Design of an Optimized Scaffold for Affibody Molecules

Affibody molecules are non-immunoglobulin-derived affinity proteins based on a three-helical bundle protein domain. Here, we describe the design process of an optimized Affibody molecule scaffold with improved properties and a surface distinctly different from that of the parental scaffold. The improvement was achieved by applying an iterative process of amino acid substitutions in the context of the human epidermal growth factor receptor 2 (HER2)-specific Affibody molecule Z_HER2:342. Replacements in the N-terminal region, loop 1, helix 2 and helix 3 were guided by extensive structural modeling using the available structures of the parent Z domain and Affibody molecules. The effect of several single substitutions was analyzed followed by combination of up to 11 different substitutions. The two amino acid substitutions N23T and S33K accounted for the most dramatic improvements, including increased thermal stability with elevated melting temperatures of up to + 12 °C. The optimized scaffold contains 11 amino acid substitutions in the nonbinding surface and is characterized by improved thermal and chemical stability, as well as increased hydrophilicity, and enables generation of identical Affibody molecules both by chemical peptide synthesis and by recombinant bacterial expression. A HER2-specific Affibody tracer, [MMA-DOTA-Cys61]-Z_HER2:2891-Cys (ABY-025), was produced by conjugating MMA-DOTA (maleimide-monoamide-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) to the peptide produced either chemically or in Escherichia coli. ABY-025 showed high affinity and specificity for HER2 (equilibrium dissociation constant, K_D, of 76 pM) and detected HER2 in tissue sections of SKOV-3 xenograft and human breast tumors. The HER2-binding capacity was fully retained after three cycles of heating to 90 °C followed by cooling to room temperature. Furthermore, the binding surfaces of five Affibody molecules targeting other proteins (tumor necrosis factor α, insulin, Taq polymerase, epidermal growth factor receptor or platelet-derived growth factor receptor β) were grafted onto the optimized scaffold, resulting in molecules with improved thermal stability and a more hydrophilic nonbinding surface.     

Synthesis, crystal structure, and magnetic properties of a new tetranuclear Cu(II) Schiff base compound

A new tetranuclear Cu(II) compound [Cu₄(HL)₂(L)₂(ClO₄)₂] (1) was synthesized from the reaction of Cu(ClO₄)₂ · 6H₂O with Schiff base ligand (H₂L) condensed from ethanolamine with 2-hydroxyacetophenone. X-ray diffraction studies revealed that 1 is formed from the self-assembly of two dinuclear units [Cu₂(HL)(L)(ClO₄)] through the doubly phenoxo bridging. The variable temperature magnetic susceptibility measurements were performed between 300 K and 2 K and show χ_MT value for 1 at 300 K is 1.395 cm³ mol⁻¹ K and fall to 0.0459 cm³ mol⁻¹ K at 2 K. These values are smaller than that expected for tetranuclear copper (II) units, indicating antiferromagnetic coupling present in the compound. This result is also confirmed from the DFT calculations.     

Design of a flexible ligand for the construction of a one-dimensional metal-organic coordination polymer

A new ligand LH (where LH = N-(picolinoyl)-biurate) has been prepared and characterized. The presence of three amide linkages make this ligand sufficiently flexible to act as N,N,O donor tridentate blocking ligand in the formation of a one dimensional metal-ligand layer like structure. Reaction of LH and dicyanamide (dca) with Co(NO₃)₂ · 6H₂O gives [CoL(dca)]_n (1). In this compound picolinamide modulated ligand L coordinated the central Co(II) ion in a meridonal-fashion. The single crystal X-ray crystallography revealed that in 1, dca acts as μ_1,5− singly bridging ligand whereas μ_1,5− doubly bridging is the more common type. This gives rise to the 1D undulated waves like structure. The Co(II) centre is surrounded in a distorted square pyramidal coordination geometry. The variable temperature magnetic (VTM) susceptibility measurements show that the global feature of the χ_MT versus T curve for 1 is characteristic of very weak antiferromagnetic interactions through the dicyanamide ligand and between 300 and 5 K the best fit parameter was determined as J = −3.52 cm⁻¹. The X-ray structure, VTM study and UV-Vis spectrum of the compound show that 1 is a low-spin square-pyramidal compound whereas high-spin compounds are more common for the five coordinated cobalt (II) compounds. The X-band EPR spectrum of 1 at room temperature shows only one isotropic band centred at g = 2.08.     

Considerations for ecological reconstruction of historic vegetation: Analysis of the spatial uncertainties in the California Vegetation Type Map dataset

Historical ecological data are valuable for reconstructing early environmental and vegetation community conditions and examining change to vegetation communities and disturbance regimes over decadal and longer temporal scales, but these data are not free from error. We examine the spatial uncertainties associated with 18,000 vegetation plots in the decades-old California Vegetation Type Mapping (VTM) dataset that has been digitized for use in modern ecological analysis. We examine the relationship between plot location error and basemap year, basemap scale, plot elevation, plot slope, and general plot habitat type. Bivariate plots and classification and regression tree analysis (CART) confirm that basemap scale and age are the strongest explanation of total error. Total error in spatial location for all plots ranged from 126.9 m to 462.3 m; plots drawn on 15-min (1:62,500-scale) basemaps had total error ranging from 126 m to 199.7 m, and plots drawn on coarser-scale basemaps (1:125,000-scale) had total errors ranging from 241 m to 461.2 m. Relocation of individual VTM plots is considerably easier for plots originally marked on 1:62,500-scale maps produced after 1904, and more difficult for plots originally marked on 1:125,000-scale maps produced before 1898. Biogeographical analyses that rely less on relocating individual plots, such as environmental niche modeling or multivariate analyses can alleviate some of these concerns, but all researchers using these kinds of data need to consider errors in spatial location of plots. The paper also discusses ways in which the differing spatial error might be reported and visualized by those using the dataset, and how the data might be used in modern environmental niche models.     

Preferential azido bridging regulating the structural aspects in cobalt(III) and copper(II)-Schiff base complexes: Syntheses, magnetostructural correlations and catalytic studies

A tridentate NNO donor Schiff base ligand [(1Z,3E)-3-((pyridin-2-yl)methylimino)-1-phenylbut-1-en-1-ol = LH] in presence of azide ions coordinates with cobalt(II) and copper(II) ions giving rise to three new coordination complexes [Co₂(L)₂(μ_1,1-N₃)₂(N₃)₂] (1), [Cu₂(L)₂(μ_1,3-N₃)]·ClO₄ (2) and [(μ_1,1-N₃)₂Cu₅(μ-OL)₂(μ_1,1-N₃)₄(μ_1,1,1-N₃)₂]_n (3). The complexes have been characterized by elemental analysis, FT-IR, UV-Vis spectral studies, and single crystal X-ray diffraction studies. These complexes demonstrate that under different synthetic conditions the azide ions and the Schiff base ligand (LH) show different coordination modes with cobalt(II) and copper(II) ions, giving rise to unusual dinuclear and polynuclear species (1, 2 and 3) whose structural variations are discussed. Magneto-structural correlation for the very rare singly μ_1,3-N₃ bridged Cu^II-Schiff base dinuclear species (2) has been studied. In addition, the catalytic properties of 1 for alkene oxidation and the general catalase-like activity behavior of 2 have been discussed.     

Enhancing a regional vegetation map with predictive models of dominant plant species in chaparral

Abstract. Data from more than 900 vegetation plots surveyed in the evergreen shrublands of southern California were used to develop predictions of the distributions of eight dominant shrub species for a 3880 km² region. The predictions, based on classification tree (CT) models, were validated using independent field data collected during a vegetation survey conducted in the 1930s. Presence and absence were correctly predicted an average of 75% of the time for the eight species. At the same time, these models minimized false positives, so that presence was predicted in the correct proportion of the cases for most species. The areal proportion of the landscape on which the species were predicted to occur was in the same rank order, and of the same magnitude, as their frequency (proportion of plots in which they occurred) within the field data sets. Predictive maps of species presence were overlaid and combined with an existing regional vegetation map. The shrub species ‘assemblages’ that resulted from this procedure had analogs with vegetation series defined using field data in previous studies. The resulting multiple species map will be used in a landscape simulation model of fire disturbance and succession.