Jong Hwa Kim

Molecular Dynamics Studies of the Transmembrane Domain of Gp41 from HIV-1

Helix-helix interactions in the putative three-helix bundle formation of the gp41 transmembrane (TM) domain may contribute to the process of virus-cell membrane fusion in HIV-1 infection. In this study, molecular dynamics is used to analyze and compare the conformations of monomeric and trimeric forms of the TM domain in various solvent systems over the course of 4 to 23-ns simulations. The trimeric bundles of the TM domain were stable as helices and remained associated in a hydrated POPE lipid bilayer for the duration of the 23-ns simulation. Several stable inter-chain hydrogen bonds, mostly among the three deprotonated arginine residues located at the center of each of the three TM domains, formed in a right-handed bundle embedded in the lipid bilayer. No such bonds were observed when the bundle was left-handed or when the central arginine residue in each of the three TM helices was replaced with isoleucine (R_I mutant), suggesting that the central arginine residues may play an essential role in maintaining the integrity of the three-helix bundle. These observations suggest that formation of the three-helix bundle of the TM domain may play a role in the trimerization of gp41, thought to occur during the virus-cell membrane fusion process.

Tautomeric energetics of xanthine oxidase substrates: xanthine, 2-oxo-6-methylpurine, and lumazine.

The stability of the tautomers of each of the three important substrates of xanthine oxidase, xanthine, 2-oxo-6-methylpurine, and lumazine, was examined by quantum mechanical calculations. The geometries of these tautomers were optimized at the AM1, Hartree-Fock (HF/6-31G), and hybrid Hartree-Fock/density functional theory (B3LYP/6-31G(d)) levels of theory. The single point energies of some of the more stable tautomers for each of the substrates were calculated at the B3LYP/6-311 +G(2d,p) level of theory. The Conductor Polarized Continuum Model (CPCM) was used to evaluate the solvent effects on the relative stabilities of these tautomers. The calculations clearly identify the lowest energy tautomeric form for xanthine and lumazine. On the other hand, there appear to be three tautomers for 2-oxo-6-methylpurine, with only minor energetic differences in vacuo. In water, however, only one of them predominates. The lowest energy tautomers presumably represent the predominant tautomeric forms at the molybdenum center of xanthine oxidase during catalysis. Implications of these computational results are discussed in the context of enzyme catalysis.

Dynamic structure of bacterial ribosomal 5S RNA helices II and III of B. megaterium 5S RNA.

A possible switch between two conformations, previously observed in an enzymatically cleaved fragment of E. coli 5S ribosomal RNA (a Gram-negative bacterium) containing helices II and III, has been examined by means of proton nuclear magnetic resonance spectroscopy (10-15 ppm) as a function of [Mg2+] and temperature for an RNase-T1 digested fragment of Bacillus megaterium 5S rRNA (a Gram-positive bacterium) containing the same helices II and III. The conformational changes induced in the fragment are not accompanied by breakage of some base-pairs and formation of others, but rather consist simply of tightening or loosening of helices with retention of existing base-pairs. Helix III is found to be more flexible than helix II. Finally, the loop conformation is conserved over a wide range of Mg2+ concentration, suggesting that the loop may serve an important role in the biological function of 5S rRNA in ribosomes.