Extensive Assessment of Various Computational Methods for Aspartate’s pK_a Shift

Abstract

A series of computational methods for pK shift prediction are extensively tested on a set of benchmark protein systems, aiming at identifying pitfalls and evaluating their performance on high variants. Including 19 ASP residues in 10 protein systems, the benchmark set consists of both residues with highly shifted pK values as well as those varying little from the reference value, with an experimental RMS free energy differences of 2.49 kcal/mol with respect to blocked amino acid, namely the RMS pK shift being 1.82 pK units. The constant pH molecular dynamics (MD), alchemical methods, PROPKA3.1, and multiconformation continuum electrostatics give RMSDs of 1.52, 2.58, 1.37, and 3.52 pK units, respectively, on the benchmark set. The empirical scoring method is the most accurate one with extremely low computational cost, and the pH-dependent model is also able to provide accurate results, while the accuracy of MD sampling incorporating alchemical free energy simulation is prohibited by convergence achievement and the performance of conformational search incorporating multiconformation continuum electrostatics is bad. Former research works did not define statistical uncertainty with care and yielded the questionable conclusion that alchemical methods perform well in most benchmarks. In this work the traditional alchemical methods are thoroughly tested for high variants. We also performed the first application of nonequilibrium alchemical methods to the pK cases.

Conformational sampling and polarization of Asp26 in pKa calculations of thioredoxin

“…Changes in the protonation states of acidic or basic residues alter the active conformations of proteins, their stability and solubility, and is directly related to the catalytic efficiency of enzymes . Prediction of the acidity constant—or its negative logarithm pK a —for ionizable side chains in proteins, therefore, is currently a challenge and has been addressed in the past with a variety of computational methods …”

“…5 Prediction of the acidity constant-or its negative logarithm pK a -for ionizable side chains in proteins, therefore, is currently a challenge and has been addressed in the past with a variety of computational methods. 1,2,6,7 Computational methods used to calculate the pK a are based on the Gibbs free energy change between the protonated and deprotontaed state of a residue in a protein. Most current common methods are empirical to achieve computational efficiency; for example, the software PROPKA.…”

Theoretical Understanding of the Thermodynamics and Interactions in Transcriptional Regulator TtgR-Ligand Binding

“…We always want to build a box as large as possible to eliminate the finite-size effect, [25][26][27][28][29] use Hamiltonians as accurate as possible, [30][31][32][33][34][35][36] and simulate our systems as long as possible to get reliable and converged estimates. [37][38][39][40][41] Normally, if there is no breaking or formation of chemical bonds, the polarization effect is not significant and the phenomena of interest happen at about several ns to ms, all-atom force fields are preferred to describe the motion of molecules. The statistical transcriptional activation of TtgABC and TtgR.…”

“…76 The free energy differences between different systems or states are obtained by alchemically switching the Hamiltonian from one state to another, and integrating the ensemble averages of the partial derivative of the alchemical Hamiltonian or reweighting via the Zwanzig equation or its derivatives. 8,41,60,68,75,[77][78][79][80][81] The integration methods are termed as thermodynamic integration (TI) 79-80 and the reweighting techniques are referred to as free energy perturbation (FEP) 82 and acceptance ratio methods. [83][84][85] Among all the equilibrium reweighting methods in the alchemical transformation, the acceptance ratio method of Bennett Acceptance Ratio (BAR) and its multistate variant named multi-state BAR (MBAR) have the best efficiency.…”

“…[83][84][85] Among all the equilibrium reweighting methods in the alchemical transformation, the acceptance ratio method of Bennett Acceptance Ratio (BAR) and its multistate variant named multi-state BAR (MBAR) have the best efficiency. 41 The nonequilibrium extensions of FEP and BAR are Jarzynski's Identity (JI) 86-87 and Crooks' Equation (CE). 88 The nonequilibrium technique uses a different simulation protocol.…”