Experiences with the shikimate-pathway enzymes as targets for rational drug design.

The background and current context of work on the shikimate-pathway enzymes as potential targets for anti-bacterial, anti-fungal and anti-parasitic drugs is reviewed. Recent work on the third enzyme of the pathway, dehydroquinase, which occurs in two structurally and mechanistically distinct forms, is used to illustrate the present state of studies into rational drug design.

High-throughput screens for postgenomics: studies of protein crystallization using microsystems technology.

This paper describes the fabrication of a micromachined miniaturized array of chambers in a 2-mm-thick single crystal (100) silicon substrate for the combinatorial screening of the conditions required for protein crystallization screening (including both temperature and the concentration of crystallization agent). The device was fabricated using standard photolithography techniques, reactive ion etching (RIE) and anisotropic silicon wet etching to produce an array of 10 x 10 microchambers, with each element having a volume of 5 microL. A custom-built temperature controller was used to drive two peltier elements in order to maintain a temperature gradient (between 12 and 40 degrees C) across the device. The performance of the microsystem was illustrated by studying the crystallization of a model protein, hen egg white lysozyme. The crystals obtained were studied using X-ray diffraction at room temperature and exhibited 1.78 A resolution. The problems of delivering a robust crystallization protocol, including issues of device fabrication, delivery of a reproducible temperature gradient, and overcoming evaporation are described.

Probing the interface between membrane proteins and membrane lipids by X-ray crystallography.

Biological membranes are composed of a complex mixture of lipids and proteins, and the membrane lipids support several key biophysical functions, in addition to their obvious structural role. Recent results from X-ray crystallography are shedding new light on the precise molecular details of the protein-lipid interface.

Structure of rabbit liver fructose 1,6-bisphosphatase at 2.3 A resolution.

The three-dimensional structure of the R form of rabbit liver fructose 1,6-bisphosphatase (Fru-1,6-Pase; E.C. 3.1.3.11) has been determined by a combination of heavy-atom and molecular-replacement methods. A model, which includes 2394 protein atoms and 86 water molecules, has been refined at 2.3 A resolution to a crystallographic R factor of 0.177. The root-mean-square deviations of bond distances and angles from standard geometry are 0.012 A and 1.7 degrees, respectively. This structural result, in conjunction with recently redetermined amino-acid sequence data, unequivocally establishes that the rabbit liver enzyme is not an aberrant bisphosphatase as once believed, but is indeed homologous to other Fru-1,6-Pases. The root-mean-square deviation of the Calpha atoms in the rabbit liver structure from the homologous atoms in the pig kidney structure complexed with the product, fructose 6-phosphate, is 0.7 A. Fru-1,6-Pases are homotetramers, and the rabbit liver protein crystallizes in space group I222 with one monomer in the asymmetric unit. The structure contains a single endogenous Mg2+ ion coordinated by Glu97, Asp118, Asp121 and Glu280 at the site designated metal site 1 in pig kidney Fru-1,6-Pase R-form complexes. In addition, two sulfate ions, which are found at the positions normally occupied by the 6-phosphate group of the substrate, as well as the phosphate of the allosteric inhibitor AMP appear to provide stability. Met177, which has hydrophobic contacts with the adenine moiety of AMP in pig kidney T-form complexes, is replaced by glycine. Binding of a non-hydrolyzable substrate analog, beta-methyl-fructose 1,6-bisphosphate, at the catalytic site is also examined.

Structural studies of thiophilic N-chloroazasteroids.

N-Chloroazasteroids form covalent S-N bonds with thiol groups and so are of interest as chemoselective irreversible binding agents for the active sites of steroid receptors and enzymes. The solid-state structures of N-chloro-3-methoxy-17-aza-D-homo-1,3,5(10)-estratrien-16-one (1), N-chloro-3-methoxy-17-aza-D-homo-1,3,5(10)-estratrien-17a-on e (2) and N-chloro-3-methoxy-16-aza-1,3,5(10)-estratrien-17-one (3) were determined to obtain information about the spatial arrangement of the N-Cl groups. Crystal data: (1) C19H24ClNO2, Mr = 333.84, orthorhombic, P2l2l2l, a = 8.0190 (3), b = 12.7175 (5), c = 16.5047 (9) A, V = 1683.2 (1) A3, Z = 4, Dx = 1.317 g cm-3, lambda(Cu K alpha) = 1.54178 A, mu = 20.9 cm-1, F(000) = 712, T = 295 K, R = 0.045 for 1786 observed reflections; (2) C19H24ClNO2, Mr = 333.84, orthorhombic, P2l2l2l, a = 10.9853 (7), b = 11.8216 (5), c = 12.9851 (9) A, V = 1686.3 (2) A3, Z = 4, Dx = 1.315 g cm-3, lambda(Cu K alpha) = 1.54178 A, mu = 20.9 cm-1, F(000) = 712, T = 295 K, R = 0.035 for 1891 observed reflections; (3) C18H22ClNO2, Mr = 319.81, monoclinic, P2l, a = 13.246 (2), b = 7.972 (2), c = 7.696 (3) A, beta = 90.24 (2) degrees, V = 812.7 (4) A3, Z = 2, Dx = 1.307 g cm-3, lambda(Cu K alpha) = 1.54178 A, mu = 21.4 cm-1, F(000) = 340, T = 295 K, R = 0.045 for 1636 observed reflections.(ABSTRACT TRUNCATED AT 250 WORDS)

Structural requirements for the binding of dexamethasone to nuclear envelopes and plasma membranes.

The specificity of dexamethasone binding sites on nuclear envelopes (NE) and plasma membranes (PM) was determined in competition studies with natural and synthetic steroids. The binding affinities for nuclear envelopes and plasma membranes were then correlated with the three-dimensional structures of the ligands. Three major factors are implicated in the ability of the steroid to bind to the membrane sites: (1) the separation between the terminal oxygen atoms substituted at atoms C3 and C17, or attached to the substituent at C17, is found to be longer than 10 A for the medium and high affinity steroids; (2) the beta-orientation of the oxygen atom in the C17-substituent to the D-ring is favored over alpha-orientation; and (3) bulky substituents and nontypical configurations are not accepted by the binding sites. A nearly linear correlation between the O3...O (substituted at C17) distance and the binding affinity of the tested steroids is observed; explanations for the lack of linear correlation of some steroids are given. A preliminary model for the interaction of steroids with these membrane sites is proposed which requires two hydrogen bonding regions that interact with the 2 oxygen atoms and some steric restriction sites that prevent the binding of steroids with large substituents. The hydrophobicities of the steroids do not correlate with binding affinities to the dexamethasone binding sites; hydrophobicity seems to play a minor role in these steroid-membrane interactions. Comparisons of the specificity of the dexamethasone binding sites on membranes to the specificity of various steroid receptors are also presented.

Structure of 5 beta-dihydrotestosterone.

17 beta-Hydroxy-5 beta-androstan-3-one, C19H30O2, Mr = 290.45, orthorhombic, P2(1)2(1)2(1), a = 11.7821 (6), b = 21.2184 (8), c = 6.5322 (2) A, V = 1633.0 (2) A3, Z = 4, D chi = 1.181 Mg m-3, lambda(Cu K alpha) = 1.54178 A, mu = 0.58 mm-1, F(000) = 640, T = 293 K, R = 0.033 for 1849 unique observed reflections. The molecular conformation of 5 beta-dihydrotestosterone shows the strong bending typical of 5 beta-steroids: the bowing angle of the A ring, relative to the remainder of the steroid, is 65.1 degrees. Bowing shortens the distance between the terminal O atoms, O(3) and O(17), to 9.824 (2) A which is ca 1 A shorter than was observed in 5 alpha-dihydrotestosterone and testosterone. The effects of both the bowing and the shorter separation between O(3) and O(17) may explain a difference in the affinity of 5 beta-dihydrotestosterone for the dexamethasone binding site on membranes compared to that of the other two compounds. A unique conformational feature of 5 beta-dihydrotestosterone is the flattening of the A ring on the side containing the C(3)--C(4) bond; this may be due to the combination of the 3-oxo substitution and the 5 beta-configuration.