Beyond CHELP: improved potential derived charges for sugars.

The partitioning of the overall molecular charge distribution into atom centered monopole charges, while quantum mechanically ill-defined, is nevertheless a technique which finds applications in several broad classes of chemical problems. Charges derived from fits to electrostatic potentials have an intuitive appeal since, in principle, these could be derived from either theoretical or experimental data. It has been noted, however, that such potential derived charges can be conformationally dependent in ways that do not appear to reflect the changes in the molecular wavefunction. Both the algorithm used for selecting points at which the molecular electrostatic potential will be fit and the density of points used in the fit have been suggested to influence the resultant charges. Recently [Stouch TR, Williams DE (1992) J Comp Chem 13: 622-32; Stouch TR, Williams DE (1993) J Comp Chem 14: 858-66] it has been noted that numerical difficulties may make it impossible to fit all the atomic charges in a molecule. Singular value decomposition (SVD) of the linear least squares matrices used in fitting atom based monopoles to molecular electrostatic potentials provides a tool for evaluating the integrity of the calculated charges. Based on the SVD analysis for a selected group of molecules we have noted particularly that increasing the molecular size reduces the fraction of charges which can be validly assigned. Users of PD derived charges, especially those who are using those charges for tasks other than reproduction of the MEP, should be aware that there is a high probability that a significant portion of those charges are statistically unreliable. Therefore, charges in many biological molecules, such as sugars, prove to be difficult to obtain by potential derived (PD) methods such as CHELP or CHELPG. Results from the SVD can be used to both assess PD charges and to generate an improved, albeit incomplete, set. Improved PD fits are presented for a series of simple saccharides.

NMR and molecular modeling study of the conformations of taxol 2'-acetate in chloroform and aqueous dimethyl sulfoxide solutions.

Taxol 2'-acetate, an analog of the antitumor drug taxol, displays no significant in vitro microtubule polymerization activity, thus underscoring the importance of a free 2'-OH group to the biological activity of taxol. Previous work had suggested that the inactivity of taxol 2'-acetate is not due to steric interference by the acetyl group. The present study examined the conformations of taxol 2'-acetate in deuteriochloroform and (2)H2O-deuteriodimethyl sulfoxide solutions and found them to be essentially the same as the respective conformations adopted by taxol itself. Thus, neither destabilization of an active taxol conformation by the acetyl group nor the formation of an important taxol conformation determining role for the 2'-OH group appears likely. The implication of these findings is that the taxol 2'-OH group interacts directly with a protein residue in the taxol-microtubule complex, perhaps as a hydrogen bond donor.

Orientations of amphipathic helical peptides in membrane bilayers determined by solid-state NMR spectroscopy.

Solid-state NMR spectroscopy was used to determine the orientations of two amphipathic helical peptides associated with lipid bilayers. A single spectral parameter provides sufficient orientational information for these peptides, which are known, from other methods, to be helical. The orientations of the peptides were determined using the 15N chemical shift observed for specifically labeled peptide sites. Magainin, an antibiotic peptide from frog skin, was found to lie in the plane of the bilayer. M2 delta, a helical segment of the nicotinic acetylcholine receptor, was found to span the membrane, perpendicular to the plane of the bilayer. These findings have important implications for the mechanisms of biological functions of these peptides.