Thomas C. Bruice

The near attack conformation approach to the study of the chorismate to prephenate reaction

Standard free energies (ΔGN°) for formation of near attack conformers, those ground state conformers that can convert directly to the transition state, were calculated for the Claisen rearrangement of chorismate to prephenate in six different environments: water, wild-type enzymes from Bacillus subtilis and Escherichia coli, their Arg90Cit and Glu52Ala mutants, and the 1F7 catalytic antibody. Values of the calculated ΔGN°s and the experimentally determined activation energies (ΔG‡) are linearly related with the slope of ≈1. This demonstrates that the relative rate of the chorismate → prephenate reaction is overwhelmingly dependent on the efficiency of formation of near attack conformers in the ground state.

Parameterization of OPLS–AA force field for the conformational analysis of macrocyclic polyketides

The parameters for the OPLS–AA potential energy function have been extended to include some functional groups that are present in macrocyclic polyketides. Existing OPLS–AA torsional parameters for alkanes, alcohols, ethers, hemiacetals, esters, and ketoamides were improved based on MP2/aug‐cc‐pVTZ and MP2/aug‐cc‐pVDZ calculations. Nonbonded parameters for the sp3 carbon and oxygen atoms were refined using Monte Carlo simulations of bulk liquids. The resulting force field predicts conformer energies and torsional barriers of alkanes, alcohols, ethers, and hemiacetals with an overall RMS deviation of 0.40 kcal/mol as compared to reference data. Densities of 19 bulk liquids are predicted with an average error of 1.1%, and heats of vaporization are reproduced within 2.4% of experimental values. The force field was used to perform conformational analysis of smaller analogs of the macrocyclic polyketide drug FK506. Structures that adopted low‐energy conformations similar to that of bound FK506 were identified. The results show that a linker of four ketide units constitutes the shortest effector domain that allows binding of the ketide drugs to FKBP proteins. It is proposed that the exact chemical makeup of the effector domain has little influence on the conformational preference of tetraketides.

A correlation of thyroxine-like activity and chemical structure

Abstract A correlation of structure vs. thyroxine-like activity for 47 analogs of thyroxine, of structure A, has been attempted where X, X′ = halogen, H, CH3, NO2; R′ = H or CH3; R = ionizable groups as alanyl, COOH, etc. It is proposed that: 1. 1. The thyromimetic activities of these analogs in amphibia and mammalia are related to the electronic character of the diphenyl ether nucleus, as affected by the abilities of the groups X, X′, and OR′ to attract or release electrons, with electron-releasing groups favoring higher activity. 2. 2. The abilities of the substituents X and X′ to form hydrogen bonds influence thyromimetic response, activity increasing with enhanced ability to form such bonds. 3. 3. Activity is related to the pK of the side chain, R. The empirical nature of the correlation is stressed and its deficiencies and possible uses are noted.

Enzymatic mechanism and product specificity of SET-domain protein lysine methyltransferases

Molecular dynamics and hybrid quantum mechanics/molecular mechanics have been used to investigate the mechanisms of +AdoMet methylation of protein-Lys-NH2 catalyzed by the lysine methyltransferase enzymes: histone lysine monomethyltransferase SET7/9, Rubisco large-subunit dimethyltransferase, viral histone lysine trimethyltransferase, and the Tyr245Phe mutation of SET7/9. At neutrality in aqueous solution, primary amines are protonated. The enzyme reacts with Lys-NH3+ and +AdoMet species to provide an Enz·Lys-NH3+·+AdoMet complex. The close positioning of two positive charges lowers the pKa of the Lys-NH3+ entity, a water channel appears, and the proton escapes to the aqueous solvent; then the reaction Enz·Lys-NH2·+AdoMet → Enz·Lys-N(Me)H2+·AdoHcy occurs. Repeat of the sequence provides dimethylated lysine, and another repeat yields a trimethylated lysine. The sequence is halted at monomethylation when the conformation of the Enz·Lys-N(Me)H2+·+AdoMet has the methyl positioned to block formation of a water channel. The sequence of reactions stops at dimethylation if the conformation of Enz·Lys-N(Me)2H+·+AdoMet has a methyl in position, which forbids the formation of the water channel.

The mechanism of catalysis of the chorismate to prephenate reaction by the Escherichia coli mutase enzyme

Molecular dynamics studies of the Escherichia coli chorismate mutase (EcCM), containing at the active site chorismate and in turn the transition state (TS), have been performed. The simulations show that TS is not bound any tighter than chorismate. Comparison of average polar interactions show they are virtually identical for interactions of EcCM with chorismate and the TS, whereas hydrophobic interactions with TS are much weaker than with chorismate. Interactions and the mechanism of catalysis of chorismate → prephenate by the EcCM enzyme are discussed.

Comparison of formation of reactive conformers for the SN2 displacements by CH3CO2 in water and by Asp124-CO2 in a haloalkane dehalogenase

The SN2 displacement of Cl− from 1,2-dichloroethane by acetate (CH3CO\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{2}^{-}}}\end{equation*}\end{document}) in water and by the carboxylate of the active site aspartate in the haloalkane dehalogenase of Xanthobacter autothropicus have been compared by using molecular dynamics simulations. In aqueous solution, six families of contact-pair structures (I–VI) were identified, and their relative concentrations and dissociation rate constants were determined. The near attack conformers (NACs) required for the SN2 displacement reaction are members of the IV (CH3COO−⋅ ⋅ ⋅CH2(Cl)CH2Cl) family and are formed in the sequence II→III→IV→NAC. The NAC subclass is defined by the —COO−⋅ ⋅ ⋅C—Cl contact distance of ≤3.41 Å and the —COO−⋅ ⋅ ⋅C—Cl angle of 157–180°. The mole percentage of NACs is 0.16%, based on the 1 M standard state. This result may be compared with 13.4 mole percentage of NACs in the Michaelis complex in the enzyme. It follows that NAC formation in the enzyme is favored by 2.6 kcal/mol. Because reaction coordinates from S to TS, both in water and in the enzyme, pass via NAC (i.e., S → NAC → TS), the reduction in the S → NAC barrier by 2.6 kcal/mol accounts for ≈25% of the reduction of total barrier in the S → TS (10.7 kcal/mol). The remaining 75% of the advantage of the enzymatic reaction revolves around the efficiency of NAC → TS step. This process, based on previous studies, is discussed briefly.

Solid-phase synthesis of positively charged deoxynucleic guanidine (DNG) modified oligonucleotides containing neutral urea linkages: effect of charge deletions on binding and fidelity

A solid-phase synthesis for a DNA analogue with a mixed guanidinium and urea backbone is reported. This material is nearly identical in structure to deoxynucleic guanidine (DNG) but the neutral urea internucleoside linkages can be used to attenuate the overall positive charge on the oligomer. The opposite charge attraction between urea containing DNG oligomers (DNGUs) and complimentary DNA can be controlled so that the affinity of DNG for DNA does not overwhelm the base-pairing discrimination necessary for specific binding. Octameric DNGU containing between 1 and 3 urea substitutions covered the range between very tight and very weak bonding. Each deletion of a positive charge reduced the thermal denaturation temperature (Tm) by approximately 5 degrees C. Mismatches in the DNA oligomers reduced the Tm values by 3 to 5 degrees C for each of the DNGU oligomers. DNGUs were found to bind in a 2:1 fashion to complimentary DNA in the same manner as DNG.

Ten-nanosecond molecular dynamics simulation of the motions of the horse liver alcohol dehydrogenase⋅PhCH2O− complex

Molecular dynamics simulations have been carried out for a period of 10 ns with the dimeric enzyme horse liver alcohol dehydrogenase (HLADH) present as the reactive complex HLADH⋅NAD+⋅ PhCH2O−. Cross-correlation analysis of the trajectory was carried out with the latter from 500 ps to 10 ns. The resulting cross-correlation map allowed the identification of the correlated and anticorrelated motions, which involve the entire protein. Anticorrelated and correlated motions are carried into the active site-aligned residues.

Consequences of breaking the Asp-His hydrogen bond of the catalytic triad: effects on the structure and dynamics of the serine esterase cutinase.

The objective of this study has been to investigate the effects on the structure and dynamics that take place with the breaking of the Asp-His hydrogen bond in the catalytic triad Asp175-His188-Ser120 of the serine esterase cutinase in the ground state. Four molecular dynamics simulations were performed on this enzyme in solution. The starting structures in two simulations had the Asp175-His188 hydrogen bond intact, and in two simulations the Asp175-His188 hydrogen bond was broken. Conformations of the residues comprising the catalytic triad are well behaved during both simulations containing the intact Asp175-His188 hydrogen bond. Short contacts of less than 2.6 A were observed in 1.2% of the sampled distances between the carboxylate oxygens of Asp175 and the NE2 of His188. The simulations showed that the active site residues exhibit a great deal of mobility when the Asp175-His188 hydrogen bond is broken. In the two simulations in which the Asp175-His188 hydrogen bond is not present, the final geometries for the residues in the catalytic triad are not in catalytically productive conformations. In both simulations, Asp175 and His188 are more than 6 A apart in the final structure from dynamics, and the side chains of Ser120 and Asp175 are in closer proximity to the NE2 of His188 than to ND1. Nonlocal effects on the structure of cutinase were observed. A loop formed by residues 26-31, which is on the opposite end of the protein relative to the active site, was greatly affected. Further changes in the dynamics of cutinase were determined from quasiharmonic mode analysis. The frequency of the second lowest mode was greatly reduced when the Asp175-His188 hydrogen bond was broken, and several higher modes showed lower frequencies. All four simulations showed that the oxyanion hole, composed of residues Ser42 and Gln121, is stable. Only one of the hydrogen bonds (Ser42 OG to Gln121 NE2) observed in the crystal structure that stabilize the conformation of Ser42 OG persisted throughout the simulations. This hydrogen bond appears to be enough for the oxyanion hole to retain its structural integrity.

Molecular dynamic study of orotidine-5′-monophosphate decarboxylase in ground state and in intermediate state: A role of the 203–218 loop dynamics

Molecular dynamics simulations have been used to derive the structures of ground (orotidine-5′-monophosphate decarboxylase⋅orotidine 5′-monophosphate; ODC⋅OMP) and intermediate (ODC⋅intermediate; ODC⋅I−) states in the ODC-catalyzed decarboxylation of OMP. For comparison, a molecular dynamics simulation of the conformers of OMP dissolved in water was also studied. This structural information is unavailable from present crystal structures. The electrostatic network in the active site around the carboxylate moiety of OMP exhibits remarkable stability. The conformation of enzyme-bound OMP is very similar to the conformation of OMP in water. Thus, the proposed Circe effect mechanism for ODC catalysis is unlikely. Comparison of ground state and intermediate state structures shows that on decarboxylation C6 takes the position of the carboxylate O8. This significant movement of the ligand is accompanied by a placement of the C6 carbanion in the vicinity of the protonated Lys-93 and is enforced by a change of the 203–218 loop from an unstructured form to an ordered β-hairpin. Previously proposed mechanisms involving protonation at O2, O4, or C5 have in common internal stabilization of the anionic intermediate by conjugation with positive charge on the pyrimidine ring. These mechanisms are not supported because there are no proton sources near O2, O4, and C5. We propose that the stabilization of intermediate ODC⋅I− is achieved by movement of the carbanion toward the external cation Lys-93 on decarboxylation and organization of the 203–218 loop. Because the intermediate and transition state are energetically similar, stabilization of the former decreases the free energy content of the latter.