Toward accurate prediction of pK_a values for internal protein residues: The importance of conformational relaxation and desolvation energy

Abstract

Proton uptake or release controls many important biological processes, such as energy transduction, virus replication, and catalysis. Accurate pK(a) prediction informs about proton pathways, thereby revealing detailed acid-base mechanisms. Physics-based methods in the framework of molecular dynamics simulations not only offer pK(a) predictions but also inform about the physical origins of pK(a) shifts and provide details of ionization-induced conformational relaxation and large-scale transitions. One such method is the recently developed continuous constant pH molecular dynamics (CPHMD) method, which has been shown to be an accurate and robust pK(a) prediction tool for naturally occurring titratable residues. To further examine the accuracy and limitations of CPHMD, we blindly predicted the pK(a) values for 87 titratable residues introduced in various hydrophobic regions of staphylococcal nuclease and variants. The predictions gave a root-mean-square deviation of 1.69 pK units from experiment, and there were only two pK(a)'s with errors greater than 3.5 pK units. Analysis of the conformational fluctuation of titrating side-chains in the context of the errors of calculated pK(a) values indicate that explicit treatment of conformational flexibility and the associated dielectric relaxation gives CPHMD a distinct advantage. Analysis of the sources of errors suggests that more accurate pK(a) predictions can be obtained for the most deeply buried residues by improving the accuracy in calculating desolvation energies. Furthermore, it is found that the generalized Born implicit-solvent model underlying the current CPHMD implementation slightly distorts the local conformational environment such that the inclusion of an explicit-solvent representation may offer improvement of accuracy.

All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water

“…In practice, 0 and 1 are replaced with two cutoffs, λ P and λ U , for defining the protonated and deprotonated states, respectively. Previous CpHMD studies 7–9,16,25,40,41 as well as current work show the calculated p K a ’s are insensitive to the exact cutoffs, e.g., 0.1/0.9 or 0.2/0.8. This topic will be further discussed in Computational Details.…”

“…1,3,8 The latter is also referred to as the hybrid-solvent constant pH MD. These methods enabled p K a predictions of proteins 9,10 as well as lipids and surfactants, 11,12 and mechanistic studies of pH-coupled conformational dynamics (see a recent review 13 for references). However, the underlying approximations in the implicit-solvent models hinders the systematic improvement of accuracy and generalization to systems that necessitate fully explicit-solvent description, for example, highly charged molecules such as nucleic acids and those involving heterogeneous dielectric environments such as transmembrane proteins.…”

pH‐sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stability

“…The shift in the log K d profile can be attributed to an underestimation of the desolvation energy and has been shown to lead to a systematic underestimation of the pK a values (from which the dissociation constant profiles are derived). 59 Henceforth, discussions of the computed dissociation constant profile will be in reference to the shifted profile (CPHMD shifted ).…”

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

“…[1][2][3][4][5] In the continuous approach, an additional titration degree of freedom is added for every titratable site and the titration degrees of freedom are propagated alongside conformational dynamics. [6][7][8] Among these methods, the continuous pH molecular dynamics (pHMD) method 7,8 based on λ dynamics, 9 which will be referred to as CpHMD hereafter, has been successfully applied to pK a predictions 10 and pH-dependent protein folding 11 and conformational dynamics. 12,13 The first version of the CpHMD technique makes use of the generalized Born (GB) implicit-solvent model for propagating both conformational and titration coordinates and the temperature-based a) Present address: Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, USA.…”