We report 250–800 nm UV-Vis monomeric protein absorption originating from protein backbone–sidechain and sidechain–sidechain charge transfer transitions involving Lys/Glu residues.

Catalytic oxidation of nanoconfined benzylic C─H bonds by light, water, and O2.

The absorption of light by proteins can induce charge transfer (CT) transitions in the UV-visible range of the electromagnetic spectrum. Metal-ligand complexes or active site prosthetic groups which absorb in the visible region exhibit prominent CT transitions. Furthermore, the protein backbone also exhibits CT transitions in the far UV range. In this manuscript, we present a detailed computational study of new near UV-visible CT transitions that involve amino acids with charged side chains. Specifically, using time dependent density functional theory calculations, we examine the absorption spectra of naturally charged amino acids (Lys, Glu, Arg, Asp and His), extracted from solution phase protein structures generated by classical molecular dynamics simulations, and phosphorylated amino acids (Tyr, Thr and Ser) from experimentally determined protein structures. We show that amino acids with charged sidechains present a directed electronic donor-bridge-acceptor paradigm, with the lowest energy optical excitations demonstrating peptide backbone-sidechain charge separations. The UV-visible spectral range of the backbone-sidechain CT transitions is determined by the chemical nature of the donor, bridge and acceptor groups within each amino acid, amino acid conformation and the protein secondary structure where the amino acids are located. Photoinduced CT occurs in opposite directions for the anionic and cationic amino acids along the ground state dipole moment vector for the chromophores. We find that photoinduced charge separation is more facile for the anionic amino acids (Asp, Glu, pSer, pThr and pTyr) relative to that for the cationic amino acids (Lys, Arg and Hsp). Our results provide a foundation for the development of spectroscopic markers based on the recently proposed Protein Charge Transfer Spectra (ProCharTS) which are relevant for the study of DNA-binding or intrinsically disordered proteins that are rich in charged amino acids.

Recent reports of distinctive UV−vis absorption profiles for monomeric proteins rich in charged amino acids that span 250−800 nm have opened up a new label-free optical spectral window for probing biomolecular structure and interactions. Combined experimental-computational studies have revealed that such broad absorption profiles of these proteins arise from photoexcited charge transfer (CT) transitions in spatially proximal charged amino acids such as lysine (Lys) and glutamate (Glu). Here, using time-dependent density functional theory (TDDFT) with an optimally tuned CAM-B3LYP functional, we refine the computed UV−vis spectra for Lys-Glu dimers within protein folds and quantify the percentage CT character of the constituent transitions. The optimally tuned functionals are derived through a careful analysis of the CAM-B3LYP parameter space for Lys-Glu dimers as a function of amino-acid conformation and side chain separation. Our studies reveal that the tuned Lys-Glu dimer spectrum spans 150−650 nm and possesses 5 specific types of CT excitations with diverse and large spatial charge separation length scales of 2− 10 Å. These include inter-/intra-residue peptide backbone to peptide backbone (BB-CT) excitations spanning 160−210 nm, inter-/intra-residue peptide backbone to side chain (BS-CT) excitations spanning 160−260 nm, and side chain to side chain (SS-CT) excitations, which show the broadest absorption range spanning 260−650 nm.

Dimitra Markovitsi replied: Your papers have indeed been very stimulating for our studies. However, in our experiments, using much lower excitation intensities (<4 mW cm À2) than yours (>4 mW cm À2), we found that the one-photon ionization of mono-nucleosides and mono-nucleotides is lower than 3 Â 10 À4 , which corresponds to our detection limit. In contrast, when using similar excitation intensities to those reported in your 2002 paper we do observe ionization from the buffer. The fact that we observe one-photon ionization only for oligomers Faraday Discussions Discussions