Hybrid-lipid Coated Silver Nanoparticles as an Antimicrobial

Silver has been known to be an antimicrobial for hundreds of years, but wasn’t thought to be useful in the medical field until the 1960’s. In more recent years people have been designing different methods of synthesis for silver nanoparticles, yet none of these methods prevent the oxidized silver (Ag+), which is toxic. As the use of silver nano materials for antimicrobial activity has expanded there has been an increase in interest in the medical field, and how silver nanoparticles can be used as an antimicrobial without having toxic effects. While there is a large availability of silver nanoparticles (AgNp’s) design strategies for controlling the rate of release of Ag+ is not well defined. Having well defined design strategies for release rate can help provide control for items that need both slow and quick release such as mesh, bandages, catheters, and other medical tubing. Consequently, there is a gap in our understanding of how to control the release rate of silver for the purpose of controlled release of Ag+, and therefore be stabilized and used for a range of antimicrobial applications. Because of the critical need for non-toxic antimicrobial agents that can target and kill bacteria in medical implants such as mesh and tubing, this study is of significant interest. With the increased interest in nanoparticles as an antimicrobial this has led us to the research question: How does surface chemistry affect the antimicrobial abilities of AgNp’s? Within this question we have a subset of questions this research should be able to answer; Can the AgNp’s successfully kill without releasing silver? How does shape and size affect the killing ability of the nanoparticles? How does varying Ag+ release rate affect killing ability

Crystal Structure of Fosfomycin Resistance Kinase FomA from Streptomyces wedmorensis*S⃞

The fosfomycin resistance protein FomA inactivates fosfomycin by phosphorylation of the phosphonate group of the antibiotic in the presence of ATP and Mg(II). We report the crystal structure of FomA from the fosfomycin biosynthetic gene cluster of Streptomyces wedmorensis in complex with diphosphate and in ternary complex with the nonhydrolyzable ATP analog adenosine 5′-(β,γ-imido)-triphosphate (AMPPNP), Mg(II), and fosfomycin, at 1.53 and 2.2Å resolution, respectively. The polypeptide exhibits an open αβα sandwich fold characteristic for the amino acid kinase family of enzymes. The diphosphate complex shows significant disorder in loops surrounding the active site. As a result, the nucleotide-binding site is wide open. Binding of the substrates is followed by the partial closure of the active site and ordering of the α2-helix. Structural comparison with N-acetyl-l-glutamate kinase shows several similarities in the site of phosphoryl transfer: 1) preservation of architecture of the catalytical amino acids of N-acetyl-l-glutamate kinase (Lys9, Lys216, and Asp150 in FomA); 2) good superposition of the phosphate acceptor groups of the substrates, and 3) good superposition of the diphosphate molecule with the β- and γ-phosphates of AMPPNP, suggesting that the reaction could proceed by an associative in-line mechanism. However, differences in conformations of the triphosphate moiety of AMPPNP molecules, the long distance (5.1Å) between the phosphate acceptor and donor groups in FomA, and involvement of Lys18 instead of Lys9 in binding with the γ-phosphate may indicate a different reaction mechanism. The present work identifies the active site residues of FomA responsible for substrate binding and specificity and proposes their roles in catalysis

The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis.

There is enormous interest in studying HIV pathogenesis for improving the treatment of patients with HIV infection. HIV infection has become one of the best-studied systems for understanding how a virus can hijack a cell. To help facilitate discovery, we previously built HIVToolbox, a web system for visual data mining. The original HIVToolbox integrated information for HIV protein sequence, structure, functional sites, and sequence conservation. This web system has been used for almost 40,000 searches. We report improvements to HIVToolbox including new functions and workflows, data updates, and updates for ease of use. HIVToolbox2, is an improvement over HIVToolbox with new functions. HIVToolbox2 has new functionalities focused on HIV pathogenesis including drug-binding sites, drug-resistance mutations, and immune epitopes. The integrated, interactive view enables visual mining to generate hypotheses that are not readily revealed by other approaches. Most HIV proteins form multimers, and there are posttranslational modification and protein-protein interaction sites at many of these multimerization interfaces. Analysis of protease drug binding sites reveals an anatomy of drug resistance with different types of drug-resistance mutations regionally localized on the surface of protease. Some of these drug-resistance mutations have a high prevalence in specific HIV-1 M subtypes. Finally, consolidation of Tat functional sites reveals a hotspot region where there appear to be 30 interactions or posttranslational modifications. A cursory analysis with HIVToolbox2 has helped to identify several global patterns for HIV proteins. An initial analysis with this tool identifies homomultimerization of almost all HIV proteins, functional sites that overlap with multimerization sites, a global drug resistance anatomy for HIV protease, and specific distributions of some DRMs in specific HIV M subtypes. HIVToolbox2 is an open-access web application available at [http://hivtoolbox2.bio-toolkit.com]

The Geogenomic Mutational Atlas of Pathogens (GoMAP) web system.

We present a new approach for pathogen surveillance we call Geogenomics. Geogenomics examines the geographic distribution of the genomes of pathogens, with a particular emphasis on those mutations that give rise to drug resistance. We engineered a new web system called Geogenomic Mutational Atlas of Pathogens (GoMAP) that enables investigation of the global distribution of individual drug resistance mutations. As a test case we examined mutations associated with HIV resistance to FDA-approved antiretroviral drugs. GoMAP-HIV makes use of existing public drug resistance and HIV protein sequence data to examine the distribution of 872 drug resistance mutations in ∼ 502,000 sequences for many countries in the world. We also implemented a broadened classification scheme for HIV drug resistance mutations. Several patterns for geographic distributions of resistance mutations were identified by visual mining using this web tool. GoMAP-HIV is an open access web application available at http://www.bio-toolkit.com/GoMap/project

Multimerization of HIV proteins.

<p>*Bolded residues are known multimerization inhibitors.</p

Protease DRM landscape.

<p>A collection of DRM surface plots for HIV protease generated with HIVToolbox2. All plots are for a structure of Amprenavir (ball and stick) bound to one subunit of protease (1HPV, chain A). The top-left panel shows functional sites and the adjacent panel shows all known immune epitopes from the IEDB ids 32326, 40375, 64343, and 71361. All other panels show resistance to different FDA-approved HIV protease inhibitors. The last panel shows a compendium of DRMs identify regions of the protease with different types of DRMs. The coloring of DRMs is as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098810#pone-0098810-g002" target="_blank"><b>Fig. 2</b></a>.</p