A primer to scaffolded DNA origami

Molecular self-assembly with scaffolded DNA origami enables building custom-shaped nanometer-scale objects with molecular weights in the megadalton regime. Here we provide a practical guide for design and assembly of scaffolded DNA origami objects. We also introduce a computational tool for predicting the structure of DNA origami objects and provide information on the conditions under which DNA origami objects can be expected to maintain their structure.     

Comparing global models of terrestrial net primary productivity (NPP): analysis of the seasonal atmospheric CO2 signal

Eight terrestrial biospheric models (TBMs) calculating the monthly distributions of both net primary productivity (NPP) and soil heterotrophic respiration (R_H) in the Potsdam NPP Model Intercomparison workshop are used to simulate seasonal patterns of atmospheric CO₂ concentration. For each model, we used net ecosystem productivity (NEP = NPP – R_H) as the source function in the TM2 atmospheric transport model from the Max-Planck Institute for Meteorology. Comparing the simulated concentration fields with detrended measurements from 25 monitoring stations spread over the world, we found that the decreasing seasonal amplitude from north to south is rather well reproduced by all the models, though the amplitudes are slightly too low in the north. The agreement between the simulated and observed seasonality is good in the northern hemisphere, but poor in the southern hemisphere, even when the ocean is accounted for. Based on a Fourier analysis of the calculated zonal atmospheric signals, tropical NEP plays a key role in the seasonal cycle of the atmospheric CO₂ in the whole southern hemisphere. The relatively poor match between measured and predicted atmospheric CO₂ in this hemisphere suggests problems with all the models. The simulation of water relations, a dominant regulator of NEP in the tropics, is a leading candidate for the source of these problems.     

Structure, Evolutionary Conservation, and Conformational Dynamics of Homo sapiens Fascin-1, an F-actin Crosslinking Protein

Eukaryotes have several highly conserved actin-binding proteins that crosslink filamentous actin into compact ordered bundles present in distinct cytoskeletal processes, including microvilli, stereocilia and filopodia. Fascin is an actin-binding protein that is present predominantly in filopodia, which are believed to play a central role in normal and aberrant cell migration. An important outstanding question regards the molecular basis for the unique localization and functional properties of fascin compared with other actin crosslinking proteins. Here, we present the crystal structure of full-length Homo sapiens fascin-1, and examine its packing, conformational flexibility, and evolutionary sequence conservation. The structure reveals a novel arrangement of four tandem β-trefoil domains that form a bi-lobed structure with approximate pseudo 2-fold symmetry. Each lobe has internal approximate pseudo 2-fold and pseudo 3-fold symmetry axes that are approximately perpendicular, with β-hairpin triplets located symmetrically on opposite sides of each lobe that mutational data suggest are actin-binding domains. Sequence conservation analysis confirms the importance of hydrophobic core residues that stabilize the β-trefoil fold, as well as interfacial residues that are likely to stabilize the overall fascin molecule. Sequence conservation also indicates highly conserved surface patches near the putative actin-binding domains of fascin, which conformational dynamics analysis suggests to be coupled via an allosteric mechanism that might have important functional implications for F-actin crosslinking by fascin.     

A finite element framework for computation of protein normal modes and mechanical response

A computational framework based on the Finite Element Method is presented to calculate the normal modes and mechanical response of proteins and their supramolecular assemblies. Motivated by elastic network models, proteins are treated as continuum elastic solids with molecular volume defined by their solvent-excluded surface. The discretized Finite Element representation is obtained using a surface simplification algorithm that facilitates the generation of models of arbitrary prescribed spatial resolution. The procedure is applied to a mutant of T4 phage lysozyme, G-actin, syntenin, cytochrome-c', beta-tubulin, and the supramolecular assembly filamentous actin (F-actin). Equilibrium thermal fluctuations of alpha-carbon atoms and their inter-residue correlations compare favorably with all-atom-based results, the Rotational-Translational Block procedure, and experiment. Additionally, the free vibration and compressive buckling responses of F-actin are in quantitative agreement with experiment. The proposed methodology is applicable to any protein or protein assembly and facilitates the incorporation of specific atomic-level interactions, including aqueous-electrolyte-mediated electrostatic effects and solvent damping. The procedure is equally applicable to proteins with known atomic coordinates as it is to electron density maps of proteins, protein complexes, and supramolecular assemblies of unknown atomic structure.     

Initial antigen encounter programs CD8+ T cells competent to develop into memory cells that are activated in an antigen-free, IL-7- and IL-15-rich environment

Although much is known concerning the immunobiology of CD8+ T memory cells, the initial events favoring the generation of CD8+ T memory cells remain poorly defined. Using a culture system that yields memory-like CD8+ T cells, we show that 1 day after Ag encounter, Ag-activated T cells developed into memory-like T cells, but this optimally occurred 3 days after Ag encounter. Key phenotypic, functional, and molecular properties that typify central memory T cells were expressed within 48 h when the activated CD8+ T cells were cultured with IL-7 or IL-15 in the absence of Ag or following transfer into normal mice. These data support a model whereby Ag activation of naive CD8+ T cells not only programs effector cell expansion and contraction but the potential to develop into a memory cell which ensues in an Ag-free environment containing IL-7 or IL-15.     

Strategy to sequence the genome of Corynebacterium glutamicum ATCC 13032: use of a cosmid and a bacterial artificial chromosome library

The initial strategy of the Corynebacterium glutamicum genome project was to sequence overlapping inserts of an ordered cosmid library. High-density colony grids of approximately 28 genome equivalents were used for the identification of overlapping clones by Southern hybridization. Altogether 18 contiguous genomic segments comprising 95 overlapping cosmids were assembled. Systematic shotgun sequencing of the assembled cosmid set revealed that only 2.84 Mb (86.6%) of the C. glutamicum genome were represented by the cosmid library. To obtain a complete genome coverage, a bacterial artificial chromosome (BAC) library of the C. glutamicum chromosome was constructed in pBeloBAC11 and used for genome mapping. The BAC library consists of 3168 BACs and represents a theoretical 63-fold coverage of the C. glutamicum genome (3.28 Mb). Southern screening of 2304 BAC clones with PCR-amplified chromosomal markers and subsequent insert terminal sequencing allowed the identification of 119 BACs covering the entire chromosome of C. glutamicum. The minimal set representing a 100% genome coverage contains 44 unique BAC clones with an average overlap of 22 kb. A total of 21 BACs represented linking clones between previously sequenced cosmid contigs and provided a valuable tool for completing the genome sequence of C. glutamicum.