Identification of protein interaction partners and protein-protein interaction sites

Rigid-body docking has become quite successful in predicting the correct conformations of binary protein complexes, at least when the constituent proteins do not undergo large conformational changes upon binding. However, determining whether two given proteins interact is a more difficult problem. Successful docking procedures often give equally good scores for proteins that do not interact experimentally. This is the case for the multiple minimization approach we use here. An analysis of the results where all proteins within a set are docked with all other proteins (complete cross-docking) shows that the predictions can be greatly improved if the location of the correct binding interface on each protein is known, since the experimental complexes are much more likely to bring these two interfaces into contact, at the same time as yielding good interaction energy scores. While various methods exist for identifying binding interfaces, it is shown that simply studying the interaction of all potential protein pairs within a data set can itself help to identify the correct interfaces.     

Identification of a novel protein complex containing annexin A4, rabphilin and synaptotagmin

Rabphilin is a synaptic vesicle-associated protein proposed to play a role in regulating neurotransmitter release. Here we report the isolation and identification of a novel protein complex containing rabphilin, annexin A4 and synaptotagmin 1. We show that the rabphilin C2B domain interacts directly with the N-terminus of annexin A4 and mediates the co-complexing of these two proteins in PC12 cells. Analyzing the cellular localisation of these co-complexing proteins we find that annexin A4 is located on synaptic membranes and co-localises with rabphilin at the plasma membrane in PC12 cells. Given that rabphilin and synaptotagmin are synaptic vesicle proteins involved in neurotransmitter release, the identification of this complex suggests that annexin A4 may play a role in synaptic exocytosis.     

Analysis of the adaptor function of the LIM domain-containing protein FHL2 using an affinity chromatography approach

Containing four LIM domains and an N-terminal half LIM domain, FHL2 has been predicted to have an adaptor function in the formation of higher order molecular complexes in the nucleus and the cytoplasm of cells. We expressed recombinant FHL2 in insect cells using the baculovirus system and used it to isolate direct or indirect interaction partners from the cytosolic fraction of fibroblasts by affinity chromatography. These were identified by their peptide mass fingerprints using MALDI-TOF mass spectrometry. Cytoskeleton-associated proteins present among the bound proteins were shown to co-localise with FHL2 in cell lamellipodia by indirect immunofluorescence staining.     

Quantitative analysis of complex protein mixtures using isotope-coded affinity tags.

We describe an approach for the accurate quantification and concurrent sequence identification of the individual proteins within complex mixtures. The method is based on a class of new chemical reagents termed isotope-coded affinity tags (ICATs) and tandem mass spectrometry. Using this strategy, we compared protein expression in the yeast Saccharomyces cerevisiae, using either ethanol or galactose as a carbon source. The measured differences in protein expression correlated with known yeast metabolic function under glucose-repressed conditions. The method is redundant if multiple cysteinyl residues are present, and the relative quantification is highly accurate because it is based on stable isotope dilution techniques. The ICAT approach should provide a widely applicable means to compare quantitatively global protein expression in cells and tissues.     

Analysis of selective, high protein-protein binding interaction of cohesin-dockerin complex using biosensing methods

Optical biosensors that use fluorescence are promising tools for the analysis of target materials such as protein, DNA and other biomaterial. To analyze the binding properties of a protein-protein interaction, we constructed fluorescent biomarkers based on the cohesin-dockerin interaction, which coordinates the assembly of cellulolytic enzymes and scaffolding proteins to produce a cell surface multiprotein complex known as the "cellulosome" in some anaerobic bacteria. Our 2D-PAGE results displayed diverse binding profiles to the dockerin containing cellulosomal proteins produced by Clostridium cellulovorans grown on different carbon sources, such as Avicel, xylan and AXP (Avicel:xylan:pectin (3:1:1)). Fluorescence intensity analysis indicated that EngE and EngH bound more efficiently to Coh6 than to Coh2 or Coh9 (2-fold to 6-fold and 1.5-fold to 5-fold, respectively), while others cellulosomal proteins displayed similar results. In addition, both an enzyme-linked interaction assay (ELIA) and surface plasmon resonance (SPR) analyses demonstrated that both EngE and EngH preferentially bound cohesin6 versus the other two cohesin molecules. This work demonstrated the analysis of the binding patterns between interacting proteins using fluorescent biomarkers. We also illustrated the potential of this sensitive approach to quantify specific target analytical materials via the example of the cohesin-dockerin interaction.     

Protein-protein interaction analysis using an affinity peptide tag and hydrophilic polystyrene plate

A sandwich ELISA method using peptide tags showing a specific affinity to a hydrophilic polystyrene surface (PS-tags), PS 19 composed of RAFIASRRIKRP and KPS19R10 of KRAFIASRRIRRP and a hydrophilic polystyrene (phi-PS) plate was used to analyze protein-protein interactions. An Escherichia coli cysteine synthase complex, in which serine acetyltransferase (SAT) interacts with O-acetylserine sulfhydrylase-A (OASS) was used as a model system. When the interaction was detected by the conventional sandwich ELISA method using a hydrophobic polystyrene (pho-PS) plate, for the exclusive use of ELISA, the signal intensity was barely detectable due to conformational change of the ligand protein, OASS in the adsorbed state. On the contrary, when OASS, genetically fused with PS19 (OASS-PS19) or chemically conjugated with KPS19R10 (OASS-KPS19R10), was immobilized on the phi-PS plate, a high signal intensity was detected. Furthermore, by applying the two-step sandwich ELISA, in which OASS-PS19 or OASS-KPS19R10 formed a complex with SAT in the blocking solution before immobilization on the phi-PS plate, the signal intensity was further increased with a much shorter operational time, because SAT in the blocking solution formed a complex with OASS-PS19 or OASS-KPS19R10 without any steric hindrance.     

Identification of a PDZ domain containing Golgi protein, GOPC, as an interaction partner of frizzled

The frizzled gene is evolutionally conserved in a wide variety of organisms including mammals, and in Drosophila, frizzled is implicated in the development of planar polarity. We describe here the isolation and characterization of a Golgi protein, GOPC, as a frizzled interacting protein. GOPC comprises one PDZ domain, two coiled-coil motifs and two evolutionally conserved regions. Immunofluorescence studies indicated that a significant fraction of GOPC protein was localized in the Golgi apparatus. Using a series of deletion mutants, we show that both coiled-coil motifs and a C-terminal conserved region were required for its Golgi localization. Interestingly, deletion mutants that lack a N-terminal conserved region or coiled-coil motifs formed aggresome-like perinuclear structure. Interaction of GOPC and frizzled was observed both in vivo and in vitro, and the PDZ domain of GOPC and the C-terminal Ser/Thr-X-Val motif of frizzled were required for their interaction. Immunofluorescence studies indicated that, although frizzled was a membrane protein, it was localized at the Golgi apparatus as well, and colocalization of GOPC and frizzled at the Golgi apparatus was observed. Furthermore, when GOPC was coexpressed with frizzled, translocation of GOPC to the plasma membrane was observed. Importantly, brefeldin A interrupted not only the localization of GOPC to the Golgi apparatus but also the translocation of frizzled to the plasma membrane, indicating that the Golgi structure was required for the proper subcellular localization of frizzled. Taken together, these results indicate that GOPC may play a role in the vesicle transport of frizzled from the Golgi apparatus to the plasma membrane.     

Identification of an uncommon haptoglobin type using DNA and protein analysis

The inherited variations in haptoglobin phenotypes are attributed to the homozygous and heterozygous combinations of three common autosomal alleles:HP ^* 1F,HP ^* 1S andHP ^* 2.HP ^* 1F andHP ^* 1S encode polypeptides that differ by two amino acids at positions 51 and 53. The formation ofHP ^* 2 is postulated to have resulted from a breakage and subsequent reunion event at non-homologous positions of twoHP ^* 1 alleles. The most common form ofHP ^* 2 isHP ^* 2FS in which the 5 end ofHP ^* 2 resemblesHP ^* 1F and the 3 end resemblesHP ^* 1S. Homologous crossing over betweenHP ^* 2 and either anHP ^* 1F orHP ^* 1S allele inHP ^* 2/HP ^* 1 heterozygotes can change the usual type ofHP ^* 2 to three other forms:HP ^* 2SS,HP ^* 2FF orHP ^* 2SF. We describe a nuclear family in which the uncommon genotypeHP ^* 2SS in one parent caused initial confusion in assigning genotypes to the rest of the nuclear family. The data demonstrate the need for a cautious approach when deducing haptoglobin genotypes from molecular analysis alone.     

BLOC-3, a protein complex containing the Hermansky-Pudlak syndrome gene products HPS1 and HPS4

The Hermansky-Pudlak syndrome (HPS) is a genetic disorder characterized by defective lysosome-related organelles. HPS results from mutations in either one of six human genes named HPS1 to HPS6, most of which encode proteins of unknown function. Here we report that the human HPS1 and HPS4 proteins are part of a complex named BLOC-3 (for biogenesis of lysosome-related organelles complex 3). Co-immunoprecipitation experiments demonstrated that epitope-tagged and endogenous HPS1 and HPS4 proteins assemble with each other in vivo. The HPS1.HPS4 complex is predominantly cytosolic, with a small amount being peripherally associated with membranes. Size exclusion chromatography and sedimentation velocity analyses of the cytosolic fraction indicate that HPS1 and HPS4 form a moderately asymmetric protein complex with a molecular mass of approximately 175 kDa. HPS4-deficient fibroblasts from light ear mice display normal distribution and trafficking of the lysosomal membrane protein, Lamp-2, in contrast to fibroblasts from AP-3-deficient pearl mice (HPS2), which exhibit increased trafficking of this lysosomal protein via the plasma membrane. Similarly, light ear fibroblasts display an apparently normal accumulation of Zn2+ in intracellular vesicles, unlike pearl fibroblasts, which exhibit a decreased intracellular Zn2+ storage. Taken together, these observations demonstrate that the HPS1 and HPS4 proteins are components of a cytosolic complex that is involved in the biogenesis of lysosomal-related organelles by a mechanism distinct from that operated by AP-3 complex.     

The role of protein dynamics in increasing binding affinity for an engineered protein-protein interaction established by H/D exchange mass spectrometry

It is generally accepted that protein and solvation dynamics play fundamental roles in the mechanisms of protein-protein binding; however, assessing their contribution meaningfully has not been straightforward. Here, hydrogen/deuterium exchange mass spectrometry (H/D-Ex) was employed to assess the role of dynamics for a high-affinity human growth hormone variant (hGHv) and the wild-type growth hormone (wt-hGH) each binding to the extracellular domain of their receptor (hGHbp). Comparative analysis of the transient fluctuations in the bound and unbound states revealed that helix-1 of hGHv undergoes significant transient unfolding in its unbound state, a characteristic that was not found in wt-hGH or apparent in the temperature factor data from the X-ray analysis of the unbound hGHv structure. In addition, upon hormone binding, an overall increase in stability was observed for the beta-sheet structure of hGHbp which included sites distant from the binding interface. On the basis of the stability, binding kinetics, and thermodynamic data presented, the increase in the binding free energy of hGHv is primarily generated by factors that appear to increase the energy of the unbound state relative to the free energy of the bound complex. This implies that an alternate route to engineer new interactions aiming to increase protein-protein association energies may be achieved by introducing certain mutations that destabilize one of the interacting molecules without destabilizing the resulting bound complex. Importantly, although the hGHv molecule is less stable than its wt-hGH counterpart, its resulting active ternary complex with two copies of hGHbp has comparable stability to the wt complex.     

Identification of significant pathways in gastric cancer based on protein-protein interaction networks and cluster analysis

Gastric cancer is one of the most common and lethal cancers worldwide. However, despite its clinical importance, the regulatory mechanisms involved in the aggressiveness of this cancer are still poorly understood. A better understanding of the biology, genetics and molecular mechanisms of gastric cancer would be useful in developing novel targeted approaches for treating this disease. In this study we used protein-protein interaction networks and cluster analysis to comprehensively investigate the cellular pathways involved in gastric cancer. A primary immunodeficiency pathway, focal adhesion, ECM-receptor interactions and the metabolism of xenobiotics by cytochrome P450 were identified as four important pathways associated with the progression of gastric cancer. The genes in these pathways, e.g., ZAP70, IGLL1, CD79A, COL6A3, COL3A1, COL1A1, CYP2C18 and CYP2C9, may be considered as potential therapeutic targets for gastric cancer.     

Cloning and deletion mutagenesis using direct protein-protein interaction on an expression vector. Identification of the calmodulin binding domain of alpha-fodrin

We have screened a lambda gt11 library, constructed with mouse macrophage cDNA, in order to isolate clones that code for calmodulin binding proteins. We have developed a new approach for this purpose using radioactive calmodulin (produced by genetic engineering) to detect fusion proteins that interact with this protein with high affinity. A cDNA clone that codes for mouse macrophage fodrin was isolated, sequenced and identified. By deleting part of the sequence the calmodulin binding domain was located on the fodrin sequence. The site is situated on repeat 11 of fodrin and probably on the extra arm of this repeat. The method we developed is widely applicable to site-directed mutagenesis of interacting proteins.     

Electron donation between copper containing nitrite reductases and cupredoxins: the nature of protein-protein interaction in complex formation.

In denitrifying organisms with copper containing dissimilatory nitrite reductases, electron donation from a reduced cupredoxin is an essential step in the reduction of nitrite to nitric oxide. Copper nitrite reductases are categorised into two subgroups based on their colour, green and blue, which are found in organisms where the cupredoxins are pseudoazurins and azurins, respectively. In view of this and some in vitro electron donation experiments, it has been suggested that copper nitrite reductases have specific electron donors and that electron transfer takes place in a specific complex of the two proteins. We report results from the first comprehensive electron donation experiments using three copper nitrite reductases, one green and two blue, and five cupredoxins, one pseudoazurin and four azurins. Our data show that pseudoazurin can readily donate electrons to both blue and green copper nitrite reductases. In contrast, all of the azurins react very sluggishly as electron donors to the green nitrite reductase. These results are discussed in terms of surface compatibility of the component proteins, complex formation, overall charges, charge distribution, hydrophobic patches and redox potentials. A docking model for the complexes is proposed.     

Affinity mass spectrometry-based approaches for the analysis of protein-protein interaction and complex mixtures of peptide-ligands.

Combined applications of affinity purification procedures and mass-spectrometric analyses (affinity mass spectrometry or affinity-directed mass spectrometry) have gained broad interest in various fields of biological sciences. We have extended these techniques to the purification and analysis of closely related peptides from complex mixtures and to the characterization of binding motifs and relative affinities in protein-protein interactions. The posttranslational modifications in the carboxy-terminal region of porcine brain tubulin are used as an example for the applicability of affinity mass spectrometry in the characterization of complex patterns of related peptides. We also show that affinity mass spectrometry allows the mapping of sequential binding motifs of two interacting proteins. Using the ActA/Mena protein-protein complex as a model system, we show that we can selectively purify Mena-binding peptides from a tryptic digest of ActA. The results from this assay are compared to data sets obtained earlier by classical methods using synthetic peptides and molecular genetic experiments. As a further expansion of affinity mass spectrometry, we have established an internally standardized system that allows comparison of the affinities of related ligands for a given protein. Here the affinities of two peptide ligands for the monoclonal tubulin-specific antibody YL1/2 are determined in terms of half-maximal competition.     

The analysis of peptide affinity and its binding kinetics to DR1DW1 major histocompatibility complex protein.

The connection between experimentally measured values of ED50 (concentration of added peptide required to bind half of the protein), which characterize peptide-protein binding and the equilibrium dissociation constant of peptide-protein complex Kd (affinity) is considered. It is shown and confirmed by experimental studies that in certain cases, as a result of the absence of equilibrium in the system, the value of Kd could be much less than the experimental value of ED50, but not equal to that as commonly assumed. This is especially applicable to the formation of peptide-MHC complexes with low dissociation rates (strong binding), which may require longer time-intervals to reach equilibrium. Thus the search of the good binding peptides based on finding ones with the smallest measured values' of ED50 may result in missing the best binders with the lowest values of dissociation constant (highest affinity). To analyze the problem we considered the formal chemical kinetics of peptide-protein binding. Experimental studies of peptide binding was performed to obtain the parameters of the kinetic model. According to the predictions of the model, it was confirmed that peptide binding occurs through the preceding step, which is either a release of an endogenous peptide or some conformational change of the molecule. The half decay time for this process was determined to be approximately 3 h. Based on the model developed, a new effective method for determination of the dissociation rates of peptide-MHC complexes and the equilibrium dissociation constants Kd was proposed, which implies the comparison of binding levels (ED50) at different instants of time. This method works especially well for the peptide-MHC complexes with relatively slow dissociation rates (stable complexes), for which the direct off-rate measurements as well as obtaining equilibrium binding data to determine Kd are highly time consuming and not very reliable.     

Mass spectrometry analysis of the native protein complex containing actinin-4 in prostate cancer cells

Actinin-4 was originally identified as an actin-binding protein associated with cell motility and cancer invasion and metastasis. However, actinin-4 forms complexes with a large number of different partner proteins and is speculated to have several distinct functions depending on its partner. The level of actinin-4 expression was found to be significantly lower in prostate cancer cells than in non-cancerous basal cells, and restoration of actinin-4 expression inhibited cell proliferation by prostate cancer cell line 22RV1. Immunoprecipitation and mass spectrometry analysis revealed that actinin-4 forms native complexes with several partner proteins in 22RV1 cells, including with beta/gamma-actin, calmodulin, the clathrin heavy chain, non-muscular myosin heavy chain, heterogeneous nuclear ribonucleoprotein A1, and Ras-GTPase-activating protein SH3 domain-binding protein. Clathrin is a coat protein that covers the internalized membrane pit that forms during early endocytosis. We found that other clathrin-related and unrelated cargo proteins, including dynamin, adaptin-delta, beta subunit of neuronal adaptin-like protein, and p47A, also interact with actinin-4. Immunofluorescence microscopy revealed that dynamin and clathrin co-localized with actinin-4 at the sites of membrane ruffling, and transfection of actinin-4 cDNA facilitated the transport of transferrin into perinuclear endosomes. Endocytosis terminates signaling evoked by cell surface receptors and regulates the recycling of receptors and ligands. We identified a panel of proteins whose expression and/or subcellular localization was regulated by actinin-4 by performing organelle fractionation and ICAT-LC-MS/MS. The decreased expression of actinin-4 protein in prostate cancer cells may cause aberrations in the intracellular trafficking of various cell surface molecules and contribute to carcinogenesis.     

Identification of a novel mitochondrial complex containing mitofusin 2 and stomatin-like protein 2

A reverse genetics approach was utilized to discover new proteins that interact with the mitochondrial fusion mediator mitofusin 2 (Mfn2) and that may participate in mitochondrial fusion. In particular, in vivo formaldehyde cross-linking of whole HeLa cells and immunoprecipitation with purified Mfn2 antibodies of SDS cell lysates were used to detect an approximately 42-kDa protein. This protein was identified by liquid chromatography and tandem mass spectrometry as stomatin-like protein 2 (Stoml2), previously described as a peripheral plasma membrane protein of unknown function associated with the cytoskeleton of erythrocytes (Wang, Y., and Morrow, J. S. (2000) J. Biol. Chem. 275, 8062-8071). Immunoblot analysis with anti-Stoml2 antibodies showed that Stoml2 could be immunoprecipitated specifically with Mfn2 antibody either from formaldehyde-cross-linked and SDS-lysed cells or from cells lysed with digitonin. Subsequent immunocytochemistry and cell fractionation experiments fully supported the conclusion that Stoml2 is indeed a mitochondrial protein. Furthermore, demonstration of mitochondrial membrane potential-dependent import of Stoml2 accompanied by proteolytic processing, together with the results of sublocalization experiments, suggested that Stoml2 is associated with the inner mitochondrial membrane and faces the intermembrane space. Notably, formaldehyde cross-linking revealed a "ladder" of high molecular weight protein species, indicating the presence of high molecular weight Stoml2-Mfn2 hetero-oligomers. Knockdown of Stoml2 by the short interfering RNA approach showed a reduction of the mitochondrial membrane potential, without, however, any obvious changes in mitochondrial morphology.     

Structural,energetic, and functional analysis of a protein-protein interface at distinct stages of affinity maturation

Due to a paucity of studies that synthesize structural, energetic, and functional analyses of a series of protein complexes representing distinct stages in an affinity maturation pathway, the biophysical basis for the molecular evolution of protein-protein interactions is poorly understood. Here, we combine crystal structures and binding-free energies of a series of variant superantigen (SAG)-major histocompatibility complex (MHC) class II complexes exhibiting increasingly higher affinity to reveal that this affinity maturation pathway is controlled largely by two biophysical factors: shape complementarity and buried hydrophobic surface. These factors, however, do not contribute equivalently to the affinity maturation of the interface, as the former dominates the early steps of the maturation process while the latter is responsible for improved binding in later steps. Functional assays reveal how affinity maturation of the SAG-MHC interface corresponds to T cell activation by SAGs.