Short-Form CDYLb but not long-form CDYLa functions cooperatively with histone methyltransferase G9a in hepatocellular carcinomas.

In hepatocellular carcinomas (HCCs), the levels of histone H3 dimethylation at lysine 9 (H3K9me2) and its corresponding histone methyltransferase G9a are significantly elevated. Recently, G9a was reported to form a complex with the H3K9 methylation effector protein CDYL, but little is known about the expression of CDYL in HCC patients. The human CDYL gene produces two transcripts, a long form (CDYLa) and a short form (CDYLb), but it is unclear whether the protein products have different functions.

Enhancement of survivin-specific anti-tumor immunity by adenovirus prime protein-boost immunity strategy with DDA/MPL adjuvant in a murine melanoma model.

As an ideal tumor antigen, survivin has been widely used for tumor immunotherapy. Nevertheless, no effective protein vaccine targeting survivin has been reported, which may be due to its poor ability to induce cellular immunity. Thus, a suitable immunoadjuvant and optimized immunization strategy can greatly enhance the cellular immune response to this protein vaccine.

Prediction of deleterious nonsynonymous single-nucleotide polymorphism for human diseases.

The identification of genetic variants that are responsible for human inherited diseases is a fundamental problem in human and medical genetics. As a typical type of genetic variation, nonsynonymous single-nucleotide polymorphisms (nsSNPs) occurring in protein coding regions may alter the encoded amino acid, potentially affect protein structure and function, and further result in human inherited diseases. Therefore, it is of great importance to develop computational approaches to facilitate the discrimination of deleterious nsSNPs from neutral ones.

Characteristics of neutralizing antibodies to adenovirus capsid proteins in human and animal sera.

Although it is known that Ad5-specific neutralizing antibodies (NAbs) against three major viral capsid components (hexon, penton and fiber) are generated, differences in the frequency and nature of these pre-existing NAbs remain unclear. The results emphasized the contribution of anti-fiber antibodies to Ad5 neutralization responses generated during natural viral infection. Additionally, Ad5-specific NAbs against the fiber knob protein were present in over 90% of the positive serum samples while 42% of the sera had NAbs against hexon in this study based on neutralization assay of anti-HVR and anti-knob subtracted sera and Western blotting analysis.

Overexpression of inactive tetherin delGPI mutant inhibits HIV-1 Vpu-mediated antagonism of endogenous tetherin.

Tetherin/BST-2/CD317 inhibits HIV-1 release from infected cells, but the viral Vpu protein efficiently antagonizes this antiviral activity through direct interaction between the transmembrane (TM) domains of each protein. Here, we demonstrated that overexpression of an inactive tetherin delGPI mutant, the TM domain of which could competitively block Vpu targeting of endogenous tetherin, potently inhibited HIV-1 release from human tetherin-positive cells in both transient and stable expression conditions. These results also suggest that heterologous dimerization occurred between the delGPI mutant and endogenous tetherin.

Vertical etching with isolated catalysts in metal-assisted chemical etching of silicon.

Metal assisted chemical etching with interconnected catalyst structures has been used to create a wide array of organized nanostructures. However, when patterned catalysts are not interconnected, but are isolated instead, vertical etching to form controlled features is difficult. A systematic study of the mechanism and catalyst stability of metal assisted chemical etching (MACE) of Si in HF and H(2)O(2) using Au catalysts has been carried out.

Identification of disease-related nsSNPs via the integration of protein sequence features and domain-domain interaction data.

Recent studies have suggested the common disease-rare variant (CD-RV) hypothesis in the mapping of disease-related genetic variants and have proposed a number of statistical methods to detect associations between rare variants and human inherited diseases. However, most of these methods take the selection of functional variants as a preliminary step in order to maximise the power of statistical tests. To meet this end, we put forward a filtration approach to identify genetic variants that are potentially associated with a query disease of interest from the perspective of one-class novelty learning.

DNA and adenovirus tumor vaccine expressing truncated survivin generates specific immune responses and anti-tumor effects in a murine melanoma model.

Survivin is overexpressed in major types of cancer and is considered an ideal "universal" tumor-associated antigen that can be targeted by immunotherapeutic vaccines. However, its anti-apoptosis function raises certain safety concerns. Here, a new truncated human survivin, devoid of the anti-apoptosis function, was generated as a candidate tumor vaccine.

Small-molecule inhibition of human immunodeficiency virus type 1 replication by targeting the interaction between Vif and ElonginC.

The HIV-1 viral infectivity factor (Vif) protein is essential for viral replication. Vif recruits cellular ElonginB/C-Cullin5 E3 ubiquitin ligase to target the host antiviral protein APOBEC3G (A3G) for proteasomal degradation. In the absence of Vif, A3G is packaged into budding HIV-1 virions and introduces multiple mutations in the newly synthesized minus-strand viral DNA to restrict virus replication.

Prioritisation of candidate Single Amino Acid Polymorphisms using one-class learning machines.

Recent advancements of the next-generation sequencing technology have enabled the direct sequencing of rare genetic variants in both case and control individuals. Although there have been a few statistical methods for uncovering potential associations between multiple rare variants and human inherited diseases, most of these methods require computational approaches to filter out non-functional variants for the purpose of maximising the statistical power. To tackle this problem, we formulate the detection of genetic variants that are associated with a specific type of disease from the perspective of one-class novelty learning.

Physical and functional antagonism between tumor suppressor protein p53 and fortilin, an anti-apoptotic protein.

Tumor suppressor protein p53, our most critical defense against tumorigenesis, can be made powerless by mechanisms such as mutations and inhibitors. Fortilin, a 172-amino acid polypeptide with potent anti-apoptotic activity, is up-regulated in many human malignancies. However, the exact mechanism by which fortilin exerts its anti-apoptotic activity remains unknown.

Identification of binding epitope for anti-rabies virus glycoprotein single-chain Fv fragment FV57.

Single-chain Fv fragment (scFv) of anti-rabies glycoprotein (G protein) has been recommended as a new agent for detecting and neutralizing lethal rabies virus. In this study, we constructed scFv that corresponded to the FV fragment of CR57, a monoclonal antibody against rabies virus, and called it FV57. Despite its virus neutralization activity, FV57 may or may not recognize the same epitope as that recognized by CR57.

Structural and functional analysis of the C-terminus of Galphaq in complex with the human thromboxane A2 receptor provides evidence of constitutive activity.

The human thromboxane A(2) (TXA(2)) receptor (TP) is known to mediate platelet aggregation and vasoconstriction. The receptor predominantly interacts with the Gq protein, thereby activating phospholipase C and increasing the intracellular calcium level. In this study, we synthesized a 15-residue peptide corresponding to the C-terminal domain of the Gq protein alpha subunit (Galphaq-Ct peptide) and characterized its interaction with recombinant TP purified from a baculovirus expression system in the presence and absence of an agonist using fluorescence and NMR spectroscopic studies.

Ligand-specific conformation determines agonist activation and antagonist blockade in purified human thromboxane A2 receptor.

The binding of an agonist to a G protein-coupled receptor (GPCR) causes its coupling to different G proteins, which mediate signaling. However, the binding of an antagonist to the same site of the GPCR could not induce coupling. To understand the molecular mechanism involved, the structural flexibility of the purified human thromboxane A2 receptor (TP) was characterized by spectroscopic approaches, while bound to an agonist or antagonist.

Involvement of non-conserved residues important for PGE2 binding to the constrained EP3 eLP2 using NMR and site-directed mutagenesis.

A peptide constrained to a conformation of second extracellular loop of human prostaglandin-E(2) (PGE(2)) receptor subtype3 (hEP3) was synthesized. The contacts between the peptide residues at S211 and R214, and PGE(2) were first identified by NMR spectroscopy. The results were used as a guide for site-directed mutagenesis of the hEP3 protein.

Characterization of the prostaglandin H2 mimic: binding to the purified human thromboxane A2 receptor in solution.

For decades, the binding of prostaglandin H(2) (PGH(2)) to multiple target proteins of unrelated protein structures which mediate diverse biological functions has remained a real mystery in the field of eicosanoid biology. Here, we report that the structure of a PGH(2) mimic, U46619, bound to the purified human TP, was determined and compared with that of its conformation bound to the COX-downstream synthases, prostacyclin synthase (PGIS) and thromboxane A(2) synthase (TXAS). Active human TP protein, glycosylated and in full length, was expressed in Sf-9 cells using a baculovirus (BV) expression system and then purified to near homogeneity.

A simple, quick, and high-yield preparation of the human thromboxane A2 receptor in full size for structural studies.

Human thromboxane A2 receptor (TP), a G protein-coupled receptor (GPCR), is one of the most promising targets for developing the next generation of anti-thrombosis and hypertension drugs. However, obtaining a sufficient amount of the full-sized and active membrane protein has been the major obstacle for structural elucidation that reveals the molecular mechanisms of the receptor activation and drug designs. Here we report an approach for the simple, quick, and high-yield preparation of the purified and active full-sized TP in an amount suitable for structural studies.

Characterization of the substrate mimic bound to engineered prostacyclin synthase in solution using high-resolution NMR spectroscopy and mutagenesis: implication of the molecular mechanism in biosynthesis of prostacyclin.

High-resolution NMR spectroscopy was used to determine the docking of a substrate (prostaglandin H2) mimic (U46619) to the engineered prostacyclin (PGI2) synthase (PGIS) in solution. The binding of U46619 to the PGIS protein was demonstrated by 1D NMR titration, and the significant perturbation of the chemical shifts of protons at C-11, H2C, and H20 of U46619 were observed upon U46619 binding to the engineered PGIS in a concentration-dependent manner. The detailed conformational change and 3D structure of the PGIS-bound U46619 were further demonstrated by 2D 1H NMR experiments using the transferred NOE technique.

Assembling NMR structures for the intracellular loops of the human thromboxane A2 receptor: implication of the G protein-coupling pocket.

It has been reported that the multiple intracellular loops (iLPs) of the thromboxane A(2) receptor (TP) are involved in the receptor G protein coupling. In this study, a high-resolution 2D NMR technique was used to determine the 3D structures of the first, second, and third iLPs of the TP using synthetic peptides constrained into the loop structures. 2D (1)H NMR spectra, TOCSY and NOESY were obtained for the two peptides from proton NMR experiments.

Solution structure of the first intracellular loop of prostacyclin receptor and implication of its interaction with the C-terminal segment of G alpha s protein.

The amino acids (residues 39-51) responsible for the interaction between the first intracellular loop (iLP1) of the human prostacyclin receptor (IP) and G alpha s protein have been identified [Zhang, L., Huang, G., Wu, J.

Solution structure of a common substrate mimetic of cyclooxygenase-downstream synthases bound to an engineered thromboxane A2 synthase using a high-resolution NMR technique.

Understanding the docking mechanism of the common substrate, prostaglandin H(2) (PGH(2)), into the active sites of different cyclooxygenase(COX)-downstream synthases is a key step toward uncovering the molecular basis of the isomerization of PGH(2) to different prostanoids. A high-resolution NMR spectroscopy was used to determine the conformational changes and solution 3D structure of U44069, a PGH(2) analogue, bound to one of the COX-downstream synthases-an engineered thromboxane A(2) synthase (TXAS). The dynamic binding was clearly observed by (1)D NMR titration.

A profile of the residues in the first intracellular loop critical for Gs-mediated signaling of human prostacyclin receptor characterized by an integrative approach of NMR-experiment and mutagenesis.

The first intracellular loop (iLP1, residues 39-51) of human prostacyclin receptor (IP) was proposed to be involved in signaling via its interaction with the Galphas protein. First, evidence of the IP iLP1 interaction with the C-terminus of the Galphas protein was observed by the fluorescence and NMR spectroscopy using the synthetic peptide (Galphas-Ct) mimicking the C-terminal 11 residues of the Galphas protein in the presence of a constrained synthetic peptide mimicking the IP iLP1. Then, the residues (Arg42, Ala44, and Arg45) in the IP iLP1 peptide possibly involved in contacting the Galphas-Ct peptide were initially assigned by observation of the significant proton resonance shifts of the side chains of the constrained IP iLP1 peptide using 2D (1)H NMR spectroscopy.