Analysis of solvent structure in proteins using neutron D2O-H2O solvent maps: pattern of primary and secondary hydration of trypsin.

A method of determining the water structure in protein crystals is described using neutron solvent difference maps. These maps are obtained by comparing the changes in diffracted intensities between two data sets, one in which H2O is the major solvent constituent, and a second in which D2O is the solvent medium. To a good first approximation, the protein atom contributions to the scattering intensities in both data sets are equal and cancel, but since H2O and D2O have very different neutron-scattering properties, their differences are accentuated to reveal an accurate representation of the solvent structure. The method also employs a series of density modification steps that impose known physical constraints on the density distribution function in the unit cell by making real space modifications directly to the density maps. Important attributes of the method are that (1) it is less subjective in the assignment of water positions than X-ray analysis; (2) there is threefold improvement in the signal-to-noise ratio for the solvent density; and (3) the iterative density modification produces a low-biased representation of the solvent density. Tests showed that water molecules with as low as 10% occupancy could be confidently assigned. About 300 water sites were assigned for trypsin from the refined solvent density; 140 of these sites were defined in the maps as discrete peaks, while the remaining were found within less-ordered channels of density. There is a very good correspondence between the sites in the primary hydration layer and waters found in the X-ray structure. Most water sites are clustered into H-bonding networks, many of which are found along intermolecular contact zones. The bound water is equally distributed between contacting apolar and polar atoms at the protein interface. A common occurrence at hydrophobic surfaces is that apolar atoms are circumvented by one or more waters that are part of a larger water network. When the effects on surface accessibility by neighboring molecules in the crystal lattice are taken into consideration, only about 29% of the surface does not interface ordered water. About 25% of the ordered water is found in the second hydration sphere. In many instances these waters bridge larger clusters of primary layer waters. It is apparent that, in certain regions of the crystal, the organization of ordered water reflects the characteristics of the crystal environment more than those of trypsin's surface alone.

Magnetic resonance imaging of the efficacy of specific inhibition of 5 alpha-reductase in canine spontaneous benign prostatic hyperplasia.

A leading role for prostatic levels of dihydrotestosterone (DHT) in the pathogenesis of benign prostatic hyperplasia is well established, if incompletely understood. The present study provides initial confirmation that 5 alpha-reductase inhibition alone is sufficient to prevent prostatic accumulation of DHT and to produce epithelial regression in the canine prostate. In dogs treated with the specific 5 alpha-reductase inhibitor finasteride, prostatic volume decreased to one-third of the baseline volume, while the prostatic concentration of DHT fell fivefold: both were constant in placebo control dogs. Demonstration that MR imaging can serve as accurate modality to assess prostatic volume was provided by serial measurements of the canine prostate and by correlation of the last imaging measurement with the weight of the excised prostate. Significant intensity changes were observed in T2-weighted images measured post-treatment; these changes correlated with the histopathology of the prostate. These results suggest that beyond quantifying regression, multiecho T2 measurements can be useful in probing accompanying changes occurring on the cellular level.

Hydroxyl hydrogen conformations in trypsin determined by the neutron diffraction solvent difference map method: relative importance of steric and electrostatic factors in defining hydrogen-bonding geometries.

Neutron diffraction maps have been used to assign the rotor conformations of the hydroxyl hydrogens in trypsin. Knowledge of these conformations is used to assess the relative importance of steric and electrostatic effects in conferring the H-bonding geometries of these groups. A general finding was that most hydroxyl groups are rotationally ordered with their highest populated conformation near the low-energy staggered orientation. For the low-energy conformers (-60 degrees, 60 degrees, 180 degrees) of serine and threonine, the trans (-180 degrees) position is most highly populated followed by +60 degrees. In trypsin, only 1 of 24 serines was found in the -60 degrees conformer. Serine hydroxyls preferentially act as H-bond acceptors and rarely are observed as H-bond donors alone. Threonines were found to be more likely than serines to participate in two H bonds; tryosines were found to prefer to act as donors. In H-bonding situations in which there was incompatibility between the energies defining the barrier to rotation and the local electrostatics, the electrostatic criteria dominated. Overall, the findings support a model of H bonding where there exists strong inherent complementarity between the low-energy hydroxyl orientations and the local electrostatic environment.

Quaternary structure of the ribosomal 30S subunit: model and its experimental testing.

In considering the structure of the 30S subunit of the Escherichia coli ribosome, we have assumed that: (i) all or almost all the proteins within the 30S particle are compact and globular, as recently shown for the isolated proteins S4, S7, S8, S15, and S16 in solution [Serdyuk, I.N., Zaccai, G. & Spirin, A.S. (1978) FEBS Lett. 94, 349-352]; (ii) the RNA within the 30S particle has approximately the same specific V-like or Y-like shape that was demonstrated for the isolated 16S RNA in a compact conformation [Vasiliev, V.D., Selivanova, O.M. & Koteliansky, V.E. (1978) FEBS Lett. 95, 273-276]. From these assumptions and using the numerous data reported on neighboring ribosomal proteins, we have constructed a model of the quaternary structure of the ribosomal 30S subunit. The model has been tested by calculation of the theoretical curves of neutron scattering at different contrasts, as well as those of x-ray scattering, and their comparison with the experimental scattering curves for E. coli 30S particles. It has been found that the calculated scattering curves for the model practically coincide with the experimental scattering curves for the 30S particles in the range of Bragg distances down to 40-55 A. The scattering curves calculated for several three-dimensional patterns of arrangement of the 30S subunit proteins proposed earlier have been shown to be inconsistent with the experiments.