Which Properties Allow Ligands to Open and Bind to the Transient Binding Pocket of Human Aldose Reductase?

The transient specificity pocket of aldose reductase only opens in response to specific ligands. This pocket may offer an advantage for the development of novel, more selective ligands for proteins with similar topology that lack such an adaptive pocket. Our aim was to elucidate which properties allow an inhibitor to bind in the specificity pocket. A series of inhibitors that share the same parent scaffold but differ in their attached aromatic substituents were screened using ITC and X-ray crystallography for their ability to occupy the pocket. Additionally, we investigated the electrostatic potentials and charge distribution across the attached terminal aromatic groups with respect to their potential to bind to the transient pocket of the enzyme using ESP calculations. These methods allowed us to confirm the previously established hypothesis that an electron-deficient aromatic group is an important prerequisite for opening and occupying the specificity pocket. We also demonstrated from our crystal structures that a pH shift between 5 and 8 does not affect the binding position of the ligand in the specificity pocket. This allows for a comparison between thermodynamic and crystallographic data collected at different pH values.

Kākāpō reproduction: Identification of steroid receptors and oestrogenic activity in native flora

<p>Kākāpō (Strigops habroptilus) are a critically endangered parrot species endemic to New Zealand that exhibit a reproductive strategy linked to “masting” years. Crucial to their survival is increased reproductive success. It has been hypothesised that their pattern of reproduction is synchronised with a steroidal “trigger” present in plants during intensive masting. If this hypothesis is valid, then Kākāpō and other closely related NZ parrots might be receptive to these masting plants in a manner different from that of other avian species. The aims of this study were firstly, to identify whether unique amino acid motifs were present in the ligand binding domains (LBD) for the steroid receptors oestrogen receptor α (ER-α), oestrogen receptor β (ER-β), androgen receptor (AR) and progesterone receptor (PR) for the New Zealand parrots Kākāpō, Kākā, Kākāriki and Kea. These LBD amino acid sequences were compared with those in an Australian parrot, the Cockatiel, as well as in Chicken and Japanese Quail. Moreover, the role of these amino acid changes on the binding of ligands (both the native ligand and other steroidogenic compounds) for ER-α was assessed by in silico modelling by comparing the most favourable binding position of the ligands in the three-dimensional structure of Kākāpō ER-α with that of human ER-α. The second aim was to test extracts of New Zealand native plants known to be a food source for Kākāpō for their seasonal variation in oestrogenic activity and hence possible involvement in the reproductive cycle of Kākāpō. The LBD for ER-β and AR of the parrot species (New Zealand and Australian) displayed 100% identity whilst those for ER-α and PR had variations. When the parrot sequences were compared with those for other avian species and human, there were a number of amino acid differences present, with the greatest disparity present in the LBD of ER-α. From in silico modelling studies, the amino acid substitutions in this receptor were predicted to have an indirect influence on the binding position of both 17β-oestradiol and a number of phytoestrogens through changes in the structure of this region. Consequently, this could have an effect on the binding affinity of certain plant chemicals for ER-α and thus their potency. Plants extracts from the foliage and fruit of native New Zealand species were screened for oestrogenic activity in a yeast bioassay transfected with the human isoform of ER-α. The results from these experiments indicated that all the plants tested (excluding Dacrycarpus dacrydioides) exhibited detectable oestrogenic activity and a number also displayed variable and sometimes seasonal trends in activity. In summary, the results in this study identified ER-α LBD amino acid motifs unique to New Zealand parrots. For the other steroid receptors, the ER-β LBD had a three amino acid combination of M, V and L that was only present in the parrot species whilst both the AR and PR LBD displayed much greater inter-species conservation. These changes, particularly those in the ER-α LBD, may influence the binding of steroidogenic compounds, known to be present in the plants consumed by Kākāpō as demonstrated by in silico modelling. Thus, this research provides evidence that the diet of Kākāpō may influence their reproductive pattern. However, it remains to be determined whether the steroidogenic potency of these plant extracts is modified when interacting with the unique LBD of native NZ parrots.</p>

Kākāpō reproduction: Identification of steroid receptors and oestrogenic activity in native flora

<p>Kākāpō (Strigops habroptilus) are a critically endangered parrot species endemic to New Zealand that exhibit a reproductive strategy linked to “masting” years. Crucial to their survival is increased reproductive success. It has been hypothesised that their pattern of reproduction is synchronised with a steroidal “trigger” present in plants during intensive masting. If this hypothesis is valid, then Kākāpō and other closely related NZ parrots might be receptive to these masting plants in a manner different from that of other avian species. The aims of this study were firstly, to identify whether unique amino acid motifs were present in the ligand binding domains (LBD) for the steroid receptors oestrogen receptor α (ER-α), oestrogen receptor β (ER-β), androgen receptor (AR) and progesterone receptor (PR) for the New Zealand parrots Kākāpō, Kākā, Kākāriki and Kea. These LBD amino acid sequences were compared with those in an Australian parrot, the Cockatiel, as well as in Chicken and Japanese Quail. Moreover, the role of these amino acid changes on the binding of ligands (both the native ligand and other steroidogenic compounds) for ER-α was assessed by in silico modelling by comparing the most favourable binding position of the ligands in the three-dimensional structure of Kākāpō ER-α with that of human ER-α. The second aim was to test extracts of New Zealand native plants known to be a food source for Kākāpō for their seasonal variation in oestrogenic activity and hence possible involvement in the reproductive cycle of Kākāpō. The LBD for ER-β and AR of the parrot species (New Zealand and Australian) displayed 100% identity whilst those for ER-α and PR had variations. When the parrot sequences were compared with those for other avian species and human, there were a number of amino acid differences present, with the greatest disparity present in the LBD of ER-α. From in silico modelling studies, the amino acid substitutions in this receptor were predicted to have an indirect influence on the binding position of both 17β-oestradiol and a number of phytoestrogens through changes in the structure of this region. Consequently, this could have an effect on the binding affinity of certain plant chemicals for ER-α and thus their potency. Plants extracts from the foliage and fruit of native New Zealand species were screened for oestrogenic activity in a yeast bioassay transfected with the human isoform of ER-α. The results from these experiments indicated that all the plants tested (excluding Dacrycarpus dacrydioides) exhibited detectable oestrogenic activity and a number also displayed variable and sometimes seasonal trends in activity. In summary, the results in this study identified ER-α LBD amino acid motifs unique to New Zealand parrots. For the other steroid receptors, the ER-β LBD had a three amino acid combination of M, V and L that was only present in the parrot species whilst both the AR and PR LBD displayed much greater inter-species conservation. These changes, particularly those in the ER-α LBD, may influence the binding of steroidogenic compounds, known to be present in the plants consumed by Kākāpō as demonstrated by in silico modelling. Thus, this research provides evidence that the diet of Kākāpō may influence their reproductive pattern. However, it remains to be determined whether the steroidogenic potency of these plant extracts is modified when interacting with the unique LBD of native NZ parrots.</p>

The Relative Binding Position of Nck and Grb2 Adaptors Dramatically Impacts Actin-Based Motility of Vaccinia Virus

ABSTRACTPhosphotyrosine (pTyr) motifs in unstructured polypeptides orchestrate important cellular processes by engaging SH2-containing adaptors to nucleate complex signalling networks. The concept of phase separation has recently changed our appreciation of such multivalent networks, however, the role of pTyr motif positioning in their function remains to be explored. We have now explored this parameter in the assembly and operation of the signalling cascade driving actin-based motility and spread of Vaccinia virus. This network involves two pTyr motifs in the viral protein A36 that recruit the adaptors Nck and Grb2 upstream of N-WASP and Arp2/3-mediated actin polymerization. We generated synthetic networks on Vaccinia by manipulating pTyr motifs in A36 and the unrelated p14 from Orthoreovirus. In contrast to predictions, we find that only specific spatial arrangements of Grb2 and Nck binding sites result in robust N-WASP recruitment, Arp2/3 driven actin polymerization and viral spread. Our results suggest that the relative position of pTyr adaptor binding sites is optimised for signal output. This finding may explain why the relative positions of pTyr motifs are usually conserved in proteins from widely different species. It also has important implications for regulation of physiological networks, including those that undergo phase transitions.

Evaluation of the correlation between porphyrin accumulation in cancer cells and functional positions for application as a drug carrier

Porphyrin derivatives accumulate selectively in cancer cells and are can be used as carriers of drugs. Until now, the substituents that bind to porphyrins (mainly at the meso-position) have been actively investigated, but the effect of the functional porphyrin positions (β-, meso-position) on tumor accumulation has not been investigated. Therefore, we investigated the correlation between the functional position of substituents and the accumulation of porphyrins in cancer cells using cancer cells. We found that the meso-derivative showed higher accumulation in cancer cells than the β-derivative, and porphyrins with less bulky substituent actively accumulate in cancer cells. When evaluating the intracellular distribution of porphyrin, we found that porphyrin was internalized by endocytosis and direct membrane permeation. As factors involved in these two permeation mechanisms, we evaluated the affinity between porphyrin-protein (endocytosis) and the permeability to the phospholipid bilayer membrane (direct membrane permeation). We found that the binding position of porphyrin affects the factors involved in the transmembrane permeation mechanisms and impacts the accumulation in cancer cells.

Small-angle neutron scattering solution structures of NADPH-dependent sulfite reductase

Sulfite reductase (SiR), a dodecameric complex of flavoprotein reductase subunits (SiRFP) and hemoprotein oxidase subunits (SiRHP), reduces sulfur reduction for biomass incorporation. Electron transfer within SiR requires intra- and inter-subunit interactions that are mediated by the relative position of each protein, governed by flexible domain movements. Using small-angle neutron scattering, we report the first solution structures of SiR heterodimers containing a single copy of each subunit. These structures show how the subunits bind and how both subunit binding and oxidation state impact SiRFP's conformation. Neutron contrast matching experiments on selectively deuterated heterodimers allow us to define the contribution of each subunit to the solution scattering. SiRHP binding induces a change in the position of SiRFP's flavodoxin-like domain relative to its ferredoxin-NADP+ reductase domain while compacting SiRHP's N-terminus. Reduction of SiRFP leads to a more open structure relative to its oxidized state, re-positioning SiRFP's N-terminal flavodoxin-like domain towards the SiRHP binding position. These structures show, for the first time, how both SiRHP binding to, and reduction of, SiRFP positions SiRFP for electron transfer between the subunits.

Fatwa Majelis Ulama Indonesia sebagai Solusi Permasalahan Umat Islam di Indonesia

The Indonesian Ulema Council (MUI) has an important role in answering the increasingly complex problems of Muslims through fatwas. However, in the Indonesian legal system, fatwas are not considered a source of material law that has legal validity as a solution to the problems of Muslims in Indonesia. Therefore, this study aims to describe the position of fatwas in the legal system in Indonesia and the existence of the fatwas of the Indonesian Ulema Council in addressing the problems of the ummah. This research is a normative legal research using three types of approaches consisting of a statutory approach, a historical approach, and a conceptual approach. The results of this study concluded that: firstly, the position of fatwas in the construction of Islamic law has a high position. Fatwas are seen as a solution that can break the ice in legal development that is not accommodated by the texts of the Quran. So, substantively and sociologically, fatwas have a strong and binding position in Islamic law. Secondly, the existence of the fatwa of the Indonesian Ulema Council in responding to the problems of the Ummah can be seen in two aspects. The first aspect, fatwas in the perspective of Islamic legal authority are binding sociologically in substance. This is because fatwas are explanations and interpreters of the texts of the Quran regarding Islamic law. The second aspect, fatwas from the perspective of the hierarchy of laws and regulations, legally and formally, do not have any position in the ranking of legal norms. However, it is constitutionally guaranteed through Article 29 of the 1945 Constitution that guarantees the realization of the fulfillment of all Islamic law for Muslims in Indonesia.

Electron cryotomography analysis of Dam1C/DASH at the kinetochore–spindle interface in situ

In dividing cells, depolymerizing spindle microtubules move chromosomes by pulling at their kinetochores. While kinetochore subcomplexes have been studied extensively in vitro, little is known about their in vivo structure and interactions with microtubules or their response to spindle damage. Here we combine electron cryotomography of serial cryosections with genetic and pharmacological perturbation to study the yeast chromosome segregation machinery in vivo. Each kinetochore microtubule has one (rarely, two) Dam1C/DASH outer kinetochore assemblies. Dam1C/DASH contacts the microtubule walls and does so with its flexible “bridges”; there are no contacts with the protofilaments’ curved tips. In metaphase, ∼40% of the Dam1C/DASH assemblies are complete rings; the rest are partial rings. Ring completeness and binding position along the microtubule are sensitive to kinetochore attachment and tension, respectively. Our study and those of others support a model in which each kinetochore must undergo cycles of conformational change to couple microtubule depolymerization to chromosome movement.