Do scale-free regulatory networks allow more expression than random ones?

In this paper, we compile the network of software packages with regulatory interactions (dependences and conflicts) from Debian GNU/Linux operating system and use it as an analogy for a gene regulatory network. Using a trace-back algorithm we assemble networks from the pool of packages with both scale-free (real data) and exponential (null model) topologies. We record the maximum number of packages that can be functionally installed in the system (i.e., the active network size). We show that scale-free regulatory networks allow a larger active network size than random ones. This result might have implications for the number of expressed genes at steady state. Small genomes with scale-free regulatory topologies could allow much more expression than large genomes with exponential topologies. This may have implications for the dynamics, robustness and evolution of genomes.     

New supramolecular complexes generated from Mn, Fe, Co, Zn, Fe with a bent dipyridyl ligand: Metal- and anion-directed assembly

Assemblies of an angular dipyridyl ligand 2,5-bis(4-pyridyl)-1,3,4-oxadiazole (4-bpo) with a series of metal perchlorate afford five new supramolecular complexes with the general formula of [M(4-bpo)₂(H₂O)₄] · (4-bpo)₂ · (anion) · (solvent), in which M = Mn^II for 1, Fe^II for 2, Co^II for 3, Zn^II for 4, and Fe^III for 5. Although similar molecular structures and compositions are found for these mononuclear complexes, they display two types of supramolecular lattices. Complexes 1, 4 and 5 similarly crystallize in space group P2/n or P2/c. The complex cations, free 4-bpo and lattice water are linked to generate 2D layered frameworks with the aid of hydrogen bonding, and the counter anions are located within and between (also methanol in 5) these 2D arrays. However, complexes 2 and 3 are isostructural in space group . Two types of alternate 2D layers consisting of complex cations and free 4-bpo components, respectively, are observed with the anions and lattice water locating between them. These motifs are interlinked by complicated hydrogen-bonding to form a 3D intercalated network. Moreover, when Co(NO₃)₂ is used instead of Co(ClO₄)₂ in the assembly of 3, a 1D polymeric chain complex {[Co(4-bpo)(H₂O)₂(NO₃)₂](H₂O)₃}_n (6) is generated. These results indicate that the choice of metal ion and anion exerts a significant influence on governing the target complexes. A comparison of the structural features for all metal perchlorate complexes with 4-bpo is also briefly discussed.     

Why is the microtubule lattice helical?

Microtubules polymerize from identical tubulin heterodimers, which form a helical lattice pattern that is the microtubule. This pattern always has left-handed chirality, but it is not known why. But as tubulin, similar to other proteins, evolved for a purpose, the question of the title of this artcile appears to be meaningful. In a computer simulation that explores the 'counterfactual biology' of microtubules without helicity, we demonstrate that these have the same mechanical properties as Nature's microtubules with helicity. Thus only a dynamical reason for helicity is left as potential explanation. We find that helicity solves 'the problem of the blind mason', i.e. how to correctly build a structure, guided only by the shape of the bricks. This answer in turn raises some new questions for researchers to address.     

The heparin III-binding domain of fibronectin (III4–5 repeats) binds to fibronectin and inhibits fibronectin matrix assembly

Fibronectin matrix assembly involves interactions among various regions of the molecule, which contribute to elongation and stabilization of the fibrils. In this study, we examined the possible role of the heparin III domain of fibronectin (repeats III4-5) in fibronectin fibrillogenesis. We show that a recombinant fragment comprising these repeats (FNIII4-5 fragment) blocked fibronectin fibril formation and the incorporation of 125I-fibronectin into cell layers. Binding assays using a biosensor revealed that FNIII4-5 bound fibronectin and the amino-terminal 70 kDa and 29 kDa fragments. It also bound to itself, indicating a previously unidentified self-association site in repeats III4-5. These interactions were specific since FNIII4-5 did not bind to the FNIII7-10 fragment, representing a central region in fibronectin. The fibronectin-binding property of the III4-5 domain, but not its matrix assembly inhibitory function, was apparently cryptic in larger fragments. By mutating the arginine residues in the WTPPRAQITGYRLTVGLTRR proteoglycan-binding sequence (HBP/III5 site) of FNIII4-5 [Moyano, J.V., Carnemolla, B., Albar, J.P., Leprini, A., Gaggero, B., Zardi, L., Garcia-Pardo, A., 1999. Cooperative role for activated alpha4beta1 integrin and chondroitin sulfate proteoglycans in cell adhesion to the heparin III domain of fibronectin. Identification of a novel heparin and cell binding sequence in repeat III5. J. Biol. Chem. 274, 135-142.], we found that the first two arginine residues in HBP/III5 were involved in the fibronectin-binding property of FNIII4-5, while the last two arginine residues in HBP/III5 were required for inhibition of matrix assembly and the binding of 125I-fibronectin to cell layers. Both properties appear to function independently from each other, depending on the conformation of the fibronectin dimer.     

Thiamine diphosphate binds to intermediates in the assembly of adenovirus fiber knob trimers in Escherichia coli

Assembly of the adenovirus (Ad) homotrimeric fiber protein is nucleated by its C-terminal knob domain, which itself can trimerize when expressed as a recombinant protein fragment. The non-interlocked, globular structure of subunits in the knob trimer implies that trimers assemble from prefolded monomers through a dimer intermediate, but these intermediates have not been observed and the mechanism of assembly therefore remains uncharacterized. Here we report that expression of the Ad serotype 2 (Ad2) knob was toxic for thi- strains of Escherichia coli, which are defective in de novo synthesis of thiamine (vitamin B1). Ad2 knob trimers isolated from a thi+ strain copurified through multiple chromatography steps with a small molecule of mass equivalent to that of thiamine diphosphate (ThDP). Mutant analysis did not implicate any specific site for ThDP binding. Our results suggest that ThDP may associate with assembly intermediates and become trapped in assembled trimers, possibly within one of several large cavities that are partially solvent-accessible or buried completely within the trimer interior.     

The Galleria mellonella Hologenome Supports Microbiota-Independent Metabolism of Long-Chain Hydrocarbon Beeswax

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Probing the role of sequence in the assembly of three‐dimensional DNA crystals

DNA is a widely used biopolymer for the construction of nanometer‐scale objects due to its programmability and structural predictability. One long‐standing goal of the DNA nanotechnology field has been the construction of three‐dimensional DNA crystals. We previously determined the X‐ray crystal structure of a DNA 13‐mer that forms a continuously hydrogen bonded three‐dimensional lattice through Watson‐Crick and non‐canonical base pairs. Our current study sets out to understand how the sequence of the Watson‐Crick duplex region influences crystallization of this 13‐mer. We screened all possible self‐complementary sequences in the hexameric duplex region and found 21 oligonucleotides that crystallized. Sequence analysis showed that one specific Watson‐Crick pair influenced the crystallization propensity and the speed of crystal self‐assembly. We determined X‐ray crystal structures for 13 of these oligonucleotides and found sequence‐specific structural changes that suggests that this base pair may serve as a structural anchor during crystal assembly. Finally, we explored the crystal self‐assembly and nucleation process. Solution studies indicated that these oligonucleotides do not form base pairs in the absence of cations, but that the addition of divalent cations leads to rapid self‐assembly to higher molecular weight complexes. We further demonstrate that crystals grown from mixtures of two different oligonucleotide sequences contain both oligonucleotides. These results suggest that crystal self‐assembly is nucleated by the formation of the Watson‐Crick duplexes initiated by a simple chemical trigger. This study provides new insight into the role of sequence for the assembly of periodic DNA structures. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 618–626, 2015.