What Strengthens Protein-Protein Interactions: Analysis and Applications of Residue Correlation Networks.

Identifying residues critical to protein-protein binding and efficient design of stable and specific protein binders are challenging tasks. Extending beyond the direct contacts in a protein-protein binding interface, our study employs computational modeling to reveal the essential network of residue interactions and dihedral angle correlations critical in protein-protein recognition. We hypothesized that mutating residues exhibiting highly correlated dynamic motion within the interaction network could efficiently optimize protein-protein interactions to create tight and selective protein binders. We tested this hypothesis using the ubiquitin (Ub) and MERS coronaviral papain-like protease (PLpro) complex, since Ub is a central player in multiple cellular functions and PLpro is an antiviral drug target. Our designed ubiquitin variant (UbV) hosting three mutated residues displayed a ∼3,500-fold increase in functional inhibition relative to wild-type Ub. Further optimization of two C-terminal residues within the Ub network resulted in a KD of 1.5 nM and IC50 of 9.7 nM for the five-point Ub mutant, eliciting 27,500-fold and 5,500-fold enhancements in affinity and potency, respectively, as well as improved selectivity, without destabilizing the UbV structure. Our study highlights residue correlation and interaction networks in protein-protein interactions, and introduces an effective approach to design high-affinity protein binders for cell biology research and future therapeutics.

Robust Design of Effective Allosteric Activators for Rsp5 E3 Ligase Using the Machine Learning Tool ProteinMPNN.

We used the deep learning tool ProteinMPNN to redesign ubiquitin (Ub) as a specific and functionally stimulating/enhancing binder of the Rsp5 E3 ligase. We generated 20 extensively mutated─up to 37 of 76 residues─recombinant Ub variants (UbVs), named R1 to R20, displaying well-folded structures and high thermal stabilities. These UbVs can also form stable complexes with Rsp5, as predicted using AlphaFold2. Three of the UbVs bound to Rsp5 with low micromolar affinity, with R4 and R12 effectively enhancing the Rsp5 activity six folds. AlphaFold2 predicts that R4 and R12 bind to Rsp5's exosite in an identical manner to the Rsp5-Ub template, thereby allosterically activating Rsp5-Ub thioester formation. Thus, we present a virtual solution for rapidly and cost-effectively designing UbVs as functional modulators of Ub-related enzymes.

What Strengthens Protein-Protein Interactions: Analysis and Applications of Residue Correlation Networks.

Identifying critical residues in protein-protein binding and efficiently designing stable and specific protein binders to target another protein is challenging. In addition to direct contacts in a protein-protein binding interface, our study employs computation modeling to reveal the essential network of residue interaction and dihedral angle correlation critical in protein-protein recognition. We propose that mutating residues regions exhibited highly correlated motions within the interaction network can efficiently optimize protein-protein interactions to create tight and selective protein binders. We validated our strategy using ubiquitin (Ub) and MERS coronaviral papain-like protease (PLpro) complexes, where Ub is one central player in many cellular functions and PLpro is an antiviral drug target. Molecular dynamics simulations and experimental assays were used to predict and verify our designed Ub variant (UbV) binders. Our designed UbV with 3 mutated residues resulted in a ~3,500-fold increase in functional inhibition, compared with the wild-type Ub. Further optimization by incorporating 2 more residues within the network, the 5-point mutant achieved a KD of 1.5 nM and IC50 of 9.7 nM. The modification led to a 27,500-fold and 5,500-fold enhancements in affinity and potency, respectively, as well as improved selectivity, without destabilizing the UbV structure. Our study illustrates the importance of residue correlation and interaction networks in protein-protein interaction and introduces a new approach that can effectively design high affinity protein binder for cell biology studies and future therapeutic solution.

What Strengthens Protein-Protein Interactions: Analysis and Applications of Residue Correlation Networks.

Identifying critical residues in protein-protein binding and efficiently designing stable and specific protein binders is challenging. In addition to direct contacts in a protein-protein binding interface, our study employs computation modeling to reveal the essential network of residue interaction and dihedral angle correlation critical in protein-protein recognition. We propose that mutating residues regions exhibited highly correlated motions within the interaction network can efficiently optimize protein-protein interactions to create tight and selective protein binders. We validated our strategy using ubiquitin (Ub) and MERS coronaviral papain-like protease (PLpro) complexes, where Ub is one central player in many cellular functions and PLpro is an antiviral drug target. Our designed UbV with 3 mutated residues resulted in a ~3,500-fold increase in functional inhibition, compared with the wild-type Ub. Further optimization by incorporating 2 more residues within the network, the 5-point mutant achieved a KD of 1.5 nM and IC50 of 9.7 nM. The modification led to a 27,500-fold and 5,500-fold enhancements in affinity and potency, respectively, as well as improved selectivity, without destabilizing the UbV structure. Our study highlights residue correlation and interaction networks in protein-protein interaction, introduces an effective approach to design high affinity protein binders for cell biology and future therapeutics solutions.

Clinical characteristics and outcomes of mixed virus or bacterial infection in children with laboratory-confirmed influenza infection.

BACKGROUND/PURPOSE: This study investigated the demographic characteristics and influenza complications of paediatric patients and explored the association of different influenza virus types and viral and bacterial coinfections with disease severity. METHODS: This retrospective cohort study used data collected in 2010-2016 from the Chang Gung Research Database (CGRD), the largest collection of multi-institutional electronic medical records in Taiwan. Data were retrieved for children aged 0-18 years with laboratory-confirmed influenza. We extracted and analysed the demographic characteristics and the data on clinical features, complications, microbiological information, and advanced therapies of each case. RESULTS: We identified 6193 children with laboratory-confirmed influenza, of whom 1964 (31.7%) were hospitalised. The age of patients with influenza A infection was lower than that of patients with influenza B (4.48 vs. 6.68, p < 0.001). Patients with influenza B infection had a higher incidence of myositis or rhabdomyolysis (4.4%, p < 0.001) and a higher need for advanced therapies (OR, 1.96; 95% CI, 1.32-2.9, p < 0.001). In addition to bacterial (OR, 9.07; 95% CI, 5.29-15.54, p < 0.001) and viral coinfection (OR, 7.73; 95% CI, 5.4-11.07, p < 0.001), dual influenza A and B infection was also a risk factor for influenza complications (OR, 2.13; 95% CI, 1.47-3.09, p < 0.001). CONCLUSION: Dual influenza A and B infection and bacterial coinfection can contribute to influenza complications. Early recognition of any influenza complication is critical for the timely initiation of organ-specific advanced therapies to improve influenza-associated outcomes.

Anticancer efficacy of unique pyridine-based tetraindoles.

Results of previous studies demonstrated that the tetraindole, SK228, which has a high lipid but low water solubility, displayed moderate anticancer efficacy in a xenograft model of breast cancer. This finding led to the proposal that new, pyridine based tetraindole (PBT) analogs of SK228, containing tetraindole moieties distributed about central protonated pyridine cores, would have enhanced bioavailabilities and anticancer efficacies. Among the PBTs prepared and subjected to biological studies, 3f (FCW81) was observed to display the highest antiproliferative activity against the two triple negative breast cancer (TNBCs) cell lines, MDA-MB-231 and BT549. In addition, its mode of action was shown to involve G2/M arrest of the cell cycle along with the promotion of increased levels of cyclin B1 and p-chk2 and a decreased level of p-cdc2. DNA damage and induction of apoptosis caused by FCW81 was found to be associated with a decrease in DNA repair. Significantly, FCW81 displays therapeutic efficacy in a xenograft model of human breast cancer by not only serving to inhibit markedly the growth of cancer cells but also to block effectively cancer cell metastasis. Collectively, the results of these studies have led to the identification of novel pyridine-tetraindole based anticancer agents with potential use in TNBC therapy.

Apoptotic Effect of Extract from Medicinal Mushroom from Taiwan Taiwanofungus salmoneus (Higher Basidiomycetes) Mycelium Combined with or without Cisplatin on Hepatocellular Carcinoma Cells.

Hepatocellular carcinoma is a cancer of high mortality; therefore, the effective therapy on this cancer is an imperative issue. Recently, anticancer agent combined with natural products has been demonstrated to increase apoptosis of various cancer cells effectively. Accordingly, we investigated the apoptotic effect and possible mechanism of the ethanol extract from Taiwanofungus salmoneus (=Antrodia salmonea) mycelium (TsE) alone or in combination with cisplatin in SK-Hep-1 cells. In this study, the proliferation of SK-Hep-1 cells could be inhibited at various concentrations of TsE for 24 h whereas TsE combined with cisplatin would inhibit the cell proliferation more notably. Moreover, the DNA damage and the interruption of cell cycle of SK-Hep-1 cells would be effectively raised after incubation with TsE combined with cisplatin for 24 h. The apoptosis of cells was dramatically induced, and the expression of caspases 3, 8, and 9, apoptosis-related protein, were significantly upregulated. Therefore, we proposed that the TsE combined with cisplatin inhibited cell proliferation by elevating sub-G1 phase, inducing DNA damage, activating caspases 3, 8, and 9 activities, and triggering cells apoptosis. These results reveal that TsE could be a potential adjuvant chemotherapeutic agent.