RESUMO
We show by quantum mechanical/molecular mechanical (QM/MM) simulations that phenylbenzothiazoles undergoing an excited-state proton transfer (ESPT) can be used to probe protein binding sites. For 2-(2'-hydroxy-4'-aminophenyl)benzothiazole (HABT) bound to a tyrosine kinase, the absolute and relative intensities of the fluorescence bands arising from the enol and keto forms are found to be strongly dependent on the active-site conformation. The emission properties are tuned by hydrogen-bonding interactions of HABT with the neighboring amino acid T766 and with active-site water. The use of ESPT tuners opens the possibility of creating two-color fluorescent markers for protein binding sites, with potential applications in the detection of mutations in cancer cell lines.
Assuntos
Corantes Fluorescentes/química , Proteínas Quinases/química , Sítios de Ligação , Domínio Catalítico , Simulação de Dinâmica Molecular , Proteínas Quinases/metabolismo , Prótons , Teoria Quântica , Espectrometria de Fluorescência , Termodinâmica , Tiazóis/químicaRESUMO
Retinitis pigmentosa (RP) is a pathological condition associated with blindness due to progressive retinal degeneration. RP-linked mutations lead to changes at the retinal binding pocket and in the absorption spectra. Here, we evaluate the geometries, electronic effects, and vertical excitation energies in the dark state of mutated human rhodopsins carrying the abnormal substitutions M207R or S186W at the retinal binding pocket. Two models are used, the solvated protein and the protein in a solvated POPC lipid bilayer. We apply homology modeling, classical molecular dynamics simulations, density functional theory (DFT), and quantum mechanical/molecular mechanical (QM/MM) methods. Our results for the wild type bovine and human rhodopsins, used as a reference, are in good agreement with experiment. For the mutants, we find less twisted QM/MM ground-state chromophore geometries around the C(11)-C(12) double bond and substantial blue shifts in the lowest vertical DFT excitation energies. An analysis of the QM energies shows that the chromophore-counterion region is less stable in the mutants compared to the wild type, consistent with recent protein folding studies. The influence of the mutations near the chromophore is discussed in detail to gain more insight into the properties of these mutants. The spectral tuning is mainly associated with counterion effects and structural features of the retinal chain in the case of the hM207R mutant, and with the presence of a neutral chromophore with deprotonated Lys296 in the case of the hS186W mutant.
Assuntos
Simulação de Dinâmica Molecular , Mutação , Retinose Pigmentar/genética , Rodopsina/química , Rodopsina/genética , Animais , Sítios de Ligação , Bovinos , Cristalografia por Raios X , Humanos , Bicamadas Lipídicas/química , Modelos Moleculares , Dados de Sequência Molecular , Estrutura Molecular , Conformação Proteica , Teoria Quântica , Retinaldeído/química , Retinaldeído/metabolismo , Rodopsina/metabolismoRESUMO
NMR J-couplings across hydrogen bonds reflect the static and dynamic character of hydrogen bonding. They are affected by thermal and solvent effects and can therefore be used to probe such effects. We have applied density functional theory (DFT) to compute the NMR (n)J(N,H) scalar couplings of a prototypical Chagas disease drug (metronidazole). The calculations were done for the molecule in vacuo, in microsolvated cluster models with one or few water molecules, in snapshots obtained from molecular dynamics simulations with explicit water solvent, and in a polarizable dielectric continuum. Hyperconjugative and electrostatic effects on spin-spin coupling constants were assessed through DFT calculations using natural bond orbital (NBO) analysis and atoms in molecules (AIM) theory. In the calculations with explicit solvent molecules, special attention was given to the nature of the hydrogen bonds formed with the solvent molecules. The results highlight the importance of properly incorporating thermal and solvent effects into NMR calculations in the condensed phase.
Assuntos
Antiparasitários/química , Metronidazol/química , Temperatura , Antiparasitários/uso terapêutico , Doença de Chagas/tratamento farmacológico , Ligação de Hidrogênio , Espectroscopia de Ressonância Magnética , Metronidazol/uso terapêutico , Simulação de Dinâmica Molecular , Solventes/químicaRESUMO
We have examined the electronic and molecular structure of 1H-phenalen-1-one (phenalenone) in the electronic ground state and in the lowest excited states, as well as intersystem crossing. The electronic structure was calculated using a combination of density functional theory and multi-reference configuration interaction. Intersystem crossing rates were determined using Fermi's golden rule and taking direct and vibronic spin-orbit coupling into account. The required spin-orbit matrix elements were obtained applying a non-empirical spin-orbit mean-field approximation. Our calculated electronic energies are in good agreement with experimental data. We find the lowest excited singlet states to be of the npi* (S1) and pipi* (S2) type. Energetically accessible from S1 are two triplet states of the pipi* (T1) and npi* (T2) type, the latter being nearly degenerate to S1. This ordering of states is retained when the molecular structure in the electronically excited states is relaxed. We expect very efficient intersystem crossing between S1 and T1. Our calculated intersystem crossing rate is approximately 2 x 10(10) s(-1), which is in excellent agreement with the experimental value of 3.45 x 10(10) s(-1). Our estimated phosphorescence and fluorescence rates are many orders of magnitude smaller. Our results are in agreement with the experimentally observed behavior of phenalenone, including the high efficiency of 1O2 production.