Benchmarking TriadAb using targets from the second antibody modeling assessment.

Computational modeling and design of antibodies has become an integral part of today's research and development in antibody therapeutics. Here we describe the Triad Antibody Homology Modeling (TriadAb) package, a functionality of the Triad protein design platform that predicts the structure of any heavy and light chain sequences of an antibody Fv domain using template-based modeling. To gauge the performance of TriadAb, we benchmarked against the results of the Second Antibody Modeling Assessment (AMA-II). On average, TriadAb produced main-chain carbonyl root-mean-square deviations between models and experimentally determined structures at 1.10 Å, 1.45 Å, 1.41 Å, 3.04 Å, 1.47 Å, 1.27 Å, 1.63 Å in the framework and the six complementarity-determining regions (H1, H2, H3, L1, L2, L3), respectively. The inaugural results are comparable to those reported in AMA-II, corroborating with our internal bench-based experiences that models generated using TriadAb are sufficiently accurate and useful for antibody engineering using the sequence design capabilities provided by Triad.

Attempts to develop an enzyme converting DHIV to KIV.

Dihydroxy-acid dehydratase (DHAD) catalyzes the dehydration of R-2,3-dihydroxyisovalerate (DHIV) to 2-ketoisovalerate (KIV) using an Fe-S cluster as a cofactor, which is sensitive to oxidation and expensive to synthesize. In contrast, sugar acid dehydratases catalyze the same chemical reactions using a magnesium ion. Here, we attempted to substitute the high-cost DHAD with a cost-efficient engineered sugar acid dehydratase using computational protein design (CPD). First, we tried without success to modify the binding pocket of a sugar acid dehydratase to accommodate the smaller, more hydrophobic DHIV. Then, we used a chemically activated substrate analog to react with sugar acid dehydratases or other enolase superfamily enzymes. Mandelate racemase from Pseudomonas putida (PpManR) and the putative sugar acid dehydratase from Salmonella typhimurium (StPutD) showed beta-elimination activity towards chlorolactate (CLD). CPD combined with medium-throughput selection improved the PpManR kcat/KM for CLD by four-fold. However, these enzyme variants did not show dehydration activity towards DHIV. Lastly, assuming phosphorylation could also be a good activation mechanism, we found that mevalonate-3-kinase (M3K) from Picrophilus torridus (PtM3K) exhibited adenosine triphosphate (ATP) hydrolysis activity when mixed with DHIV, indicating phosphorylation activity towards DHIV. Engineering PpManR or StPutD to accept 3-phospho-DHIV as a substrate was performed, but no variants with the desired activity were obtained.

Bacillus subtilis spore display of laccase for evolution under extreme conditions of high concentrations of organic solvent.

Protein libraries were displayed on the spore coat of Bacillus subtilis, and this method was demonstrated as a tool for directed evolution under extreme conditions. Escherichia coli, yeast, and phage display suffer from protein folding, and viability issues. On the other hand, spores avoid folding concerns by the natural sporulation process, and they remain viable under harsh chemical and physical environments. The naturally occurring B. subtilis spore coat protein, CotA, was evolved for improved activity under conditions of high organic solvent concentrations. CotA is a laccase, which is a copper-containing oxidase enzyme. A CotA library was expressed on the spore coat, and ∼ 3000 clones were screened at 60% dimethyl sulfoxide (DMSO). A Thr480Ala variant (Thr480Ala-CotA) was identified that was 2.38-fold more active than the wild-type CotA. In addition, Thr480Ala-CotA was more active with different concentrations of DMSO ranging from 0 to 70%. The mutant was also found to be more active compared with the wild-type CotA in different concentrations of methanol, ethanol, and acetonitrile.

CCR5 is essential for NK cell trafficking and host survival following Toxoplasma gondii infection.

The host response to intracellular pathogens requires the coordinated action of both the innate and acquired immune systems. Chemokines play a critical role in the trafficking of immune cells and transitioning an innate immune response into an acquired response. We analyzed the host response of mice deficient in the chemokine receptor CCR5 following infection with the intracellular protozoan parasite Toxoplasma gondii. We found that CCR5 controls recruitment of natural killer (NK) cells into infected tissues. Without this influx of NK cells, tissues from CCR5-deficient (CCR5-/-) mice were less able to generate an inflammatory response, had decreased chemokine and interferon gamma production, and had higher parasite burden. As a result, CCR5-/- mice were more susceptible to infection with T. gondii but were less susceptible to the immune-mediated tissue injury seen in certain inbred strains. Adoptive transfer of CCR5+/+ NK cells into CCR5-/- mice restored their ability to survive lethal T. gondii infection and demonstrated that CCR5 is required for NK cell homing into infected liver and spleen. This study establishes CCR5 as a critical receptor guiding NK cell trafficking in host defense.

Coinfection modulates inflammatory responses and clinical outcome of Helicobacter felis and Toxoplasma gondii infections.

The host immune response plays a critical role in determining disease manifestations of chronic infections. Inadequate immune response may fail to control infection, although in other cases the specific immune response may be the cause of tissue damage and disease. The majority of patients with chronic infections are infected by more than one organism yet the interaction between multiple active infections is not known, nor is the impact on disease outcome clear. Using the BALB/c strain of mice, we show that Toxoplasma gondii infection in a host infected with Helicobacter felis alters the natural outcome of T. gondii infection, allowing uncontrolled tachyzoite replication and severe organ damage. Survival rates decrease from 95% in T. gondii infection alone to 50% in dual-infected mice. In addition, infection with T. gondii alters the specific H. felis immune response, converting a previously resistant host to a susceptible phenotype. Gastric mucosal IFN-gamma and IL-12 were significantly elevated and IL-10 substantially reduced in dual-infected mice. These changes were associated with severe gastric mucosal inflammation, parietal cell loss, atrophy, and metaplastic cell changes. These data demonstrate the profound interactions between the immune response to unrelated organisms, and suggest these types of interactions my impact clinical disease.

CD1d-restricted T cells regulate dendritic cell function and antitumor immunity in a granulocyte-macrophage colony-stimulating factor-dependent fashion.

CD1d-restricted T cells contribute to tumor protection, but their precise roles remain unclear. Here we show that tumor cells engineered to secrete granulocyte-macrophage colony-stimulating factor induce the expansion of CD1d-restricted T cells through a mechanism that involves CD1d and macrophage inflammatory protein 2 expression by CD8 alpha-, CD11c+ dendritic cells (DCs). The antitumor immunity stimulated by vaccination with irradiated, granulocyte-macrophage colony-stimulating factor-secreting tumor cells was abrogated in CD1d- and J alpha 281-deficient mice, revealing a critical role for CD1d-restricted T cells in this response. The loss of antitumor immunity was associated with impaired tumor-induced T helper 2 cytokine production, although IFN-gamma secretion and cytotoxicity were preserved. DCs from immunized CD1d-deficient mice showed compromised maturation and function. Together, these results delineate a role for CD1d-restricted T cell-DC cross talk in the shaping of antitumor immunity.