Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces

Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with the physicochemical complementarity features based on the non-covalent interaction data derived from protein interiors

Photo-reduction and adsorption in aqueous Cr(VI) solution by titanium dioxide, carbon nanotubes and their composite

Background: This study compared the removal of aqueous Cr(VI) by multi-walled carbon nanotubes (CNTs) modified by sulfuric acid, titanium dioxide (TiO_2) and composite of CNTs and TiO_2. Results: More than 360 h contact time was needed to completely adsorb 3 mg L^(−1) of Cr(VI) by CNTs, indicating that the rate of adsorption by CNTs alone was slow. The reaction time approaching equilibrium depended on the Cr(VI) concentration. XPS analysis of CNTs after adsorbing Cr(VI) showed that the Cr(VI) on the surface of CNTs was partially reduced to Cr(III). A 3 mg L^(−1) solution of Cr(VI) was fully photocatalyzed by commercial TiO_2 (Degussa P25) in less than 0.5 h under UV irradiation. Unlike P25, reduction by another commercial TiO_2 (Hombikat UV100) took 4 h and more than 2 h were necessary for reduction by the composite. Thus the efficiency of Cr(VI) photo-reduction by the composite was lower than by TiO_2, but higher than that by CNTs. XPS analysis of TiO_2 and composite showed the existence of both Cr(VI) and Cr(III) on their surfaces. Conclusion: In contrast to TiO_2, the reduction rate of aqueous Cr(VI) using CNTs as adsorbent was slow. P25 had a markedly higher photocatalytic efficiency than the composite or UV100 alone. Using P25 to reduce aqueous Cr(VI) has a higher potential for practical application. The diameters of TiO_2 and CNTs and the ratio of TiO_2/CNTs are key problems in the preparation of TiO_2/CNTs composite

The Tzs Protein and Exogenous Cytokinin Affect Virulence Gene Expression and Bacterial Growth of Agrobacterium tumefaciens

The soil phytopathogen Agrobacterium tumefaciens causes crown galldisease in a wide range of plant species. The neoplastic growth at theinfection sites is caused by transferring, integrating, and expressingtransfer DNA (T-DNA) from A. tumefaciens into plant cells. A transzeatinsynthesizing (tzs) gene is located in the nopaline-type tumor-inducingplasmid and causes trans-zeatin production in A. tumefaciens.Similar to known virulence (Vir) proteins that are induced by the vir geneinducer acetosyringone (AS) at acidic pH 5.5, Tzs protein is highlyinduced by AS under this growth condition but also constitutively expressedand moderately upregulated by AS at neutral pH 7.0. We foundthat the promoter activities and protein levels of several AS-induced virgenes increased in the tzs deletion mutant, a mutant with decreasedtumorigenesis and transient transformation efficiencies, in Arabidopsisroots. During AS induction and infection of Arabidopsis roots, the tzsdeletion mutant conferred impaired growth, which could be rescued bygenetic complementation and supplementing exogenous cytokinin. Exogenouscytokinin also repressed vir promoter activities and Vir proteinaccumulation in both the wild-type and tzs mutant bacteria with ASinduction. Thus, the tzs gene or its product, cytokinin, may be involved inregulating AS-induced vir gene expression and, therefore, affect bacterialgrowth and virulence during A. tumefaciens infection

Comparative leaf proteomic profiling of salt-treated natural variants of Imperata cylindrica

Cogon grass (Imperata cylindrica (L.) Beauv. var. major (Nees) Hubb.) is one of the top-ten weeds worldwide. It is also a C4 medicinal plant. In particular, an ecotype from Chuwei (CW) mangrove forest was found to be salt tolerant. Comparative proteomic analysis using two-dimensional (2D)-difference in gel electrophoresis coupled with liquid chromatography-mass spectrometry (LC-MS) was carried out to identify responsive leaf proteins in the CW ecotype and salt-intolerant Sarlun (SL) population following three days of 150 mM sodium chloride salt stress treatment. We identified five photosynthesis proteins including Rubisco small subunit, uncharacterized protein LOC100194054, Cyt b6-f, oxygen-evolving enhancer 2, and photosystem I reaction center subunit IV which were significantly up- or down-regulated by salt stress in CW ecotype but not SL population. Gene ontology enrichment analysis showed that photosynthesis was over-represented. The mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD008482. Taken together, our proteomic study identified differentially accumulated proteins which provide additional evidence of ecophysiological variation in two natural variants of I. cylindrica

Raman Spectroscopic Characteristics of Zeolite Group Minerals

In this work, Raman spectroscopic experiments are conducted on zeolites, including a total of 33 varieties and seven groups with different secondary structural frameworks, for which characteristic vibration modes are studied. Most of the zeolites show prominent Raman peaks in the spectral range between 200–1200 cm−1. Different groups of zeolites can be recognized by differences in the wavenumbers of the T-O-T (T = Si and Al, O = oxygen) modes in the range 379–538 cm−1, the M-O (M = metal,) modes in the range 250–360 cm−1 and the T-O bending modes in the range 530–575 cm−1. All zeolites show characteristic Raman peaks in the range 379–529 cm−1, except for natrolite group (fibrous) zeolites, which are characterized by T-O-T modes in the 433–447 cm−1 range and T-O bending modes in the 528–538 cm−1 range. The analcime group (with singly connected four-ring chains) zeolites show T-O-T modes in the 379–392 cm−1 and 475–497 cm−1 ranges. The gismondine group (with doubly connected four-ring chains) zeolites have T-O-T modes in the 391–432 cm−1 and 463–497 cm−1 ranges. The chabazite group (with a six-cyclic ring) zeolites are characterized by M-O modes in the 320–340 cm−1 range and T-O-T modes in the 477–509 cm−1 range. The Raman modes of mordenite group zeolites (397–410 cm−1 and 470–529 cm−1) overlap with those of heulandite group zeolites (402–416 cm−1 and 480–500 cm−1). Moreover, the mordenite group has a characteristic peak in the 502–529 cm−1 range, and an additional peak in the 800–965 cm−1 range. Another recognizable peak for the heulandite group is in the 612–620 cm−1 range. The unknown zeolites (cowlesite) have unique characteristic peaks at 534 cm−1, which can aid in the verification of their identity

Sympathovagal imbalance in prehypertension status

Background: Heart rate variability (HRV) had been promoted for longer than half a century to monitor the activity of autonomic nerve systems. Previous studies have not clarified the relationship between HRV and prehypertension (pre-HTN) status compared with the normal group. We aimed to figure out the optimal model or cutoff point for predicting the possible pre-HTN status. Patients and Methods: We retrospectively collected and reviewed 2586 Asian people who had joined annual physical examination in Tri-Service General Hospital at 2013. The patient profiles such as age, gender, body height, body weight, body weight index, waist circumferences, and serological biochemistry data were analyzed and correlated with HRV parameter. Results: A total number of 909 patients were enrolled in our study. The physical stress index (PSI) owed a small but most significant Spearman's relation coefficient (r = 0.118, P58.4. Early intervention to these participants may decrease cardiovascular events in the coming future

Aqueous Ocimum gratissimum extract induces cell apoptosis in human hepatocellular carcinoma cells

Treatment of advanced hepatocellular carcinoma (HCC) has exhibited a poor overall survival rate of only six to ten months, and the urgency of the development of more effective novel agents is ever present. In this line of research, we aimed to investigate the effects and inhibitive mechanisms of aqueous Ocimum gratissimum leaf extract (OGE), the extract of Ocimum gratissimum, which is commonly used as a therapeutic herb for its numerous pharmacological properties, on malignant HCC cells. Our results showed that OGE decreased the cell viability of HCC SK-Hep1 and HA22T cells in a dose-dependent manner (from 400 to 800 µg/mL), while there is little effect on Chang liver cells. Moreover, cell-cycle analysis shows increased Sub-G1 cell count in SK-Hep1 and HA22T cells which is not observed in Chang liver cells. These findings raise suspicion that the OGE-induced cell death may be mediated through proteins that regulate cell cycle and apoptosis in SK-Hep1 and HA22T cells, and further experimentation revealed that OGE treatment resulted in a dose-dependent decrease in caspase 3 and PARP expressions and in CDK4and p-ERK1/2expressions. Moreover, animal tests also exhibited decreased HCC tumor growth by OGE treatment. We therefore suggest that the inhibition of cell viability and tumor growth induced by OGE may be correlated to the alteration of apoptosis-related proteins

Involvement of extracellular signal-regulated kinase (ERK) in CXCL12-induced connective tissue growth factor (CTGF) expression in WI-38 cells.

<p>A, Cells were pretreated with 10 and 30 µM PD98059 for 30 min and then stimulated with CXCL12 (10 ng/ml) for another 2 h. Whole-cell lysates were prepared and immunodetected with specific antibodies for the CTGF or α-tubulin. Data are presented as the mean ± S.E. of three experiments. *<i>p</i><0.05, compared to CXCL12 treatment. B, Cells were treated with CXCL12 (10 ng/ml) for 0∼20 min. Whole-cell lysates were prepared and immunodetected with specific antibodies for phospho-ERK Tyr 204 or ERK2. Data are presented as the mean ± S.E. of three experiments. *<i>p</i><0.05, compared to the control without CXCL12 stimulation.</p

Schematic summary of the signal transduction pathway by which CXCL12 induces connective tissue growth factor (CTGF) expression in human lung fibroblasts (WI-38).

<p>CXCL12 acts on CXCR4 to activate the Rac/extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK) signaling pathways, which in turn initiates activator protein-1 (AP-1) activation, and ultimately causes CTGF expression. Moreover, CTGF mediates CXCL12-induced α-smooth muscle actin (α-SMA) expression in human lung fibroblasts.</p