Isomerization mechanism of the HcRed fluorescent protein chromophore

Sun, Qiao; Li, Zhen; Lan, Zhenggang; Pfisterer, Christoph; Doerr, Markus; Fischer, Stefan; Smith, Sean C.; Thiel, Walter

doi:10.1039/c2cp41217a

Cited by 23 publications

(33 citation statements)

References 83 publications

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“…The method allows determination of the mechanism of complex reactions in proteins. CPR has been used successfully in conjunction with QM/MM energy functions, for example to study proton transfer along proton wires (52,53), the cleavage of P ̶ O bonds (9,31), or isomerization reactions (54)(55)(56). Unlike molecular dynamics simulations, the MEP shows only the motions that are essential for the reaction, but gives no information on the time needed to get from one movie frame to the next.…”

Section: Methodsmentioning

confidence: 99%

Catalytic strategy used by the myosin motor to hydrolyze ATP

Kiani

Fischer

2014

Proc. Natl. Acad. Sci. U.S.A.

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Myosin is a molecular motor responsible for biological motions such as muscle contraction and intracellular cargo transport, for which it hydrolyzes adenosine 5'-triphosphate (ATP). Early steps of the mechanism by which myosin catalyzes ATP hydrolysis have been investigated, but still missing are the structure of the final ADP·inorganic phosphate (P i ) product and the complete pathway leading to it. Here, a comprehensive description of the catalytic strategy of myosin is formulated, based on combined quantumclassical molecular mechanics calculations. A full exploration of catalytic pathways was performed and a final product structure was found that is consistent with all experiments. Molecular movies of the relevant pathways show the different reorganizations of the H-bond network that lead to the final product, whose γ-phosphate is not in the previously reported HP γ O 4 2− state, but in the H 2 P γ O 4 − state. The simulations reveal that the catalytic strategy of myosin employs a three-pronged tactic: (i) Stabilization of the γ-phosphate of ATP in a dissociated metaphosphate (P γ O 3 − ) state. (ii) Polarization of the attacking water molecule, to abstract a proton from that water. (iii) Formation of multiple proton wires in the active site, for efficient transfer of the abstracted proton to various product precursors. The specific role played in this strategy by each of the three loops enclosing ATP is identified unambiguously. It explains how the precise timing of the ATPase activation during the force generating cycle is achieved in myosin. The catalytic strategy described here for myosin is likely to be very similar in most nucleotide hydrolyzing enzymes.T he molecular motor myosin cyclically interacts with the actin filament to generate the mechanical force that is used in living cells to achieve muscle contraction (1), cytokinesis (2, 3), and intracellular cargo transport (4). Hydrolysis of one ATP molecule per cycle provides the free energy that drives the actomyosin interaction cycle, as originally described by Lymn and Taylor (5). ATP is the common energy currency in biology, and is extremely stable in aqueous solution (6, 7). ATPases, the enzymes that catalyze the hydrolysis of the P β -O-P γ anhydride linkage in ATP, are ubiquitous in biology because they are needed to accelerate the release of free energy stored in ATP. Myosin manages to speed up the hydrolysis by a factor of 10 7 over the uncatalyzed rate in solution. The experimental uncatalyzed energy barrier is 29 kcal mol −1 (7,8), and the catalyzed barrier has been determined experimentally between 14.4 kcal mol −1 (9) and 14.8 kcal mol −1 (10). Understanding how myosin achieves its ATPase function is necessary to understand how myosin works as a motor, but also helps one to understand the functioning of the multitude of other nucleotide hydrolyzing enzymes. The catalytic mechanism of ATP hydrolysis in myosin has been studied extensively with methods such as protein crystallography (11)(12)(13)(14), mutagenesis (15, 16), photochemical kinet...

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Section: Methodsmentioning

confidence: 99%

Catalytic strategy used by the myosin motor to hydrolyze ATP

Kiani

Fischer

2014

Proc. Natl. Acad. Sci. U.S.A.

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“…Nonetheless, in some cases the trans isomers are predominant . The cis–trans isomerization can be achieved via slow and spontaneous relaxation in the dark or by accelerated photoactivation by irradiation, which has been confirmed through experimental and theoretical studies …”

Section: Introductionmentioning

confidence: 64%

Electric Field Effect on trans‐p‐Hydroxybenzylideneimidazolidinone: A DFT Study and Implication to Green Fluorescent Protein

Kang

Baek

Lee

2015

Bulletin Korean Chem Soc

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In the present study, density function theory (DFT) calculations were carried out regarding the electric field effect on the trans-p-hydroxybenzylideneimidazolidinone (HBDI), which represents the green fluorescent protein (GFP) chromophore. Structures in the absence or presence of electric fields were fully optimized with the CAM-B3LYP functional, and the corresponding absorption properties were obtained by the timedependent DFT method. It was found that electric field parallel to the x-axis (Fx) has the strongest effect on the charge distribution, and, hence the structure and dipole moment, of the ground state. Furthermore, the absorption energy of the neutral and anionic HBDI monomer was significantly affected by Fx.

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“…CPR has been used successfully to calculate minimum energy paths (MEPs) for proton transfer, 81,[83][84][85] hydrolysis of ATP, 86 and isomerization reactions. [87][88][89][90] CPR starts with an initial guess of the path that consists of energy-optimized reactants and product states, with or without intermediate configurations, and finds a MEP that connects the reactant and the product by identifying the first-order saddle point(s) along the path. The selected local minima along the MEPs were further geometry optimized using the same convergence criterion as for the reactant and product states.…”

Section: Proton-transfer Calculationsmentioning

confidence: 99%