A fast method for the determination of fractional contributions to solvation in proteins

Abstract

A fast method for the calculation of residue contributions to protein solvation is presented. The approach uses the exposed polar and apolar surface of protein residues and has been parametrized from the fractional contributions to solvation determined from linear response theory coupled to molecular dynamics simulations. Application of the method to a large subset of proteins taken from the Protein Data Bank allowed us to compute the expected fractional solvation of residues. This information is used to discuss when a residue or a group of residues presents an uncommon solvation profile.Keywords: protein solvation; protein structure; molecular dynamics; protein stability Supplemental material: see www.proteinscience.orgThe solvation free energy is the reversible work needed to transfer the solute from the gas phase to solution at constant pressure, temperature, and concentration (Böttcher 1952;Tomasi and Persico 1994;Rivail and Rinaldi 1995;Cramer and Truhlar 1999;Orozco and Luque 2000). From a computational point of view, it is convenient to partition such process into three steps: (1) creation of a solute-shaped cavity in the solvent, (2) switching on the steric properties of the solute inside the cavity, and (3) building up of the charge distribution of the solute. According to this partitioning scheme, the solvation free energy (DG solv ) is determined as the addition of electrostatic (DG ele ), cavitation (DG cav ), and van der Waals (DG vw ) terms (Equation 1), though these two latter contributions are often grouped into the ''steric'' contribution (DG ster ).The experimental determination of DG solv is difficult even for small molecules and impossible for large macromolecules. This has fueled the development of accurate theoretical approaches to calculate DG solv of small and medium molecules in water with an error <1 kcal/mol (see discussion in Tomasi and Persico 1994; Rivail and 9 These authors contributed equally to this work. Reprint requests to: Modesto Orozco, Molecular Modeling and Bioinformatics Unit, Institut de Rercerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain; e-mail: modesto@mmb.pcb.ub.es; fax: +34-93-4037158.Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi

Characterization of Protein-Protein Interaction Interfaces from a Single Species

“…In addition, the energy is similar between the binding interface (whether rim or core) and the non-interfacial protein surface (see Table 2 ). The solvation energy is dependent on the types of amino acids present [40] : since there are compositional differences between the interface and the rest of the surface, we may expect that the average solvation energy per residue would differ. The lack of such a difference suggests that there are other factors that compensate for the expected differences in solvation energy.…”

“…The ΔG solvation was calculated by using the fractional solvation method (equation 8) of DT [40] . This method takes into account the different contributions to the solvation energy made by the polar and apolar parts of the amino acids.…”