A fast and accurate computational approach to protein ionization

Abstract

We report a very fast and accurate physics-based method to calculate pH-dependent electrostatic effects in protein molecules and to predict the pK values of individual sites of titration. In addition, a CHARMm-based algorithm is included to construct and refine the spatial coordinates of all hydrogen atoms at a given pH. The present method combines electrostatic energy calculations based on the Generalized Born approximation with an iterative mobile clustering approach to calculate the equilibria of proton binding to multiple titration sites in protein molecules. The use of the GBIM (Generalized Born with Implicit Membrane) CHARMm module makes it possible to model not only water-soluble proteins but membrane proteins as well. The method includes a novel algorithm for preliminary refinement of hydrogen coordinates. Another difference from existing approaches is that, instead of monopeptides, a set of relaxed pentapeptide structures are used as model compounds. Tests on a set of 24 proteins demonstrate the high accuracy of the method. On average, the RMSD between predicted and experimental pK values is close to 0.5 pK units on this data set, and the accuracy is achieved at very low computational cost. The pH-dependent assignment of hydrogen atoms also shows very good agreement with protonation states and hydrogen-bond network observed in neutron-diffraction structures. The method is implemented as a computational protocol in Accelrys Discovery Studio and provides a fast and easy way to study the effect of pH on many important mechanisms such as enzyme catalysis, ligand binding, protein-protein interactions, and protein stability.

Protein Ionizable Groups: pK Values and Their Contribution to Protein Stability and Solubility

“…He recognized that net charge on a protein would influence the ionization of individual groups and incorporated this into the first model developed to understand acid/base properties of proteins. This model was extended by Tanford and Kirkwood (9) in an important paper that triggered an interest in factors that determine pK values of the ionizable groups in proteins that continues to the present day (10).…”

Dengue Envelope Domain III-Peptide Binding Analysis <i>via</i> Tryptophan Fluorescence Quenching Assay

“…Secondly, the binding sites of insulin chain A is not present in the EIII as indicated by the pairwise sequence alignment and superimposition of the crystal structures of EIII 2) and insulin receptor extracellular domain. [13][14][15][16]) These evidences increased the confidence level that insulin chain A oxidized ammonium salt should not have any interaction with EIII. Each individual plate contained the reference and negative controls.…”

A generalised Davydov-Scott model for polarons in linear peptide chains

“…The subscript x denotes differentiation with respect to x. We seek φ(x) which satisfies equation (36) for all x, not just when x = n − N/2. Then, from such a φ(x) we will be able to recover the discrete solution ψ n (τ ) via ξ = xR and equation (30).…”

“…β = 1), then equation (36) reduces to the nonlinear Schrödinger equation with a cubic nonlinearity, which has a well-known solution satisfying all the above constraints [9],…”