Role of Active Site Tyrosine in Glutathione S-Transferase: Insights from a Theoretical Study on Model Systems

On the Inhibition Mechanism of Glutathione Transferase P1 by Piperlongumine. Insight From Theory

Piperlongumine (PL) is an anticancer compound whose activity is related to the inhibition of human glutathione transferase of pi class (GSTP1) overexpressed in cancerous tumors and implicated in the metabolism of electrophilic compounds. In the present work, the inhibition mechanism of hydrolyzed piperlongumine (hPL) has been investigated employing QM and QM/MM levels of theory. The potential energy surfaces (PESs) underline the contributions of Tyr residue close to G site in the catalytic pocket of the enzyme. The proposed mechanism occurs through a one-step process represented by the nucleophilic addition of the glutathione thiol to electrophilic species giving rise to the simultaneous C-S and H-C bonds formation. Both the used methods give barrier heights (19.8 and 21.5 kcal mol⁻¹ at QM/MM and QM, respectively) close to that experimentally measured for the C-S bond formations (23.8 kcal mol⁻¹).

Fluorinated amino acids: compatibility with native protein structures and effects on protein-protein interactions

Fluorinated analogues of the canonical α-L-amino acids have gained widespread attention as building blocks that may endow peptides and proteins with advantageous biophysical, chemical and biological properties. This critical review covers the literature dealing with investigations of peptides and proteins containing fluorinated analogues of the canonical amino acids published over the course of the past decade including the late nineties. It focuses on side-chain fluorinated amino acids, the carbon backbone of which is identical to their natural analogues. Each class of amino acids--aliphatic, aromatic, charged and polar as well as proline--is presented in a separate section. General effects of fluorine on essential properties such as hydrophobicity, acidity/basicity and conformation of the specific side chains and the impact of these altered properties on stability, folding kinetics and activity of peptides and proteins are discussed (245 references).

Cryogenic and laser photoexcitation studies identify multiple roles for active site residues in the light-driven enzyme protochlorophyllide oxidoreductase

The light-activated enzyme NADPH-protochlorophyllide oxidoreductase (POR) catalyzes the trans addition of hydrogen across the C-17-C-18 double bond of protochlorophyllide (Pchlide), a key step in chlorophyll biosynthesis. Similar to other members of the short chain alcohol dehydrogenase/reductase family of enzymes, POR contains a conserved Tyr and Lys residue in the enzyme active site, which are implicated in a proposed reaction mechanism involving proton transfer from the Tyr hydoxyl group to Pchlide. We have analyzed a number of POR variant enzymes altered in these conserved residues using a combination of steady-state turnover, laser photoexcitation studies, and low temperature fluorescence spectroscopy. None of the mutations completely abolished catalytic activity. We demonstrate their importance to catalysis by defining multiple roles in the overall reaction pathway. Mutation of either residue impairs formation of the ground state ternary enzyme-substrate complex, pointing to a key role in substrate binding. By analyzing the most active variant (Y193F), we show that Tyr-193 participates in proton transfer to Pchlide and stabilizes the Pchlide excited state, enabling hydride transfer from NADPH to Pchilde. Thus, in addition to confirming the probable identity of the proton donor in Pchlide reduction, our work defines additional roles for these residues in facilitating hydride transfer through stabilization of the ground and excited states of the ternary enzyme complex.

Phenol vs Water Molecule Interacting with Various Molecules: σ-type, π-type, and χ-type Hydrogen Bonds, Interaction Energies, and Their Energy Components

The nature of interactions of phenol with various molecules (Y = HF, HCl, H2O, H2S, NH3, PH3, MeOH, MeSH) is investigated using ab initio calculations. The optimized geometrical parameters and spectra for the global energy minima of the complexes match the available experimental data. The contribution of attractive (electrostatic, inductive, dispersive) and repulsive (exchange) components to the binding energy is analyzed. HF favors sigma O-type H-bonding, while H2O, NH3, and MeOH favor sigma H-type H-bonding, where sigma O-/sigma H-type is the case when a H-bond forms between the phenolic O/H atom and its interacting molecule. On the other hand, HCl, H2S, and PH3 favor pi-type H-bonding, which are slightly favored over sigma O-, sigma H-, sigma H-type bonding, respectively. MeSH favors chi H-type bonding, which has characteristics of both pi and sigma H. The origin of these conformational preferences depending on the type of molecules is elucidated. Finally, phenol-Y complexes are compared with water-Y complexes. In the water-Y complexes where sigma O/sigma H-type involves the H-bond by the water O/H atom, HF and HCl favor sigma O-type, H2O involves both sigma O-/sigma H-type, and H2S, NH3, PH3, MeOH, and MeSH favor sigma H-type bonding. Except for HF, seven other species have larger binding energies with a phenol molecule than a water molecule.

Universal iterative strategy for the divergent synthesis of dendritic macromolecules from conventional monomers by a combination of living radical polymerization and irreversible TERminator multifunctional INItiator (TERMINI)

A new synthetic concept named TERMINI that stands for irreversible TERminator Multifunctional INItiator is reported. Suitable combinations of TERMINI and living polymerizations provide access to strategies for the design and synthesis of unprecedented complex molecular and macromolecular architectures from a diversity of commercial monomers. TERMINI represents a masked multifunctional initiator designed to quantitatively and irreversibly interrupt a chain organic reaction or a living polymerization. After demasking, the TERMINI repeat unit enables the quantitative reinitiation, in the presence or absence of a catalyst, of the same or a different living polymerization or a chain organic reaction in more than one direction, thus becoming a branching point. The demonstration of this concept was made by using a combination of metal-catalyzed living radical polymerization (LRP) and (1,1-dimethylethyl)[[1-[3,5-bis(S-phenyl 4-N,N'-diethylthiocarbamate)phenyl]ethenyl]oxy]dimethylsilane as TERMINI, to elaborate a novel iterative divergent method for the synthesis of dendritic macromolecules based on methyl methacrylate (MMA).

Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9,10-oxide

Glutathione S-transferases (GSTs) play an important role in the detoxification of xenobiotics in mammals. They catalyze the conjugation of glutathione to a wide range of electrophilic compounds. Phenanthrene 9,10-oxide is a model substrate for GSTs, representing an important group of epoxide substrates. In the present study, combined quantum mechanical/molecular mechanical (QM/MM) simulations of the conjugation of glutathione to phenanthrene 9,10-oxide, catalyzed by the M1-1 isoenzyme from rat, have been carried out to obtain insight into details of the reaction mechanism and the role of solvent present in the highly solvent accessible active site. Reaction-specific AM1 parameters for sulfur have been developed to obtain an accurate modeling of the reaction, and QM/MM solvent interactions in the model have been calibrated. Free energy profiles for the formation of two diastereomeric products were obtained from molecular dynamics simulations of the enzyme, using umbrella sampling and weighted histogram analysis techniques. The barriers (20 kcal/mol) are in good agreement with the overall experimental rate constant and with the formation of equal amounts of the two diastereomeric products, as experimentally observed. Along the reaction pathway, desolvation of the thiolate sulfur of glutathione is observed, in agreement with solvent isotope experiments, as well as increased solvation of the epoxide oxygen of phenanthrene 9,10-oxide, illustrating an important stabilizing role for active site solvent molecules. Important active site interactions have been identified and analyzed. The catalytic effect of Tyr115 through a direct hydrogen bond with the epoxide oxygen of the substrate, which was proposed on the basis of the crystal structure of the (9S,10S) product complex, is supported by the simulations. The indirect interaction through a mediating water molecule, observed in the crystal structure of the (9R,10R) product complex, cannot be confirmed to play a role in the conjugation step. A selection of mutations is modeled. The Asn8Asp mutation, representing one of the differences between the M1-1 and M2-2 isoenzymes, is identified as a possible factor contributing to the difference in the ratio of product formation by these two isoenzymes. The QM/MM reaction pathway simulations provide new and detailed insight into the reaction mechanism of this important class of detoxifying enzymes and illustrate the potential of QM/MM modeling to complement experimental data on enzyme reaction mechanisms.

Isolation and characterization of glutathione-S-transferase isozyme Q3 from the northern quahog, Mercinaria mercinaria

Three glutathione-S-transferase (GST) isozymes (Q1, Q2, and Q3) from the northern quahog (Mercinaria mercinaria) were purified and separated with a combination of affinity and ion exchange chromatography. SDS-PAGE analysis of the separated quahog GSTs indicated there are four distinct subunits of the enzyme with molecular masses ranging between 23 and 27 kDa. The electrophoretic analysis in combination with GST information from literature indicates that among the quahog GST isozymes, there is a single homodimer and two heterodimers. Enzymatic kinetic analysis of the homodimeric quahog GST (Q3) using 1-chloro-2,4-dinitrobenzene and glutathione as reactants resulted in Vmax and Km values of 33.2 micromol min(-1) mg(-1) and 0.40 mM, respectively. A pH profile analysis of the Q3 GST indicates that the optimum catalytic pH is 7.6. The Q3 isozyme composes about 28% of the ion exchange purified GSTs but accounts for only 9% of the total GST enzymatic activity (25 micromol min(-1) mg(-1). An analysis investigating the dependence of the Q3 GST activity on temperature resulted in a retention of enzymatic activity (50-30% at temperature extremes from -13 degrees C to 100 degrees C), suggesting a unconventional role for the Q3 GST in quahog metabolism.

Ab initio calculations on hidden modulators of theta class glutathione transferase activity

The glutathione transferases decrease the pKa of glutathione, allowing its deprotonation and the formation of the more reactive thiolate anion. The thiolate is maintained in the active site through a weak conventional hydrogen bond first sphere interaction donated by a Tyr hydroxyl in the Alpha, Mu, Pi, and Sigma glutathione transferase classes that can be modified by other second sphere or indirect thiolate contacts. However, the Theta and Delta class isoforms use a Ser hydroxyl for stabilizing the GSH thiolate, and as such, have a different chemical system compared with that of the Tyr possessed by other classes. We have used high level ab initio methods to investigate this interaction by using a simple methanol methanethiol system as a model. The hydrogen bond strength of this initial first sphere interaction was calculated to be less than that of the Tyr interaction. A putative second sphere interaction exists in the Theta and Delta class structures between Cys or Ser-14 and Ser-11 in the mammalian Theta subclass 1 and 2, respectively. The effect of this interaction on the first sphere interaction has also been investigated and found to significantly increase the energy of the bond.

N5-(L-1-carboxyethyl)-L-ornithine synthase: physical and spectral characterization of the enzyme and its unusual low pKa fluorescent tyrosine residues

N5-(L-1-carboxyethyl)-L-ornithine synthase [E.C. 1.5.1.24] (CEOS) from Lactococcus lactis has been cloned, expressed, and purified from Escherichia coli in quantities sufficient for characterization by biophysical methods. The NADPH-dependent enzyme is a homotetramer (Mr approximately equal to 140,000) and in the native state is stabilized by noncovalent interactions between the monomers. The far-ultraviolet circular dichroism spectrum shows that the folding pattern of the enzyme is typical of the alpha,beta family of proteins. CEOS contains one tryptophan (Trp) and 19 tyrosines (Tyr) per monomer, and the fluorescence spectrum of the protein shows emission from both Trp and Tyr residues. Relative to N-acetyltyrosinamide, the Tyr quantum yield of the native enzyme is about 0.5. All 19 Tyr residues are titratable and, of these, two exhibit the uncommonly low pKa of approximately 8.5, 11 have pKa approximately 10.75, and the remaining six titrate with pKa approximately 11.3. The two residues with pKa approximately 8.5 contribute approximately 40% of the total tyrosine emission, implying a relative quantum yield >1, probably indicating Tyr-Tyr energy transfer. In the presence of NADPH, Tyr fluorescence is reduced by 40%, and Trp fluorescence is quenched completely. The latter result suggests that the single Trp residue is either at the active site, or in proximity to the sequence GSGNVA, that constitutes the beta alphabeta fold of the nucleotide-binding domain. Chymotrypsin specifically cleaves native CEOS after Phe255. Although inactivated by this single-site cleavage of the subunit, the enzyme retains the capacity to bind NADPH and tetramer stability is maintained. Possible roles in catalysis for the chymotrypsin sensitive loop and for the low pKa Tyr residues are discussed.

Molecular dynamics simulations of a protein-protein dimer: particle-mesh Ewald electrostatic model yields far superior results to standard cutoff model

In this article we present two 1000 ps molecular dynamics simulations on the rat micro-glutathione S-transferase dimeric enzyme in complex with the product 1-(S-glutathionyl)-2,4-dinitrobenzene, in a periodic box with explicit solvent molecules, and investigate the effect of long-range electrostatics models on the structure and dynamics of the dimer and its components. One simulation used the standard cutoff method (10A), whilst the other used the particle-mesh Ewald (PME) method. We monitored the root mean-square atomic deviation (RMSD) from the initial crystal structure to examine the convergence of both simulations, as well as several other structural parameters such as the distance between active sites, rigid body rotation between domains in subunits, radius of gyration, B-factors, number of hydrogen bonds and salt bridges and solvent-accessible surface area. For example, with the PME method, the dimer structure remains much closer to the initial crystallographic structure with an average RMSD of 1.3A +/- 0.1A and 1.0A +/- 0.1A for all heavy and backbone atoms, respectively, in the last 200 ps; the respective values for the cutoff simulation are 4.7A +/- 0.3A and 4.2A +/- 0.3A. The large deviations observed in the cutoff simulation severely affected the stability of the enzyme dimer and its complex with the bound product. This finding is contrary to that found in a similar study of the monomeric protein ubiquitin [Fox, T. & Kollman, P. A. Proteins Struct. Func. Genet. 25, 315-334 (1996)]. Unlike the earlier published work, the present study provides evidence that the standard cutoff method is not generally valid for the study of protein complexes, or their subunits.

Quantum mechanical calculations on biological systems

Improvements in quantum chemical methods have led to increased applications to biological problems, including the development of potential energy functions for molecular mechanics and modeling of the reactive chemistry in enzyme active sites, with particularly interesting progress being made for metal-containing systems. An important direction is the development and application of hybrid quantum chemical-molecular mechanics methods.

Catalytic mechanism and role of hydroxyl residues in the active site of theta class glutathione S-transferases. Investigation of Ser-9 and Tyr-113 in a glutathione S-transferase from the Australian sheep blowfly, Lucilia cuprina

Spectroscopic and kinetic studies have been performed on the Australian sheep blowfly Lucilia cuprina glutathione S-transferase (Lucilia GST; EC 2.5.1.18) to clarify its catalytic mechanism. Steady state kinetics of Lucilia GST are non-Michaelian, but the quite hyperbolic isothermic binding of GSH suggests that a steady state random sequential Bi Bi mechanism is consistent with the anomalous kinetics observed. The rate-limiting step of the reaction is a viscosity-dependent physical event, and stopped-flow experiments indicate that product release is rate-limiting. Spectroscopic and kinetic data demonstrate that Lucilia GST is able to lower the pKa of the bound GSH from 9.0 to about 6.5. Based on crystallographic suggestions, the role of two hydroxyl residues, Ser-9 and Tyr-113, has been investigated. Removal of the hydroxyl group of Ser-9 by site-directed mutagenesis raises the pKa of bound GSH to about 7.6, and a very low turnover number (about 0.5% of that of wild type) is observed. This inactivation may be explained by a strong contribution of the Ser-9 hydroxyl group to the productive binding of GSH and by an involvement in the stabilization of the ionized GSH. This serine residue is highly conserved in the Theta class GSTs, so the present findings may be applicable to all of the family members. Tyr-113 appears not to be essential for the GSH activation. Stopped-flow data indicate that removal of the hydroxyl group of Tyr-113 does not change the rate-limiting step of reaction but causes an increase of the rate constants of both the formation and release of the GSH conjugate. Tyr-113 resides on alpha-helix 4, and its hydroxyl group hydrogen bonds directly to the hydroxyl of Tyr-105. This would reduce the flexibility of a protein region that contributes to the electrophilic substrate binding site; segmental motion of alpha-helix 4 possibly modulates different aspects of the catalytic mechanism of the Lucilia GST.