emPDBA: protein-DNA binding affinity prediction by combining features from binding partners and interface learned with ensemble regression model.

Protein-deoxyribonucleic acid (DNA) interactions are important in a variety of biological processes. Accurately predicting protein-DNA binding affinity has been one of the most attractive and challenging issues in computational biology. However, the existing approaches still have much room for improvement. In this work, we propose an ensemble model for Protein-DNA Binding Affinity prediction (emPDBA), which combines six base models with one meta-model. The complexes are classified into four types based on the DNA structure (double-stranded or other forms) and the percentage of interface residues. For each type, emPDBA is trained with the sequence-based, structure-based and energy features from binding partners and complex structures. Through feature selection by the sequential forward selection method, it is found that there do exist considerable differences in the key factors contributing to intermolecular binding affinity. The complex classification is beneficial for the important feature extraction for binding affinity prediction. The performance comparison of our method with other peer ones on the independent testing dataset shows that emPDBA outperforms the state-of-the-art methods with the Pearson correlation coefficient of 0.53 and the mean absolute error of 1.11 kcal/mol. The comprehensive results demonstrate that our method has a good performance for protein-DNA binding affinity prediction. Availability and implementation: The source code is available at https://github.com/ChunhuaLiLab/emPDBA/.

Specific recognition between YTHDF3 and m6 A-modified RNA: An all-atom molecular dynamics simulation study.

The YTH domain of YTHDF3 belongs to a class of protein "readers" recognizing the N6-methyladenosine (m6 A) modification in mRNA. Although static crystal structure reveals m6 A recognition by a conserved aromatic cage, the dynamic process in recognition and importance of aromatic cage residues are not completely clear. Here, molecular dynamics (MD) simulations are performed to explore the issues and negative selectivity of YTHDF3 toward unmethylated substrate. Our results reveal that there exist conformation selectivity and induced-fit in YTHDF3 binding with m6 A-modified RNA, where recognition loop and loop6 play important roles in the specific recognition. m6 A modification enhances the stability of YTHDF3 in complex with RNA. The methyl group of m6 A, like a warhead, enters into the aromatic cage of YTHDF3, where Trp492 anchors the methyl group and constraints m6 A, making m6 A further stabilized by π-π stacking interactions from Trp438 and Trp497. In addition, the methylation enhances the hydrophobicity of adenosine, facilitating water molecules excluded out of the aromatic cage, which is another reason for the specific recognition and stronger intermolecular interaction. Finally, the comparative analyses of hydrogen bonds and binding free energy between the methylated and unmethylated complexes reveal the physical basis for the preferred recognition of m6 A-modified RNA by YTHDF3. This study sheds light on the mechanism by which YTHDF3 specifically recognizes m6 A-modified RNA and can provide important information for structure-based drug design.

Key Residues in δ Opioid Receptor Allostery Explored by the Elastic Network Model and the Complex Network Model Combined with the Perturbation Method.

Opioid receptors, a kind of G protein-coupled receptors (GPCRs), mainly mediate an analgesic response via allosterically transducing the signal of endogenous ligand binding in the extracellular domain to couple to effector proteins in the intracellular domain. The δ opioid receptor (DOP) is associated with emotional control besides pain control, which makes it an attractive therapeutic target. However, its allosteric mechanism and key residues responsible for the structural stability and signal communication are not completely clear. Here we utilize the Gaussian network model (GNM) and amino acid network (AAN) combined with perturbation methods to explore the issues. The constructed fcfGNMMD, where the force constants are optimized with the inverse covariance estimation based on the correlated fluctuations from the available DOP molecular dynamics (MD) ensemble, shows a better performance than traditional GNM in reproducing residue fluctuations and cross-correlations and in capturing functionally low-frequency modes. Additionally, fcfGNMMD can consider implicitly the environmental effects to some extent. The lowest mode can well divide DOP segments and identify the two sodium ion (important allosteric regulator) binding coordination shells, and from the fastest modes, the key residues important for structure stabilization are identified. Using fcfGNMMD combined with a dynamic perturbation-response method, we explore the key residues related to the sodium ion binding. Interestingly, we identify not only the key residues in sodium ion binding shells but also the ones far away from the perturbation sites, which are involved in binding with DOP ligands, suggesting the possible long-range allosteric modulation of sodium binding for the ligand binding to DOP. Furthermore, utilizing the weighted AAN combined with attack perturbations, we identify the key residues for allosteric communication. This work helps strengthen the understanding of the allosteric communication mechanism in δ opioid receptor and can provide valuable information for drug design.

Standardized measurement of mid-surface shift of brain based on deep Hough transform.

The measurement of mid-surface shift (MSS), the geometric displacement between the actual mid-surface and the ideal midsagittal plane (iMSP), is of great significance for accurate diagnosis, treatment and prognosis of patients with intracranial hemorrhage (ICH). Most previous studies are subject to inherent inaccuracy on account of calculating midline shift (MLS) based on 2D slices and ignoring pathological conditions. In this study, we propose a novel standardized measurement model to quantify the distance and the overall volume of mid-surface shift (MSS-D, MSS-V). Our work has four highlights. First, we develop an end-to-end network architecture with multiple sub-tasks including the actual mid-surface segmentation, hematoma segmentation and iMSP detection, which significantly improves the efficiency and accuracy of MSS measurement by taking advantage of the common properties among tasks. Second, an efficient iMSP detection scheme is proposed based on the differentiable deep Hough transform (DHT), which converts and simplifies the plane detection problem in the image space into a keypoint detection problem in the Hough space. Third, we devise a sparse DHT strategy and a weighted least square (WLS) method to increase the sparsity of features, improving inference speed and greatly reducing computation cost. Fourth, we design a joint loss function to comprehensively consider the correlation of features between multi-tasks and multi-domains. Extensive validation on our large in-house dataset (519 patients) and the public CQ500 dataset (491 patients), demonstrates the superiority of our method over the state-of-the-art methods.

Insight into the nucleoside transport and inhibition of human ENT1.

The human equilibrative nucleoside transporter 1 (hENT1) is an effective controller of adenosine signaling by regulating its extracellular and intracellular concentration, and has become a solid drug target of clinical used adenosine reuptake inhibitors (AdoRIs). Currently, the mechanisms of adenosine transport and inhibition for hENT1 remain unclear, which greatly limits the in-depth understanding of its inner workings as well as the development of novel inhibitors. In this work, the dynamic details of hENT1 underlie adenosine transport and the inhibition mechanism of the non-nucleoside AdoRIs dilazep both were investigated by comparative long-time unbiased molecular dynamics simulations. The calculation results show that the conformational transitions of hENT1 from the outward open to metastable occluded state are mainly driven by TM1, TM2, TM7 and TM9. One of the trimethoxyphenyl rings in dilazep serves as the adenosyl moiety of the endogenous adenosine substrate to competitively occupy the orthosteric site of hENT1. Due to extensive and various VDW interactions with N30, M33, M84, P308 and F334, the other trimethoxyphenyl ring is stuck in the opportunistic site near the extracellular side preventing the complete occlusion of thin gate simultaneously. Obviously, dilazep shows significant inhibitory activity by disrupting the local induce-fit action in substrate binding cavity and blocking the transport cycle of whole protein. This study not only reveals the nucleoside transport mechanism by hENT1 at atomic level, but also provides structural guidance for the subsequent design of novel non-nucleoside AdoRIs with enhanced pharmacologic properties.

Allosteric mechanism for SL RNA recognition by polypyrimidine tract binding protein RRM1: An atomistic MD simulation and network-based study.

Polypyrimidine tract-binding protein (PTB), an RNA-binding protein, is involved in the regulation of diverse processes in mRNA metabolism. However, the allosteric modulation of its binding with RNA remains unclear. We explore the dynamic characteristics of PTB RNA recognition motif 1 (RRM1) in its RNA-free and wild-type/mutant RNA-bound states to understand the issues using molecular dynamics (MD) simulation, perturbation response scanning (PRS) and protein structure network (PSN) models. It is found that RNA binding strengthens RRM1 stability, while L151G mutation in α3 helix far away from the interface makes the complex unstable. The latter is caused by long-distance dynamic couplings, which makes intermolecular electrostatic and entropy energies unfavorable. The weakened couplings between interface ß sheets and C-terminal parts upon mutation reveal RNA recognition is co-regulated by these regions. Interestingly, PRS analysis reveals the allostery caused by the perturbation on α3 helix has already been pre-encoded in the equilibrium dynamics of the protein structure. PSN analysis shows the details of the allosteric signal transmission, revealing the necessity of strong couplings between α3 helix and interface for maintaining the high binding affinity. This study sheds light on the mechanisms of PTB allostery and RNA recognition and can provide important information for drug design.

Clinical study on the wrist-ankle acupuncture treatment for 30 cases of diabetic peripheral neuritis.

OBJECTIVE: To study the mechanisms of wrist-ankle acupuncture for prevention and treatment of diabetic peripheral neuritis. METHODS: Ninety cases of diabetic peripheral neuritis were randomly divided into 3 groups, and treated respectively with wrist-ankle acupuncture, body-acupuncture, and the western routine medical treatment, with 30 cases in each of the groups; and therapeutic effects and laboratory results compared. RESULTS: It is proved that the therapeutic effects of the wrist-ankle acupuncture group and body acupuncture group were significantly superior to those of the control group, with no significant differences between the former two groups. CONCLUSION: Wrist-ankle acupuncture has the actions of improving the metabolisms of blood sugar and blood-lipid, lowering down blood viscosity, and restoring the functions of peripheral nerve cells, thus giving definite therapeutic effects for diabetic peripheral neuritis.

Downregulation of growth differentiation factor-15 in trichostatin A-induced apoptosis could play a role in progression of gastric cancer.

AIM: To investigate the effect of trichostatin A (TSA) on gastric cancer cell line BGC-823, and identify the differentially expressed genes induced by TSA, which might participate in the progression of gastric cancer. METHODS: MTT, fluorescence microscopy, and flow cytometry were used to detect the effect of TSA on growth inhibition and apoptosis of BGC-823 cells. Using gene microarray, we analyzed the changes in gene expression. Change in growth differentiation factor-15 (GDF-15) was verified by qRT-PCR and Western blotting. The expression of GDF-15 in gastric cancer and adjacent normal tissues was detected by immunohistochemistry. RESULTS: Apoptosis of BGC-823 cells induced by TSA (75 ng/mL for 48 h) was demonstrated by flow cytometry. There were significant variations between TSA treated groups and control groups (P = 0.02). Nuclear chromatin condensation and fluorescence intensity were observed by fluorescence microscopy. GDF-15 gene expression and protein level were significantly reduced in the TSA treated group (75 ng/mL for 48 h). Immunohistochemistry demonstrated that the expression of GDF-15 in gastric adenocarcinoma was significantly higher than in the surrounding normal tissues (P < 0.05). CONCLUSION: Lower GDF-15 gene expression due to TSA-induced apoptosis was found in gastric cancer cell line BGC-823. Higher GDF-15 gene expression was seen in gastric adenocarcinoma tissues.

Differential expression of glycoprotein non-metastatic melanoma protein B (GPNMB) involved in trichostatin A-induced apoptosis in gastric cancer.

In this study, we investigated the effect of trichostatin A (TSA) on the gastric cancer cell line BGC-823. The effect of TSA on growth inhibition and apoptosis of BGC-823 cells was examined. The gene expression profile was determined by microarray. Western blotting was used to study the levels of acetylated histone H4 and Glycoprotein non-metastatic melanoma protein B (GPNMB) proteins. GPNMB gene expression was measured by real-time PCR. GPNMB protein levels in gastric adenocarcinoma tissues and adjoining normal tissues were detected by immunohistochemistry. The results showed that a significant decrease in cell population following treatment with 75 ng/mL TSA for 48 h (0.87 ± 0.04) as compared to control (1.14 ± 0.06) (P = 0.02). Apoptotic cells were increased in TSA (75 ng/mL for 48 h) treated group as compared to the control group (from 2.02% to 19.74%) by flow cytometry. The expression of acetylated histone H4 was increased in TSA treated (75 ng/mL for 48 h) group (from 1.00 ± 0.26 to 1.87 ± 0.33, F = 5.862, P = 0.0038) as compared to the control group by Western blotting. After 48 h TSA treatment (75 ng/mL), BGC-823 cells showed decrease in GPNMB gene expression (from 1.00 ± 0.21 to 0.59 ± 0.11, F = 6.214, P = 0.0018). Immunohistochemistry showed that GPNMB expression in gastric adenocarcinoma was significantly higher than the adjoining normal tissues (P = 0.000). To conclusion, our results support that TSA can induce apoptosis, and increase acetylated histone H4 in BGC-823 cells. GPNMB expression is decreased in BGC-823 cells after TSA treatment. GPNMB is overexpressed in gastric adenocarcinoma tissue. GPNMB involved in TSA-induced apoptosis might participate in gastric cancer.

Experience of congenital choledochal cyst in adults:treatment, surgical procedures and clinical outcome in the Second Affiliated Hospital of Harbin Medical University.

This study was undertaken to analyze and evaluate the diagnosis and principal treatment methods for congenital choledochal cyst, focusing on various surgical procedures and clinical outcome. A comprehensive, retrospective study was conducted on 72 adult patients who presented with choledochal cyst from 1985 to 2002. Surgical procedures were cyst excision with hepaticojejunostomy in 25 cases for type I or type IV-B, extrahepatic cyst excision with hepaticojejunostomy in 8 cases for type IV-A, extrahepatic cyst excision with modified hepaticojejunostomy in 2 cases for type IV-B, non-cyst excision with or without hepaticojejunostomy in 27 cases for types I, II, IV-A, IV-B. The early postoperative morbidity and mortality rate were 16.1% (9/62) and 6.5% (4/62) respectively, and the complication rate related to surgical procedure was 30.6% (19/62). The incidence of cholangiocarcinoma with non-cyst excision or non-operated congenital choledochal cyst was 10.8% (4/37). One patient died of primary hepatocellular carcinoma after cyst excision with hepatojejunostomy. In conclusion, our results showed that complete excision of choledochal cyst for types I, II, and IV-B and complete excision of extrahepatic choledochal cyst from the hepatic hilum in type IV-A with hepaticojejunostomy or modified hepaticojejunostomy are the treatment of choice for choledochal cyst in adult patients.