What is the Optimal Size of the Quantum Region in Embedding Calculations of Two-Photon Absorption Spectra of Fluorescent Proteins?

Dawid Grabarek,Tadeusz Andruniów

doi:10.1021/acs.jctc.0c00602

Abstract

We systematically investigate an impact of the size and content of a quantum (QM) region, treated at the density functional theory level, in embedding calculations on one- (OPA) and two-photon absorption (TPA) spectra of the following fluorescent proteins (FPs) models: Aequorea victoria green FP (avGFP) with neutral (avGFP-n) and anionic (avGFP-a) chromophore as well as Citrine FP. We find that amino acid (a.a.) residues as well as water molecules hydrogen-bonded (h-bonded) to the chromophore usually boost both OPA and TPA processes intensity. The presence of hydrophobic a.a. residues in the quantum region also non-negligibly affects both absorption spectra but decreases absorption intensity. We conclude that to reach a quantitative description of OPA and TPA spectra in multiscale modeling of FPs, the quantum region should consist of a chromophore and most of a.a. residues and water molecules in a radius of 0.30–0.35 nm (ca. 200–230 atoms) when the remaining part of the system is approximated by the electrostatic point-charges. The optimal size of the QM region can be reduced to 80–100 atoms by utilizing a more advanced polarizable embedding model. We also find components of the QM region that are specific to a FP under study. We propose that the F165 a.a. residue is important in tuning the TPA spectrum of avGFP-n but not other investigated FPs. In the case of Citrine, Y203 and M69 a.a. residues must definitely be part of the QM subsystem. Furthermore, we find that long-range electrostatic interactions between the QM region and the rest of the protein cannot be neglected even for the most extensive QM regions (ca. 350 atoms).

Highlights

Since early works[1,2] on the Aequorea victoria jellyfish bioluminescence system, fluorescent proteins (FPs) became a versatile tool in modern biology and biochemistry
In some FPs, a sizable impact of polarization interactions on ΔE may be detected.[30]. This is the case when coupling between the MM region polarization and electronic excitation is accounted for, using an electronic-statespecific response of the environment to the excitation in the QM region.[30,31]. All these results clearly show that polarization interactions cannot be neglected in calculations of OPA and two-photon absorption (TPA) spectra as shown for different Aequorea victoria green FP (avGFP) models in other FPs.[21,31−33] the excitation energy for avGFP-a is converged only if polarization interactions with a.a. residues and water molecules within at least 20 Å radius from the chromophore are included.[33,34]
All ΔE, σTPA, and f values obtained with different QM subsystems are available in Tables: S10−S12, S13− S15, and S16−S18 (Citrine) in the Supporting Information depending on the level of theory used to describe the MM subsystem: NE, EE, and polarizable embedding (PE)

Summary

Introduction

Since early works[1,2] on the Aequorea victoria jellyfish bioluminescence system, fluorescent proteins (FPs) became a versatile tool in modern biology and biochemistry. They are utilized as biosensors and for the visualization of various processes in vivo.[3−5] The vital part of each FP is a chromophore created autocatalytically from three consecutive amino acids and embedded in a characteristic β-barrel polypeptide fold consisting of 11 β-strands (Scheme 1). Available FPs differ in terms of spectral, photochemical, and photophysical properties which are dictated by: (i) chromophore structure and (ii) chromophore’s protein environment. Tertiary avGFP Structure (PDB Code: 1GFL) with the Chromophore in Neutral Protonation State Emphasized

Objectives

Methods

Results

Conclusion