Testing the Validity of Single-Particle Maps at Low and High Resolution.

Single-particle electron cryomicroscopy may be used to determine the structure of biological assemblies by aligning and averaging low-contrast projection images recorded in the electron microscope. Recent progress in both experimental and computational methods has led to higher resolution three-dimensional maps, including for more challenging low molecular weight proteins, and this has highlighted the problems of model bias and over-fitting during iterative refinement that can potentially lead to incorrect map features at low or high resolution. This chapter discusses the principles and practice of specific validation tests that demonstrate the consistency of a 3D map with projection images. In addition, the chapter describes tests that detect over-fitting during refinement and lead to more robust assessment of both global and local map resolution. Application of several of these tests together demonstrates the reliability of single-particle maps that underpins their correct biological interpretation.

Strain-specific antiviral activity of iminosugars against human influenza A viruses.

OBJECTIVES: Drugs that target host cell processes can be employed to complement drugs that specifically target viruses, and iminosugar compounds that inhibit host α-glucosidases have been reported to show antiviral activity against multiple viruses. Here the effect and mechanism of two iminosugar α-glucosidase inhibitors, N-butyl-deoxynojirimycin (NB-DNJ) and N-nonyl-deoxynojirimycin (NN-DNJ), on human influenza A viruses was examined. METHODS: The viruses examined were a recently circulating seasonal influenza A(H3N2) virus strain A/Brisbane/10/2007, an older H3N2 strain A/Udorn/307/72, and A/Lviv/N6/2009, a strain representative of the currently circulating pandemic influenza A(H1N1)pdm09 virus. RESULTS: The inhibitors had the strongest effect on Brisbane/10 and NN-DNJ was more potent than NB-DNJ. Both compounds showed antiviral activity in cell culture against three human influenza A viruses in a strain-specific manner. Consistent with its action as an α-glucosidase inhibitor, NN-DNJ treatment resulted in an altered glycan processing of influenza haemagglutinin (HA) and neuraminidase (NA), confirmed by MS. NN-DNJ treatment was found to reduce the cell surface expression of the H3 subtype HA. The level of sialidase activity of NA was reduced in infected cells, but the addition of exogenous sialidase to the cells did not complement the NN-DNJ-mediated inhibition of virus replication. Using reassortant viruses, the drug susceptibility profile was determined to correlate with the origin of the HA. CONCLUSIONS: NN-DNJ inhibits influenza A virus replication in a strain-specific manner that is dependent on the HA.

Methotrexate combined with isoniazid treatment for latent tuberculosis is well tolerated in patients with rheumatoid arthritis: experience from an urban arthritis clinic.

OBJECTIVES: Reactivation of Mycobacterium tuberculosis (TB) is a significant problem with all available tumour necrosis factor (TNF) antagonists when used to treat rheumatoid arthritis (RA), psoriatic arthritis, psoriasis and other inflammatory diseases. Concerns have been raised regarding the appropriate management of patients with latent TB (LTB) exposure (or active TB infection) before initiating TNF antagonists as the safety data of combined treatment with two potentially hepatotoxic medications, methotrexate (MTX) and isoniazid (INH), is lacking. The goal of this study was to investigate the toxicity of MTX and INH treatment in patients with RA before initiating TNF antagonists. METHODS: To investigate the toxicity of MTX and INH treatment in patients with RA we performed a retrospective chart review of patients seen at the Bellevue Hospital Arthritis Clinic in New York City between 2002 and 2006. Forty-four patients who were concomitantly treated with both drugs were included. The primary outcome investigated was increase in liver function tests (LFT). RESULTS: Transient increases in LFT were seen in 11% of patients, but in no case was this more than twice the upper limit of normal values. All abnormal LFT resolved spontaneously without intervention. In addition, no patient has developed signs or symptoms of TB reactivation. CONCLUSIONS: The use of INH for LTB was well tolerated in patients with RA on a background regimen of MTX. While the risks and benefits of all treatment must always be considered, in our experience the additive risk of INH to MTX in terms of hepatotoxicity was low. None the less it is prudent to follow LFT closely on patients taking this combination.

X-ray crystallographic determination of the structure of the influenza C virus haemagglutinin-esterase-fusion glycoprotein.

The structure of the haemagglutinin-esterase-fusion (HEF) glycoprotein from influenza C virus has been determined to 3.2 A resolution by X-ray crystallography. A synthetic mercury-containing esterase inhibitor and receptor analogue, 9-acetamidosialic acid alpha-thiomethylmercuryglycoside, was designed as the single isomorphous heavy-atom derivative. The asymmetric unit of one crystal form (form I; P4322, a = b = 155.4, c = 414.4 A) contained an HEF trimer. Six mercury sites identifying the three haemagglutination and three esterase sites were located by difference Patterson map analysis of a 6.5 A resolution derivative data set. These positions defined the molecular threefold-symmetry axis of the HEF trimer. A molecular envelope was defined by averaging a 7.0 A resolution electron-density map, phased by single isomorphous replacement (SIR), about the non-crystallographic threefold-symmetry axis. Iterative non-crystallographic symmetry averaging in real space, solvent flattening and histogram matching were used to extend the phases to 3.5 A resolution. Molecular replacement of the model into a second crystal form (form II; P43212, a = b = 217.4, c = 421.4 A) containing two HEF trimers per asymmetric unit permitted iterative ninefold averaging of the electron density. The 3.5 A electron-density map allowed an unambiguous tracing of the polypeptide chain and identification of N-linked carbohydrates. The model has been refined by least squares to 3.2 A resolution (Rfree = 26.7%).

Structure of the haemagglutinin-esterase-fusion glycoprotein of influenza C virus.

The spike glycoproteins of the lipid-enveloped orthomyxoviruses and paramyxoviruses have three functions: to recognize the receptor on the cell surface, to mediate viral fusion with the cell membrane, and to destroy the receptor. In influenza C virus, a single glycoprotein, the haemagglutinin-esterase-fusion (HEF) protein, possesses all three functions. In influenza A and B, the first two activities are mediated by haemagglutinin and the third by a second glycoprotein, neuraminidase. Here we report the crystal structure of the HEF envelope glycoprotein of influenza C virus. We have identified the receptor-binding site and the receptor-destroying enzyme (9-O-acetylesterase) sites, by using receptor analogues. The receptor-binding domain is structurally similar to the sialic acid-binding domain of influenza A haemagglutinin, but binds 9-O-acetylsialic acid. The esterase domain has a structure similar to the esterase from Streptomyces scabies and a brain acetylhydrolase. The receptor domain is inserted into a surface loop of the esterase domain and the esterase domain is inserted into a surface loop of the stem. The stem domain is similar to that of influenza A haemagglutinin, except that the triple-stranded, alpha-helical bundle diverges at both of its ends, and the amino terminus of HEF2, the fusion peptide, is partially exposed. The segregation of HEF's three functions into structurally distinct domains suggests that the entire stem region, including sequences at the amino and carboxy termini of HEF1 which precede the post-translational cleavage site between HEF1 and HEF2, forms an independent fusion domain which is probably derived from an ancestral membrane fusion protein.

Crystallization and preliminary X-ray diffraction studies of the influenza C virus glycoprotein.

Influenza C virus contains a single surface glycoprotein in its lipid envelope which is the hemagglutinin-esterase-fusion glycoprotein (HEF). HEF binds cell-surface receptors, is a receptor-destroying enzyme (a 9-O-acetylesterase), and mediates the fusion of virus and host cell membranes. A bromelain-released soluble form of HEF has been crystallized. Two different tetragonal forms have been identified from crystals with the same morphology [P(1(3))22, a = b = 154.5, c = 414.4 A, and P4(1(3))2(1)2, a = b = 217.4, c = 421.4 A]. Both crystal forms share a common packing scheme. Synchrotron data collection and flash cooling of crystals have been used for high-resolution data collection.

Synthesis and inhibitory properties of a thiomethylmercuric sialic acid with application to the X-ray structure determination of 9-O-acetylsialic acid esterase from influenza C virus.

2-alpha-Thiomethylmercuryl 9-acetamido-9-deoxy-sialoside was prepared and found to inhibit the 9-O-acetylsialic acid esterase from influenza C virus in a competitive manner with a Ki of 4.2 +/- 0.5 mM. The inhibitor is being used in the X-ray determination of the crystal structure of the esterase.