Paramagnetic metal centers [such as Fe(III) found within ferriprotoporphyrin IX heme (FPIX)] exert through space effects on the relaxation rate of nearby proton spins that depend critically on the metal-proton distance. We have measured these effects for all protons of several antimalarial drugs that bind to FPIX by systematically varying the drug:heme molar ratio in high field NMR experiments. These measurements allow us to determine precise FPIX Fe-drug H distances for the solution structures of noncovalent complexes formed between FPIX mu-oxo dimers and the antimalarial drugs chloroquine (CQ), quinine (QN), and quinidine (QD). Using these distances, we then performed distance restraint calculations to determine the lowest-energy solution structures of these complexes. Structures were solved for neutral, monoprotic (+1), and diprotic (+2) forms of the drugs. Analysis of these structures allows us to visualize for the first time the stereospecific differences between QN and QD binding to FPIX and the differences in populations of QN and QD solution structures upon changes in digestive vacuolar pH for drug resistant malarial parasites [Dzekunov, S. M., et al. (2000) Mol. Biochem. Parasitol. 110, 107-124]. The data indicate a previously unrecognized key role for the CQ aliphatic chain in stabilizing FPIX-CQ complexes, and suggest how lengthening or shortening the chain might perturb stability. We also define FPIX:drug stoichiometries of 2:1 for the complexes formed at physiological FPIX concentrations, in contrast to the 4:1 and 5:1 stoichiometries previously determined at higher FPIX concentrations [Dorn, A., et al. (1998) Biochem. Pharmacol. 55, 727-736]. These atomic resolution antimalarial drug-heme structures should help elucidate how these drugs inhibit formation of hemozoin during metabolism of heme within the malarial parasite Plasmodium falciparum and assist ongoing development of strategies for circumventing antimalarial drug resistance.

To further an understanding of the nature of information available from Xe chemical shifts in cavities in biological systems, it would be advantageous to start with Xe in regular nanochannels that have well known ordered structures built from amino acid units. In this paper, we report the experimental observation of Xe NMR lineshapes in peptide channels, specifically the self-assembled nanochannels of the dipeptide L-Val-L-Ala and its retroanalog L-Ala-L-Val in the crystalline state. We carry out grand canonical Monte Carlo simulations of Xe in these channels to provide a physical understanding of the observed Xe lineshapes in these two systems.S elf-assembling structures with nanochannels have been of increasing interest (1, 2). A subset of these (peptide-based nanochannels) have demonstrated applicability as transmembrane pores and ion channels, as well as size-selective ion sensors (1). Görbitz and coworkers (3, 4) have described peptide nanochannels formed by the aggregation of dipeptides in a head-to-tail hydrogen-bonded network, forming a channel with a hydrophobic interior. Two such systems, the dipeptide L-Val-L-Ala (3) (VA) and its retroanalog, L-Ala-L-Val (4) (AV), form two distinct channels, which have been demonstrated to act as supramolecular hosts for organic molecules. These dipeptide systems are the subject of the present study.Binding of Xe within cavities in proteins is common because of several favorable factors. The Xe atom has a large electric dipole polarizability; cavities within proteins are about the correct size to hold one or more Xe atoms, and the unfavorable entropic term related to the need to orient the ligand in the binding site is absent for Xe atom. The affinity of Xe for hydrophobic cavities in the interiors of macromolecules (5-10) coupled with the development of techniques for hyperpolarization of Xe nuclear spins have inspired an array of NMR studies of Xe in proteins (11), cells, (12, 13), and tissues (14-16). For example, hyperpolarized (HP) 129 Xe has been developed as a tool for the characterization of protein cavities which bind Xe, by using its nuclear spin polarization to enhance the signals of the protons in the cavity (10, 17), by using the Xe chemical shift itself as a reporter of cavity structure in both solution and the solid state (11), and in applications to biomolecular assays (18,19).Xe adsorbed into nanochannels and cavities gives rise to an anisotropic lineshape in the NMR spectrum. Such lineshapes have been observed experimentally in 1D channels in various crystalline materials (20)(21)(22)(23), with the observed lineshape varying with changing Xe occupancy within the channel. A theoretical understanding, using the dimer tensor model in grand canonical Monte Carlo (GCMC) simulations (24), permits the prediction of the average Xe chemical shift tensor and the lineshapes that are observed in the Xe NMR spectrum of a polycrystalline sample (24, 25) or of a single crystal (26), with no adjustable parameters. The lineshapes calculated for a uniform distribution...

A molecular dynamics (MD) investigation on a series of oligo-α-arabinofuranosides (1-8) using the AMBER force field and the GLYCAM carbohydrate parameter set is reported. The validation of the method was carried out by direct comparison of experimental vicinal proton-proton coupling constants ((3)JH,H) with those obtained by using an empirically determined Karplus equation and density functional theory (DFT)-derived relationships specifically tailored for α-arabinofuranosyl systems. A simple code was developed to implement the determination of (3)JH,H by applying these relationships to the probability distributions of rotamers and ring conformations displayed by the simulations. The empirical Karplus relationship and the DFT-derived equations yielded, in most cases, the same trend as experiment for intra-ring (3)JH,H values. This direct comparison circumvents additional sources of errors that may arise from the assumptions introduced by the deconvolution procedures often used to calculate population of rotamers and ring conformations from experimental (3)JH,H.