Direct observation of protein solvation and discrete disorder with experimental crystallographic phases.

A complete and accurate set of experimental crystallographic phases to a resolution of 1.8 angstroms was obtained for a 230-residue dimeric fragment of rat mannose-binding protein A with the use of multiwavelength anomalous dispersion (MAD) phasing. An accurate image of the crystal structure could thus be obtained without resort to phases calculated from a model. Partially reduced disulfide bonds, local disorder, and differences in the mobility of chemically equivalent molecules are apparent in the experimental electron density map. A solvation layer is visible that includes well-ordered sites of hydration around polar and charged protein atoms, as well as diffuse, partially disordered solvent shells around exposed hydrophobic groups. Because the experimental phases and the resulting electron density map are free from the influence of a model, they provide a stringent test of theoretical models of macromolecular solvation, motion, and conformational heterogeneity.

Ethnic, clinical and immunological factors in systemic lupus erythematosus and the development of lupus nephritis: results from a multi-ethnic New Zealand cohort.

The aim of this study was to identify risk factors for lupus nephritis including clinical, laboratory, and ethnic factors in a cohort of lupus patients in New Zealand. A retrospective study of patients from two teaching hospitals in Auckland, New Zealand. Patients were selected if they had attended as either an inpatient, or a rheumatology outpatient between 2000 and 2005. 170 patients had SLE according to ACR classification. Lupus nephritis (LN) was diagnosed according to ACR criteria. Clinical, laboratory, and ethnic data were gathered from the patient notes. Twenty-four patients had LN at diagnosis and 32 patients developed LN after diagnosis. LN was associated with serositis (P = 0.008), cutaneous vasculitis (P = 0.026), anaemia (P = 0.005), CRP elevation >6 months (P < 0.001), hypocomplementaemia >6 months (P < 0.0001). Patients with elevated doublestranded DNA (dsDNA) (>5 x normal) were more likely to develop type IV LN (P = 0.0096). Forty-one percent of patients were Caucasian, 12% Maori, 23% Pacific People, 16% Asian, 6% Indian. Maori patients with SLE (odds ratio (OR) = 8.47, 95% confidence interval (CI) = 2.11-33.96, P = 0.002), and Pacific People (OR = 3.11, 95% CI = 1.29-11.48, P = 0.014) had increased risk for developing LN. Anaemia at presentation (hazard ratio (HR) 3.2, 95% CI = 1.4-7.1, P = 0.004), and low complement >6 months (HR = 3.4, 95% CI = 1.4-8.7, P = 0.008) were independent risk factors for developing LN after SLE diagnosis. In New Zealand, Pacific People and Maori patients with SLE have a higher incidence of LN, and patients with anaemia and hypocomplementaemia are more likely to develop LN after diagnosis. Patients with high dsDNA levels are more likely to develop Type IV lupus nephritis.

A database study of nonbonded intramolecular sulfur-nucleophile contacts.

A search of the Cambridge Structural Database (1991, version 4.5) was performed to investigate nonbonded intramolecular 1,4 S...O close contacts of the kind seen in the thiazole nucleoside tiazofurin and other classes of compounds. The search yielded 362 structures with 1,4 S...O connectivity. S...O distances in 70% of these structures were less than the sum of the sulfur and oxygen van der Waals radii. Findings indicate that 1,4 S...O close contacts are common and so probably result from intramolecular interactions rather than from external crystal packing forces. A structure containing a sulfur atom in a conjugated ring system is more likely to exhibit 1,4 S...O close contacts than a structure containing a sulfur atom in an unconjugated and/or acyclic environment. Sulfur-nitrogen contacts were also investigated and were found to show similar properties. These results are consistent with findings from previous quantum-chemical-based studies performed on model fragments [Burling & Goldstein (1992). J. Am. Chem. Soc. 114, 2313-2320].

Structures of the 2',3'-dideoxy and 2',3'-didehydro-2',3'-dideoxy analogs of tiazofurin.

2',3'-Dideoxytiazofurin [2-(2',3'-dideoxy-beta-D-glycero-pentafuranosyl)thiazole-4- carboxamide]hemihydrate (1), C9H12N2O3S.1/2H2O, Mr = 237.3, monoclinic, C2, a = 23.141 (2), b = 5.912 (1), c = 8.252 (1) A, beta = 90.71 (1) degrees, V = 1128.9 (4) A3, Z = 4, Dx = 1.396 g cm-3, Cu K alpha, lambda = 1.54178 A, mu = 25.0 cm-1, F(000) = 500, T = 295 K, R = 0.0319 for all 1316 unique reflections. 2',3'-Didehydro-2',3'-dideoxytiazofurin [2-(2',3'-dideoxy-beta-D-glyceropent-2-enofuranosyl)thiazole -4-carboxamide] (2), C9H10N2O3S, Mr = 226.3, orthorhombic, P2(1)2(1)2(1), a = 22.172 (2), b = 8.019 (1), c = 5.991 (1) A, V = 1065.2 (4) A3, Z = 4, Dx = 1.411 g cm-3, Cu K alpha, lambda = 1.54178 A, mu = 25.9 cm-1, F(000) = 472, T = 295 K, R = 0.0344 for all 957 unique reflections. Both structures show a close contact between the thiazole S and the pentose O(1') atoms. S...O(1') distances are 2.834 (2) A in (1) and 2.835 (1) A in (2), resulting from C-glycosidic torsion angles of 14.1 (2) and 5.2 (3) degrees respectively. This unusual feature is conserved in the crystal structures of other thiazole nucleosides [Goldstein, Mao & Marquez (1988). J. Med. Chem. 31, 1026-1031].

Structures of the 4-cyano and 4-methylamidate analogs of tiazofurin.

4-Cyanotiazofurin [2-(beta-D-ribofuranosyl)thiazole-4-carbonitrile, (1)], C9H10N2O4S, M(r) = 242.3, monoclinic, P2(1), a = 7.329(1), b = 8.295 (1), c = 8.697(1) A, beta = 90.90 (1) degree, V = 528.7(1) A3, Z = 2, Dx = 1.52 g cm-3, Cu K alpha, lambda = 1.54178 A, mu = 27.2 cm-1, F(000) = 252, T = 293 K, R = 0.0487 for all 1171 unique reflections. 4-Methylamidatetiazofurin [methyl 2-(beta-D-ribofuranosyl)thiazole-4-carboximidate, (2)], C10H14N2O5S, M(r) = 274.3, orthorhombic, P2(1)2(1)2(1), a = 8.596(1), b = 11.060(1), c = 26.064(1) A, V = 2478.1(2) A3, Z = 8, Dx = 1.47 g cm-3, Cu K alpha, lambda = 1.54178 A, mu = 24.5 cm-1, F(000) = 1152, T = 293 K, R = 0.0374 for all 2902 unique reflections. Compound (2) crystallizes with two crystallographic unique structures in the asymmetric unit [(2a) and (2b)]. All three structures show a close contact between the thiazole sulfur and the pentose oxygen O(1'). S...O(1') distances are 2.936 (3) A in (1), 2.773 (2) A in (2a) and 2.878 (2) A in (2b), resulting from C-glycosidic torsion angles of 34.5 (4), 15.6 (3) and 27.2 (3) degrees respectively. This interesting feature is conserved in the crystal structures of other thiazole nucleosides [Burling & Goldstein (1992).

Inhibition of human immunodeficiency virus type 1 infectivity by the gp41 core: role of a conserved hydrophobic cavity in membrane fusion.

The gp41 envelope protein of human immunodeficiency virus type 1 (HIV-1) contains an alpha-helical core structure responsible for mediating membrane fusion during viral entry. Recent studies suggest that a conserved hydrophobic cavity in the coiled coil of this core plays a distinctive structural role in maintaining the fusogenic conformation of the gp41 molecule. Here we investigated the importance of this cavity in determining the structure and biological activity of the gp41 core by using the N34(L6)C28 model. The high-resolution crystal structures of N34(L6)C28 of two HIV-1 gp41 fusion-defective mutants reveal that each mutant sequence is accommodated in the six-helix bundle structure by forming the cavity with different sets of atoms. Remarkably, the mutant N34(L6)C28 cores are highly effective inhibitors of HIV-1 infection, with 5- to 16-fold greater activity than the wild-type molecule. The enhanced inhibitory activity by fusion-defective mutations correlates with local structural perturbations close to the cavity that destabilize the six-helix bundle. Taken together, these results indicate that the conserved hydrophobic coiled-coil cavity in the gp41 core is critical for HIV-1 entry and its inhibition and provides a potential antiviral drug target.

Structure of Escherichia coli uridine phosphorylase at 2.0 A.

The 2.0 A crystal structure has been determined for Escherichia coli uridine phosphorylase (UP), an essential enzyme in nucleotide biosynthesis that catalyzes the phosphorolytic cleavage of the C-N glycosidic bond of uridine to ribose-1-phosphate and uracil. The structure determination of two independent monomers in the asymmetric unit revealed the residue composition and atomic details of the apo configurations of each active site. The native hexameric UP enzyme was revealed by applying threefold crystallographic symmetry to the contents of the asymmetric unit. The 2.0 A model reveals a closer structural relationship to other nucleotide phosphorylase enzymes than was previously appreciated.