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

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

In this paper, we present a brief review of the existing computational methods for predicting proteome-wide protein-protein interaction networks from high-throughput data. The availability of various types of omics data provides great opportunity and also unprecedented challenge to infer the interactome in cells. Reconstructing the interactome or interaction network is a crucial step for studying the functional relationship among proteins and the involved biological processes. The protein interaction network will provide valuable resources and alternatives to decipher the mechanisms of these functionally interacting elements as well as the running system of cellular operations. In this paper, we describe the main steps of predicting protein-protein interaction networks and categorize the available approaches to couple the physical and functional linkages. The future topics and the analyses beyond prediction are also discussed and concluded.
Algorithms ; Artificial Intelligence ; Humans ; Models, Biological ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping ; Protein Interaction Maps ; Proteome ; genetics ; metabolism ; Proteomics ; Systems Biology

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

Avian influenza virus Nucleoprotein (NP) is important in viral transcription, replication and determining host specificity of influenza virus. Yeast two-hybrid technique was applied to screen for proteins interacting with virus nucleoprotein, so as to further elucidate the interaction between virus nucleoprotein and cellular proteins, as well as the interaction between virus and host. To explore new proteins interacted with NP protein, a human brain cDNA library was screened using yeast two-hybrid system with NP as the bait. DNA inserts of the positive AD/library plasmids were sequenced. By the BLAST analysis against the GenBank databases seven positive clones resulted in seven genes. Our results could help for the further study on the molecular mechanism of virus replication, transcription and protein-protein interaction. Further investigations were needed to characterize these interactions.
Brain ; Gene Library ; Humans ; Influenzavirus A ; chemistry ; genetics ; Nucleoproteins ; metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping ; Two-Hybrid System Techniques

OBJECTIVETo screen the hepatocyte proteins that interact with hepatitis B virus X protein (HBx).

METHODSThe recombinant plasmid pSos-HBx was constructed by inserting Sos-HBx fragment into the bait vector, and after sequence verification the plasmid was transformed into competent yeast cells. The expression and self-activation of Sos-HBx protein was detected in the yeast cells. The hepatocyte proteins interacting with the bait protein was screened with CytoTrap yeast two-hybrid technique.

RESULTSThe reconstructed plasmid harboring HBx gene expressed Sos-HBx protein in the yeast cells without self-activation of the protein. CytoTrap yeast two-hybrid system identified 6 hepatocyte proteins that interacted with HBx, including fibronectin 1, translationally controlled tumor protein, IQ motif and WD repeats 1, follistatin, orosomucoid 1, and disulfide isomerase family A member 3.

CONCLUSIONSix HBx-binding hepatocyte proteins have been identified using the CytoTrap yeast two-hybrid system, which provides clues for further investigation of the role of HBx protein in hepatitis and liver cancer.

Genetic Vectors ; Hepatocytes ; metabolism ; Humans ; Plasmids ; Protein Interaction Domains and Motifs ; Proteins ; metabolism ; Trans-Activators ; metabolism ; Two-Hybrid System Techniques

The p26, a multifunctional ubiquitin-binding protein, has been proposed to be involved in protein degradation as a component within the ubiquitin-proteasome and autophagy-lysosome systems. As a scaffolding protein with several different kinds of protein-protein interaction domains, p62 mediates various cellular functions. Importantly, p62 plays a critical role in cell's selective autophagy and oxidative stress response, which are associated with the pathogenesis of several human diseases. In this review, we describe the structure of p62 and the mechanism of connection between p62 and ubiquitin-proteasome system/autophagy, so as to provide some perspectives on p62 research.
Adaptor Proteins, Signal Transducing ; physiology ; Autophagy ; Humans ; Oxidative Stress ; Proteasome Endopeptidase Complex ; Protein Interaction Domains and Motifs ; Proteolysis ; Ubiquitin

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

Binding Sites ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Secondary ; Receptors, Metabotropic Glutamate ; chemistry ; physiology