Higher order iminodiacetic acid libraries for probing protein-protein interactions

Higher order iminodiacetic acid diamide trimer (560 compounds) and tetramer libraries (1260 compounds) are described and were assembled in a convergent multistep solution-phase synthesis for use in studying protein-protein interactions.     

Green fluorescent protein as a signal for protein-protein interactions

Green fluorescent protein (GFP) is autofluorescent. This property has made GFP useful in monitoring in vivo activities such as gene expression and protein localization. We find that GFP can be used in vitro to reveal and characterize protein-protein interactions. The interaction between the S-peptide and S-protein fragments of ribonuclease A was chosen as a model system. GFP-tagged S-peptide was produced, and the interaction of this fusion protein with S-protein was analyzed by two distinct methods: fluorescence gel retardation and fluorescence polarization. The fluorescence gel retardation assay is a rapid method to demonstrate the existence of a protein-protein interaction and to estimate the dissociation constant (Kd) of the resulting complex. The fluorescence polarization assay is an accurate method to evaluate Kd in a specified homogeneous solution and can be adapted for the high-throughput screening of protein or peptide libraries. These two methods are powerful new tools to probe protein-protein interactions.     

A hybrid method for extraction of protein-protein interactions from literature

In this work, a hybrid method is proposed to eliminate the limitations of traditional protein-pro- tein interactions (PPIs) extraction methods, such as pattern learning and machine learning. Each sentence from the biomedical literature containing a protein pair describes a PPI which is predicted by first learning syntax patterns typical of PPIs from training corpus and then using their presence as features, along with bag-of-word features in a maximum entropy model. Tested on the BioCreAtIve corpus, the PPIs extraction method, which achieved a precision rate of 64%, recall rate of 60%, improved the performance in terms of F1 value by 11% compared with the component pure pattern- based and bag-of-word methods. The results on this test set were also compared with other three ex- traction methods and found to improve the performance remarkably.     

Structure-based engineering of environmentally sensitive fluorophores for monitoring protein-protein interactions

Single, extrinsic, environmentally sensitive fluorophores can be used to quantitate formation of protein-protein complexes. These can be prepared semi-synthetically by covalent coupling to single cysteine mutations introduced at positions where the fluorophore is predicted to respond to formation of the complex without adversely affecting the interaction. The three-dimensional structure of a protein-protein interface can be used to select such locations by identifying residues that are located at the edge of a buried interfacial region, and are in partial steric contact with both partners as indicated by a change in their static solvent-accessible surface area upon complex formation. Using this design approach, cysteine mutations were introduced into the B1 domain of protein G, which successfully monitor complex formation with minimal interference. Such constructs have great utility in the analysis of solution properties of interface mutants.     

Ribosomal structure: RNA-protein and protein-protein interactions

Vitamin A and its derivatives have been postulated to play an important role in renal tubulogenesis and compensatory hypertrophy. This study examined the effects of two carboxylic derivatives of vitamin A on Lewis lung carcinoma-porcine kidney-1 (LLC-PK1) renal tubular epithelial cell mito- and motogenesis and cell size. It was found that all-trans and 13-cis retinoic acids exerted modest, dose-dependent effects to stimulate incorporation of 3H-thymidine into acid-precipitable material of LLC-PK1 cells. The effects of all-trans retinoic acid to promote 3H-thymidine uptake in LLC-PK1 cells modestly enhanced that seen with acidic fibroblastic growth factor. Similar findings of these two retinoic acid derivatives to promote 3H-thymidine uptake and to enhance 3H-thymidine uptake stimulated by another growth factor (platelet-derived growth factor BB) were also observed in cultured bovine aortic smooth muscle cells. Both retinoic acids promoted healing of denuded areas made within confluent monolayers of serum-starved LLC-PK1 cells. All-trans retinoic acid also stimulated recovery of mechanically denuded areas within bovine aortic smooth muscle monolayers. Neither all-trans nor 13-cis retinoic acids s affected cell size as assessed by forward light scatter with flow cytometry, suggesting lack of effect to induce hypertrophy. These results demonstrate that two carboxylic acid derivatives of vitamin A are capable of stimulation of basal and growth factor-induced incorporation of 3H-thymidine uptake into acid-precipitable material and healing of denuded areas in disparate cell types. These findings are compatible with a role for vitamin A and its analogues in the tissue repair process.     

Mapping protein-protein interactions by affinity-directed mass spectrometry

A precise and rapid method for identifying sites of interaction between proteins was demonstrated; the basis of the method is direct mass spectrometric readout from the complex to determine the specific components of the proteins that interact--a method termed affinity-directed mass spectrometry. The strategy was used to define the region of interaction of a protein growth factor with a monoclonal antibody. A combination of proteolytic digestion and affinity-directed mass spectrometry was used to rapidly determine the approximate location of a continuous binding epitope within the growth factor. The precise boundaries of the binding epitope were determined by affinity-directed mass spectrometric analysis of sets of synthetic peptide ladders that span the approximate binding region. In addition to the mapping of such linear epitopes, affinity-directed mass spectrometry can be applied to the mapping of other types of molecule-molecule contacts, including ligand-receptor and protein-oligonucleotide interactions.     

Molecular mechanisms for focal adhesion assembly through regulation of protein-protein interactions

Focal adhesions provide a useful model for studying cell/extracellular matrix interactions and the subsequent cytoskeletal reorganization. Recent advances have suggested potential mechanisms by which cells may regulate focal adhesion assembly following integrin-mediated cell adhesion.     

Expression of thioredoxin random peptide libraries on the Escherichia coli cell surface as functional fusions to flagellin: a system designed for exploring protein-protein interactions

The administration of high dose chemotherapy and or radiotherapy with autologous hematopoietic rescue has become a treatment modality with increasing number of indications in a variety of malignant conditions. Improvements in the conditioning regimens and supportive measures used, as well as a more refined patient selection based on prognostic factors, have resulted in progressively better results. The availability of precursor cells from peripheral blood has allowed a faster restoration of hematopoiesis, decreasing the period and intensity of myelosuppression. The following revision gives an updated image of the accumulated experience with this mode of support in malignant lymphomas.     

Peptide modulators of protein-protein interactions in intracellular signaling

Signal transduction cascades involve multiple enzymes and are orchestrated by selective protein-protein interactions that are essential for the progression of intracellular signaling events. Modulators of these protein-protein interactions have been used to dissect the role of individual components of each signaling cascade. We describe several methods that have been developed for the identification of peptides that inhibit the interaction between signaling proteins and hence selectively modulate their functions. Such peptide modulators provide important tools for basic research and have great potential as leads for the development of new classes of therapeutic drugs.     

Experimental design for kinetic analysis of protein-protein interactions with surface plasmon resonance biosensors

The exact mechanism of hemoglobin (Hb) associated vasoconstriction has not been elucidated. We investigated this problem using isolated superfused rat aortic rings with intact endothelium. Human stroma-free hemoglobin solution (SFH) at 2uM reversed vaso relaxation induced by 33uM acetylcholine (Ach). Further, pretreatment with 4uM SFH inhibited Ach(333uM) induced dilation. The SFH induced contraction was reversible by glyceryltrinitrate (GTN), a nitric oxide (NO) donor. Preincubation with a NO synthase inhibitor nitro-L-arginine-methyl ester (NAME, 0.4nM) caused almost complete inhibition of the Hb vasoactivity. Unlike SFH (ferrous oxyHb), prenitrosylated SFH (HbNO) or ferric Hb derivatives (e.g., metHb, HbCN) did not elicit vasoconstriction. The presence of 2uM SFH did not significantly reduce the vasodilatory effectiveness of endothelium independent vasodilators isoproteranol (ISO) and papaverine (PPV). These results suggest that a primary mechanism for Hb vasoconstrictor activity is ferrous Hb scavenging of endothelium derived NO, a signal for guanylate cyclase-cGMP mediated smooth muscle relaxation. Additionally, it appears that the Hb induced vasoactivities may be modulated with NO independent vasodilators.     

An in vitro transcription assay for probing drug-DNA interactions at individual drug sites

In this study, we show that oligodendrocyte differentiation is powerfully inhibited by activation of the Notch pathway. Oligodendrocytes and their precursors in the developing rat optic nerve express Notch1 receptors and, at the same time, retinal ganglion cells express Jagged1, a ligand of the Notch1 receptor, along their axons. Jagged1 expression is developmentally regulated, decreasing with a time course that parallels myelination in the optic nerve. These results suggest that the timing of oligodendrocyte differentiation and myelination is controlled by the Notch pathway and raise the question of whether localization of myelination is controlled by this pathway.     

Structural damage to lactate dehydrogenase during copper iminodiacetic acid metal affinity chromatography

The stability of the enzyme lactate dehydrogenase (LDH) was evaluated by measuring structural damage and activity loss after exposure to copper-iminodiacetic acid (IDA) immobilized metal affinity chromatography (IMAC) under oxidizing conditions at pH 7.0. Oxidizing conditions were produced by adding reductants commonly employed in bioprocessing and biomedical applications (glutathione, beta-mercaptoethanol, dithiothreitol, cysteine, or ascorbate) and/or hydrogen peroxide to the mobile phase. Most of these additives have been shown recently to give rise to metal-catalyzed oxidation (MCO) reactions on copper-iminodicaetic acid IMAC columns. Structural damage in the form of increased susceptibility to proteolytic degradation, fragmentation, and cross-linking were measured. Increased sensitivity to proteolysis was significant in virtually all cases tested, even when activity remained high (>95% specific activity recovered). In contrast fragmentation and cross-linking were minimal in all cases, even when activity was low (<50%). As the damage was believed to have been caused primarily by MCO reactions, preventative measures consistent with this reaction pathway were tested. The most successful measure for all of the conditions studied was addition of the Cu+ chelating agent bicinchoninic acid (BCA) to the mobile phase. Decreased contact time with the column decreased damage in the case where glutathione was added. Removal of dissolved oxygen by nitrogen sparging and use of Tris-acetate buffer in place of phosphate had no measurable effect. The success of BCA addition in reducing structural damage and activity loss strengthens the conclusion that MCO reactions can occur on copper-iminodiacetic acid IMAC columns. However, the addition of BCA and the other protective measures described were not successful in eliminating the increased proteolytic susceptibility observed when LDH in buffer was exposed to the copper-charged column with no oxidizing additives. This suggests that at least one other pathway for damage exists. This damage is difficult to detect as it did not cause statistically significant losses in enzymatic activity, fragmentation, or cross-linking.     

A yeast genetic system for selecting small molecule inhibitors of protein-protein interactions in nanodroplets

Cellular processes are mediated by complex networks of molecular interactions. Dissection of their role most commonly is achieved by using genetic mutations that alter, for example, protein-protein interactions. Small molecules that accomplish the same result would provide a powerful complement to the genetic approach, but it generally is believed that such molecules are rare. There are several natural products, however, that illustrate the feasibility of this approach. Split-pool synthesis now provides a simple mechanical means to prepare vast numbers of complex, even natural product-like, molecules individually attached to cell-sized polymer beads. Here, we describe a genetic system compatible with split-pool synthesis that allows the detection of cell-permeable, small molecule inhibitors of protein-protein interactions in 100- to 200-nl cell culture droplets, prepared by a recently described technique that arrays large numbers of such droplets. These "nanodroplets" contain defined media, cells, and one or more beads containing approximately 100 pmol of a photoreleasable small molecule and a controlled number of cells. The engineered Saccharomyces cerevisiae cells used in this study express two interacting proteins after induction with galactose whose interaction results in cell death in the presence of 5-fluoroorotic acid (inducible reverse two-hybrid assay). Disruption of the interaction by a small molecule allows growth, and the small molecule can be introduced into the system hours before induction of the toxic interaction. We demonstrate that the interaction between the activin receptor R1 and the immunophilin protein FKBP12 can be disrupted by the small molecule FK506 at nanomolar concentrations in nanodroplets. This system should provide a general method for selecting cell-permeable ligands that can be used to study the relevance of protein-protein interactions in living cells or organisms.     

Recovery of nickel from Orimulsion fly ash by iminodiacetic acid chelating resin

Macroporous resins containing imminodiacetic acid (IDA) groups (Lewatit TP-207, Purolite S-930 and Amberlite IRC-748) were studied under dynamic conditions for uptake of nickel ions from the sulphate solution at pH 4 deriving from preliminary acid leaching of Orimulsion fly ash and subsequent vanadium recovery and impurities removal stages. The effects of temperature and ionic medium on the Ni adsorption were investigated.     

Determining protein-protein interactions by oxidative cross-linking of a glycine-glycine-histidine fusion protein

The Ni(II) complex of the tripeptide NH2-glycine-glycine-histidine-COOH (GGH) mediates efficient protein-protein cross-linking in the presence of oxidants such as oxone and monoperoxyphthalic acid (MMPP). Here we demonstrate that GGH fused to the amino terminus of a protein can still support cross-linking. The tripeptide was expressed at the amino terminus of ecotin, a dimeric macromolecular serine protease inhibitor found in the periplasm of Escherichia coli. In the presence of Ni(OAc)2 and MMPP, GGH-ecotin is cross-linked to give a species that has an apparent molecular mass of a GGH-ecotin dimer with no observable protein degradation. The cross-linking reaction occurs between two ecotin proteins in a dimer complex. Furthermore, GGH-ecotin can be cross-linked to a serine protease target, trypsin, and the reaction is specific for proteins that interact with ecotin. The cross-linking reaction has been carried out on small peptides, and the reaction products have been analyzed by matrix-assisted laser desorption/ionization mass spectrometry. The target of the reaction is tyrosine, and the product is bityrosyl cross-links. The yield of the cross-linking is on the order of 15%. However, the reaction efficiency can be increased 4-fold by a single amino acid substitution in the carboxy terminus of ecotin that places an engineered tyrosine within 5 A of a naturally occurring tyrosine. This cross-linking methodology allows for the protein cross-linking reagent to be encoded for at the DNA level, thus circumventing the need for posttranslational modification.