Which factors determine the acidity of the phytochromobilin chromophore of plant phytochrome?

Quantum chemical calculations aimed at identifying the factors controlling the acidity of phytochromobilin, the tetrapyrrole chromophore of the plant photoreceptor phytochrome, are reported. Phytochrome is converted from an inactive (Pr) to an active form (Pfr) through a series of events initiated by a Z --> E photoisomerization of phytochromobilin, forming the Lumi-R intermediate, and much controversy exists as to whether the protonation state of the chromophore (cationic in Pr with all nitrogens protonated) changes during the photoactivation. Here, relative ground (S0) and excited-state (S1) pKa s of all four pyrrole moieties of phytochromobilin in all 64 possible configurations with respect to the three methine bridges are calculated in a protein-like environment, using a recently benchmarked level of theory. Accordingly, the relationships between acidity and chromophore geometry and charge distribution, hydrogen bonding, and light absorption are investigated in some detail, and discussed in terms of possible mechanisms making a proton transfer reaction more probable along the Pr --> Pfr reaction than in the parent cationic Pr state. It is found that charge distribution in the cationic species, intra-molecular hydrogen bonding in the neutral, and hydrogen bonding with two highly conserved aspartate and histidine residues have a significant effect on the acidity, while overall chromophore geometry and electronic state are less important factors. Furthermore, based on the calculations, two processes that may facilitate a proton transfer by substantially lowering the pKa s relative to their Pr values are identified: (i) a thermal Z,anti --> Z,syn isomerization at C5, occurring after formation of Lumi-R; (ii) a perturbation of the hydrogen bonding network which in Pr comprises the nitrogens of pyrroles A, B and C and the two aspartate and histidine residues.     

Dynamic systems view of learning a three‐tiered theory in physics: robust learning outcomes as attractors

The process of learning scientific knowledge from the dynamic systems viewpoint is studied in terms probabilistic learning model (PLM), where learning accrues from foraging in the epistemic landscape. The PLM leads to the formation of attractor‐type regions of preferred models in an epistemic landscape. The attractor‐type states correspond to robust learning outcomes which are more probable than others. These can be assigned either to the high confidence in model selection or to the dynamic evolution of a learner's proficiency, which depends on the learning history. The results suggest that robust learning states are essentially context dependent, and that learning is a continuous development between these context dependent states. © 2016 Wiley Periodicals, Inc. Complexity 21: 259–267, 2016     

Engineered biosynthesis of nonribosomal lipopeptides with modified fatty acid side chains

The biological properties of the calcium-dependent antibiotics (CDAs), daptomycin and related nonribosomal lipopeptides, depend to a large extent on the nature of the N-terminal fatty acid moiety. It is suggested that the chain length of the unusually short (C6) 2,3-epoxyhexanoyl fatty acid moiety of CDA is determined by the specificity of the KAS-II enzyme encoded by fabF3 in the CDA biosynthetic gene cluster. Indeed, deletion of the downstream gene hxcO results in three new lipopeptides, all of which possess hexanoyl side chains (hCDAs). This confirms that HxcO functions as a hexanoyl-CoA or -ACP oxidase. The absence of additional CDA products with longer fatty acid groups further suggests that the CDA lipid chain is biosynthesized on a single ACP and is then transferred directly from this ACP to the first CDA peptide synthetase (CdaPS1). Interestingly, the hexanoyl-containing CDAs retain antibiotic activity. To further modulate the biological properties of CDA by introducing alternative fatty acid groups, a mutasynthesis approach was developed. This involved mutating the key active site Ser residue of the CdaPS1, module 1 PCP domain to Ala, which prevents subsequent phosphopantetheinylation. In the absence of the natural module 1 PCP tethered intermediate, it is possible to effect incorporation of different N-acyl-L-serinyl N-acetylcysteamine (NAC) thioester analogues, leading to CDA products with pentanoyl as well as hexanoyl side chains.     

Electron-transfer induced repair of 6-4 photoproducts in DNA: a computational study

The mechanism employed by DNA photolyase to repair 6-4 photoproducts in UV-damaged DNA is explored by means of quantum chemical calculations. Considering the repair of both oxetane and azetidine lesions, it is demonstrated that reduction as well as oxidation enables a reversion reaction by creating anionic or cationic radicals that readily fragment into monomeric pyrimidines. However, on the basis of calculated reaction energies indicating that electron transfer from the enzyme to the lesion is a much more favorable process than electron transfer in the opposite direction, it is suggested that the photoenzymic repair can only occur by way of an anionic mechanism. Furthermore, it is shown that reduction of the oxetane facilitates a mechanism involving cleavage of the C-O bond followed by cleavage of the C-C bond, whereas reductive fragmentation of the azetidine may proceed with either of the intermonomeric C-N and C-C bonds cleaved as the first step. From calculations on neutral azetidine radicals, a significant increase in the free-energy barrier for the initial fragmentation step upon protonation of the carbonylic oxygens is predicted. This effect can be attributed to protonation serving to stabilize reactant complexes more than transition structures.     

Multifunctional Polyoxometalate Platforms for Supramolecular Light-Driven Hydrogen Evolution**

Multifunctional supramolecular systems are a central research topic in light-driven solar energy conversion. Here, we report a polyoxometalate (POM)-based supramolecular dyad, where two platinum-complex hydrogen evolution catalysts are covalently anchored to an Anderson polyoxomolybdate anion. Supramolecular electrostatic coupling of the system to an iridium photosensitizer enables visible light-driven hydrogen evolution. Combined theory and experiment demonstrate the multifunctionality of the POM, which acts as photosensitizer/catalyst-binding-site^[1] and facilitates light-induced charge-transfer and catalytic turnover. Chemical modification of the Pt-catalyst site leads to increased hydrogen evolution reactivity. Mechanistic studies shed light on the role of the individual components and provide a molecular understanding of the interactions which govern stability and reactivity. The system could serve as a blueprint for multifunctional polyoxometalates in energy conversion and storage.     

Intercomparison exercise on difficult to measure radionuclides in activated concrete—statistical analysis and comparison with activation calculations

Journal of Radioanalytical and Nuclear Chemistry - This paper reports the results obtained in a Nordic Nuclear Safety Research project during the second intercomparison exercise for the...     

Effect of counterion structure on rates and diastereoselectivities in α,β-unsaturated iminium-ion Diels-Alder reactions

The use of cyclic α,β-unsaturated iminium-ion dienophiles is documented in two highly diastereoselective Diels-Alder (DA) reactions. The dienophilic counterion was found to have a significant effect on reactivity.     

Desmoplakin is important for proper cardiac cell-cell interactions

Normal cardiac function is maintained through dynamic interactions of cardiac cells with each other and with the extracellular matrix. These interactions are important for remodeling during cardiac growth and pathophysiological conditions. However, the precise mechanisms of these interactions remain unclear. In this study we examined the importance of desmoplakin (DSP) in cardiac cell-cell interactions. Cell-cell communication in the heart requires the formation and preservation of cell contacts by cell adhesion junctions called desmosome-like structures. A major protein component of this complex is DSP, which plays a role in linking the cytoskeletal network to the plasma membrane. Our laboratory previously generated a polyclonal antibody (1611) against the detergent soluble fraction of cardiac fibroblast plasma membrane. In attempting to define which proteins 1611 recognizes, we performed two-dimensional electrophoresis and identified DSP as one of the major proteins recognized by 1611. Immunoprecipitation studies demonstrated that 1611 was able to directly pulldown DSP. We also demonstrate that 1611 and anti-DSP antibodies co-localize in whole heart sections. Finally, using a three-dimensional in vitro cell-cell interaction assay, we demonstrate that 1611 can inhibit cell-cell interactions. These data indicate that DSP is an important protein for cell-cell interactions and affects a variety of cellular functions, including cytokine secretion.     

Cross-intersecting sub-families of hereditary families

Families A₁,A₂,…,Ak of sets are said to be cross-intersecting if for any i and j in {1,2,…,k} with i≠j, any set in Ai intersects any set in Aj. For a finite set X, let X² denote the power set of X (the family of all subsets of X). A family H is said to be hereditary if all subsets of any set in H are in H; so H is hereditary if and only if it is a union of power sets. We conjecture that for any non-empty hereditary sub-family H≠{∅} of X² and any k?|X|+1, both the sum and the product of sizes of k cross-intersecting sub-families A₁,A₂,…,Ak (not necessarily distinct or non-empty) of H are maxima if A₁=A₂=?=Ak=S for some largest starSofH (a sub-family of H whose sets have a common element). We prove this for the case when H is compressed with respect to an element x of X, and for this purpose we establish new properties of the usual compression operation. As we will show, for the sum, the condition k?|X|+1 is sharp. However, for the product, we actually conjecture that the configuration A₁=A₂=?=Ak=S is optimal for any hereditary H and any k?2, and we prove this for a special case.