Transient receptor potential (TRP) channels are widely found throughout the animal kingdom. By serving as cellular sensors for a wide spectrum of physical and chemical stimuli, they play crucial physiological roles ranging from sensory transduction to cell cycle modulation. TRP channels are tetrameric protein complexes. While most TRP subunits can form functional homomeric channels, heteromerization of TRP channel subunits of either the same subfamily or different subfamilies has been widely observed. Heteromeric TRP channels exhibit many novel properties compared to their homomeric counterparts, indicating that co-assembly of TRP channel subunits has an important contribution to the diversity of TRP channel functions.
Animals ; Ankyrin Repeat ; Humans ; Models, Molecular ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits ; TRPC Cation Channels ; chemistry ; genetics ; physiology

Anthocyanins are a ubiquitous group of water-soluble plant pigments of the flavonoid family, with anticancer property through HER-2 signaling pathway. Nowadays, molecular docking plays an important role in exposing the active sites and obtaining the bioactive conformation involving protein-ligand interactions. According to the crystal structure of HER-2 kinase domain and 12 main antitumor compounds of anthocyanins as well as ATP, a molecular docking study was performed by MVD program. All 12 compounds could bind to the same cavity of HER-2 kinase domain by high affinity (MolDock Score < -105 kJ/mol for anthocyanidins, < -130 kJ/mol for anthocyanidins-glc), where hydrophobic force and hydrogen bond played key roles. Additionally, this cavity overlapped with ATP binding (MolDock Score = -161 kJ/mol) domain; the binding of anthocyanins presumably interfered the H bond formation between ATP and HER-2. These results indicate that anthocyanins may competitively bind to ATP binding site in HER-2 kinase domain by suppressing HER-2 activation and downstream signaling cascade. This may provide useful theoretical instruction for the molecular mechanism of HER-2 kinase activity inhibition by anthocyanins in cancer prevention and treatment.
Anthocyanins ; chemistry ; Catalytic Domain ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Molecular Docking Simulation ; Phosphorylation ; Protein Interaction Domains and Motifs ; Receptor, ErbB-2 ; chemistry

The c-Abl nonreceptor tyrosine kinase is activated in the cellular responses to genotoxic, oxidative and other forms of stress. Using tagged forms of c-Abl, the present studies demonstrate that c-Abl forms homodimers in cells. The results show that the c-Abl N-terminal regions interact with the corresponding C-terminal regions of both partners in the dimmer. Specifically, the c-Abl SH3 domain binds to a proline-rich motif at amino acids 958-982 in the c-Abl C-terminal region. Deletion of the proline-rich motif disrupts dimmer formation. These findings provide the first evidence that c-Abl forms homodimers and indicate that homodimerization can contribute to the regulation of c-Abl activity.
Humans ; Protein Multimerization ; Proto-Oncogene Proteins c-abl ; genetics ; metabolism ; src Homology Domains

Proteins are the final executive actor of cell viability and function. Protein-protein interactions determine the complexity of the organism. Research on the protein interactions can help us understand the function of the protein at the molecular level, learn the cell growth, development, differentiation, apoptosis and understand biological regulation mechanisms and other activities. They are essential for understanding the pathologies of diseases and helpful in the prevention and treatment of diseases, as well as in the development of new drugs. In this paper, we employ the single decision-tree classification model to predict protein-protein interactions in the yeast. The original data came from the existing literature. Using software Clementine, this paper analyzes how these attributes affect the accuracy of the model by adjusting the predicted attributes. The result shows that a single decision tree is a good classification model and it has higher accuracy compared to those in the previous researches.
Algorithms ; Decision Trees ; Fungal Proteins ; chemistry ; Models, Theoretical ; Protein Interaction Domains and Motifs ; Protein Interaction Maps

The cystic fibrosis transmembrane conductance regulator (CFTR) is a unique member of the ATP-binding cassette (ABC) transporter superfamily that forms a Cl(-) channel with complex regulation. CFTR is composed of five domains: two membrane-spanning domains (MSDs), two nucleotide-binding domains (NBDs) and a unique regulatory domain (RD). The MSDs assemble to form a low conductance (6-10 pS) anion-selective pore with deep intracellular and shallow extracellular vestibules separated by a selectivity filter. The NBDs form a head-to-tail dimer with two ATP-binding sites (termed sites 1 and 2) located at the dimer interface. Anion flow through CFTR is gated by the interaction of ATP with sites 1 and 2 powering cycles of NBD dimer association and dissociation and hence, conformational changes in the MSDs that open and close the channel pore. The RD is an unstructured domain with multiple consensus phosphorylation sites, phosphorylation of which stimulates CFTR function by enhancing the interaction of ATP with the NBDs. Tight spatial and temporal control of CFTR activity is achieved by macromolecular signalling complexes in which scaffolding proteins colocalise CFTR and plasma membrane receptors with protein kinases and phosphatases. Moreover, a macromolecular complex composed of CFTR and metabolic enzymes (a CFTR metabolon) permits CFTR activity to be coupled tightly to metabolic pathways within cells so that CFTR inhibition conserves vital energy stores. CFTR is expressed in epithelial tissues throughout the body, lining ducts and tubes. It functions to control the quantity and composition of epithelial secretions by driving either the absorption or secretion of salt and water. Of note, in the respiratory airways CFTR plays an additional important role in host defence. Malfunction of CFTR disrupts transepithelial ion transport leading to a wide spectrum of human disease.
Cystic Fibrosis Transmembrane Conductance Regulator ; physiology ; Epithelium ; physiology ; Humans ; Ion Transport ; Phosphorylation ; Protein Interaction Domains and Motifs

Domain database is essential for domain property research. Eliminating redundant information in database query is very important for database quality. Here we report the manual construction of a non-redundant human SH2 domain database. There are 119 human SH2 domains in 110 SH2-containing proteins. Human SH2s were aligned with ClustalX, and a homologous tree was generated. In this tree, proteins with similar known function were classified into the same group. Some proteins in the same group have been reported to have similar binding motifs experimentally. The tree might provide clues about possible functions of hypothetical proteins for further experimental verification.
Amino Acid Sequence ; Computational Biology ; Databases, Protein ; Humans ; Molecular Sequence Data ; Sequence Alignment ; src Homology Domains ; genetics

Clathrin-mediated vesicle formation is an essential step in the intracellular trafficking of the protein and lipid. Binding of clathrin assembly protein to clathrin triskelia induces their assembly into clathrin-coated vesicles (CCVs). In order to better understand a possible role of post-translational modification of CALM (clathrin assembly protein lymphoid myeloid), the homologue of AP180, in the assembly of CCVs, CALM was expressed in the cell-free reticulocyte translation system that is capable of carrying out post-translational modification. The apparent molecular weight of the expressed recombinant CALM was estimated as 105 kD. Alkaline phosphatase treatment of CALM resulted in a mobility shift on SDS-PAGE. We found that CALM was associated with the proteins harboring SH3 domain, promote assembly of clathrin triskelia into clathrin cage and bound to the preformed clathrin cage. CALM was also proteolyzed by caspase 3 and calpain but not by caspase 8. These results indicated that the post-translationally modified CALM, expressed in the eukaryotic cell-free reticulocyte translation system was able to mediate the assembly of clathrin and the coated-vesicle formation.
Alkaline Phosphatase/pharmacology ; Animal ; Brain/metabolism ; Calpain/metabolism ; Carrier Proteins/*chemistry ; Caspases/metabolism ; Cattle ; Cell-Free System ; Clathrin/*chemistry ; Electrophoresis, Polyacrylamide Gel ; Glutathione Transferase/metabolism ; Lipids/chemistry ; Membrane Proteins/*chemistry ; Phosphorylation ; Protein Binding ; Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Protein Transport ; Recombinant Proteins/chemistry/metabolism ; Reticulocytes/metabolism ; Support, Non-U.S. Gov't ; Translation, Genetic ; src Homology Domains

OBJECTIVETo study the effect of progesterone on interleukin-6 (IL-6) release from human umbilic vein endothelial cells (HUVECs) induced by high mobility group box-1 protein (HMGB1).

METHODThe recombinant expression plasmid pET14b-HMGB1 was constructed and transformed into competent E.coli BL21 cells to obtain HMGB1 protein, which was purified with chromatography on Ni-NTA Sepharose column. Cultured HUVECs were treated with purified HMGB1 protein alone at the concentrations 0, 10, 100, 500, and 1000 ng/ml, progesterone alone at the concentrations of 0, 0.1, 1, 10, 100 mmol/L, or with both HMGB1 protein (500 ng/ml) and progesterone at the terminal concentrations of 0, 0.1, 1, 10, and 100 mmol/L. Twenty-four hours later, the supernatant of the cell culture medium was collected to detect the levels of IL-6 using enzyme-linked immunosorbent assay (ELISA).

RESULTSThe IL-6 levels in HUVEC culture medium was slightly decreased after treatment with low-concentration HMGB1 but increased obviously following treatment with high-concentration HMGB1, and these effects could be dose-dependently inhibited by progesterone. Progesterone alone did not result in any noticeable changes of IL-6 levels in the cell culture medium.

CONCLUSIONSProgesterone can dose-dependently inhibit HMGB1-induced IL-6 release from HUVECs, suggesting the protective role of progesterone in endotoxemia.

Cells, Cultured ; Dose-Response Relationship, Drug ; Endothelial Cells ; cytology ; metabolism ; HMG-Box Domains ; HMGB1 Protein ; pharmacology ; Humans ; Interleukin-6 ; biosynthesis ; Progesterone ; pharmacology ; Umbilical Veins ; cytology ; metabolism

Animals ; Databases, Protein ; Humans ; Models, Molecular ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping ; methods ; Protein Interaction Maps ; Proteins ; chemistry ; metabolism ; Proteome ; chemistry ; metabolism

The cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel that belongs to the ATP-binding cassette (ABC) transporter superfamily. Defective function of CFTR is responsible for cystic fibrosis (CF), the most common lethal autosomal recessive disorder in Caucasian populations. The disease is manifested in defective chloride transport across the epithelial cells in various tissues. To date, more than 1400 different mutations have been identified as CF-associated. CFTR is regulated by phosphorylation in its regulatory (R) domain, and gated by ATP binding and hydrolysis at its two nucleotide-binding domains (NBD1 and NBD2). Recent studies reveal that the NBDs of CFTR may dimerize as observed in other ABC proteins. Upon dimerization of CFTR's two NBDs, in a head-to-tail configuration, the two ATP-binding pockets (ABP1 and ABP2) are formed by the canonical Walker A and B motifs from one NBD and the signature sequence from the partner NBD. Mutations of the amino acids that interact with ATP reveal that the two ABPs play distinct roles in controlling ATP-dependent gating of CFTR. It was proposed that binding of ATP to the ABP2, which is formed by the Walker A and B in NBD2 and the signature sequence in NBD1, is critical for catalyzing channel opening. While binding of ATP to the ABP1 alone may not increase the opening rate, it does contribute to the stabilization of the open channel conformation. Several disease-associated mutations of the CFTR channel are characterized by gating defects. Understanding how CFTR's two NBDs work together to gate the channel could provide considerable mechanistic information for future pharmacological studies, which could pave the way for tailored drug design for therapeutical interventions in CF.
Adenosine Triphosphate ; physiology ; Animals ; Binding Sites ; Cystic Fibrosis Transmembrane Conductance Regulator ; physiology ; Humans ; Hydrolysis ; Protein Interaction Domains and Motifs ; Protein Multimerization