Abstract
We propose a simple atomic multipole electrostatic model to rapidly evaluate the effects of mutation on enzyme activity and test its performance on wild-type and mutant ketosteroid isomerase. The predictions of our atomic multipole model are similar to those obtained with symmetry-adapted perturbation theory at a fraction of the computational cost. We further show that this approach is relatively insensitive to the precise amino acid side chain conformation in mutants and may thus be useful in computational enzyme (re)design.
Highlights
In silico enzymedesign, which has become increasingly popular and successful in recent years,[1−3] ideally features a fast but accurate method to predict the influence of point mutations on catalytic activity.[4−6] To be practically useful, such a method should allow computational procedures for enzymedesign that involve screening of multiple possible variants (e.g., 100s)
We first investigate how the electrostatic interaction changes during the reaction in wild-type KSI8 and the four mutants using the multipolar part of this contribution, Ee(1l,M0)TP, as calculated with the cumulative atomic multipole moment (CAMM) expansion truncated at R−5 for all available points along the reaction path (52 in total, Figure 4a), where differential intermediate state stabilization (DISS)(CAMM) converges approximately after the R−3 level for all mutants
We show that the atomic multipole component of differential transition state stabilization energy (DTSS)/DISS acts as a reasonably accurate predictor of relative activity in a typical enzyme where catalysis is dominated by electrostatic stabilization
Summary
In silico enzyme (re)design, which has become increasingly popular and successful in recent years,[1−3] ideally features a fast but accurate method to predict the influence of point mutations on catalytic activity.[4−6] To be practically useful, such a method should allow computational procedures for enzyme (re)design that involve screening of multiple possible variants (e.g., 100s). “Differential stabilization” energies can be partitioned into components defined by either symmetry-adapted perturbation theory (SAPT; for more information, see the Computational Details section)[15,16] or hybrid variation-perturbation theory (HVPT) of intermolecular interactions.[17] In the case of chorismate mutase[17] and cAMP-dependent protein kinase (PKA),[18] this decomposition analysis indicated that interactions having positive impact on the catalytic activities could be solely represented by the electrostatic term (or its multipolar component) of the differential transition state stabilization energy (DTSS; for more information, see section 2.1) This finding is in agreement with many other works indicating the importance of electrostatic interactions in enzymatic catalysis.[1,19] This electrostatic term seems to be a better estimator of the relative stability of molecular complexes when distances shorter than expected are present in modeled structures (e.g., overlapping atomic radii) compared to high level MP2 and CCSD(T) results.[20] Nonempirical evaluation of the complete electrostatic interaction term (Ee(1ls0t)) including penetration requires significant computational effort scaling as O(N4), but it can be considerably reduced by applying the cumulative atomic multiple moment (CAMM; for more details, see section 2.2). The importance of electrostatics in this system was demonstrated by computational studies[8,29] and more recently by spectroscopic experiments showing excellent correlation between the electric field in the active site and the apparent reaction barrier in a series of KSI variants,[30] the details of the source of the catalytic power of the enzyme are still a subject of discussion.[31,32] In addition to its central role in debates on enzyme catalysis, KSI has been shown to be a promising template for biocatalyst design, for example, to catalyze Diels−Alder reactions.[33]
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