Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions

Nuclear receptor ligand binding domains (LBDs) convert ligand binding events into changes in gene expression by recruiting transcriptional coregulators to a conserved activation function-2 (AF-2) surface. While most nuclear receptor LBDs form homo- or heterodimers, the human nuclear receptor pregnane X receptor (PXR) forms a unique and essential homodimer and is proposed to assemble into a functional heterotetramer with the retinoid X receptor (RXR). How the homodimer interface, which is located 30 Å from the AF-2, would affect function at this critical surface has remained unclear. By using 20- to 30-ns molecular dynamics simulations on PXR in various oligomerization states, we observed a remarkably high degree of correlated motion in the PXR–RXR heterotetramer, most notably in the four helices that create the AF-2 domain. The function of such correlation may be to create “active-capable” receptor complexes that are ready to bind to transcriptional coactivators. Indeed, we found in additional simulations that active-capable receptor complexes involving other orphan or steroid nuclear receptors also exhibit highly correlated AF-2 domain motions. We further propose a mechanism for the transmission of long-range motions through the nuclear receptor LBD to the AF-2 surface. Taken together, our findings indicate that long-range motions within the LBD scaffold are critical to nuclear receptor function by promoting a mobile AF-2 state ready to bind coactivators

Structure-Based Predictive Models for Allosteric Hot Spots

In allostery, a binding event at one site in a protein modulates the behavior of a distant site. Identifying residues that relay the signal between sites remains a challenge. We have developed predictive models using support-vector machines, a widely used machine-learning method. The training data set consisted of residues classified as either hotspots or non-hotspots based on experimental characterization of point mutations from a diverse set of allosteric proteins. Each residue had an associated set of calculated features. Two sets of features were used, one consisting of dynamical, structural, network, and informatic measures, and another of structural measures defined by Daily and Gray [1]. The resulting models performed well on an independent data set consisting of hotspots and non-hotspots from five allosteric proteins. For the independent data set, our top 10 models using Feature Set 1 recalled 68–81% of known hotspots, and among total hotspot predictions, 58–67% were actual hotspots. Hence, these models have precision P = 58–67% and recall R = 68–81%. The corresponding models for Feature Set 2 had P = 55–59% and R = 81–92%. We combined the features from each set that produced models with optimal predictive performance. The top 10 models using this hybrid feature set had R = 73–81% and P = 64–71%, the best overall performance of any of the sets of models. Our methods identified hotspots in structural regions of known allosteric significance. Moreover, our predicted hotspots form a network of contiguous residues in the interior of the structures, in agreement with previous work. In conclusion, we have developed models that discriminate between known allosteric hotspots and non-hotspots with high accuracy and sensitivity. Moreover, the pattern of predicted hotspots corresponds to known functional motifs implicated in allostery, and is consistent with previous work describing sparse networks of allosterically important residues

Resistance variation of conductive ink applied by the screen printing technique on different substrates

This research study focuses on the application of conductive ink by the screen printing technique to evaluate the potential of creating printed electrodes and to investigate the effect of washing upon electrical resistance and flexibility. Two conductive inks were applied by a conventional screen printing method on four different textile substrates, 100% cotton, 50%/50% cotton/polyester, 100% polyester and 100% polyamide. The inks were also applied on a multifibre fabric. Atmospheric plasma treatment was applied to improve the adhesion to the samples, and the resistance values were compared with those of non-treated samples. The values were measured before and after cleaning and washing tests, which were performed to simulate domestic treatment for garments to predict the behaviour of the inks after normal usage of the fabrics. Comfort properties like stiffness of the fabrics were also evaluated after five and 10 washing cycles. It was observed that PE 825 ink forms a thicker film on the fabric surface, contributing to the loss of flexibility of the textile. However, PE 825 ink also produced the best results in terms of durability and lower values of resistance. Polyamide fabrics lost their conductive property after five washing cycles due to weak bonding between the ink and the fibres, whereas cotton fibres provided the best results.This work is financed by Project“Deus ex Machina”, NORTE-01-0145-FEDER-000026, funded by CCDRN, through Sistema de Apoio à Investigação Cientifica e Tecnológica (Projetos Estruturados I&D&I) of Programa Operacional Regional do Norte, from Portugal 2020 and by Project UID/CTM/00264/2019 of 2C2T –Centro de Ciência e Tecnologia Têxtil, funded by National Founds through FCT/MCTES.Derya Tama thanks FCT for fellowship 2C2T-BPD-08-2017

Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein

The periplasmic lysine-, arginine-, ornithine-binding protein (LAOBP) traps its ligands by a large hinge bending movement between two globular domains. The overall geometry of the binding site remains largely unchanged between the open (unliganded) and closed (liganded) forms, with only a small number of residues exhibiting limited movement of their side chains. However, in the case of the ornithine-bound structure, the backbone peptide bond between Asp11 and Thr12 undergoes a large rotation. Molecular dynamics simulations have been used to investigate the origin and mechanism of this backbone movement. Simulations allowing flexibility of a limited region and of the whole binding site, with and without bound ligands, suggest that this conformational change is induced by the binding of ornithine, leading to the stabilisation of an energetically favourable alternative conformation