Specific Interaction Partners Research Articles

Capturing the Social Life of a Person by Integrating Experience-Sampling Methodology and Personal-Social-Network Assessments

The daily social life of a person can be captured with different methodologies. Two methods that are especially promising are personal-social-network (PSN) data collection and experience-sampling methodology (ESM). Whereas PSN data collections ask participants to provide information on their social relationships and broader social environment, ESM studies collect intensive longitudinal data on social interactions in daily life using multiple short surveys per day. In combination, the two methods enable detailed insights into someone’s social life, including information on interactions with specific interaction partners from the personal network. Despite many potential uses of such data integration, there are few studies to date using the two methods in conjunction. This is likely due to their complexity and lack of software that allows capturing the full social life of someone while keeping the burden for participants and researchers sufficiently low. In this article, we report on the development of methodology and software for an ESM/PSN integration within the established ESM tool m-Path. We describe results of a first study using the developed tool that illustrate the feasibility of the proposed method combination and show that participants consider the assessments insightful. We further outline study-design choices and ethical considerations when combining the two methodologies. We hope to encourage applications of the presented methods in research and practice across different fields.

Considering the ‘With Whom’: Differences Between Event- and Signal-Contingent ESM Data of Person-Specific Social Interactions

Experience sampling studies often aim to capture social interactions. A central methodological question in such studies is whether to use event- or signal-contingent sampling. The little existing research on this issue has not taken into account that social interactions occur with unique interaction partners (e.g., Anna or Tom). We analyze one week of social interaction data of 286 students from the University of Pittsburgh (60.8% male, mean age 19.2 years), taking into account the unique interaction partners of each student. Specifically, we investigate the differences between event- and signal contingent sampling in (1) the total number of unique interaction partners captured, as well as (2) the kinds of relationships, and (3) the quality of social interactions with these captured interaction partners. Apart from a larger quantity of interactions and unique interaction partners in the event-contingent sampling design, our analyses indicate subtle differences between the two designs when aiming to assess social interactions with more distant interaction partners, such as coworkers or strangers. Most importantly, in our analyses, specific interaction partners and social roles explained a considerable amount of variance in the quality of social interactions (up to 20.5%), suggesting that future research would benefit greatly from considering “with whom” individuals interact.

Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partner

Protein interaction networks underlie countless biological mechanisms. However, most protein interaction predictions are based on biological evidence that are biased to well-known protein interaction or physical evidence that exhibits low accuracy for weak interactions and requires high computational power. In this study, a novel method has been suggested to predict protein interaction partners by investigating narrow funnel-like interaction energy distribution. In this study, it was demonstrated that various protein interactions including kinases and E3 ubiquitin ligases have narrow funnel-like interaction energy distribution. To analyze protein interaction distribution, modified scores of iRMS and TM-score are introduced. Then, using these scores, algorithm and deep learning model for prediction of protein interaction partner and substrate of kinase and E3 ubiquitin ligase were developed. The prediction accuracy was similar to or even better than that of yeast two-hybrid screening. Ultimately, this knowledge-free protein interaction prediction method will broaden our understanding of protein interaction networks.

Constraining and Modifying Peptides Using Pd-Mediated Cysteine Allylation.

Over the past decades, several strategies for inducing and stabilizing secondary structure formation in peptides have been developed to increase their proteolytic stability and their binding affinity to specific interaction partners. Here, we report how our recently introduced chemoselective Pd-catalyzed cysteine allylation reaction can be extended to stapling and how the resulting alkene-containing staples themselves can be further modified to introduce additional probes into such stabilized peptides. The latter is demonstrated by introducing a fluorophore as well as a PEG moiety into different stapled peptides using bioorthogonal thiol-ene and Diels-Alder reactions. Furthermore, we investigated structural implications of our allyl staples when used to replace conformationally relevant disulfide bridges. To this end, we chose a selective binder of integrin α3 β1 (LXY3), which is only active in its cyclic disulfide form. We replaced the disulfide bridge by different stapling reagents in order to increase stability and binding affinity towards integrin α3 β1 .

Measuring Interpersonal Trust towards Virtual Humans with a Virtual Maze Paradigm.

Virtual humans, including virtual agents and avatars, play an increasingly important role as VR technology advances. For example, virtual humans are used as digital bodies of users in social VR or as interfaces for AI assistants in online financing. Interpersonal trust is an essential prerequisite in real-life interactions, as well as in the virtual world. However, to date, there are no established interpersonal trust measurement tools specifically for virtual humans in virtual reality. This study fills the gap, by contributing a novel validated behavioural tool to measure interpersonal trust towards a specific virtual social interaction partner in social VR. This validated paradigm is inspired by a previously proposed virtual maze task that measures trust towards virtual characters. In the current study, a variant of this paradigm was implemented. The task of the users (the trustors) is to navigate through a maze in virtual reality, where they can interact with a virtual human (the trustee). They can choose to 1) ask for advice and 2) follow the advice from the virtual human if they want to. These measures served as behavioural measures of trust. We conducted a validation study with 70 participants in a between-subject design. The two conditions did not differ in the content of the advice but in the appearance, tone of voice and engagement of the trustees (alleged as avatars controlled by other participants). Results indicate that the experimental manipulation was successful, as participants rated the virtual human as more trustworthy in the trustworthy condition than in the untrustworthy condition. Importantly, this manipulation affected the trust behaviour of our participants, who, in the trustworthy condition, asked for advice more often and followed advice more often, indicating that the paradigm is sensitive to assessing interpersonal trust towards virtual humans. Thus, our paradigm can be used to measure differences in interpersonal trust towards virtual humans and may serve as a valuable research tool to study trust in virtual reality.

Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins.

Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequences of two interacting protein families, one can use phylogeny or residue coevolution to infer which paralogs are specific interaction partners within each species. We show that these two signals can be combined to improve the performance of the inference of interaction partners among paralogs. For this, we first align the sequence-similarity graphs of the two families through simulated annealing, yielding a robust partial pairing. We next use this partial pairing to seed a coevolution-based iterative pairing algorithm. This combined method improves performance over either separate method. The improvement obtained is striking in the difficult cases where the average number of paralogs per species is large or where the total number of sequences is modest.

On How to Be Liked in First Encounters: The Effects of Agentic and Communal Behaviors on Popularity and Unique Liking

When meeting other people for the first time, how should one behave in order to be liked? We investigated the effects of agentic and communal behaviors on two forms of being liked: popularity (being generally liked by others) and unique liking (being uniquely liked by specific interaction partners). In a round-robin study, 139 unacquainted German adults had dyadic conversations and provided liking ratings afterward. The conversations were recorded on video, and four agentic behaviors (leading, dominant, confident, boastful) and four communal behaviors (polite, benevolent, warm, friendly) were each rated by trained observers. Participants who generally showed agentic and communal behavior were also generally liked (popularity). When participants’ level of communal, but not agentic, behavior exceeded their personal standards during an interaction, they were particularly well-liked by the respective interaction partner (unique liking). The behavioral predictors of being liked thus differ, depending on whether one focuses on popularity or unique liking.

Prediction of α-MORFS and folding free energies in intrinsically disordered peptides.

Intrinsically disordered proteins (IDPs) and disordered regions (IDRs) of folded proteins play significant roles in cell signaling, regulation, and recognition. However, the lack of well-defined structures challenges our ability to predict the biological role and working mechanisms of IDPs. Computer simulations provide a powerful tool to characterize the conformational ensembles explored by IDPs. Here, we use free energy calculations in atomistic simulations to explore the applicability of binding-induced folding mechanisms for the development of ligands that specifically bind to intrinsically disordered proteins. Molecular recognition features (MoRFs) are functional regions located within longer intrinsically disordered regions that undergo disorder-to-order transitions upon binding their specific interaction partners. A subgroup called α-MoRFs undergoes disordered to α-helix transitions upon binding. In principle, MoRFs can also be utilized as targets for the design of drug molecules that bind to such regions in disease-causing IDPs and render them inactive or modulate their properties. We quantify the free energy cost involved in transitions from intrinsically disordered peptide states into folded secondary structure motifs for variable peptide sequences. We compare α-MoRFs and fully disordered sequences from several known proteins and compare our results to state-of-the-art structure predictions. In contrast to structure prediction tools, our atomistic simulation protocol not only allows us to determine the minimum free energy structure but also quantifies the free energy difference between folded and disordered conformational states. The latter is critical for the development of drugs targeting a specific IDR in a folded conformation because the binding free energy needs to overcompensate the free energy cost of folding. Our general strategy aims to reduce the “undruggability” of IDPs and IDRs, which lack an inherent structure and represent a significant fraction of the proteome.

Signal Peptide Features Determining the Substrate Specificities of Targeting and Translocation Components in Human ER Protein Import

In human cells, approximately 30% of all polypeptides enter the secretory pathway at the level of the endoplasmic reticulum (ER). This process involves cleavable amino-terminal signal peptides (SPs) or more or less amino-terminal transmembrane helices (TMHs), which serve as targeting determinants, at the level of the precursor polypeptides and a multitude of cytosolic and ER proteins, which facilitate their ER import. Alone or in combination SPs and TMHs guarantee the initial ER targeting as well as the subsequent membrane integration or translocation. Cytosolic SRP and SR, its receptor in the ER membrane, mediate cotranslational targeting of most nascent precursor polypeptide chains to the polypeptide-conducting Sec61 complex in the ER membrane. Alternatively, fully-synthesized precursor polypeptides and certain nascent precursor polypeptides are targeted to the ER membrane by either the PEX-, SND-, or TRC-pathway. Although these targeting pathways may have overlapping functions, the question arises how relevant this is under cellular conditions and which features of SPs and precursor polypeptides determine preference for a certain pathway. Irrespective of their targeting pathway(s), most precursor polypeptides are integrated into or translocated across the ER membrane via the Sec61 channel. For some precursor polypeptides specific Sec61 interaction partners have to support the gating of the channel to the open state, again raising the question why and when this is the case. Recent progress shed light on the client spectrum and specificities of some auxiliary components, including Sec62/Sec63, TRAM1 protein, and TRAP. To address the question which precursors use a certain pathway or component in intact human cells, i.e., under conditions of fast translation rates and molecular crowding, in the presence of competing precursors, different targeting organelles, and relevant stoichiometries of the involved components, siRNA-mediated depletion of single targeting or transport components in HeLa cells was combined with label-free quantitative proteomics and differential protein abundance analysis. Here, we present a summary of the experimental approach as well as the resulting differential protein abundance analyses and discuss their mechanistic implications in light of the available structural data.

The potential mechanism of PPP2R3A in myocardial cells and its interacting proteins.

PPP2R3A plays a key role in the cardiac pathological and physiological processes, yet little is known about how the protein involved in normal myocardium formation and the protein-protein interaction pathways involved. To address this issue, we investigated the role of PPP2R3A in cardiac myocytes and identify PPP2R3A specific protein interaction partners to accelerate the developmental process of the mechanistic studies. PPP2R3A-silenced primary myocardial cell of neonatal rats and H9c2 cells were established by infecting shRNA lentiviral particles. RT-PCR and Western blot were used to determine the expression of PPP2R3A and silencing efficiency. The cell viability was analyzed by CCK-8 kit, then the cell cycles and apoptosis assays were detected by flow cytometry. Novel protein-protein interactions of PPP2R3A were detected by Yeast Two-Hybrid assays using a high-quality human primary cardiomyocyte cDNA library. PPP2R3A-silencing rat primary cardiomyocytes and H9c2 cells were established successfully, and the expression of PPP2R3A was downregulated significantly as confirmed by RT-PCR and Western blot. PPP2R3A silencing can inhibit the myocardial cell proliferation, arrest the cell cycle in the S phase and promote the cardiomyocytes apoptosis. 19 potential candidates like COL1A2, GIPC1and BCL6 specifically interact with PPP2R3A, and COL1A2 was the highest screening frequency, covering 12.5% of the 24 clones. These partners are highly enriched in signaling pathways associated with a variety of cellular processes. A series of studies have discovered that PPP2R3A was closely associated with heart failure and arrhythmia. Our data further confirmed PPP2R3A plays an important role in the cardiomyocytes and PPP2R3A in the regulation of cardiac events via its interaction partners. Therefore, it is a potential therapeutic target for the disease.

No effects of synchronicity in online social dilemma experiments: A registered report

AbstractOnline experiments have become a valuable research tool for researchers interested in the processes underlying cooperation. Typically, online experiments are asynchronous, participants complete an experiment individually and are matched with partners after data collection has been completed. We conducted a registered report to compare asynchronous and synchronous designs, where participants interact and receive feedback in real-time. We investigated how two features of synchronous designs, pre-decision matching and immediate feedback, influence cooperation in the prisoners dilemma. We hypothesized that 1) pre-decision matching (assigning participants to specific interaction partners before they make decisions) would lead to decreased social distance and increased cooperation; 2) immediate feedback would reduce feelings of aversive uncertainty and lead to increased cooperation; and 3) individuals with prosocial Social Value Orientations would be more sensitive to the differences between synchronous and asynchronous designs. We found no support for these hypotheses. In our study (N = 1,238), pre-decision matching and immediate feedback had no significant effects on cooperative behavior or perceptions of the interaction; and their effects on cooperation were not significantly moderated by Social Value Orientation. The present results suggest that synchronous designs have little effect on cooperation in online social dilemma experiments.

Methods to study circRNA-protein interactions.

Circular RNAs (circRNAs) have been studied extensively in the last few years, uncovering functional roles in a diverse range of cell types and organisms. As shown for a few cases, these functions may be mediated by trans-acting factors, in particular RNA-binding proteins (RBPs). However, the specific interaction partners for most circRNAs remain unknown. This is mainly due to technical difficulties in their identification and in differentiating between interactors of circRNAs and their linear counterparts. Here we review the currently used methodology to systematically study circRNA-protein complexes (circRNPs), focusing either on a specific RNA or protein, both on the gene-specific or global level, and discuss advantages and challenges of the available approaches.

Listening to the Whispers in Neuroimmune Crosstalk: A Comprehensive Workflow to Investigate Neurotrophin Receptor p75NTR Under Endogenous, Low Abundance Conditions.

Inflammatory conditions are critically influenced by neuroimmune crosstalk. Cytokines and neurotrophic factors shape the responses of both nervous and immune systems. Although much progress has been made, most findings to date are based on expression of recombinant (tagged) proteins. The examination of receptor interactions by immunoprecipitation (IP) at endogenous levels provides further insight into the more subtle regulations of immune responses. Here, we present a comprehensive workflow and an optimized IP protocol that provide step-by-step instructions to investigate neurotrophin receptor p75NTR at endogenous, low abundance levels: from lysate preparation and confirmation of receptor expression to antibody validation and successful detection of protein-protein interactions. We employ human melanoma cell line A375 to validate specific antibodies and IP conditions, and apply these methods to explore p75NTR interactions in human leukemic plasmacytoid dendritic cell line PMDC05 detecting 14-3-3ϵ:p75NTR interaction in this cell type. With p75NTR as an exemplary protein, our approach provides a strategy to detect specific interaction partners even under endogenous, low abundance expression conditions.

Proximity-Dependent Biotinylation (BioID) of Integrin Interaction Partners.

Integrins are heterodimeric adhesion receptors that maintain cell-extracellular matrix (ECM) interactions in diverse tissue microenvironments. They mediate cell adhesion and signaling through the assembly of large cytoplasmic multiprotein complexes that focally connect with the cytoskeleton. Integrin adhesion complexes (IAC) are specialized by the type of integrin-ECM contact and are sensitive to mechanical forces. Thus, they encrypt context-dependent information about the microenvironment in their composition. Signals mediated through IACs modulate many aspects of cell behavior, which allows cells to adapt to their surroundings. To gain insights into their function, IACs have been isolated from cultured cells and explored by proteomics. IACs are insoluble by nature and held together by transient/weak interactions, which makes it challenging to isolate intact IACs. Usually all IACs coupled to a specified ECM, which may employ different integrins, are isolated. Here we describe an alternative method based on proximity-dependent biotin identification (BioID), where specific integrin interaction partners are labeled in live cells and isolated without the need to isolate intact IACs.

Caspr2 interacts with type 1 inositol 1,4,5-trisphosphate receptor in the developing cerebellum and regulates Purkinje cell morphology

Contactin-associated protein-like 2 (Caspr2) is a neurexin-like protein that has been associated with numerous neurological conditions. However, the specific functional roles that Caspr2 plays in the central nervous system and their underlying mechanisms remain incompletely understood. Here, we report on a functional role for Caspr2 in the developing cerebellum. Using a combination of confocal microscopy, biochemical analyses, and behavioral testing, we show that loss of Caspr2 in the Cntnap2−/− knockout mouse results in impaired Purkinje cell dendritic development, altered intracellular signaling, and motor coordination deficits. We also find that Caspr2 is highly enriched at synaptic specializations in the cerebellum. Using a proteomics approach, we identify type 1 inositol 1,4,5-trisphosphate receptor (IP3R1) as a specific synaptic interaction partner of the Caspr2 extracellular domain in the molecular layer of the developing cerebellum. The interaction of the Caspr2 extracellular domain with IP3R1 inhibits IP3R1-mediated changes in cellular morphology. Together, our work defines a mechanism by which Caspr2 controls the development and function of the cerebellum and advances our understanding of how Caspr2 dysfunction might lead to specific brain disorders.

The ubiquitin-like modifier FAT10 - much more than a proteasome-targeting signal.

Human leukocyte antigen (HLA)-F adjacent transcript 10 (FAT10) also called ubiquitin D (UBD) is a member of the ubiquitin-like modifier (ULM) family. The FAT10 gene is localized in the MHC class I locus and FAT10 protein expression is mainly restricted to cells and organs of the immune system. In all other cell types and tissues, FAT10 expression is highly inducible by the pro-inflammatory cytokines interferon (IFN)-γ and tumor necrosis factor (TNF). Besides ubiquitin, FAT10 is the only ULM which directly targets its substrates for degradation by the 26S proteasome. This poses the question as to why two ULMs sharing the proteasome-targeting function have evolved and how they differ from each other. This Review summarizes the current knowledge of the special structure of FAT10 and highlights its differences from ubiquitin. We discuss how these differences might result in differential outcomes concerning proteasomal degradation mechanisms and non-covalent target interactions. Moreover, recent insights about the structural and functional impact of FAT10 interacting with specific non-covalent interaction partners are reviewed.

Single molecule distribution of RhD binding epitopes on ultraflat erythrocyte ghosts.

The Rh blood group system plays a key role in transfusion and organ transplant medicine. The complex transmembrane Rh polypeptides RhD and RhCE carry numerous antigens, including the extremely immunogenic D antigen. The Rh polypeptides form multimolecular Rh complexes with certain transmembrane and skeletal proteins, with so far only incompletely understood physiological functions. Determination of the energy landscape of individual Rh binding epitopes towards their specific interaction partners as well as their localization across the red blood cell (RBC) membrane requires single molecule approaches including large area high resolution recognition imaging. Atomic force microscopy based molecular recognition force spectroscopy in combination with single molecule recognition imaging fulfills these requirements. For unbiased single molecule results, nano-mechanical influences due to cell elasticity have to be eliminated. This is realized by generation of ultra flat erythrocyte ghosts on a solid support. We developed a protocol for the preparation of complete ultraflat erythrocyte ghosts and determined the molecular binding behaviour of different anti-D antibodies towards their binding epitopes on RhD positive and negative erythrocytes. Performing optimized topography and recognition imaging at 16 Mpixel resolution allowed localisation of individual RhD molecules at the single molecule level across an entire RBC. A map of Rh antigens across integer ultraflat RBC ghosts was generated with nanometer resolution. Here we show a homogeneous distribution on rim and dimple regions with comparable receptor densities. Furthermore, differences in the energy landscape between specific monoclonal antibodies were determined at the single molecule level.

TPX2-LIKE PROTEIN3 Is the Primary Activator of α-Aurora Kinases and Is Essential for Embryogenesis.

Aurora kinases are key regulators of mitosis. Multicellular eukaryotes generally possess two functionally diverged types of Aurora kinases. In plants, including Arabidopsis (Arabidopsis thaliana), these are termed α- and β-Auroras. As the functional specification of Aurora kinases is determined by their specific interaction partners, we initiated interactomics analyses using both Arabidopsis α-Aurora kinases (AUR1 and AUR2). Proteomics results revealed that TPX2-LIKE PROTEINS2 and 3 (TPXL2/3) prominently associated with α-Auroras, as did the conserved TPX2 to a lower degree. Like TPX2, TPXL2 and TPXL3 strongly activated the AUR1 kinase but exhibited cell-cycle-dependent localization differences on microtubule arrays. The separate functions of TPX2 and TPXL2/3 were also suggested by their different influences on AUR1 localization upon ectopic expressions. Furthermore, genetic analyses showed that TPXL3, but not TPX2 and TPXL2, acts nonredundantly to enable proper embryo development. In contrast to vertebrates, plants have an expanded TPX2 family and these family members have both redundant and unique functions. Moreover, as neither TPXL2 nor TPXL3 contains the C-terminal Kinesin-5 binding domain present in the canonical TPX2, the targeting and activity of this kinesin must be organized differently in plants.

Neuroticism and interpersonal perception: Evidence for positive, but not negative, biases.

Personality dispositions predict how individuals perceive, interpret, and react to social interactions with others. A still unresolved question is (a) whether these personality-congruent interpersonal perceptions reflect perception biases, which occur when perceivers' dispositions systematically predict deviations between perceivers' and other people's perceptions of the same interaction, and/or selection effects, which occur when perceivers' dispositions predict their selection of interaction partners, and (b) whether these effects feed back into perceivers' personality. Data from 110 psychology freshmen involving repeated assessments of Neuroticism and repeated interpersonal perceptions of social interactions with fellow students were analyzed to address these questions, focusing on Neuroticism. There is evidence for a Neuroticism-related positivity bias in interpersonal perceptions (i.e., perceivers high in Neuroticism tended to make more positive judgments of others' sociability and warmth), but little evidence for personality-congruent selection effects (i.e., Neuroticism-related preferences for interaction partners). The positivity bias did not predict intrapersonal changes in Neuroticism over time, but the selection of specific interaction partners did. These findings help to shed light on the interpersonal perception dynamics of Neuroticism in a real-life context and add to our understanding of the psychological mechanisms underlying the interplay of personality and interpersonal perceptions.

Adolescent idiopathic scoliosis associated POC5 mutation impairs cell cycle, cilia length and centrosome protein interactions.

Adolescent Idiopathic Scoliosis (AIS) is a spinal deformity that affects approximately 3 percent of human adolescents. Although the etiology and molecular basis of AIS is unclear, several genes such as POC5 have been identified as possible causes of the condition. In order to understand the role of POC5 in the pathogenesis of AIS, we investigated the subcellular localization of POC5 in cilia of cells over-expressing either the wild type (wt) or an AIS-related POC5 variant POC5A429V. Mutation of POC5 was found to alter its subcellular localization and to induce ciliary retraction. Furthermore, we observed an impaired cell-cycle progression with the accumulation of cells in the S-phase in cells expressing POC5A429V. Using immunoprecipitation coupled to mass spectrometry, we identified specific protein interaction partners of POC5, most of which were components of cilia and cytoskeleton. Several of these interactions were altered upon mutation of POC5. Altogether, our results demonstrate major cellular alterations, disturbances in centrosome protein interactions and cilia retraction in cells expressing an AIS-related POC5 mutation. Our study suggests that defects in centrosomes and cilia may underlie AIS pathogenesis.