Structural and thermodynamic consequences of burial of an artificial ion pair in the hydrophobic interior of a protein

Abstract

An artificial charge pair buried in the hydrophobic core of staphylococcal nuclease was engineered by making the V23E and L36K substitutions. Buried individually, Glu-23 and Lys-36 both titrate with pK a values near 7. When buried together their pK a values appear to be normal. The ionizable moieties of the buried Glu-Lys pair are 2.6 Å apart. The interaction between them at pH 7 is worth 5 kcal/mol. Despite this strong interaction, the buried Glu-Lys pair destabilizes the protein significantly because the apparent Coulomb interaction is sufficient to offset the dehydration of only one of the two buried charges. Save for minor reorganization of dipoles and water penetration consistent with the relatively high dielectric constant reported by the buried ion pair, there is no evidence that the presence of two charges in the hydrophobic interior of the protein induces any significant structural reorganization. The successful engineering of an artificial ion pair in a highly hydrophobic environment suggests that buried Glu-Lys pairs in dehydrated environments can be charged and that it is possible to engineer charge clusters that loosely resemble catalytic sites in a scaffold protein with high thermodynamic stability, without the need for specialized structural adaptations.electrostatics | internal charge | low-barrier hydrogen bond | dielectric constant | enzyme design P aired ionizable groups buried in hydrophobic environments inside proteins are an uncommon but essential structural motif necessary for H + transport (1), e − transfer (2), catalysis (3-5), and other important biochemical processes. Despite their importance, the properties of these buried ionizable pairs are poorly understood because they are difficult to study experimentally in the proteins where they play functional roles. When the pair consists of a basic and an acidic group it is usually assumed to be charged, but this is often just speculation without direct experimental support (6, 7). In principle, a Coulomb interaction between two ionizable groups of opposite polarity buried in a dehydrated environment inside a protein can be very strong, but this has not been established experimentally. Simulations suggest that buried ion pairs are always destabilizing (8); however, from an experimental perspective it is not known if the favorable Coulomb interaction would be sufficient to compensate for the unfavorable dehydration of the two buried charges or if the net effect of the pair on the thermodynamic stability of a protein would be stabilizing or not. These issues were examined in detail with an artificial ion pair buried in the hydrophobic interior of staphylococcal nuclease (SNase).The buried ion pair was engineered by introducing the V23E and L36K substitutions in a highly stable form of SNase. The pK a values of Glu-23 and Lys-36 introduced individually are anomalous (pK a of 7.1 for ref. 9; ref. 10), consistent with the groups existing in hydrophobic environments that are neither as polar nor as polarizable as water (11-13). Structural modeli...

Affinity-controlled protein encapsulation into sub-30 nm telodendrimer nanocarriers by multivalent and synergistic interactions

“…The presence of hydrophobic moieties in telodendrimer decreases the polarity around charge interactions between telodendrimer and protein, therefore it may further stabilize the “salt bridges” in the nanocomplex by decreasing the static dielectric constants of surroundings,[43, 44] which is well-known to protein structures. [54] We also introduced amphiphilic riboflavin (Rf) into telodendrimers, PEG 5k (ArgArg-L-Rf) 4 , intending to match both polar and nonpolar surfaces of protein in addition to the charge interactions.…”

“…(ii) Multivalent interactions can dramatically increase the binding affinities. (iii) The charge interactions between telodendrimer and protein will be enhanced and stabilized by the decreased polarity of the surroundings[43, 44] because of the closely adjacent hydrophobic moieties in the telodendrimers. In this study, we engineered the ionic strength, charge density and the structure of the hydrophobic groups in telodendrimers to fine-tune the binding affinity of protein-nanocarrier and to study the mechanism for protein loading and release.…”

An Internal Disulfide Locks a Misfolded Aggregation-Prone Intermediate in Cataract-Linked Mutants of Human Gamma-D Crystallin

“…The purified protein was stable for weeks in storage at 4 °C, but aggregated in a redox-dependent manner when shifted to a higher temperature ( Figure 1B). Accommodation of charged residues in protein cores has been the subject of intensive study (52,53), thus it was of interest to compare the charged (W42R) and neutral (W42Q) core substitutions. DSC ( Figure 1C) revealed that there was almost no difference in the temperature of the two mutants' unfolding transitions.…”

Driving Forces of Translocation Through Bacterial Translocon SecYEG

“…A pK a shift of 3–5 pH units was reported for pH-sensitive dyes in dioxane-water mixtures upon lowering the dielectric constant ε r from 80 to 10 (Fernandez und Fromherz 1977). Similarly, pK a shifts of up to 5 pH units were observed for both acidic (Isom et al 2010) and basic residues (Isom et al 2011; Robinson et al 2014), when transferring them into apolar proteinaceous surroundings.pH within the translocon pore is more basic than in the cytoplasm. This is due to SecY’s moderate anionic selectivity: Since the permeability for anions is sevenfold higher than for cations (Sachelaru et al 2017), positively charged particles must be partially excluded from the pore.…”

“…A pK a shift of 3–5 pH units was reported for pH-sensitive dyes in dioxane-water mixtures upon lowering the dielectric constant ε r from 80 to 10 (Fernandez und Fromherz 1977). Similarly, pK a shifts of up to 5 pH units were observed for both acidic (Isom et al 2010) and basic residues (Isom et al 2011; Robinson et al 2014), when transferring them into apolar proteinaceous surroundings.…”