Dynamics simulations of excited-state triple proton transfer in 7-azaindole complexes with water, water–methanol and methanol

Excited-state triple proton transfer (ESTPT) reactions in 7-azaindole (7AI) complexed with two water, with one water and one methanol, and with two methanol molecules were investigated by dynamics simulations in the first excited state computed with the second order algebraic-diagrammatic construction (ADC (2)) method. The results show that photoexcitation may trigger ultrafast an asynchronous concerted proton transfer via two solvent molecules along an intermolecular hydrogen-bonded network. The probability of occurrence of ESTPT ranges from 32% for 7AI(H2O–MeOH) to 64% for 7AI(MeOH)2. The average time for completing the ESTPT varies between 58 and 85 fs depending on the complex. The proton transfer (rather than hydrogen transfer) nature of the reaction was suggested by the nonexistence of crossings between the ππ* and πσ* states

Molecular Docking and NMR Binding Studies to Identify Novel Inhibitors of Human Phosphomevalonate Kinase

Phosphomevalonate kinase (PMK) phosphorylates mevalonate-5-phosphate (M5P) in the mevalonate pathway, which is the sole source of isoprenoids and steroids in humans. We have identified new PMK inhibitors with virtual screening, using autodock. Promising hits were verified and their affinity measured using NMR-based 1H–15N heteronuclear single quantum coherence (HSQC) chemical shift perturbation and fluorescence titrations. Chemical shift changes were monitored, plotted, and fitted to obtain dissociation constants (Kd). Tight binding compounds with Kd’s ranging from 6–60 μM were identified. These compounds tended to have significant polarity and negative charge, similar to the natural substrates (M5P and ATP). HSQC cross peak changes suggest that binding induces a global conformational change, such as domain closure. Compounds identified in this study serve as chemical genetic probes of human PMK, to explore pharmacology of the mevalonate pathway, as well as starting points for further drug development

Substrate Induced Structural and Dynamics Changes in Human Phosphomevalonate Iinase and Implications for Mechanism

Phosphomevalonate kinase (PMK) catalyzes an essential step in the mevalonate pathway, which is the only pathway for synthesis of isoprenoids and steroids in humans. PMK catalyzes transfer of the γ-phosphate of ATP to mevalonate 5-phosphate (M5P) to form mevalonate 5-diphosphate. Bringing these phosphate groups in proximity to react is especially challenging, given the high negative charge density on the four phosphate groups in the active site. As such, conformational and dynamics changes needed to form the Michaelis complex are of mechanistic interest. Herein, we report the characterization of substrate induced changes (Mg-ADP, M5P, and the ternary complex) in PMK using NMR-based dynamics and chemical shift perturbation measurements. Mg-ADP and M5P Kd\u27s were 6–60 μM in all complexes, consistent with there being little binding synergy. Binding of M5P causes the PMK structure to compress (τc = 13.5 nsec), whereas subsequent binding of Mg-ADP opens the structure up (τc = 15.6 nsec). The overall complex seems to stay very rigid on the psec-nsec timescale with an average NMR order parameter of S2 ∼0.88. Data are consistent with addition of M5P causing movement around a hinge region to permit domain closure, which would bring the M5P domain close to ATP to permit catalysis. Dynamics data identify potential hinge residues as H55 and R93, based on their low order parameters and their location in extended regions that connect the M5P and ATP domains in the PMK homology model. Likewise, D163 may be a hinge residue for the lid region that is homologous to the adenylate kinase lid, covering the “Walker-A” catalytic loop. Binding of ATP or ADP appears to cause similar conformational changes; however, these observations do not indicate an obvious role for γ-phosphate binding interactions. Indeed, the role of γ-phosphate interactions may be more subtle than suggested by ATP/ADP comparisons, because the conservative O to NH substitution in the β-γ bridge of ATP causes a dramatic decrease in affinity and induces few chemical shift perturbations. In terms of positioning of catalytic residues, binding of M5P induces a rigidification of Gly21 (adjacent to the catalytically important Lys22), although exchange broadening in the ternary complex suggests some motion on a slower timescale does still occur. Finally, the first nine residues of the N-terminus are highly disordered, suggesting that they may be part of a cleavable signal or regulatory peptide sequence. Proteins 2009. © 2008 Wiley-Liss, Inc

Molecular Dynamics simulations of supercritical ammonia and metal-ammonia solutions

The results of Molecular Dynamics simulations of supercritical ammonia are reported for the first time. Qualitative agreement is found with neutron diffraction studies, the only experimental evidence on the structure of supercritical ammonia, so far. Based on the experiences with aqueous electrolyte solutions, it is discussed how the potentials describing ion-ammonia interactions in dilute and concentrated metal-ammonia solutions at subcritical conditions have to be modified for supercritical simulations.Вперше представлені результати моделювання методом молекулярної динаміки аміаку в надкритичному стані. Встановлено якісне узгодження з дослідженнями за дифракцією нейтронів, які є єдиним експериментальним свідченням про структуру аміаку у надкритичному стані. На основі відомих даних про водні розчини електролітів обговорюється питання про те, в який спосіб необхідно модифікувати потенціали, що описують взаємодії іон-аміак у розведених та концентрованих розчинах металів у аміаку, з метою їх застосування у моделюванні аміаку в надкритичному стані

Theoretical study on excited-state intermolecular proton transfer reactions of 1H-pyrrolo[3,2-h]quinoline with water and methanol

The dynamics of the ultrafast excited-state multiple intermolecular proton transfer (PT) reactions in gas-phase complexes of 1H-pyrrolo[3,2-h]quinoline with water and methanol (PQ(H2O)n and PQ(MeOH)n , where n = 1, 2) is modeled using quantum-chemical simulations. The minimum energy ground-state structures of the complexes are determined. Molecular dynamics simulations in the first excited state are employed to determine reaction mechanisms and the time evolution of the PT processes. Excited-state dynamics results for all complexes reveal synchronous excited-state multiple proton transfer via solvent-assisted mechanisms along an intermolecular hydrogen-bonded network. In particular, excited-state double proton transfer is the most effective, occurring with the highest probability in the PQ(MeOH) cluster. The PT character of the reactions is suggested by nonexistence of crossings between ππ* and πσ* states