Glutathione Peroxidase Revisited—Simulation of the Catalytic Cycle by Computer-Assisted Molecular Modelling

Glutathione peroxidase, the first example of selenoproteins identified in mammals, was subjected to force field calculations and molecular dynamics in order to enable a clearer comprehension of enzymatic selenium catalysis. Starting from the established X-ray structure of bovine GPX, all kinetically defined intermediates and enzyme substrate complexes were modelled. The models thus obtained support the hypothesis that the essential steps of the catalysis are three distinct redox changes of the active site selenium which, in the ground state, presents itself at the surface of selenoperoxidases as the center of a characteristic triad built by selenocysteine, glutarnine and tryptophan. In GPX, four arginine residues and a lysine residue provide an electrostatic architecture which, in each reductive step, directs the donor substrate GSH towards the catalytic center in such a way that 1ts sulfhydryl group must react with the selenium moiety. To this end, different equally efficient modes of substrate binding appear possible. The models are consistent with substrate specificity data, kinetic pattern and other functional characteristics of the enzyme. Comparison of molecular models of GPX with those of other members of the GPX superfamily reveals that the cosubstrate binding mechanisrns are unique for the classical type of cytosolic glutathione peroxidases but cannot operate e. g. in plasma GPX and phospholipid hydroperoxide GPX. The structural differences between the selenoperoxidases, shown to be relevant to their specificities, are discussed in terms of functional diversification within the GPX superfamily

Palladium-catalyzed dicarbonylation of 1,3-butadiene with bidentate phosphine ligands:A density functional theory study

DFT calculations have been performed to discover the mechanism for the synthesis of dimethyl adipate(DMA)by 1,3-butadiene(BD)dicarbonylation catalyzed by a complex consisting of palladium and a bidentate diphosphine ligand.The computational results indicate that BD dicarbonylation involves two catalytic stages with the same reaction mechanism including terminal alkenyl insertion,CO migratory insertion,and methanolysis.Four different reaction routes have been explored,the pathway yielding linear DMA has the lowest alkenyl C-H insertion barrier with an overall barrier of 13.4 kcal·mol^(-1)(1 kcal·mol^(-1)=4.184 kJ·mol^(-1)).The regioselectivity of the BD dicarbonylation depends mainly on the barrier of the alkenyl insertion into the palladium-hydrogen complex site.The computations well reproduced the experimentally observed linear selectivity.

Organophosphorus catalytic reaction based on reduction of phosphine oxide

The special electronic configuration of phosphorus atoms endows organophosphorus reagents with unique chemical properties,which enable them to be used to catalyze various organic reactions,such as the Wittig reaction,Staudinger reaction,Appel reaction and Mitsunobu reaction.However,the catalytic process will be accompanied by the generation of large amounts of phosphine oxide waste,resulting in the reduction of atom utilization of the reaction,and it is difficult to separate the product.Therefore,it is essential to explore a greener and more sustainable organic synthesis route based on the catalytic cycle of phosphine oxide as a model.This paper summarizes the catalytic cycle and recycling of phosphorus with or without reducing agents and reviews the related developments in recent decades:from the addition of stoichiometric strong reducing agents,to the design of ring phosphines with specific structures,to the development of new energy inputs(electrochemistry),to the addition of a series of compounds to activate the P(V)––O double bond,driving the catalytic cycle of phosphine oxide through chemical transformation.This review also points out the development potential of this field in the future,which will promote its development and progress in a greener direction.

P-glycoprotein(ABCB1)-weak dipolar interactions provide the key to understanding allocrite recognition,binding,and transport

P-glycoprotein(ABCB1)is the first discovered mammalian member of the large family of ATP binding cassette(ABC)transporters.It facilitates the movement of compounds(called allocrites)across membranes,using the energy of ATP binding and hydrolysis.Here,we review the thermodynamics of allocrite binding and the kinetics of ATP hydrolysis by ABCB1.In combination with our previous molecular dynamics simulations,these data lead to a new model for allocrite transport by ABCB1.In contrast to previous models,we take into account that the transporter was evolutionarily optimized to operate within a membrane,which dictates the nature of interactions.Hydrophobic interactions drive lipid-water partitioning of allocrites,the transport process’s first step.Weak dipolar interactions(including hydrogen bonding,π-π stacking,and π-cation interactions)drive allocrite recognition,binding,and transport by ABCB1 within the membrane.Increasing the lateral membrane packing density reduces allocrite partitioning but enhances dipolar interactions between allocrites and ABCB1.Allocrite flopping(or reorientation of the polar part towards the extracellular aqueous phase)occurs after hydrolysis of one ATP molecule and opening of ABCB1 at the extracellular side.Rebinding of ATP re-closes the transporter at the extracellular side and expels the potentially remaining allocrite into the membrane.The high sensitivity of the steady-state ATP hydrolysis rate to the nature and number of dipolar interactions,as well as to the dielectric constant of the membrane,points to a flopping process,which occurs to a large extent at the membrane-transporter interface.The proposed unidirectional ABCB1 transport cycle,driven by weak dipolar interactions,is consistent with membrane biophysics.