Shape: automatic conformation prediction of carbohydrates using a genetic algorithm

<p>Abstract</p> <p>Background</p> <p>Detailed experimental three dimensional structures of carbohydrates are often difficult to acquire. Molecular modelling and computational conformation prediction are therefore commonly used tools for three dimensional structure studies. Modelling procedures generally require significant training and computing resources, which is often impractical for most experimental chemists and biologists. <monospace>Shape</monospace> has been developed to improve the availability of modelling in this field.</p> <p>Results</p> <p>The <monospace>Shape</monospace> software package has been developed for simplicity of use and conformation prediction performance. A trivial user interface coupled to an efficient genetic algorithm conformation search makes it a powerful tool for automated modelling. Carbohydrates up to a few hundred atoms in size can be investigated on common computer hardware. It has been shown to perform well for the prediction of over four hundred bioactive oligosaccharides, as well as compare favourably with previously published studies on carbohydrate conformation prediction.</p> <p>Conclusion</p> <p>The <monospace>Shape</monospace> fully automated conformation prediction can be used by scientists who lack significant modelling training, and performs well on computing hardware such as laptops and desktops. It can also be deployed on computer clusters for increased capacity. The prediction accuracy under the default settings is good, as it agrees well with experimental data and previously published conformation prediction studies. This software is available both as open source and under commercial licenses.</p

Norovirus-glycan interactions

Noroviruses (NVs) are among the most common viral pathogens which target the gastrointestinal (GI) tract and cause severe diarrhea, vomiting and episodes of abdominal cramps with fever. Millions of people around the world get infected with NVs annually, of which 200,000 cases are estimated to be fatal. Yet for decades, the failure of propagating the human NVs in a cell-culture model has hampered NV infection research and consequently treatment and vaccine development. Thus, the research has mainly been focused on epidemiology and studies on the interaction of model virus-like particles (VLPs) with potential host receptors or attachment factors to gain understanding of the first steps of the infection in order to successfully pave the way for effective clinical therapy or prophylaxis. Motivated by this theme, the emphasis of the present work is mainly on protein-carbohydrate interactions of host glycans with NV VLPs. About 80 % of NV outbreaks reported to date are caused by GII.4 genocluster of NVs. Therefore, due to its dominating clinical importance GII.4 NV-like particles and capsid protein dimers are used for in vitro and in silico studies included in the thesis work. NVs have been shown to recognize host histo-blood group antigens (HBGAs) as viral receptors or attachment factors. To investigate the molecular details of interactions of GII.4 NVs with a repertoire of fucosylated HBGAs, molecular dynamics studies were initially carried out based on the crystal structure of B-trisaccharide HBGA in complex with VA387 GII.4 norovirus P dimer. The results, which were later confirmed by crystallographic studies, could explain, on an atomic level, the binding characteristics from a mutagenesis study carried out earlier on the same NV strain. Along with the modelling studies theoretical binding energies were also estimated for different HBGAs binding to VA387 P dimers. The atomic details of binding modes revealed how a single fucose binding site could exploit two different binding modes of the same glycan. This was supported by a literature review of the occurrence of similar fucose binding sites and modes observed in nature for fucose binding lectins and antibodies. One of the objectives of the thesis was to understand the dynamics of virus host interactions at the cell surface membrane, as it holds clues to very early steps of virus infection. Therefore, total internal reflection fluorescent microscopy (TIRFM) was developed to study the binding events of glycosphingolipid (GSL)-containing vesicles to single NV like particles bound to a supported lipid bilayer (SLB). The advantage of this single vesicle binding assay is the ability to analyze the attachment-detachment kinetics both in transient and steady state conditions. Therefore, it enabled us, for the first time, to discriminate between compositionally different GSL-containing vesicles based on their detachment activation energy. This relates directly to the binding strength of the virus-vesicle complex thereby providing new insights into the characteristics of binding virus-like particles to various lipid bound glycans. Moreover, the differences in the distribution of detachment energy of activation for different GSL-containing vesicles were also analyzed. Microdomains or clustered patches of GSLs with or without cholesterol are dynamic integral parts of most of the plasma membranes. Their role has been implicated in virus infection of HIV and influenza virus but not in NVs. However for the first time, NVs were shown to recognize galactosylceramide (GalCer) microdomains in supported lipid bilayers. The atomic details of the binding mode of these interactions are, however, still to be clarified. In conclusion, the thesis describes details of viral protein - host carbohydrate interactions at the molecular level, of relevance for understanding virus infection and design of novel anti-viral strategies