Combined quantum‐mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution

Abstract

Combined quantum mechanical molecular mechanics (QM/MM) calculations have become a popular methodology for efficient and accurate description of large molecular systems. In this work we introduce our development of a QM/MM framework based on two well-known codes-NWChem and AMBER. As an initial application area we are focused on excited state properties of small molecules in an aqueous phase using an analogue of the green fluorescent protein (GFP) chromophore as a particular test case. Our approach incorporates high level coupled cluster theory for the analysis of excited states providing a reliable theoretical analysis of effects of an aqueous solvation environment on the photochemical properties of the GFP chromophore. Using a systematic approach, which involves comparison of gas phase and aqueous phase results for different protonation states and conformations, we resolve existing uncertainties regarding the theoretical interpretation of experimental data. We observe that the impact of aqueous environment on charged states generally results in blue shifts of the absorption spectra, but the magnitude of the effect is sensitive to both protonation state and conformation and can be rationalized based on charge movement into the area of higher/lower external electrostatic potentials. At neutral pH levels the experimentally observed absorption signal is most likely coming from the phenol protonated form. Our results also show that the high level electron correlated method is essential for a proper description of excited states of GFP. © 2017 Wiley Periodicals, Inc.

Improving the Design of the Triple-Decker Motif in Red Fluorescent Proteins

“…As one can see, XMCQDTP2 excitation energies agree well with observed absorption band maxima in mCherry, mRojoA, and mRojoA-VYGV. We note that errors in calculations of the absolute electronic excitation energies for the GFP-type chromophores typically exceed 0.1 eV. − Here, the discrepancies between the experimental and XMCQDT2 values are fairly small (as well as in other organic chromophores, e.g., ref ). As expected, TD-DFT produces blue-shifted excitation energies.…”

Prediction of Fluorophore Brightness in Designed Mini Fluorescence Activating Proteins

“…As an initial test of this hypothesis, we ran simulations of free DFHBI in water to determine whether the observed rotation kinetics would quantitatively agree with experimental measurements of the quantum yield. While hybrid quantum mechanics/molecular mechanics (QM/MM) simulations would ordinarily be suited for this purpose, 18 their computational cost would have been prohibitive for accumulating enough statistics to obtain converged estimates of the time it takes to cross the energy barriers, especially for the long rotation times expected in the context of a protein. Instead, we chose to use the gas-phase QM potential energies to reparametrize GAFF molecular mechanics (MM) parameters for the two dihedral angles.…”

“…The GFP chromophore upon which DFHBI was based has been very well studied. − Like DFHBI, the GFP chromophore has a phenolate group attached to an imidazole group by a methine bridge. However, the imidazole group is covalently attached to the protein backbone because the chromophore is autocatalytically formed from several residues of the GFP protein. , This covalent attachment of the GFP chromophore is a restriction on the dynamic freedom not shared by the DFHBI chromophore.…”

“…, we used 200 different DFHBI poses derived from docking to a designed model of mFAP1. Those ligand conformations were transferred onto to the mFAP-A structure by superimposing the Cα atoms of the mFAP1 binding site residues(14,15,16,18,22,23, 24,25,26,27,28,42,43,44,45,46, 50, 52, 72, 75, 78, 98, and 104) onto the equivalent residues of mFAP-A via sequence alignment. The ligand poses included all four major permutations of the ligand structure (i.e., from combinations of 180°rotations about the major and minor ligand axes).…”

Temperature-Dependent Fluorescence of mPlum Fluorescent Protein from 295 to 20 K

“…In general, the complex structure and dynamics of proteins lead to a combination of spectral congestion and molecular motions over many orders of magnitude in time, which makes it difficult to clearly assign their excited-state processes with either frequency- or time-resolved spectroscopy. Many studies rely on theoretical calculations for the interpretation of excited-state processes, − but this is challenging due to the limitations in the accuracy and range of timescales accessible to quantum mechanical (QM) calculations on such large systems. Low-temperature fluorescence spectroscopy is one approach for simplifying the dynamics of complex systems.…”