Molecular Dynamic Simulation to Explore the Molecular Basis of Btk-PH Domain Interaction with Ins(1,3,4,5)P4

Bruton’s tyrosine kinase contains a pleckstrin homology domain, and it specifically binds inositol 1,3,4,5-tetrakisphosphate (Ins(1,3,4,5)P4), which is involved in the maturation of B cells. In this paper, we studied 12 systems including the wild type and 11 mutants, K12R, S14F, K19E, R28C/H, E41K, L11P, F25S, Y40N, and K12R-R28C/H, to investigate any change in the ligand binding site of each mutant. Molecular dynamics simulations combined with the method of molecular mechanics/Poisson-Boltzmann solvent-accessible surface area have been applied to the twelve systems, and reasonable mutant structures and their binding free energies have been obtained as criteria in the final classification. As a result, five structures, K12R, K19E, R28C/H, and E41K mutants, were classified as “functional mutations,” whereas L11P, S14F, F25S, and Y40N were grouped into “folding mutations.” This rigorous study of the binding affinity of each of the mutants and their classification provides some new insights into the biological function of the Btk-PH domain and related mutation-causing diseases

Catalytic Mechanism Investigation of Lysine-Specific Demethylase 1 (LSD1): A Computational Study

Lysine-specific demethylase 1 (LSD1), the first identified histone demethylase, is a flavin-dependent amine oxidase which specifically demethylates mono- or dimethylated H3K4 and H3K9 via a redox process. It participates in a broad spectrum of biological processes and is of high importance in cell proliferation, adipogenesis, spermatogenesis, chromosome segregation and embryonic development. To date, as a potential drug target for discovering anti-tumor drugs, the medical significance of LSD1 has been greatly appreciated. However, the catalytic mechanism for the rate-limiting reductive half-reaction in demethylation remains controversial. By employing a combined computational approach including molecular modeling, molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations, the catalytic mechanism of dimethylated H3K4 demethylation by LSD1 was characterized in details. The three-dimensional (3D) model of the complex was composed of LSD1, CoREST, and histone substrate. A 30-ns MD simulation of the model highlights the pivotal role of the conserved Tyr761 and lysine-water-flavin motif in properly orienting flavin adenine dinucleotide (FAD) with respect to substrate. The synergy of the two factors effectively stabilizes the catalytic environment and facilitated the demethylation reaction. On the basis of the reasonable consistence between simulation results and available mutagenesis data, QM/MM strategy was further employed to probe the catalytic mechanism of the reductive half-reaction in demethylation. The characteristics of the demethylation pathway determined by the potential energy surface and charge distribution analysis indicates that this reaction belongs to the direct hydride transfer mechanism. Our study provides insights into the LSD1 mechanism of reductive half-reaction in demethylation and has important implications for the discovery of regulators against LSD1 enzymes

Network modelling reveals the mechanism underlying colitis-associated colon cancer and identifies novel combinatorial anti-cancer targets

The connection between inflammation and tumourigenesis has been well established. However, the detailed molecular mechanism underlying inflammation-associated tumourigenesis remains unknown because this process involves a complex interplay between immune microenvironments and epithelial cells. To obtain a more systematic understanding of inflammation-associated tumourigenesis as well as to identify novel therapeutic approaches, we constructed a knowledge-based network describing the development of colitis-associated colon cancer (CAC) by integrating the extracellular microenvironment and intracellular signalling pathways. Dynamic simulations of the CAC network revealed a core network module, including P53, MDM2, and AKT, that may govern the malignant transformation of colon epithelial cells in a pro-tumor inflammatory microenvironment. Furthermore, in silico mutation studies and experimental validations led to a novel finding that concurrently targeting ceramide and PI3K/AKT pathway by chemical probes or marketed drugs achieves synergistic anti-cancer effects. Overall, our network model can guide further mechanistic studies on CAC and provide new insights into the design of combinatorial cancer therapies in a rational manner

Molecular Basis of NDM-1, a New Antibiotic Resistance Determinant

The New Delhi Metallo-β-lactamase (NDM-1) was first reported in 2009 in a Swedish patient. A recent study reported that Klebsiella pneumonia NDM-1 positive strain or Escherichia coli NDM-1 positive strain was highly resistant to all antibiotics tested except tigecycline and colistin. These can no longer be relied on to treat infections and therefore, NDM-1 now becomes potentially a major global health threat

Probing NaCl hydrate formation from aqueous solutions by Terahertz Time-Domain Spectroscopy

The cooling-induced formation of hydrate in aqueous NaCl solutions was probed using terahertz time-domain spectroscopy (THz-TDS). It was found that the NaCl hydrate formation is accompanied with emergence of four new absorption peaks at 1.60, 2.43, 3.34 and 3.78 THz. Combining the X-ray diffraction measurement with the solid-state based density functional theory (DFT) calculations, we assign the observed terahertz absorption peaks to the vibrational modes of the formed NaCl⋅2H2O hydrate during cooling. This work dedicates THz-TDS based analysis great potential in studying ionic hydrate and the newly revealed collective vibrational modes could be the sensitive indicators to achieve quantitative analysis in phase transitions and lattice dynamics

Investigation of the Acetylation Mechanism by GCN5 Histone Acetyltransferase

The histone acetylation of post-translational modification can be highly dynamic and play a crucial role in regulating cellular proliferation, survival, differentiation and motility. Of the enzymes that mediate post-translation modifications, the GCN5 of the histone acetyltransferase (HAT) proteins family that add acetyl groups to target lysine residues within histones, has been most extensively studied. According to the mechanism studies of GCN5 related proteins, two key processes, deprotonation and acetylation, must be involved. However, as a fundamental issue, the structure of hGCN5/AcCoA/pH3 remains elusive. Although biological experiments have proved that GCN5 mediates the acetylation process through the sequential mechanism pathway, a dynamic view of the catalytic process and the molecular basis for hGCN5/AcCoA/pH3 are still not available and none of theoretical studies has been reported to other related enzymes in HAT family. To explore the molecular basis for the catalytic mechanism, computational approaches including molecular modeling, molecular dynamic (MD) simulation and quantum mechanics/molecular mechanics (QM/MM) simulation were carried out. The initial hGCN5/AcCoA/pH3 complex structure was modeled and a reasonable snapshot was extracted from the trajectory of a 20 ns MD simulation, with considering post-MD analysis and reported experimental results. Those residues playing crucial roles in binding affinity and acetylation reaction were comprehensively investigated. It demonstrated Glu80 acted as the general base for deprotonation of Lys171 from H3. Furthermore, the two-dimensional QM/MM potential energy surface was employed to study the sequential pathway acetylation mechanism. Energy barriers of addition-elimination reaction in acetylation obtained from QM/MM calculation indicated the point of the intermediate ternary complex. Our study may provide insights into the detailed mechanism for acetylation reaction of GCN5, and has important implications for the discovery of regulators against GCN5 enzymes and related HAT family enzymes

Computational Analysis of the Binding Specificities of PH Domains

Pleckstrin homology (PH) domains share low sequence identities but extremely conserved structures. They have been found in many proteins for cellular signal-dependent membrane targeting by binding inositol phosphates to perform different physiological functions. In order to understand the sequence-structure relationship and binding specificities of PH domains, quantum mechanical (QM) calculations and sequence-based combined with structure-based binding analysis were employed in our research. In the structural aspect, the binding specificities were shown to correlate with the hydropathy characteristics of PH domains and electrostatic properties of the bound inositol phosphates. By comparing these structure properties with sequence-based profiles of physicochemical properties, PH domains can be classified into four functional subgroups according to their binding specificities and affinities to inositol phosphates. The method not only provides a simple and practical paradigm to predict binding specificities for functional genomic research but also gives new insight into the understanding of the basis of diseases with respect to PH domain structures

Risk factors associated with obstructive sleep apnea-hypopnea syndrome in Chinese children: A single center retrospective case-control study.

Pediatric obstructive sleep apnea-hypopnea syndrome is caused by multiple factors. The present study aimed to investigate the potential risks of pediatric obstructive sleep apnea hypopnea syndrome (OSAHS) and their correlation with the disease severity. A total of 338 pediatric patients with OSAHS (polysomnography (PSG) diagnosis) were enrolled between June 2008 and October 2010. These pediatric patients were divided into mild, moderate and severe subgroups according to the obstructive apnea index (OAI) and/or apnea hypoventilation index (AHI). A total of 338 pediatric patients with vocal nodules who were without obstruction of the upper respiratory tract were enrolled as the control group. The patients were analyzed retrospectively. The average number of upper respiratory tract infections each year and tonsil hypertrophy, adenoid hypertrophy, positive serum tIgE, chronic sinusitis, nasal stenosis, craniofacial features and obesity were significantly higher in OSAHS compared with controls (P<0.01). The parameters the average number of upper respiratory tract infections each year (OR: 1.395, 95% CI: 1.256-1.550), adenoid hypertrophy (OR: 8.632, 95% CI: 3.990-18.672), tonsil hypertrophy (OR: 9.138, 95% CI: 4.621-18.073), nasal stenosis (8.023, 95% CI: 3.633-17.717) and chronic sinusitis (OR: 27.186, 95% CI: 13.310-55.527) were independent factors of pediatric OSAHS (P<0.01). The distribution of chronic sinusitis, nasal stenosis, craniofacial features and obesity indicated a gradual increasing trend in the severity of OSAHS (P<0.01). Number of upper respiratory tract infections per year, adenoid hypertrophy, tonsil hypertrophy, chronic sinusitis, nasal stenosis, infections, allergic reactions, craniofacial features and obesity may be potential risk factors of pediatric OSAHS

LMD Method and Multi-Class RWSVM of Fault Diagnosis for Rotating Machinery Using Condition Monitoring Information

Timely and accurate condition monitoring and fault diagnosis of rotating machinery are very important to maintain a high degree of availability, reliability and operational safety. This paper presents a novel intelligent method based on local mean decomposition (LMD) and multi-class reproducing wavelet support vector machines (RWSVM), which is applied to diagnose rotating machinery faults. First, the sensor-based vibration signals measured from the rotating machinery are preprocessed by the LMD method and product functions (PFs) are produced. Second, statistic features are extracted to acquire more fault characteristic information from the sensitive PF. Finally, these features are fed into a multi-class RWSVM to identify the rotating machinery health conditions. The experimental results validate the effectiveness of the proposed RWSVM method in identifying rotating machinery fault patterns accurately and effectively and its superiority over that based on the general SVM