Abstract
The Automatic Rhodopsin Modeling (ARM) protocol has recently been proposed as a tool for the fast and parallel generation of basic hybrid quantum mechanics/molecular mechanics (QM/MM) models of wild type and mutant rhodopsins. However, in its present version, input preparation requires a few hours long user's manipulation of the template protein structure, which also impairs the reproducibility of the generated models. This limitation, which makes model building semiautomatic rather than fully automatic, comprises four tasks: definition of the retinal chromophore cavity, assignment of protonation states of the ionizable residues, neutralization of the protein with external counterions, and finally congruous generation of single or multiple mutations. In this work, we show that the automation of the original ARM protocol can be extended to a level suitable for performing the above tasks without user's manipulation and with an input preparation time of minutes. The new protocol, called a-ARM, delivers fully reproducible (i.e., user independent) rhodopsin QM/MM models as well as an improved model quality. More specifically, we show that the trend in vertical excitation energies observed for a set of 25 wild type and 14 mutant rhodopsins is predicted by the new protocol better than when using the original. Such an agreement is reflected by an estimated (relative to the probed set) trend deviation of 0.7 ± 0.5 kcal mol-1 (0.03 ± 0.02 eV) and mean absolute error of 1.0 kcal mol-1 (0.04 eV).
Highlights
These models are built on the basis of chain A and the side-chain rotamer with the highest occupancy, a chromophore cavity generated by Fpocket and including the Lys covalently linked to the retinal protonated Schiff base (rPSB) and MC and SC residues, ionization states predicted at the crystallographic pH with a neutral HID tautomer of histidine and automatic counterion placement decided by the PUTION code.[52]
We are interested in answering the question of whether the a-Automatic Rhodopsin Modeling (ARM) models generated using the input files PDBARM, cavity, and seqmut are suitable for predicting trends of ΔES1–S0 of wild type and mutant rhodopsins
Considering the compelling importance of having a high quality model for bR, we found that the default cavity does not include the Asp-96, Asp-115, and Glu-194 residues, which are crucial for the proton pump function,[87] and may sensibly interact with the surrounding and even the rPSB chromophore
Summary
Vertebrate, invertebrate, and microbial rhodopsins constitute an ecologically widespread class of membrane photoresponsive proteins driving fundamental biological functions such as vision, photoentrainment, chromatic adaptation, ion-gating, and ion-pumping.[1,2,3] The recent discovery of a new family of light-sensing microbial rhodopsins[4,5,6,7] indicates that we do not still fully comprehend the vast distribution and functional diversity of these systems, which are likely to exploit, globally, an amount of sun-light energy larger than that harnessed by photosynthetic systems. We will show that, when adopting certain default choices/parameters, a-ARM is capable of performing automatically (i.e., avoiding user manipulation) the following four key steps: (A) definition of the chromophore cavity, (B) assignment of protonation states of ionizable residues side chain, (C) placement of OS and IS counterions, and (D) congruous generation of single or multiple point mutations, allowing in principle for a faster and parallel model building Such an automated approach, called a-ARMdefault, adopts a set of default values for the choices determining how the QM/MM model is built.
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