A general Temperature-Guided Language model to engineer enhanced Stability and Activity in Proteins

Designing protein mutants with high stability and activity is a critical yet challenging task in protein engineering. Here, we introduce PRIME, an innovative deep learning approach for the zero-shot prediction of both protein stability and enzymatic activity. PRIME leverages temperature-guided language modelling, providing robust and precise predictions without relying on prior experimental mutagenesis data. Tested against 33 protein datasets, PRIME demonstrated superior predictive performance and generalizability compared to current state-of-the-art modelsComment: arXiv admin note: text overlap with arXiv:2304.0378

Identification of Prognostic Immune-Related Genes in Pancreatic Adenocarcinoma and Establishment of a Prognostic Nomogram: A Bioinformatic Study

Background. The prognosis of pancreatic adenocarcinoma (PAAD) is extremely poor and has not been improved. Thus, an effective method to assess the prognosis of patients must be established to improve their survival rate. Method. This study investigated immune-related genes that could be used as potential therapeutic targets for PAAD. Level 3 gene expression data from the PAAD cohort and the relevant clinical information were obtained from The Cancer Genome Atlas (TCGA) database. For validation, other PAAD datasets (DSE62452) were downloaded from the Gene Expression Omnibus (GEO) database. The PAAD datasets from TCGA and GEO were used to screen immune-related genes through the Molecular Signatures Database using gene set enrichment analysis. Then, the overlapping immune-related genes of the two datasets were identified. Coexpression networks of the immune-related genes were constructed. Results. A signature of three immune-related genes (CKLF, ERAP2, and EREG) was identified in patients with PAAD. The signature could be used to divide the patients with PAAD into high- and low-risk groups based on their median risk score. Multivariate Cox regression analysis was performed to determine the independent prognostic factors of PAAD. Time-dependent receiver operating characteristic (ROC) curve analysis was conducted to assess the prediction accuracy of the prognostic signature. Last, a nomogram was established to assess the individualized prognosis prediction model based on the clinical characteristics and risk score of the TCGA PAAD dataset. The accuracy of the prognostic signature was further evaluated through functional evaluation and principal component analysis. Conclusions. The results indicated that the signature of three immune-related genes had excellent predictive value for PAAD. These findings might help improve personalized treatment and medical decisions

Enhanced proton and electron reservoir abilities of polyoxometalate grafted on graphene for high-performance hydrogen evolution

A beneficial &quot;microenvironment effect&quot; on the efficiency of confined electrocatalysts is predicted by theory. However, examples of its experimental confirmation are scarce for catalysts based on polyoxometalates for the hydrogen evolution reaction (HER). For this purpose, the cyclic 48-tungsto-8-phosphate [H7P8W48O184](33) (P8W48) was fixed in a 3D configuration on reduced graphene oxide sheets (rGO) to boost its HER activity. The HRTEM imaging and the solid state P-31 NMR spectrum of P8W48/rGO reveal a strong interaction between individual P8W48 and transparent rGO sheets. The calculation of the interaction between P8W48 and graphene (G) sheets is difficult to perform within a reasonable period of time because of the large size and very high overall negative charge of P8W48. However, as P8W48 is symmetrical, a quarter of its structure [H2P2W12O48](12-) (P2W12) was extracted as a DFT calculation model. As P8W48 in P8W48/rGO is neutral, due to surrounding counter cations, the calculation model P2W12 is neutral with protons considering the affordable computational time. The adsorption energy for P2W12 on G (-1.55 eV) and the charge transfer between P2W12 and G (0.66 vertical bar e vertical bar) indicate that a strong interaction between P2W12 and G sheets exists. Kinetic studies show that the P8W48/rGO hybrids display excellent HER activity in acid, further confirmed by reproducible generation of hydrogen with quantitative faradaic yield and a high turnover frequency (11 s(-1) at 295 mV overpotential) for a noble metal-free electrocatalyst. Importantly, the overpotentials required for the HER compare well with those of the commercial Pt/C (20 wt% Pt), which indicates that P8W48/rGO is a promising cheap HER electrocatalyst. We demonstrate here the most convincing experimental evidence of the &quot;microenvironment effect&quot; on HER electrocatalysis by a polyoxometalate.</p