A novel biclustering approach to association rule mining for predicting HIV-1-human protein interactions

Identification of potential viral-host protein interactions is a vital and useful approach towards development of new drugs targeting those interactions. In recent days, computational tools are being utilized for predicting viral-host interactions. Recently a database containing records of experimentally validated interactions between a set of HIV-1 proteins and a set of human proteins has been published. The problem of predicting new interactions based on this database is usually posed as a classification problem. However, posing the problem as a classification one suffers from the lack of biologically validated negative interactions. Therefore it will be beneficial to use the existing database for predicting new viral-host interactions without the need of negative samples. Motivated by this, in this article, the HIV-1-human protein interaction database has been analyzed using association rule mining. The main objective is to identify a set of association rules both among the HIV-1 proteins and among the human proteins, and use these rules for predicting new interactions. In this regard, a novel association rule mining technique based on biclustering has been proposed for discovering frequent closed itemsets followed by the association rules from the adjacency matrix of the HIV-1-human interaction network. Novel HIV-1-human interactions have been predicted based on the discovered association rules and tested for biological significance. For validation of the predicted new interactions, gene ontology-based and pathway-based studies have been performed. These studies show that the human proteins which are predicted to interact with a particular viral protein share many common biological activities. Moreover, literature survey has been used for validation purpose to identify some predicted interactions that are already validated experimentally but not present in the database. Comparison with other prediction methods is also discussed.     

A network of protein-protein interactions in yeast

A global analysis of 2,709 published interactions between proteins of the yeast Saccharomyces cerevisiae has been performed, enabling the establishment of a single large network of 2,358 interactions among 1,548 proteins. Proteins of known function and cellular location tend to cluster together, with 63% of the interactions occurring between proteins with a common functional assignment and 76% occurring between proteins found in the same subcellular compartment. Possible functions can be assigned to a protein based on the known functions of its interacting partners. This approach correctly predicts a functional category for 72% of the 1,393 characterized proteins with at least one partner of known function, and has been applied to predict functions for 364 previously uncharacterized proteins.     

Dye-Ligand Affinity Chromatography: The Interaction of Cibacron Blue F3GA® with Proteins and Enzyme

Abstract

The dye Cibacron Blue F3GA has a high affinity for many proteins and enzymes. It has therefore been attached to various solid supports such as Sephadex, Sepharose, polyacrylamide, and the like. In the immobilized form the dye has rapidly been exploited as an affinity chromatographic medium to separate and purify a variety of proteins including dehydrogenases, kinases, serum albumin, interferons, several plasma proteins, and a host of other proteins. Such a diversity shown by the blue dye in binding several unrelated classes of proteins has generated considerable work in terms of studies of the chromophore itself and also the immobilized ligand. As a prelude to realizing the full potential of the immobilized Cibacron Blue F3GA, an understanding of the basic interactions of the dye with its surroundings must be gained. It has been recognized that the dye is capable of hydrophobic and/or electrostatic interactions at the instance of the ambient conditions. The study of interactions of the dye with salts, solvents, and other small molecules indicates the nature of the interactions of the dye with different kinds of groups at the interacting sites of proteins. The review will cover such interactions of the dye with the proteins, the interactions of the proteins with the immobilized ligand, and the media used to elute the bound protein in several cases, and thus consolidate the available information on such studies into a cogent and comprehensive explanation.     

Structural properties of lipid-binding sites in cytoskeletal proteins

Several cytoskeletal proteins have been shown to interact in vitro with, and in some cases are regulated by, specific membrane lipids. In some cases, evidence for in situ interactions has been provided. The molecular basis for such interactions is now being unravelled. At least five structurally distinct types of lipid-binding sites in cytoskeletal proteins have been identified. However, our understanding of the physiological role of such interactions is still limited. Precise knowledge about the binding-site structures and the actual amino acid residues involved should now enable the expression of mutant proteins that specifically lack the ability to interact with lipids. The impact of these mutations on protein location and function can then be assessed.     

Yeast two hybrid analyses reveal novel binary interactions between human cytomegalovirus-encoded virion proteins

Human cytomegalovirus (HCMV) is the largest human herpesvirus and its virion contains many viral encoded proteins found in the capsid, tegument, and envelope. In this study, we carried out a yeast two-hybrid (YTH) analysis to study potential binary interactions among 56 HCMV-encoded virion proteins. We have tested more than 3,500 pairwise combinations for binary interactions in the YTH analysis, and identified 79 potential interactions that involve 37 proteins. Forty five of the 79 interactions were also identified in human cells expressing the viral proteins by co-immunoprecipitation (co-IP) experiments. To our knowledge, 58 of the 79 interactions revealed by YTH analysis, including those 24 that were also identified in co-IP experiments, have not been reported before. Novel potential interactions were found between viral capsid proteins and tegument proteins, between tegument proteins, between tegument proteins and envelope proteins, and between envelope proteins. Furthermore, both the YTH and co-IP experiments have identified 9, 7, and 5 interactions that were involved with UL25, UL24, and UL89, respectively, suggesting that these "hub" proteins may function as the organizing centers for connecting multiple virion proteins in the mature virion and for recruiting other virion proteins during virion maturation and assembly. Our study provides a framework to study potential interactions between HCMV proteins and investigate the roles of protein-protein interactions in HCMV virion formation or maturation process.     

Interactions of heparin/heparan sulfate with proteins: appraisal of structural factors and experimental approaches

Over the past decade, the glycosaminoglycans heparin and heparan sulfate have been shown to bind and regulate the activities of many proteins. Established techniques have provided both qualitative and quantitative information regarding these interactions, leading to a general view that proteins bind with a variety of affinities to particular sequences within heparin or heparan sulfate chains. The mechanism by which heparan sulfate regulates the activity of proteins through such interactions has, however, proved more elusive. We survey some relevant details of the structural characteristics of heparin/heparan sulfate and the approaches used to investigate their interactions with proteins. For the latter, the interactions of heparin/heparan sulfate with fibroblast growth factors and their receptors will be emphasized, because these proteins have been the subject of many studies. We reflect on the information that various techniques have provided, points regarding their use, and some relevant theoretical considerations regarding the study of protein-heparin/heparan sulfate interactions. A perspective of new and developing approaches, which may aid advances in this field, is also provided.     

Protein-protein interactions in pathogen recognition by plants

Protein-protein interactions have emerged as key determinants of whether plant encounters with pathogens result in disease or successful plant defense. Genetic interactions between plant resistance genes and pathogen avirulence genes enable pathogen recognition by plants and activate plant defense. These gene-for-gene interactions in some cases have been shown to involve direct interactions of the products of the genes, and have indicated plant intracellular localization for certain avirulence proteins. Incomplete specificity of some of the interactions in laboratory assays suggests that additional proteins might be required to confer specificity in the plant. In many cases, resistance and avirulence protein interactions have not been demonstrable, and in some cases, other plant components that interact with avirulence proteins have been found. Investigation to date has relied heavily on biochemical and cytological methods including in vitrobinding assays and immunoprecipitation, as well as genetic tools such as the yeast two-hybrid system. Observations so far, however, point to the likely requirement for multiple, interdependent protein associations in pathogen recognition, for which these techniques can be insufficient. This article reviews the protein-protein interactions that have been described in pathogen recognition by plants, and provides examples of how rapid future progress will hinge on the adoption of new and developing technologies.     

Direct visualization of Bcl-2 family protein interactions using live cell fluorescent protein redistribution assays

Bcl-2 family proteins have important roles in tumor initiation, progression and resistance to therapy. Pro-survival Bcl-2 proteins are regulated by their interactions with pro-death BH3-only proteins making these protein–protein interactions attractive therapeutic targets. Although these interactions have been extensively characterized biochemically, there is a paucity of tools to assess these interactions in cells. Here, we address this limitation by developing quantitative, high throughput microscopy assays to characterize Bcl-2 and BH3-only protein interactions in live cells. We use fluorescent proteins to label the interacting proteins of interest, enabling visualization and quantification of their mitochondria-localized interactions. Using tool compounds, we demonstrate the suitability of our assays to characterize the cellular activity of putative therapeutic molecules that target the interaction between pro-survival Bcl-2 and pro-death BH3-only proteins. In addition to the relevance of our assays for drug discovery, we anticipate that our work will contribute to an improved understanding of the mechanisms that regulate these important protein–protein interactions within the cell.     

Role of cation-pi interactions to the stability of thermophilic proteins

Elucidating the factors responsible for exhibiting extreme thermal stability of thermophilic proteins is very important for an understanding of the mechanism of protein stability, as well as to design stable proteins. In this work, we have analyzed the influence of cation-pi interactions to enhance the stability from mesophilic to thermophilic proteins. The favorable residue pairs forming such a system of interactions have been brought out. We found that the Tyr has a greater number of such interactions with Lys in thermophilic proteins. Specifically, the same Lys would experience a greater number of cation-pi interactions with several Tyr residues in thermophiles. On the other hand, the influence of Phe in making cation-pi interactions is higher in mesophiles than in thermophiles. Further, a network of cation-pi interactions are maintained by Lys in thermophiles, whereas Arg plays a major role in mesophilic proteins. Moreover, atoms that have a substantial positive charge in both Lys and Arg make a more significant contribution for cation-pi interactions than do cationic group atoms.     

Computation of non-covalent interactions in TNF proteins and interleukins

The roles played by the non-covalent interactions have been investigated for a set of six TNF proteins and nine Interleukins. The stabilizing residues have been identified by a consensus approach using the concepts of available surface area, medium and long-range interactions and conservation of amino acid residues. The cation-pi interactions have been computed based on a geometric approach such as distance and energy criteria. We identified an average of 1 energetically significant cation-pi interactions in every 94 residues in TNF proteins and 1 in every 62 residues in Interleukins. In TNF proteins, the cationic groups Lys preferred to be in helix while Arg preferred to be in strand regions while in Interleukins the Arg residues preferred to be in helix and Lys preferred to be in strand regions. From the available surface area calculations, we found that, almost all the cation and pi residues in TNF proteins and Interleukins were either in buried or partially buried regions and none of them in the exposed regions. Medium and long-range interactions were predominant in both TNF proteins and Interleukins. It was observed that the percentage of stabilizing centers were more in TNF proteins as compared to the Interleukins, while the percentage of conserved residues were more in Interleukins than in TNF proteins. In the stabilizing residues Lys was observed to be a stabilizing residue in both TNF proteins and Interleukins. Among the aromatic group, Phe was seen to be a stabilizing residue in both TNF and Interleukins. We suggest that this study on the computation of cation-pi interactions in TNF proteins and Interleukins would be very helpful in further understanding the structure, stability and functional similarity of these proteins.     

The protein-lipid interface: perspectives from magnetic resonance and crystal structures

Lipid-protein interactions in membranes are dynamic, and consequently are well studied by magnetic resonance spectroscopy. More recently, lipids associated with integral membrane proteins have been resolved in crystals by X-ray diffraction, mostly at cryogenic temperatures. The conformation and chain ordering of lipids in crystals of integral proteins are reviewed here and are compared and contrasted with results from magnetic resonance and with the crystal structures of phospholipid bilayers. Various aspects of spin-label magnetic resonance studies on lipid interactions with single integral proteins are also reviewed: specificity for phosphatidylcholine, competition with local anaesthetics, oligomer formation of single transmembrane helices, and protein-linked lipid chains. Finally, the interactions between integral proteins and peripheral or lipid-linked proteins, as reflected by the lipid-protein interactions in double reconstitutions, are considered.     

The use of immobilized ubiquitin for biosensor analysis of the mitochondrial subinteractome

Protein ubiquitination is an important mechanism responsible not only for specific labeling of proteins for their subsequent degradation; it also determines localization of proteins in the cell and regulation of protein-protein interactions. In the context of protein-protein interactions binding of (mono/poly)ubiquitinated molecules to proteins containing specific ubiquitin binding domains plays the decisive role. Formation of the ubiquitin interactome has been demonstrated for cytosol. Involvement of mitochondria and associated extramitochondrial proteins into such interactions still requires detailed investigation. In this study using an optical biosensor we have demonstrated binding of proteins of mouse brain mitochondrial lysates to immobilized monomeric ubiquitin. Model purified proteins, which are known to be associated with the outer mitochondrial compartment (glyceraldehyde-3-phosphate dehydorgenase, creatine phosphokinase), interacted with immobilized ubiquitin as well as with each other. This suggests that (poly)ubiquitinated chains may be involved in protein-protein interactions between ubiquitinated and non-ubiquitinated proteins and thus may contribute to formation of (mitochondrial) ubiquitin subinteractome.     

Matricellular proteins: extracellular modulators of cell function

The term 'matricellular' has been applied to a group of extracellular proteins that do not contribute directly to the formation of structural elements in vertebrates but serve to modulate cell-matrix interactions and cell function. Our understanding of the mode of action of matricellular proteins has been advanced considerably by the recent elucidation of the phenotypes of mice that are deficient in these proteins. In many cases, aspects of these phenotypes have illuminated previously unsuspected consequences of the lack of appropriate interactions of cells with their environment.     

Role of medium--and long-range interactions in discriminating globular and membrane proteins.

The analysis of inter-residue interactions in protein structures provides considerable insight to understand their folding and stability. We have previously analyzed the role of medium- and long-range interactions in the folding of globular proteins. In this work, we study the distinct role of such interactions in the three-dimensional structures of membrane proteins. We observed a higher number of long-range contacts in the termini of transmembrane helical (TMH) segments, implying their role in the stabilization of helix-helix interactions. The transmembrane strand (TMS) proteins are having appreciably higher long-range contacts than that in all-beta class of globular proteins, indicating closer packing of the strands in TMS proteins. The residues in membrane spanning segments of TMH proteins have 1.3 times higher medium-range contacts than long-range contacts whereas that of TMS proteins have 14 times higher long-range contacts than medium-range contacts. Residue-wise analysis indicates that in TMH proteins, the residues Cys, Glu, Gly, Pro, Gln, Ser and Tyr have higher long-range contacts than medium-range contacts in contrast with all-alpha class of globular proteins. The charged residue pairs have higher medium-range contacts in all-alpha proteins, whereas hydrophobic residue pairs are dominant in TMH proteins. The information on the preference of residue pairs to form medium-range contacts has been successfully used to discriminate the TMH proteins from all-alpha proteins. The statistical significance of the results obtained from the present study has been verified using randomized structures of TMH and TMS protein templates.     

植物与病原菌互作的蛋白质组学研究进展

深入认识植物与病原菌的识别方式、亲和性或非亲和性的互作模式,对于揭示植物-病原菌互作机制研究具有重要意义.利用蛋白质组学方法研究病原菌侵染植物过程,分析相关的基因和蛋白,有助于从分子水平上探究植物-病原菌相互作用机制.本文概述了植物-病原菌的互作机制,系统介绍了差异蛋白质组学分析方法在植物-病原真菌、植物-病原细菌两类互作系统中的应用,分析了植物与病原菌互作过程中可能涉及的差异表达功能蛋白,并对当前蛋白质组学技术在植物与病原菌互作研究中存在的诸多问题进行了探讨.     

Exploring protein interactions by interaction-induced folding of proteins from complementary peptide fragments

The study of protein--protein interactions is central to understanding the chemical machinery that makes up the living cell. Until recently, facile methods to study these processes in intact, living cells have not existed. Furthermore, the assignment of function to novel proteins relies on demonstrating interactions of these proteins with proteins of known function. This review describes an experimental strategy, devised to study protein--protein interactions in any intact living cells based on protein-fragment complementation assays. Applications to quantitative analysis of interactions, allosteric processes and cDNA library screening are discussed. Recently, the feasibility of employing this strategy in genome-wide biochemical pathway mapping efforts has been demonstrated.     

Bacterial proteins binding to the mammalian extracellular matrix

Pathogenic bacteria frequently express surface proteins with affinity for components of the mammalian extracellular matrix, i.e. collagens, laminin, fibronectin or proteoglycans. This review summarizes our current knowledge on the mechanisms of bacterial adherence to extracellular matrices and on the biological significance of these interactions. The best-characterized bacterial proteins active in these interactions are the mycobacterial fibronectin-binding proteins, the fibronectin- and the collagen-binding proteins of staphylococci and streptococci, specific enterobacterial fimbrial types, as well as the polymeric surface proteins YadA of yersinias and the A-protein of Aeromonas. Some of these bacterial proteins are highly specific for an extracellular matrix protein, some are multifunctional and express binding activities towards a number of target proteins. The interactions can be based on a protein-protein or on a protein-carbohydrate interaction, or on a bridging mechanism mediated by a bivalent soluble target protein. Many of the interactions have also been demonstrated on tissue sections or in vivo, and adherence to the extracellular matrix has been shown to promote bacterial colonization of damaged tissues.