Role of the isoprenyl pocket of the G protein beta gamma subunit complex in the binding of phosducin and phosducin-like protein.

Phosducin (Pdc) and phosducin-like protein (PhLP) regulate G protein-mediated signaling by binding to the betagamma subunit complex of heterotrimeric G proteins (Gbetagamma) and removing the dimer from cell membranes. The binding of Pdc induces a conformational change in the beta-propeller structure of Gbetagamma, creating a pocket between blades 6 and 7. It has been proposed that the isoprenyl group of Gbetagamma inserts into this pocket, stabilizing the Pdc.Gbetagamma structure and decreasing the affinity of the complex for the lipid bilayer. To test this hypothesis, the binding of Pdc and PhLP to several Gbetagamma dimers containing variants of the beta or gamma subunit was measured. These variants included modifications of the isoprenyl group (gamma), residues involved in the conformational change (beta), and residues lining the proposed prenyl pocket (beta). Switching prenyl groups from farnesyl to geranylgeranyl or vice versa had little effect on binding. However, alanine substitution of one residue in the beta subunit involved in the conformational change (W332) decreased binding 5-fold. Alanine substitution of certain residues within the prenyl pocket caused only minor decreases in binding, while a lysine substitution of T329 within the pocket inhibited binding 10-fold. Molecular modeling of the binding energy of the Pdc.Gbeta(1)gamma(2) complex required insertion of the geranylgeranyl group into the prenyl pocket in order to accurately predict the effects of prenyl pocket amino acid substitutions. Finally, a dimer containing a gamma subunit with no prenyl group (gamma(2)-C68S) decreased binding by nearly 20-fold. These results support the structural model in which the prenyl group escapes contact with the aqueous milieu by inserting into the prenyl pocket and stabilizing the Pdc-binding conformation of Gbetagamma.

Molecular modeling of the binding of 5-substituted 2'-deoxyuridine substrates to thymidine kinase of herpes simplex virus type-1.

In an earlier study, De Winter and Herdewijn (J. Med. Chem. 1996, 37, 4727-4737) studied the binding of various 5-substituted 2'-deoxyuridine substrates to thymidine kinase of herpes simplex virus type-1. They used a computational procedure that achieves good correlation with experimentally determined IC50 values. We applied an alternative procedure to the same deoxyuridine substrates, using only three readily calculated quantities-the binding energy, the molecular surface area, and a flexibility factor. Our simplified method achieves the same degree of correlation with the IC50 values as did the earlier procedure. We then applied this procedure to examine the binding of various 5-substituted pyrimidine 1,5-anhydrohexitol substrates to thymidine kinase.

Kinetic and molecular modeling of nucleoside and nucleotide inhibition of malate dehydrogenase.

We studied the inhibition of mitochondrial malate dehydrogenase (mMDH) by the nucleotides cAMP, AMP, ADP, ATP. The experimental kinetic studies showed that the nucleotides were competitive inhibitors and that cAMP was probably the most potent inhibitor. To explain these observations, we used molecular modeling to determine the location, orientation, and relative binding energy of the nucleotides to mMDH. The order of the calculated binding energies, from lowest (most favorable) to highest, was cAMP, AMP, ADP, and ATP, which corresponded somewhat to the order of the experimentally determined inhibition constants.

Procedure for selecting starting conformations for energy minimization of nucleosides and nucleotides.

The purpose of this study was to carry out a thorough search of the conformational space of various adenine-containing nucleotides, applying a previously published searching procedure, known as the representative method. This method, which reduces the number of starting conformations required to explore all the important regions of conformational space, appears to be successful in finding all (or nearly all) the putative low-energy conformations of each molecule.

Self-Inclusion Complexes Derived from Cyclodextrins: Synthesis and Characterization of 6(A),6(B)-Bis-O-[p-(allyloxy)phenyl]-Substituted beta-Cyclodextrins.

The syntheses, structures, and spectroscopic properties of 6(A),6(B)-bis-O-[p-(allyloxy)phenyl]-substituted beta-cyclodextrins have been investigated. Selective activation of the 6(A),6(B)-hydroxy groups was carried out by treating heptakis(2,3-di-O-methyl)-beta-cyclodextrin (1) with 2,4-dimethoxybenzene-1,5-disulfonyl chloride to give 6(A),6(B)-bissulfonate ester 2 in a yield of only 3%. This material was treated with sodium p-(allyloxy)phenoxide in DMF to form 6(A),6(B)-bis-O-[p-(allyloxy)phenyl]-heptakis(2,3-di-O-methyl)-beta-cyclodextrin (3), which had two isomers. One (3A) has the two p-(allyloxy)phenyl arms directed away from the cyclodextrin cavity, and the other (3B) has one of the p-(allyloxy)phenyl groups through the cavity to form a self-inclusion complex. When either 3A or 3B was treated with methyl iodide and sodium hydride, the resulting permethylated 6(A),6(B)-bis-O-[p-(allyloxy)phenyl]heptakis(2,3-di-O-methyl)-6(C),6(D),6(E),6(F),6(G)-penta-O-methyl-beta-cyclodextrin (4) was composed of two isomers, in which 4B is a self-inclusion complex. 3A and 3B also can be converted into a mixture of 3A and 3B in strong base but not when melted in the absence of base. 4A and 4B do not isomerize. Detailed 1D and 2D NMR spectroscopic studies were carried out to characterize the structures of these new compounds, and molecular mechanics techniques were used to explain the experimental facts.