ProteoMutaMetrics: machine learning approaches for solute carrier family 6 mutation pathogenicity prediction.

The solute carrier transporter family 6 (SLC6) is of key interest for their critical role in the transport of small amino acids or amino acid-like molecules. Their dysfunction is strongly associated with human diseases such as including schizophrenia, depression, and Parkinson's disease. Linking single point mutations to disease may support insights into the structure-function relationship of these transporters. This work aimed to develop a computational model for predicting the potential pathogenic effect of single point mutations in the SLC6 family. Missense mutation data was retrieved from UniProt, LitVar, and ClinVar, covering multiple protein-coding transcripts. As encoding approach, amino acid descriptors were used to calculate the average sequence properties for both original and mutated sequences. In addition to the full-sequence calculation, the sequences were cut into twelve domains. The domains are defined according to the transmembrane domains of the SLC6 transporters to analyse the regions' contributions to the pathogenicity prediction. Subsequently, several classification models, namely Support Vector Machine (SVM), Logistic Regression (LR), Random Forest (RF), and Extreme Gradient Boosting (XGBoost) with the hyperparameters optimized through grid search were built. For estimation of model performance, repeated stratified k-fold cross-validation was used. The accuracy values of the generated models are in the range of 0.72 to 0.80. Analysis of feature importance indicates that mutations in distinct regions of SLC6 transporters are associated with an increased risk for pathogenicity. When applying the model on an independent validation set, the performance in accuracy dropped to averagely 0.6 with high precision but low sensitivity scores.

Experimental and Computational Analysis of Newly Identified Pathogenic Mutations in the Creatine Transporter SLC6A8.

Creatine is an essential metabolite for the storage and rapid supply of energy in muscle and nerve cells. In humans, impaired metabolism, transport, and distribution of creatine throughout tissues can cause varying forms of mental disability, also known as creatine deficiency syndrome (CDS). So far, 80 mutations in the creatine transporter (SLC6A8) have been associated to CDS. To better understand the effect of human genetic variants on the physiology of SLC6A8 and their possible impact on CDS, we studied 30 missense variants including 15 variants of unknown significance, two of which are reported here for the first time. We expressed these variants in HEK293 cells and explored their subcellular localization and transport activity. We also applied computational methods to predict variant effect and estimate site-specific changes in thermodynamic stability. To explore variants that might have a differential effect on the transporter's conformers along the transport cycle, we constructed homology models of the inward facing, and outward facing conformations. In addition, we used mass-spectrometry to study proteins that interact with wild type SLC6A8 and five selected variants in HEK293 cells. In silico models of the protein complexes revealed how two variants impact the interaction interface of SLC6A8 with other proteins and how pathogenic variants lead to an enrichment of ER protein partners. Overall, our integrated analysis disambiguates the pathogenicity of 15 variants of unknown significance revealing diverse mechanisms of pathogenicity, including two previously unreported variants obtained from patients suffering from the creatine deficiency syndrome.

Generating water/MeOH-soluble and luminescent polymers by grafting 2,6-bis(1,2,3-triazol-4-yl)pyridine (btp) ligands onto a poly(ethylene-alt-maleic anhydride) polymer and cross-linking with terbium(III).

The synthesis of two new polymers made from P(E-alt-MA) (poly(ethylene-alt-maleic anhydride) and possessing 2,6-bis(1,2,3-triazol-4-yl)pyridine (btp) ligand side chains in 3 and 6 mol%, respectively (P1 and P2, respectively) is described. These polymers were shown to be soluble in MeOH solution and, in the case of P1, also in water, while P2 needed prolonged heating to enable water dissolution. Btp ligands are known for coordinating both d- and f-metal ions and so, herein, we demonstrate by using both UV-Vis absorption, fluorescence emission, as well as time-gated phosphorescence spectroscopies, that both P1 and P2 can bind to Tb(III) ions to give rise to luminescent polymers. From the analysis of the titration data, which demonstrated large changes in the emission intensity properties of the polymer upon Tb(III) binding (ground state changes were also clearly observed, with the absorption being red-shifted at lower energy), we show that the dominant stoichiometry in solution is 1 : 2 (M : L; Tb(III) : btp ratio) which implies that two btp ligands from the polymer background are able to crosslink through lanthanide coordination and that the backbone of the polymer is very likely to aid in coordinating the ions.

Luminescent lanthanide (Eu(iii)) cross-linked supramolecular metallo co-polymeric hydrogels: the effect of ligand symmetry.

Two lanthanide luminescent naphthyl-dipicolinic amide (dpa) methacrylate monomers for the synthesis of grafted supramolecular co-polymer gels (hydrogels), and their use as additional crosslinks in robust covalently cross-linked HEMA hydrogels is presented; the results demonstrate the importance of the ligand symmetry for the Eu(iii) emission from the hydrogels.

Recent advances in the development of luminescent lanthanide-based supramolecular polymers and soft materials.

Combination of different properties has always proven effective in the generation of hybrid materials with novel interesting properties. Ln(iii) containing materials possessing multiple properties are useful in a wide range of applications. In this article, key and recent examples of metallo-supramolecular polymers in the formation of gels, soft polymeric materials and films are discussed. There is a focus on the use of trivalent lanthanide, Ln(iii), ions to provide soft materials with advanced mechanical and luminescence properties for applications in developing electronic- and bio-technologies. This frontier article has been written with the intention of reaching a broad range of readers from various backgrounds such as chemistry, materials chemistry, spectroscopy and biochemistry. Additionally, we evaluate how the unique and versatile properties of such hybrid materials can be tuned and explored to enhance the efficiency, as well as research, for new ones. Finally, an assessment of the current state-of-the-art and our outlook for the future of this field is made.

Surface-Modified Gold Nanoparticles Possessing Two-Channel Responsive EuIII /TbIII Cyclen Complexes as Luminescent Logic Gate Mimics.

The development of material-supported molecular logic gate mimics (MGLMs) for contained application and device fabrication has become of increasing interest. Herein, we present the formation of ≈5 nm gold nanoparticles (AuNPs) that have been surface-modified (via a thiol linkage) with heptadentate cyclen-based complexes of europium and terbium for sensing applications using delayed lanthanide luminescence and as integrated logic gate mimics within competitive media.

Luminescent Lanthanide Cyclen-Based Enzymatic Assay Capable of Diagnosing the Onset of Catheter-Associated Urinary Tract Infections Both in Solution and within Polymeric Hydrogels.

Herein we present a supramolecular (delayed luminescent) Eu(III)-based pH-responsive probe/sensor with the ability to detect the urease-mediated hydrolysis of urea in aqueous solution. A series of photophysical titrations show this Eu(III) chelate behaves as an "on-off" luminescent switching probe, with its luminescence being quenched upon urea being enzymatically converted into ammonia and carbon dioxide. Calculation of the rate constant (k) and activation energy (Ea) for this hydrolysis reaction are detailed; the results demonstrate a direct observation of enzymatic activity in solution by the sensor. The potential application of this probe in detecting the onset of catheter-associated urinary tract infections (CAUTIs) is also demonstrated by incorporating 1.Eu into water-permeable hydrogels that can be utilized as an alternative coating for catheters.

Lanthanide luminescent logic gate mimics in soft matter: [H(+)] and [F(-)] dual-input device in a polymer gel with potential for selective component release.

The non-covalent incorporation of responsive luminescent lanthanide, Ln(III), complexes with orthogonal outputs from Eu(III) and Tb(III) in a gel matrix allows for in situ logic operation with colorimetric outputs. Herein, we report an exemplar system with two inputs ([H(+)] and [F(-)]) within a p(HEMA-co-MMA) polymer organogel acting as a dual-responsive device and identify future potential for such systems.

Quantifying the formation of chiral luminescent lanthanide assemblies in an aqueous medium through chiroptical spectroscopy and generation of luminescent hydrogels.

Herein we present the synthesis and the photophysical evaluation of water-soluble chiral ligands (2·(R,R) and 2·(S,S)) and their application in the formation of lanthanide directed self-assembled structures. These pyridine-2,6-dicarboxylic amide based ligands, possessing two naphthalene moieties as sensitising antennae, that can be used to populate the excited state of lanthanide ions, were structurally modified using 3-propanesultone and caesium carbonate, allowing for the incorporation of a water-solubilising sulfonate motif. We show, using microwave synthesis, that Eu(III) forms chiral complexes in 1 : 3 (M : L) stoichiometries (Eu·[2·(R,R)]3 and Eu·[2·(S,S)]3) with these ligands, and that the red Eu(III)-centred emission arising from these complexes has quantum yields (Φtot) of 12% in water. Both circular dichroism (CD) and circular polarised luminescence (CPL) analysis show that the complexes are chiral; giving rise to characteristic CD and CPL signatures for both the Λ and the Δ complexes, which both possess characteristic luminescence dissymmetry factors (g(lum)), describing the structure in solution. The self-assembly process was also monitored in situ by observing the changes in the ligand absorption and fluorescence emission, as well as in the Eu(III) luminescence. The change, fitted using non-linear regression analysis, demonstrated high binding affinity for Eu(III) which in part can be assigned to being driven by additional hydrophobic effects. Moreover, using CD spectroscopy, the changes in the chiroptical properties of both (2·(R,R) and 2·(S,S)) were monitored in real time. Fitting the changes in the CD spectra allowed for the step-wise binding constants to be determined for these assemblies; these matched well with those determined from both the ground and the excited state changes. Both the ligands and the Eu(III) complexes were then used in the formation of hydrogels; the Eu(III)-metallogels were luminescent to the naked-eye.