg, Lys, Asp, and Glu. Here, we deploy a Thermodynamic Cycle-based Proton Dissociation (TCPD) approach in conjunction with data from direct measurements to obtain estimates for the free energies of hydration for model compounds that mimic the side chains of Arg + , Lys + , Asp – , and Glu – . Irrespective of the choice made for the hydration free energy of the proton, the TCPD approach reveals clear trends regarding the free energies of hydration for Arg + , Lys + , Asp – , and Glu – . These trends include asymmetries between the hydration free energies of acidic (Asp – and Glu – ) and basic (Arg + and Lys + ) residues. Further, the TCPD analysis, which relies on a combination of experimental data, shows that the free energy of hydration of Arg + is less favorable than that of Lys + . We sought a physical explanation for the TCPD-derived trends in free energies of hydration. To this end, we performed temperature-dependent calculations of free energies of hydration and analyzed hydration structures from simulations that use the polarizable Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field and water model. At 298 K, the AMOEBA model generates estimates of free energies of hydration that are consistent with TCPD values with a free energy of hydration for the proton of ca. −259 kcal/mol. Analysis of temperature-dependent simulations leads to a structural explanation for the observed differences in free energies of hydration of ionizable residues and reveals that the heat capacity of hydration is positive for Arg + and Lys + and negative for Asp – and Glu – .

Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins

“…These new values highlight the more hydrophobic nature of Arg when compared to Lys, and more favorable hydration of Asp / Glu when compared to Arg or Lys (see details in the SI Appendix ). Using the recalibrated free energies of hydration (42, 62), we computed free energy profiles with x = ( R g / N 0.5 ) as the reaction coordinate (see details in SI Appendix ). Note that x ≡ x FRC ≈ 2.5 Å per residue sets a useful reference length scale (63).…”

“…We tested this hypothesis using ABSINTH-based simulations of (GRESRE) 7 , (GKDSKD) 7 , and (GRDSRD) 7 . Being able to capture distinct preferences of Arg- vs. Lys-containing sequences requires a formal accounting of the differences in free energies of hydration that were derived recently using a combination of experimentally derived quantities and free energy calculations (42, 62). These results indicate that despite being a strong base, arginine is more hydrophobic than lysine, the physical basis for which has been discussed recently by Fossat et al, (42).…”

“…As noted by Tesei et al, (93) different hydrophobicity scales show a lack of consensus regarding the apparent hydrophobicity of Arg vs. Lys. Arriving at a consensus will require the assessment of differences in intrinsic differences in free energies of hydration and in the context dependent effects of Arg vs. Lys and Glu vs. Asp (42, 62). Additionally, the sensitivity of a sequence to the effects of charge regulation are also likely to be highly dependent on the identities of ionizable residues as well as sequence contexts (53, 94).…”

“…show two-state behavior: Simulations were performed using an adaptation of recently recalibrated free energies of hydration (42,62). These new values highlight the more hydrophobic nature of Arg when compared to Lys, and more favorable hydration of Asp / Glu when compared to Arg or Lys (see details in the SI Appendix).…”

“…Charged residues are key determinants of sequence-ensemble relationships of IDRs (19,(39)(40)(41). They contribute through highly favorable free energies of hydration (42) and long-range electrostatic interactions. Net charge per residue (19,39,40) and the patterning of oppositely charged residues (43)(44)(45) have been used as order parameters for describing sequence-ensemble relationships and interactions of charge-rich IDRs (46).…”