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Development of a Structure-Based, pH-Dependent Lipophilicity Scale of Amino Acids from Continuum Solvation Calculations
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Lipophilicity is a fundamental property to characterize the structure and function of proteins, motivating the development of lipophilicity scales. Here we report a versatile strategy to derive a pH-adapted scale that relies on theoretical estimates of distribution coefficients from conformational ensembles of amino acids. This is accomplished by using an accurately parametrized version of the IEFPCM/MST continuum solvation model, as an effective way to describe the partitioning between n-octanol and water, in conjunction with a formalism that combines partition coefficients of neutral and ionic species of residues, and the corresponding pKa of ionizable groups. Two weighting schemes are considered to derive solvent-like and protein-like scales, which have been calibrated by comparison with other experimental scales developed in different chemical/biological environments and pH conditions, as well as by examining properties such as the retention time of small peptides and the recognition of antigenic peptides. A straightforward extension to nonstandard residues is enabled by this efficient methodological strategy.
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ZAMORA RAMÍREZ, William J., CAMPANERA ALSINA, Josep Maria and LUQUE GARRIGA, F. Xavier. Development of a Structure-Based, pH-Dependent Lipophilicity Scale of Amino Acids from Continuum Solvation Calculations. Journal of Physical Chemistry Letters. 2019. Vol. 10, num. 4, pags. 883-889. ISSN 1948-7185. [consulted: 22 of May of 2026]. Available at: https://hdl.handle.net/2445/168798