MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling - PubMed (original) (raw)

MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling

Yifan Song et al. J Comput Chem. 2009.

Abstract

Multiconformation continuum electrostatics (MCCE) explores different conformational degrees of freedom in Monte Carlo calculations of protein residue and ligand pK(a)s. Explicit changes in side chain conformations throughout a titration create a position dependent, heterogeneous dielectric response giving a more accurate picture of coupled ionization and position changes. The MCCE2 methods for choosing a group of input heavy atom and proton positions are described. The pK(a)s calculated with different isosteric conformers, heavy atom rotamers and proton positions, with different degrees of optimization are tested against a curated group of 305 experimental pK(a)s in 33 proteins. QUICK calculations, with rotation around Asn and Gln termini, sampling His tautomers and torsion minimum hydroxyls yield an RMSD of 1.34 with 84% of the errors being <1.5 pH units. FULL calculations adding heavy atom rotamers and side chain optimization yield an RMSD of 0.90 with 90% of the errors <1.5 pH unit. Good results are also found for pK(a)s in the membrane protein bacteriorhodopsin. The inclusion of extra side chain positions distorts the dielectric boundary and also biases the calculated pK(a)s by creating more neutral than ionized conformers. Methods for correcting these errors are introduced. Calculations are compared with multiple X-ray and NMR derived structures in 36 soluble proteins. Calculations with X-ray structures give significantly better pK(a)s. Results with the default protein dielectric constant of 4 are as good as those using a value of 8. The MCCE2 program can be downloaded from http://www.sci.ccny.cuny.edu/\~mcce.

2009 Wiley Periodicals, Inc.

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Figures

Figure 1

Figure 1

Fragment of lysozyme structure 4LZT. (a) Single conformation dielectric boundary used to calculate the reaction field energy ΔΔ_G_rxn; and the reference pairwise interactions ΔGAi,BjES (bold lines) between the only conformer with partial charges (a conformer of Arg128 here) and the native conformer of all other residues; (b) Multiconformer dielectric boundary has more low dielectric boundary material so all pairwise interactions, ΔGAi,BjM have larger absolute values than ΔGAi,BjES. The raw pairwise interaction to each non-native conformer is corrected with eq. (6) to give ΔGAi:BjC.

Figure 2

Figure 2

Comparison of pairwise interactions of 1200 conformers in Barnase (1A2P chain A) at ε_p of 4. Δ_G_ES is calculated with only the interacting conformers present (Fig. 1a) whereas Δ_GM uses the standard multiconformation boundary conditions for calculating pairwise interactions (Fig. 1b, Table 1). ΔGAi,BjM versus ΔGAi,BjES for (a) 1613 charge–charge and (c) 9679 charge–dipole interactions and (e) 16641 dipole–dipole interactions. Lines show slope 1 and best-fit lines through the points. ΔGAi:BjC eq. (6) versus ΔGAi,BjES for (c) charge–charge and (c) charge–dipole interactions. Dipole–dipole interactions are generally small and no corrections are used. Line of slope 1 is shown.

Figure 3

Figure 3

Comparison of calculated p_K_a values using FULL MCCE conformer flexibility with experimentally measured values. The error bars represent the standard deviation of the values for different structures. The thick central line is the ideal where p_K_a (calc) = p_K_a (expt); the solid line bracket errors <1 pH unit and the dashed lines errors <2 pH units. Circled points highlight residues buried in the protein with desolvation energies >2.04 kcal/mol (1.5 pH units) or with p_K_as perturbed by >1.5 pH units from the solution value. (A) 305 averaged p_K_as obtained starting with 86 structures obtained by X-ray crystallography of 33 proteins; (B) 265 p_K_as obtained starting with 696 structures obtained by NMR methods of 24 proteins. The calculated and experimental p_K_as are provided in supporting information Table S2.

Figure 4

Figure 4

Shifts in calculated experimental p_K_as versus those calculated with a protein dielectric constant of 4 (●) or 8 (Δ). The dashed and dotted lines show errors of ±1 and ±2 pH units.

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