Analysis of Protein-Protein Interaction by Co-IP in Human Cells

While there are various approaches available to analyze protein-protein interactions, coimmunoprecipitation (co-IP) remains one of the most classic and commonly used methods to discover novel protein interactions or to determine the physical association of proteins. The assay begins with the preparation of total cell or tissue lysate in an appropriate lysis buffer. Protein of interest in the lysate is captured using a specific antibody and precipitated along with its binding proteins using a resin. After a series of washes to remove nonbound proteins in the lysate, the resultant immune complexes are subjected to immunoblotting, in-gel protein staining, or mass spectrometry to determine the protein-protein interaction of interest. In this chapter, a standard IP/co-IP protocol is described and potential problems and troubleshooting are discussed.

Identification of the kinesin KifC3 as a new player for positioning of peroxisomes and other organelles in mammalian cells

The attachment of organelles to the cytoskeleton and directed organelle transport is essential for cellular morphology and function. In contrast to other cell organelles like the endoplasmic reticulum or the Golgi apparatus, peroxisomes are evenly distributed in the cytoplasm, which is achieved by binding of peroxisomes to microtubules and their bidirectional transport by the microtubule motor proteins kinesin-1 (Kif5) and cytoplasmic dynein. KifC3, belonging to the group of C-terminal kinesins, has been identified to interact with the human peroxin PEX1 in a yeast two-hybrid screen. We investigated the potential involvement of KifC3 in peroxisomal transport. Interaction of KifC3 and the AAA-protein (ATPase associated with various cellular activities) PEX1 was confirmed by in vivo colocalization and by coimmunoprecipitation from cell lysates. Furthermore, knockdown of KifC3 using RNAi resulted in an increase of cells with perinuclear-clustered peroxisomes, indicating enhanced minus-end directed motility of peroxisomes. The occurrence of this peroxisomal phenotype was cell cycle phase independent, while microtubules were essential for phenotype formation. We conclude that KifC3 may play a regulatory role in minus-end directed peroxisomal transport for example by blocking the motor function of dynein at peroxisomes. Knockdown of KifC3 would then lead to increased minus-end directed peroxisomal transport and cause the observed peroxisomal clustering at the microtubule-organizing center.

TLR5 recognizes Aeromonas hydrophila flagellin and interacts with MyD88 in Nile tilapia

Toll-like receptor 5 (TLR5) is responsible for bacterial flagellin recognition in vertebrates. In the present study, TLR5M was identified in the Nile tilapia Oreochromis niloticus (OnTLR5), containing a conserved LRR domain, a transmembrane region and a C-terminal TIR domain, similar to that of other fishes and mammals. OnTLR5 was broadly expressed in all the tissues examined, presenting the highest expression levels in the blood and the lowest in the kidney. OnTLR5 was detected from 2 d postfertilization (dpf) to 8 dpf during embryonic development. Moreover, expression levels of OnTLR5 were clearly altered in all five tissues examined in response to Streptococcus agalactiae infection in vivo. Overexpression of OnTLR5 in HEK293T cells revealed that OnTLR5 was distributed in the cytoplasm and significantly increased NF-κB activation. In response to cotransfection with OnMyd88, OnTLR5 significantly upregulated OnMyd88-induced NF-κB activation. Pulldown assays showed that OnTLR5 interacts with OnMyd88 and revealed an interaction between TLR5 and Aeromonas hydrophila flagellin. Taken together, these findings suggest that OnTLR5 plays important roles in TLR/IL-1R signalling pathways and the immune response to pathogen invasion.

Coimmunoprecipitation of proteins from yeast

This protocol outlines a procedure for testing whether two proteins interact. A target protein will be immunoprecipitated using an antibody that recognizes it (or a tagged version of the protein). The immunoprecipitated material will be separated by SDS-PAGE and analyzed by Western blotting to assess the presence of a candidate interacting protein(s).

Modulation of CaMKIIa-GluN2B interaction in levodopa-induced dyskinesia in 6-OHDA-lesioned Parkinson's rats

Long-term treatment with L-dopa leads to involuntary aimless movements called L-dopa-induced dyskinesia (LID) has hindered its use in Parkinson's disease (PD) patients. Emerging evidence suggests a possible role of CaMKIIa and its interacting partners in the development of LID. In this study, we found that CaMKIIa was found to form complexes with GluN2B after chronic administration of L-dopa in adult rat striatal neurons. Intrastriatal injection of KN-93 significantly reduced the level of GluN2B in CaMKIIa precipitates with a dose dependent response, as well as reduced the Global ALO AIM score without ablation of the therapeutic response to L-dopa. In parallel, intrastriatal injection of MK-801 significantly alleviated the level of CaMKIIa in GluN2B precipitates compared to LID group (p < 0.01), and this is accompanied by realizing improvement of the Global ALO AIM score also without affect the efficacy of L-dopa. In summary, the present study indicated that CaMKIIa-GluN2B interaction had an important role in the development of LID. Disrupt of this link by intrastriatal infusion of KN-93 or MK-801 ameliorated dyskinesia in 6-OHDA-lesioned PD rats.

Analysis of protein-protein interactions by coimmunoprecipitation

Proteins generally act by binding to other molecules, including proteins. When proteins bind to other proteins, we speak of protein-protein interactions. It has become apparent that protein-protein interactions are critically important to many processes that take place in the cell, including signal transduction, regulation of gene expression, vesicular transport, nuclear import and export, and cell migration (Pawson and Nash, 2003). This has led to the recognition of protein-protein interactions as targets for drug development and to an increased interest in the identification of novel protein-protein interactions (Fry and Vassilev, 2005; Fry, 2006; Tord et al., 2007). Coimmunoprecipitation is a technique that is used to confirm novel protein-protein interactions in the context of a living cell or organism. In addition, coimmunoprecipitation is also used to study the dynamics of protein-protein interactions in response to intra- or extracellular stimuli, or can be used to study the effect of mutations on the ability of a protein to engage its binding partner. In a coimmunoprecipitation experiment, a protein of interest is isolated by immunoprecipitation. Subsequently, the presence of binding partners can be assessed by immunoblotting (see Western Blotting using Chemiluminescent Substrates).

The RNA-dependent RNA polymerase of Citrus tristeza virus forms oligomers

The RNA-dependent RNA polymerases (RdRp) from Citrus tristeza virus (CTV) were tagged with HA and FLAG epitopes. Differentially tagged proteins were expressed either individually or concomitantly in Escherichia coli. Immunoprecipitation of the expressed proteins with anti-FLAG antibody followed by Western blot with anti-HA antibody demonstrated that molecules of RdRp from CTV interact to form oligomers. Yeast two-hybrid assays showed that molecules of RdRp interact in eukaryotic cells. Co-immunoprecipitation with anti-FLAG antibody of truncated HA-tagged RdRps (RdRpΔ1-166-HA, RdRpΔ1-390-HA, RdRp1-169-HA) co-expressed with full-length RdRp-FLAG showed that only RdRp1-169-HA interacted with the full-length FLAG-RdRp. Yeast two-hybrid assays with truncated RdRp constructs confirmed that the oligomerization site resides in the N-terminal region and that the first 169 aa of CTV RdRp are necessary and sufficient for oligomerization both in bacterial and yeast cells. Development of control strategies targeting viral RdRp oligomer formation may inhibit virus replication and prove useful in control of CTV.

Coimmunoprecipitation of Interacting Proteins in Plants

Protein-protein interactions discovered by yeast two-hybrid systems must be confirmed in vivo in a homologous system. In the case of plants, one of the easiest and fastest methods to validate protein interactions in vivo is the transient expression of the proteins in Nicotiana benthamiana leaves followed by coimmunoprecipitation. This method consists of the following steps: growth of the appropriate Agrobacterium tumefaciens cultures, preparation of the infiltration mixtures, infiltration into N. benthamiana leaves, protein extraction and immunoprecipitation. The utilization of epitope tags to immunoprecipitate and detect the proteins of interest is very useful in this procedure. In this chapter we describe a standard protocol to coimmunoprecipitate proteins expressed in N. benthamiana leaves.

TH2BS11ph histone mark is enriched in the unsynapsed axes of the XY body and predominantly associates with H3K4me3-containing genomic regions in mammalian spermatocytes

Background

TH2B is a major histone variant that replaces about 80–85% of somatic H2B in mammalian spermatocytes and spermatids. The post-translational modifications (PTMs) on TH2B have been well characterised in spermatocytes and spermatids. However, the biological function(s) of these PTMs on TH2B have not been deciphered in great detail. In our attempt to decipher the unique function(s) of histone variant TH2B, we detected the modification in the N-terminal tail, Serine 11 phosphorylation on TH2B (TH2BS11ph) in spermatocytes.

Results

The current study is aimed at understanding the function of the TH2BS11ph modification in the context of processes that occur during meiotic prophase I. Immunofluorescence studies with the highly specific antibodies revealed that TH2BS11ph histone mark is enriched in the unsynapsed axes of the sex body and is associated with XY body-associated proteins like Scp3, γH2AX, pATM, ATR, etc. Genome-wide occupancy studies as determined by ChIP sequencing experiments in P20 C57BL6 mouse testicular cells revealed that TH2BS11ph is enriched in X and Y chromosomes confirming the immunofluorescence staining pattern in the pachytene spermatocytes. Apart from the localisation of this modification in the XY body, TH2BS11ph is majorly associated with H3K4me3-containing genomic regions like gene promoters, etc. These data were also found to corroborate with the ChIP sequencing data of TH2BS11ph histone mark carried out in P12 C57BL6 mouse testicular cells, wherein we found the predominant localisation of this modification at H3K4me3-containing genomic regions. Mass spectrometry analysis of proteins that associate with TH2BS11ph-containing mononucleosomes revealed key proteins linked with the functions of XY body, pericentric heterochromatin and transcription.

Conclusions

TH2BS11ph modification is densely localised in the unsynapsed axes of the XY body of the pachytene spermatocyte. By ChIP sequencing studies in mouse P12 and P20 testicular cells, we demonstrate that TH2BS11ph is predominantly associated with H3K4me3 positive genomic regions like gene promoters, etc. We propose that TH2BS11ph modification could act alone or in concert with other histone modifications to recruit the appropriate transcription or XY body recombination protein machinery at specific genomic loci.

A Powerful Method for Studying Protein-Protein Interactions in Plants: Coimmunoprecipitation (Co-IP) Assay

With the continuous application of molecular biology technologies in the field of plant virology, growing evidence shows that the interactions between viral proteins or virus and host are essential in almost all steps of virus infection. Various methods used to study protein-protein interactions have been extensively adapted for plant virology research. Among them, coimmunoprecipitation (Co-IP) is considered as a standard and powerful tool by molecular biologists to analyze the occurrence of protein-protein interactions in living cells. This method can help us gain a deeper understanding of the functions of target proteins, which interact with other proteins or belong to some functional complexes. In this chapter, we detail a protocol for the Co-IP assay and highlight challenges associated with this method.

Biochemical assay of G protein-coupled receptor oligomerization: adenosine A1 and thromboxane A2 receptors form the novel functional hetero-oligomer

G protein-coupled receptors (GPCRs) are classified into a family of seven transmembrane receptors. Receptor oligomerization may be the key to the expression and function of these receptors, for example, ligand binding, desensitization, membrane trafficking, and signaling. The accumulation of evidence that GPCRs form an oligomerization with a functional alternation may change the strategy for the discovery of novel drugs targeting GPCRs. Identification of the oligomer is essential to elucidate GPCR oligomerization. GPCR oligomerizations have been demonstrated using various biochemical approaches, which include the coimmunoprecipitation method, fluorescence resonance energy transfer assay, and bioluminescence RET assay. Thus, various assays are useful for the study of GPCR oligomerization, and we should choose the best method to match the purpose. We previously targeted adenosine A1 and thromboxane A2 (TP) receptors to form a functionally novel hetero-oligomer, since both receptors function in the same cells. This chapter describes the methods used to detect GPCR oligomerization and alterations in the signaling pathways, principally according to our findings on oligomerization between adenosine A1 and TPα receptors.

Thioredoxin Reductase 2 Synergizes with Cytochrome c, Somatic to Alleviate Doxorubicin-Induced Oxidative Stress in Cardiomyocytes and Mouse Myocardium

Doxorubicin (DOX) may cause multiple side effects, which include cardiotoxicity. Hence, to ascertain the impact of thioredoxin reductase 2 (TXNRD2) and cytochrome c, somatic (CYCS) on DOX-induced oxidative stress (OS) in cardiomyocytes and mouse myocardium, this study was implemented. DOX was utilized to treat cardiomyocytes and mice, and TXNRD2 and CYCS expression in cell supernatant and mouse myocardial tissues was detected. TXNRD2 and/or CYCS were overexpressed in DOX-induced cardiomyocytes and mice. In cardiomyocytes, cell viability and the levels of reactive oxygen species (ROS), superoxide dismutase (SOD), catalase (CAT), malondialdehyde (MDA), and glutathione (GSH) were measured. In mice, pathologic changes of the heart, ejection fraction (EF), fractional shortening (FS), and heart weight (HW) /tibial length (TL) ratio, and the contents of lactic dehydrogenase (LDH), creatine kinase-MB (CK-MB), and cardiac troponin I (cTnI) were analyzed. To assess the binding between TXNRD2 and CYCS, coimmunoprecipitation and glutathione S-transferase pull-down assays were performed. TXNRD2 and CYCS were downregulated in DOX-treated cardiomyocytes and mice. Mechanistically, TXNRD2 interacted with CYCS. Overexpression of TXNRD2 or CYCS augmented viability and SOD, CAT, and GSH levels but reduced ROS and MDA contents in DOX-induced cardiomyocytes, which was further facilitated by simultaneous overexpression of TXNRD2 or CYCS. Moreover, TXNRD2 or CYCS upregulation improved the pathologic changes in myocardial tissues, along with increases in EF, FS, and HW/TL ratio of the heart and SOD, CAT, and GSH levels and decreases in LDH, CK-MB, cTnI, ROS, and MDA levels. TXNRD2 coordinated with CYCS to alleviate DOX-induced OS in cardiomyocytes and mouse myocardium.

A Coinfection Model to Evaluate Chlamydia Inc Protein Interactions

Chlamydia trachomatis resides and replicates within a membranous vacuole, termed the inclusion. A group of Type III secreted effector proteins, the inclusion membrane proteins (Inc), are embedded within the inclusion membrane and facilitate the interaction of the inclusion with host cell organelles. These interactions are vital for bacterial replication and allow for the acquisition of essential nutrients from the host cell. However, it is not known if Inc proteins function independently or require interactions with other Inc proteins to function. This chapter describes a system to test the homotypic/heterotypic interactions of Inc proteins through the coinfection of Chlamydia strains expressing differently tagged inclusion membrane proteins. Our approach takes advantage of the natural homotypic fusion of inclusions and allows for the study of Inc protein interactions when they are embedded within the inclusion membrane.

Analysis of Cytomegalovirus Glycoprotein and Cellular Receptor Interactions

Human cytomegalovirus (HCMV) entry into host cells is a complex process involving interactions between an array of viral glycoproteins with multiple host cell surface receptors. A significant amount of research has been devoted toward identifying these glycoprotein and cellular receptor interactions as the broad cellular tropism of HCMV suggests a highly regulated yet adaptable process that controls viral binding and penetration. However, deciphering the initial binding and cellular receptor activation events by viral glycoproteins remains challenging. The relatively low abundance of receptors and/or interactions with glycoproteins during viral entry, the hydrophobicity of membrane receptors, and the rapid degradation and recycling of activated receptors have complicated the analysis of HCMV entry and the cellular signaling pathways initiated by HCMV engagement to the host membrane. Here, we describe the different methodologies used in our laboratory and others to analyze the interactions between HCMV glycoproteins and host cellular receptors during the entry stage of the viral life cycle.

Detection of RIPK1 in the FADD-Containing Death Inducing Signaling Complex (DISC) During Necroptosis

FAS-associated protein with death domain (FADD) is a signaling molecule required by members of the TNF receptor superfamily (TNFRSF) such as FAS and TNFR1 to induce apoptosis. FADD is a small adapter molecule that functions as a scaffold to recruit procaspase-8 and other regulators. The FADD-containing signaling complex that initiates the apoptotic cascade has been termed the death inducing signaling complex (DISC). In the absence of FADD, death receptors cannot induce apoptosis and in appropriate cell types, these death receptors then induce necroptosis. Necroptosis can also be induced by death receptors in FADD-sufficient cells when caspase-8 is inhibited, usually accomplished by the addition of caspase inhibitors. Under such necroptotic conditions, the immunoprecipitation of FADD to isolate the DISC can be utilized to examine components of this complex. Here, we describe the immunoprecipitation of FADD and subsequent western-blotting to identify RIPK1 in this complex during necroptosis.

Investigation of Novel Cavin-1/Suppressor of Cytokine Signaling 3 (SOCS3) Interactions by Coimmunoprecipitation, Peptide Pull-Down, and Peptide Array Overlay Approaches

The ability of inducible regulator suppressor of cytokine signaling 3 (SOCS3) to inhibit Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling requires interaction with specific cytokine receptors, JAKs, and components of the cellular ubiquitylation machinery. However, it is now clear that additional protein interactions are essential for effective inhibition of JAK-STAT signaling that have also identified new roles for SOCS3. For example, we have demonstrated that SOCS3 interaction with cavin-1, a core component of caveolae essential for their formation, is required for effective inhibition of interleukin (IL)-6 signaling and maintenance of cellular levels of caveolae. This is achieved through cavin-1 interaction with a discrete motif within the SOCS3 SH2 domain. Here, we describe in detail three methods (coimmunoprecipitation; peptide pull-down; peptide array overlay) we have used to validate and characterize cavin-1/SOCS3 interactions in vitro.

Functional Integrin Regulation Through Interactions with Tetraspanin CD9

Integrins are adhesion receptors that mediate many intercellular and cell-extracellular matrix interactions with relevance in physiology and pathology. Unlike other cellular receptors, integrins critically require activation for ligand binding. Through interaction in cis with other molecules and the formation of tetraspanin-enriched membrane microdomains (TEMs), the tetraspanin CD9 regulates integrin activity and avidity. Here we present three techniques used to study CD9-integrin interactions and integrin activation.

Validation of Nuclear Pore Complex Protein-Protein Interactions by Transient Expression in Plants

The nuclear pore complex (NPC) is the largest protein complex, consisting of multiple copies of over 30 different nucleoporins. The interactions between the nucleoporins are critical elements for the NPC functions of the nuclear envelope in plant cells. In recent years, transient expression-based validations of protein-protein interactions have been widely used in plants. Bimolecular fluorescence complementation assay and coimmunoprecipitation assays are powerful tools to identify the molecules that interact with specific proteins. Here, as an example, we describe these techniques using nucleoporin protein interactions in plants.

Affinity Purification and Coimmunoprecipitation of Transenvelope Protein Complexes in Gram-Negative Bacteria

Multiprotein complexes are important machineries that organize a large number of different proteins into functional units. Studying protein-protein interactions in the complexes, rather than individual proteins, is a fundamental step to gaining functional insights into a biological process. Here, we present the sequential affinity purification and coimmunoprecipitation system that was applied to enable the efficient purification of all the proteins that compose the Lpt system complex in Escherichia coli and their identification by western blotting and mass spectrometry (MS).

Tissue factor regulates autophagy in pulmonary artery endothelial cells from chronic thromboembolic pulmonary hypertension rats via the p38 MAPK-FoxO1 pathway

AIMS

To detect the expression of autophagy components, p38 MAPK (p38) and phosphorylated forkhead box transcription factor O-1 (pFoxO1) in pulmonary vascular endothelial cells of chronic thromboembolic pulmonary hypertension (CTEPH) rats and to investigate the possible mechanism through which tissue factor (TF) regulates autophagy.

METHODS

Pulmonary artery endothelial cells (PAECs) were isolated from CTEPH (CTEPH group) and healthy rats (control group (ctrl group)) which were cocultured with TF at different time points including 12 h, 24 h, 48 h and doses including 0 nM,10 nM, 100 nM, 1µM, 10µM, 100µM and cocultured with TFPI at 48 h including 0 nM, 2.5 nM, 5 nM. The expression of forkhead box transcription factor O-1 (FoxO1), pFoxO1, p38, Beclin-1 and LC3B in PAECs was measured. Coimmunoprecipitation (co-IP) assays were used to detect the interaction between FoxO1 and LC3.

RESULTS

The protein expression of p-FoxO1/FoxO1 was significantly lower in the CTEPH groups (cocultured with TF from 0 nM to 100 µM) than in the ctrl group at 12 h, 24 h, and 48 h (P < 0.05) and was significantly lower in the CTEPH groups (cocultured with TFPI from 0 nM to 5 nM) than in the ctrl group at 48 h (P < 0.05). The protein expression of p38 in the CTEPH groups treated with 0 nM, 10 nM, 100 nM or 1 µM TF for 48 h significantly increased than ctrl groups (P < 0.05) and was significantly increased in the CTEPH groups (cocultured with TFPI concentration from 0 nM to 5 nM) than in the ctrl group at 48 h (P < 0.05). The protein expression of Beclin1 at the same concentration (cocultured with TF from 0 nM to 100 µM) was significantly lower in the CTEPH groups than ctrl groups after 24 h and 48 h (P < 0.05) and was significantly decreased in the CTEPH groups (cocultured with TFPI concentration from 2.5 nM to 5 nM) than in the ctrl group at 48 h (P < 0.05). The protein expression of LC3-II/LC3-I at the same concentration (cocultured with TF 0 nM, 1 µM, 10 µM, and 100 µM) was significantly lower in the CTEPH than in the ctrl groups after 12 h (P < 0.05) and was significantly lower in the CTEPH groups (cocultured with TFPI concentration from 0 nM to 5 nM) than in the ctrl group at 48 h (P < 0.05). There were close interactions between FoxO1 and LC3 in the control and CTEPH groups at different doses and time points.

CONCLUSION

The autophagic activity of PAECs from CTEPH rats was disrupted. TF, FoxO1 and p38 MAPK play key roles in the autophagic activity of PAECs. TF may regulate autophagic activity through the p38 MAPK-FoxO1 pathway.

Affinity Purification Followed by Liquid Chromatography-Tandem Mass Spectrometry to Identify Proteins Interacting with ABA Signaling Components

Abscisic acid (ABA) is a key phytohormone involved in plant development, seed germination and responses to osmotic stresses, such as drought and high salinity. SNF1-related protein kinases (SnRK2s) play important roles in ABA-dependent and ABA-independent osmotic stress signaling. SnRK2s phosphorylate transcription factors and ion channels in response to ABA or osmotic stress to induce the expression of stress-responsive genes and stomatal closure, respectively, to confer osmotic stress tolerance. The activity of SnRK2s is directly or indirectly regulated by several protein factors. Identification of downstream substrates or upstream regulators of SnRK2s is very useful for elucidating protein components that regulate ABA and osmotic stress signaling. Here, we describe the use of affinity purification by coimmunoprecipitation and liquid chromatography-tandem mass spectrometry to identify protein complexes involved in ABA and osmotic stress signaling in plants. We previously identified several protein factors that regulate ABA and osmotic stress signaling by using this method.

In Vivo Protein Cross-Linking and Coimmunoprecipitation in Haloferax volcanii

Coimmunoprecipitation is a powerful and commonly used method to identify protein-protein interactions in a physiological context. Here, we report a coimmunoprecipitation protocol that was adapted and optimized for the haloarchaeon Haloferax volcanii to identify interacting partners to the LonB protease. This protocol includes the in vivo cross-linking of H. volcanii proteins using two different crosslinker agents, dithiobis(succinimidyl propionate) and formaldehyde, followed by immunoprecipitation with anti-LonB antibody conjugated to Protein A - Sepharose beads. Tryptic on-bead protein digestion was performed combined with Mass Spectrometry analysis of peptides for the identification and quantification of LonB ligands.

Affinity Purification and Preparation of Peptides for Mass Spectrometry from C. elegans

Affinity purification of a target protein followed by mass spectrometry of the purified peptides can be used to identify physical interactors of the protein of interest. Using this biochemical approach on proteins from whole organisms such as C. elegans can reveal novel in vivo protein interactions that cannot be identified using homology-based predictions or in vitro approaches. Here we describe affinity purification of a GFP-tagged target protein from whole worm lysates, digestion of the purified proteins into peptides, and preparation of the peptides for analysis by mass spectrometry. This protocol has been optimized for ChromoTek GFP-Trap® Magnetic Agarose beads, but it may be used with other tags and antibody-conjugated beads.

Biochemical and Cellular Assays to Study Mechanisms of PCP Signaling in Axon Guidance

Understanding biochemical and cellular mechanisms of how PCP components regulate axon guidance is important for understanding brain development and may lead to new therapeutic approaches for neural repair. Meanwhile, axonal growth cones are a highly polarized structure and are a great experimental system. Therefore, some of these novel mechanisms we are uncovering for axon guidance may be applicable for PCP signaling in general. In this chapter, we introduce some of the techniques we used or developed: (1) protein localization and trafficking; (2) protein phosphorylation; and (3) protein-protein interactions in the same cell and across the two neighboring cells.

HLA Class I and Class II-Induced Intracellular Signaling and Molecular Associations in Primary Human Endothelial Cells

The signaling capacity of HLA molecules in vascular cells has been well established. Intracellular signaling and association with the coreceptor integrin β4 has been well-studied for HLA class I. However, little is known regarding HLA class II intracellular signaling in human endothelial cells. Investigation of HLA class II has been challenging due to the loss of HLA class II expression in cultured primary cells. Herein, we describe methods for inducing expression of endogenous alleles and loci of HLA class II molecules, as well as for studying intracellular signaling. This includes siRNA knockdown of proteins and coimmunoprecipitation of putative coreceptors for HLA in primary human aortic endothelial cells.