Internal ionizable groups are quite rare in water-soluble globular proteins. Presumably, this reflects the incompatibility between charges and the hydrophobic environment in the protein interior. Here we show that proteins can have an inherently high tolerance for internal ionizable groups. The 25 internal positions in staphylococcal nuclease were substituted one at a time with Lys, Glu, or Asp...

Ionizable residues play important roles in protein structure and activity, and proton binding is a valuable reporter of electrostatic interactions in these systems. We use molecular dynamics free energy simulations (MDFE) to compute proton pKa shifts, relative to a model compound in solution, for three aspartate side chains in two proteins. Simulations with explicit solvent and with an implicit...

The superior adsorption capacity of carbon nanotubes has been well recognized and there is a wealth of information in the literature concerning the adsorption of unionized organic pollutants on carbon nanotubes. Recently, the adsorption of emerging environmental pollutants, most of which are ionizable, has attracted increasing attention due to the heightened concerns about the accumulation of t...

Full or partial burial of ionizable groups in the hydrophobic interior of proteins underlies the large modulation in group properties (modified pK value, high nucleophilicity, enhanced capability of interaction with chemical moieties of the substrate, etc.) linked to biological function. Indeed, the few internal ionizable residues found in proteins are known to play important functional roles i...

Molecular dynamics simulations of triclinic hen egg white lysozyme in aqueous solution were performed to calculate the intrinsic pKas of 14 ionizable residues. An all-atom model was used for both solvent and solute, and a single 180 ps simulation in conjunction with a Gaussian fluctuation analysis method was used. An advantage of the Gaussian fluctuation method is that it only requires a single...

Ionizable Lipid Nanoparticles nanoparticle (LNP) systems are currently the leading nonviral delivery for enabling clinical potential of mRNA drugs. lipid is critical component nanoparticles. In article 2202590 by Gengshen Song, Jing Yang, Shengqi Wang, and co-workers, a novel ionizable YK009 designed developed LNP formulation. The YK009-LNP shows high efficacy good safety. An vaccine against SA...

A new computational method for analyzing the protonation states of protein-ligand complexes with multiple ionizable groups is applied to the structurally characterized complex between the peptide Glu-Asp-Leu and HIV-1 protease. This complex has eight ionizable groups at the active site: four from the ligand and four Asp residues on the protein. Correlation, with an error of ca. 0.6 kcal mol-1, ...