Scalable rule-based modelling of allosteric proteins and biochemical networks

Much of the complexity of biochemical networks comes from the information-processing abilities of allosteric proteins, be they receptors, ion-channels, signalling molecules or transcription factors. An allosteric protein can be uniquely regulated by each combination of input molecules that it binds. This "regulatory complexity" causes a combinatorial increase in the number of parameters required to fit experimental data as the number of protein interactions increases. It therefore challenges the creation, updating, and re-use of biochemical models. Here, we propose a rule-based modelling framework that exploits the intrinsic modularity of protein structure to address regulatory complexity. Rather than treating proteins as "black boxes", we model their hierarchical structure and, as conformational changes, internal dynamics. By modelling the regulation of allosteric proteins through these conformational changes, we often decrease the number of parameters required to fit data, and so reduce over-fitting and improve the predictive power of a model. Our method is thermodynamically grounded, imposes detailed balance, and also includes molecular cross-talk and the background activity of enzymes. We use our Allosteric Network Compiler to examine how allostery can facilitate macromolecular assembly and how competitive ligands can change the observed cooperativity of an allosteric protein. We also develop a parsimonious model of G protein-coupled receptors that explains functional selectivity and can predict the rank order of potency of agonists acting through a receptor. Our methodology should provide a basis for scalable, modular and executable modelling of biochemical networks in systems and synthetic biology

Fluorescent pseudo-peptide linear vasopressin antagonists: Design, synthesis, and applications

Fluoresceinyl and rhodamyl groups have been coupled by an amide link to side-chain amino groups at positions 1, 6, and 8 of pseudo-peptide linear vasopressin antagonists (Manning et al. Int. J. Pept. Protein Res. 1992, 40, 261-267) through different positions on the fluorophore, to give tetraethylrhodamyl-DTyr(Me)-Phe-Gln-Asn-Arg-Pro-Arg-Tyr-NH2 (2), 4- HOPh(CH2)2-CO-DTyr(Me)-Phe-Gln-Asn-Lys(5-carboxyfluoresceinyl)-Pro-Arg- NH2 (4), 4-HOPh(CH2)2CO-DTyr(Me)-Phe-Gln-Asn-Lys(5- or 6- carboxytetramethylrhodamyl)-Pro-Arg-NH2 (5, 6), 4-HOPh-(CH2)2CO-DTyr(Me)- Phe-Gln-Asn-Arg-Pro-Lys(5- or 6- carboxyfluoresceinyl)-NH2 (8, 9), and 4- HOPh(CH2)2CO-DTyr(Me)-Phe-Gln-Asn-Arg-Pro-Lys(5- or 6- carboxytetramethylrhodamyl)-NH2 (10, 11). The closer to the C-terminus the fluorophore, the higher the affinities of the fluorescent derivatives for the human vasopressin V(1a) receptor transfected in CHO cells. The compound 10 has a K(i) of 70 pM, as determined by competition experiments with [125I]- 4-HOPh-CH2CO-DTyr(Me)-Phe-Gln-Asn-Arg-Pro-Arg-NH2. It showed a good selectivity for human V(1a) receptor versus human OT (K(i) = 1.2 nM), human vasopressin V(1b) (K(i) approximately 27 nM), and human vasopressin V2 (K(i) > 5000 nM) receptor subtypes. All fluorescent analogues were antagonists as shown by the inhibition of vasopressin induced inositol phosphate accumulation. These fluorescent ligands are efficient for labeling cells expressing the human V(1a) receptor subtype, as shown by flow cytofluorometric experiments or fluorescence microscopy. They are also appropriate tools for structural analysis of the vasopressin receptors by fluorescence

Building a new conceptual framework for receptor heteromers

Receptor heteromers constitute a new area of research that is reshaping our thinking about biochemistry, cell biology, pharmacology and drug discovery. In this commentary, we recommend clear definitions that should facilitate both information exchange and research on this growing class of transmembrane signal transduction units and their complex properties. We also consider research questions underlying the proposed nomenclature, with recommendations for receptor heteromer identification in native tissues and their use as targets for drug development

Global food security, contributions from sustainable potato agri-food systems.

In the coming decades, feeding the expanded global population nutritiously and sustainably will require substantial improvements to the global food system worldwide. The main challenge will be to produce more food with the same or fewer resources. Food security has four dimensions: food availability, food access, food use and quality, and food stability. Among several other food sources, the potato crop is one that can help match all these requirements worldwide due to its highly diverse distribution pattern, and its current cultivation and demand, particularly in developing countries with high levels of poverty, hunger, and malnutrition. After an overview of the current situation of global hunger, food security, and agricultural growth, followed by a review of the importance of the potato in the current global food system and its role played as a food security crop, this chapter analyzes and discusses how potato research and innovation can contribute to sustainable agri-food systems with reference to food security indicators. It concludes with a discussion about the challenges for sustainable potato cropping considering the needs to increase productivity in developing countries while promoting better resource management and optimization