Preprocessing of rotamers for protein design calculations

We have developed a process that significantly reduces the number of rotamers in computational protein design calculations. This process, which we call Vegas, results in dramatic computational performance increases when used with algorithms based on the dead-end elimination (DEE) theorem. Vegas estimates the energy of each rotamer at each position by fixing each rotamer in turn and utilizing various search algorithms to optimize the remaining positions. Algorithms used for this context specific optimization can include Monte Carlo, self-consistent mean field, and the evaluation of an expression that generates a lower bound energy for the fixed rotamer. Rotamers with energies above a user-defined cutoff value are eliminated. We found that using Vegas to preprocess rotamers significantly reduced the calculation time of subsequent DEE-based algorithms while retaining the global minimum energy conformation. For a full boundary design of a 51 amino acid fragment of engrailed homeodomain, the total calculation time was reduced by 12-fold.     

Exact rotamer optimization for protein design

Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to perform previously intractable designs of entire protein core, surface, or boundary regions. Computational demonstrations include a full core design of the variable domains of the light and heavy chains of catalytic antibody 48G7 FAB with 74 residues and 10(128) conformations, a full core/boundary design of the beta1 domain of protein G with 25 residues and 10(53) conformations, and a full surface design of the beta1 domain of protein G with 27 residues and 10(60) conformations. In addition, a full sequence design of the beta1 domain of protein G is used to demonstrate the strong dependence of algorithm performance on the exact form of the potential function and the fidelity of the rotamer library. These results emphasize that search algorithm performance for protein design can only be meaningfully evaluated on physical models that have been subjected to experimental scrutiny. The new algorithm greatly facilitates ongoing efforts to engineer increasingly complex protein features.     

Phage-display selection of a human single-chain fv antibody highly specific for melanoma and breast cancer cells using a chemoenzymatically synthesized G(M3)-carbohydrate antigen

Overexpression of the cell-surface glycosphingolipid G(M3) is associated with a number of different cancers, including those of the skin, colon, breast, and lung. Antibodies against the G(M3) epitope have potential application as therapeutic agents in the treatment of these cancers. We describe the chemoenzymatic synthesis of two G(M3)-derived reagents and their use in the panning of a phage-displayed human single-chain Fv (scFv) antibody library derived from the blood of cancer patients. Three scFv-phage clones, GM3A6, GM3A8, and GM3A15, were selected for recombinant expression and were characterized using BIAcore and flow cytometry. BIAcore measurements using the purified, soluble scFvs yielded dissociation constants (K(d)) ranging from 4.2 x 10(-7) to 2.1 x 10(-5) M. Flow cytometry was used to evaluate the ability of each scFv to discriminate between normal human cells (human dermal fibroblast, HDFa), melanoma cells (HMV-1, M21, and C-8161), and breast cancer cells (BCM-1, BCM-2, and BMS). GM3A6 displayed cross-reactivity with normal cells, as well as tumor cells, and GM3A15 possessed little or no binding activity toward any of the cell lines tested. However, GM3A8 bound to five of the six tumor cell lines and showed no measurable reactivity against the HDFa cells. Hence, we have demonstrated that a synthetic G(M3) panning reagent can be used to isolate a fully human scFv that is highly specific for native G(M3) on the surface of tumor cells. The result is a significant step toward effective immunotherapies for the treatment of cancer.     

Vapoluminescent Behavior and the Single-Crystal-to-Single-Crystal Transformations of Chloroform Solvates of [Au2(μ-1,2-bis(diphenylarsino)ethane)2](AsF6)2

The mono- and di-chloroform solvates of [Au₂(μ-1,2-bis(diphenylarsino)ethane)₂](AsF₆)₂ undergo single-crystal-to-single-crystal transformations that result in gain (over 12 hours) or slow loss (over five years) of only one chloroform molecule. The change in solvation results in changes in the structure and luminescence of the digold cation. The cation consists of a pair of slightly bent As-Au-As units that are connected through the two bridging dpae ligands and by aurophilic interactions with Au⋅⋅⋅Au contacts of 3.05152(15) Å in the disolvate or 2.9570(5) Å in the monosolvate.     

The synthesis of luminescent lanthanide-based chemosensors for the detection of zinc ions

Herein, we report the synthesis of two lanthanide-based chemosensors, Tb-5 and Eu-6, designed to sense free zinc ions (Zn²⁺) in aqueous solutions. The Tb-5 complex features a bis(2-pyridinylmethyl)amine moiety as a zinc(II)-responsive lanthanide-sensitising ‘antenna’, while Eu-6 incorporates a quinoline-based moiety for this purpose. Luminescence enhancements of 210% and 340% are observed upon addition of Zn²⁺ ions to Tb-5 and Eu-6, respectively. Both sensors are selective for Zn²⁺ ions over several other cations of environmental significance.     

The contribution of 2N photon absorption in C(γ,2N) reactions for Eγ = 150–400 MeV

The ¹²C(γ,pn) and ¹²C(γ,pp) reactions have been studied using tagged photons of energy E_γ = 150–400 MeV. Recoil momentum distributions are compared to the results of Monte Carlo calculations based on a two-nucleon photon absorption model and two different phase space models. The ¹²C(γ,pn) data at low missing energy are consistent with absorption on 1p² and 1s1p nucleon pairs.     

Anion‐Mediated Effects on the Size and Mechanical Properties of Enzymatically Crosslinked Suckerin Hydrogels

The suckerin family of proteins, identified from the squid sucker ring teeth assembly, offers unique mechanical properties and potential advantages over other natural biomaterials. In this study, a small suckerin isoform, suckerin‐12, is used to create enzymatically crosslinked, macro‐scale hydrogels. Upon exposure to specific salt conditions, suckerin‐12 hydrogels contracted into a condensed state where mechanical properties are found to be modulated by the salt anion present. The rate of contraction is found to correlate well with the kosmotropic arm of the Hofmeister anion series. However, the observed changes in hydrogel mechanical properties are better explained by the ability of the salt to neutralize charges in suckerin‐12 by deprotonization or charge screening. Thus, by altering the anions in the condensing salt solution, it is possible to tune the mechanical properties of suckerin‐12 hydrogels. The potential for suckerins to add new properties to materials based on naturally‐derived proteins is highlighted.