Proximity Interactions Research Articles

Steric occlusion regulates proximal interactions of acyl carrier protein domain in fungal fatty acid synthase

The acyl carrier protein (ACP) domain shuttles substrates and reaction intermediates in type I fungal fatty acid synthases via transient protein-protein interactions. Here, using electron cryo-microscopy (cryoEM), we report the structure of a fungal FAS stalled at the dehydration reaction, which precedes the final enoyl reduction in the fatty acid biosynthesis cycle. This conformation revealed multiple contact sites between ACP and the dehydratase (DH) and enoyl reductase (ER) domains that occluded the ACP binding to the adjacent ER domain. Our data suggests a minimal path from the DH to the ER reaction site that requires minute changes in the coordinates of the structured N- and C- termini of the ACP domain.

Phosphoproteomics identifies dual-site phosphorylation in an extended basophilic motif regulating FILIP1-mediated degradation of filamin-C

The PI3K/Akt pathway promotes skeletal muscle growth and myogenic differentiation. Although its importance in skeletal muscle biology is well documented, many of its substrates remain to be identified. We here studied PI3K/Akt signaling in contracting skeletal muscle cells by quantitative phosphoproteomics. We identified the extended basophilic phosphosite motif RxRxxp[S/T]xxp[S/T] in various proteins including filamin-C (FLNc). Importantly, this extended motif, located in a unique insert in Ig-like domain 20 of FLNc, is doubly phosphorylated. The protein kinases responsible for this dual-site phosphorylation are Akt and PKCα. Proximity proteomics and interaction analysis identified filamin A-interacting protein 1 (FILIP1) as direct FLNc binding partner. FILIP1 binding induces filamin degradation, thereby negatively regulating its function. Here, dual-site phosphorylation of FLNc not only reduces FILIP1 binding, providing a mechanism to shield FLNc from FILIP1-mediated degradation, but also enables fast dynamics of FLNc necessary for its function as signaling adaptor in cross-striated muscle cells.

Second heart field-specific expression of Nkx2-5 requires promoter proximal interaction with Srf

The cardiac homeobox transcription factor Nkx2-5 is a major determinant of cardiac identity and cardiac morphogenesis. Nkx2-5 operates as part of a complex and mutually reinforcing network of early transcription factors of the homeobox, GATA zinc finger and MADS domain families to initiate the program of cardiac development and differentiation, particularly in outflow tract precursor cells in the second heart field (SHF). We have now found evidence for another aspect of cardiac transcription factor cooperativity between Nkx2-5 and the cardiac enriched MADS domain transcription factor Srf. Specifically, Srf interaction with an evolutionarily conserved binding site in the Nkx2-5 CpG island-like proximal promoter is required for cardiac specific expression mediated by an SHF enhancer, and for combinatorial activation of these elements by cardiac transcription factors. These results provide further insight into cooperative gene regulation during cardiogenesis at the level of promoter-enhancer interactions.

Motion–Force Interaction Performance Analyses of Redundantly Actuated and Overconstrained Parallel Robots With Closed-Loop Subchains

Abstract Motion–force interaction performance analyses of redundantly actuated and overconstrained parallel robots with closed-loop subchains are an open problem considering two challenges: (a) how to take all the internal wrenches into account at the same level when the mobile platform suffers uncertain loads and (b) how to disclose the influence of the structural parameters inside the closed-loop subchains on the robot’s performance. To tackle this problem, based on the blocking-and-acting strategy, this paper proposes a new screw-based method to analyze the motion–force interaction performance of such parallel robots. Two aspects of performance are focused, i.e., the distal and proximal motion–force interactability. The two proposed indices focus on reflecting the load-carrying capacity and the motion-transmission capacity, respectively. To evaluate the comprehensive performance of the parallel robot at a certain pose, a local interaction index (LII) is defined as the minimum value of indices of the minimized distal and proximal interaction performance. The feasibility and validity of the proposed indices are illustrated by the motion–force interaction analysis of some redundantly actuated and overconstrained parallel robots with closed-loop subchains.

Affinity threshold conversion: the progressive differentiation checkpoint at which the TCRα/CD3δ signaling axis controls thymic positive selection

Abstract Upon positive selection of conventional αβ T cells, CD4+ CD8+ double-positive (DP) cells transition to single-positive (SP) and reduce their responsiveness to weak peptide/MHC ligands (affinity threshold conversion, ATC). We report that ATC actually begins prior to the completion of positive selection in the DP stage, and this checkpoint is where the TCRα/CD3δ signaling axis controls positive selection. We dissected ATC in the OT1 TCR transgenic system in conjunction with several different genes whose null mutations block thymic development at DP stage: β2m, CD3δ, and/or TCRα-Connecting Peptide Motif (αCPM). In the absence of MHC class I (β2m0), CD3δ or αCPM mutants were blocked at pre-selection DP stage and displayed immature, high-sensitivity to weak TCR ligands. In contrast, when MHC class I was present (β2m+), CD3δ or αCPM mutants were blocked at DP stage but underwent partial ATC; they began positive selection but did not complete it. Upon exogenous TCR engagement of partial-ATC thymocytes, the proximal signaling protein interaction network showed overall weakened activity, notably decreasing SOS1 participation linked to the downstream Ras/Raf/ERK selection pathway. Provision of high affinity peptide/MHC in FTOC rescued completion of positive selection for partial-ATC mutant thymocytes. Finally, comparing nontransgenic, polyclonal B6 vs. CD3δ0 DP thymocytes, although most cells showed equal maturation state, a subset of cells in B6 progressed in maturation relative to CD3δ0. We propose the existence of an intermediate checkpoint inside DP stage, in which ATC already begins to reduce responsiveness to selection ligands, yet further TCR signaling is required to complete positive selection.

Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis

In higher eukaryotes, heterochromatin is mainly composed of transposable elements (TEs) silenced by epigenetic mechanisms. But, the silencing of certain heterochromatin-associated TEs is disrupted by heat stress. By comparing genome-wide high-resolution chromatin packing patterns under normal or heat conditions obtained through Hi-C analysis, we show here that heat stress causes global rearrangement of the 3D genome in Arabidopsis thaliana. Contacts between pericentromeric regions and distal chromosome arms, as well as proximal intra-chromosomal interactions along the chromosomes, are enhanced. However, interactions within pericentromeres and those between distal intra-chromosomal regions are decreased. Many inter-chromosomal interactions, including those within the KNOT, are also reduced. Furthermore, heat activation of TEs exhibits a high correlation with the reduction of chromosomal interactions involving pericentromeres, the KNOT, the knob, and the upstream and downstream flanking regions of the activated TEs. Together, our results provide insights into the relationship between TE activation and 3D genome reorganization.

Urban Network and Regions in China: An Analysis of Daily Migration with Complex Networks Model

This paper analyzed urban network and regions in China using a complex network model. Data of daily migration among 348 prefectural-level cities from the Baidu Map location-based service (LBS) Open Platform were used to calculate urban network metrics and to delineate boundaries of urban regions. Results show that urban network in China displays an obvious hierarchy in terms of attracting and distributing population and controlling regional interaction. Regional integration has become increasingly prominent, as administrative boundaries and natural barriers no longer have strong impacts on urban connections. Overall, 18 urban regions were identified according to urban connectivity, and the degree of urban connection is higher among cities in the same urban region. Due to geographical proximity and close interaction, several provincial capital cities form an urban region with cities from neighboring provinces instead of those from the same province. Identification of urban region boundaries is of significant importance for sustainable development and policymaking on the demarcation of urban economic zones, urban agglomerations, and future adjustment of provincial administrative boundaries in China.

The multidimensionality of female mandrill sociality-A dynamic multiplex network approach.

The structure and dynamics of primate social groups are shaped by the social relationships of its members. These relationships are based on different types of interactions and vary in relation to the identity of the interactants and over time. Social network analysis tools represent a powerful and comprehensive method to characterise social interactions and recent methodological advances now allow the study of the multidimensionality of sociality via multilayer networks that incorporate multiple types of interactions. Here, we use a multidimensional network approach to investigate the multidimensionality of sociality of females in a captive group of mandrills. We constructed two multiplex networks based on agonistic, proximity and grooming interactions of 6–7 mature females to analyse the multidimensionality of relationships within two independent observation periods; and three multiplex networks (one for each interaction type) to examine how relationships changed between periods. Within each period, different individuals were the most central in each layer and at the multiplex level, and different layers (i.e., interaction types) contributed non-redundant information to the multilayer structure. Across periods, relationships based on the same interaction type also contained non-redundant information. These results indicate that female mandrills engage in multidimensional and dynamic relationships, suggesting that in order to represent the full complexity of relationships, networks need to be constructed from more than a single type of interaction and across time. Our results provide evidence for the potential value of the multilayer network approach to characterise the multidimensionality of primate sociality.

Proximity mapping of the microtubule plus-end tracking protein SLAIN2 using the BioID approach.

The centrosome is the main microtubule-organizing center of animal cells, which plays key roles in critical cellular processes ranging from cell division to cellular signaling. Accordingly, defects in the structure and function of centrosomes cause various human diseases such as cancer and primary microcephaly. To elucidate the molecular defects underlying these diseases, the biogenesis and functions of the centrosomes have to be fully understood. An essential step towards addressing these questions is the identification and functional dissection of the full repertoire of centrosome proteins. Here, we used high-resolution imaging and showed that the microtubule plus-end tracking protein SLAIN2 localizes to the pericentriolar material at the proximal end of centrioles. To gain insight into its cellular functions and mechanisms, we applied in vivo proximity-dependent biotin identification to SLAIN2 and generated its proximity interaction map. Gene ontology analysis of the SLAIN2 interactome revealed extensive interactions with centriole duplication, ciliogenesis, and microtubule-associated proteins, including previously characterized and uncharacterized interactions. Collectively, our results define SLAIN2 as a component of pericentriolar material and provide an important resource for future studies aimed at elucidating SLAIN2 functions at the centrosome.

Evolution of Guangzhou Biomedical Industry Innovation Network Structure and Its Proximity Mechanism

The topological structure and multidimensional proximity evolution mechanism of Guangzhou biomedical industry innovation network are studied by using cooperative patents and cooperative papers from 1998 to 2018 with Ucinet and PLS-SEM. Research shows: ① The evolution of the Guangzhou Biomedical Industry Innovation Network can be divided into three stages, which are the primary budding stage of 1998–2005, the steady development stage of 2006–2012, and the rapid development stage of 2013–2018; ② the number of subjects in the innovation network is increasing, and the types of subjects are constantly increasing. The innovation network has gone from small to large, from closed to open, and from simple to complex. Patents and papers cooperation networks show different characteristics at various stages; ③ the relationship between geographical proximity, cognitive proximity, organizational proximity, and innovation network differs in stages. The interaction of proximity varies with the content of innovation cooperation. Based on this result, we have put forward policy recommendations for different innovative content.

The impact of street clothes among caregivers on residents with dementia in special care units: The STRECLO study.

To examine the impact of caregivers' street clothes on people living in special care units (SCUs). We hypothesised that caregivers wearing street clothes would improve residents' relationships with other residents and caregivers and, as a consequence, would improve their quality of life. Environmental factors have been recognised as important elements in the care of people with dementia. Among these factors, the importance of the caregivers' appearance and more particularly their street clothes has been raised. The Street Clothes study (STRECLO) was designed as a multicentre crossover observational study. This study was conducted in two volunteer nursing homes. It involved videotaping residents (N=24) over a 6-month period: caregivers wore uniform and then street clothes for two consecutive three-month periods. Three outcome measures were observed as follows: (a) behaviours of residents, (b) contents of conversations and (c) proximal interactions between residents and caregivers. The STROBE checklist was used to ensure quality reporting during this observational study. When caregivers wore street clothes, we observed the following: (a) greater solicitation and less anxiety in residents, (b) content of conversations between residents and caregivers included more personal and less health information, and (c) more proximal interaction between caregivers and residents. To our knowledge, this is the first study which investigated the long-term effects on residents of SCU caregivers wearing street clothes. Our study demonstrated the potential benefit of not wearing uniform on the quality of life of institutionalised people with dementia. Given the budgetary constraints faced by nursing homes, wearing street clothes for caregivers could be readily applied to clinical practice and represents a promising way to increase the quality of life of dementia residents and their families.

Parental and social factors in relation to child psychopathology, behavior, and cognitive function

Parental and social factors have long-term impact on the neurodevelopment of offspring, but tend to highly covary with each other. Thus, it is difficult to parse out which parental and social factor contributes most to neurodevelopmental outcomes. This study aimed to assess clusters of parental and social factors associated with child psychopathology, behavioral problems, and cognition. This study employed the data of 11,875 children (9 to 11 years) from the Adolescent Brain Cognitive Development (ABCD) study. Principal component analysis (PCA) was performed on 39 environmental measures and 30 child behavior and cognitive measures separately to identify clusters of parental and social factors and clusters of child psychopathology, behaviour, and cognition. Regression analysis was used to examine independent effects of each cluster of parental and social factors on child psychopathology, behavioral problems, and cognition. Greater Parent Psychopathology cluster was associated with greater Child Psychopathology cluster. Moreover, greater Socioeconomic Status cluster was associated with greater child General Cognition and Executive Function but less Behavioral Inhibition clusters. Greater Proximal Social Environment and Interaction cluster were associated with less child Impulsive Behavior and Behavioral Inhibition, but greater Behavioral Activation cluster. The environmental clusters related to birth outcomes, maternal tobacco, and drug use were not significantly related to child psychopathology, behavior, and cognition. Our findings suggest that socioeconomic status, parental psychopathology, and social environment and interactions are the strongest risks for behavioral problems and cognitive performance in a general child population. Intervention programs should target modifiable factors within these domains.

Author Correction: Mapping the proximity interaction network of the Rho-family GTPases reveals signalling pathways and regulatory mechanisms.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Using contact statistics to characterize structure transformation of biopolymer ensembles.

As a unique subset of functional polymers, many biopolymers have a set of well-defined three-dimensional (3D) structural characteristics that can be described by spatial contacts between monomers. Statistical analysis of the contacts has been extremely productive in characterizing the biopolymer structural ensemble, such as for 3D chromosome structures. Often, native contacts and compartment structures are the focus of the studies, while the generic polymer aspect, such as the overall decaying of contacts with increasing sequence distance, is analyzed separately or preemptively removed. Here, we explore insights that can be gained by performing "compartment analysis" that keeps the distance decay, which we believe is particularly useful for characterizing the structure transformation of biopolymers. We tested contact analysis on several such transformations under physical perturbation or biological processes, including (1) unfolding of proteins induced by thermal denaturation, (2) chromosome conformation transition during the cell cycle, and (3) chromosome unpacking by physicochemical perturbations. Useful score functions were developed to further quantitatively characterize the transformation judging from the contact analysis. We also find that the sinusoidal undertone of eigenvector patterns (the "unwanted," low frequency signal, in contrast to the detailed A/B compartment) that had previously been attributed to biological effects of centromere proximal and distal interactions may in fact reflect a universal feature of polymers that have relatively weaker long-range contacts.

3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells.

A major question in cell biology is genomic organization within the nuclear space and how chromatin architecture can influence processes such as gene expression, cell identity and differentiation. Many approaches developed to study the 3D architecture of the genome can be divided into two complementary categories: chromosome conformation capture based technologies (C-technologies) and imaging. While the former is based on capturing the chromosome conformation and proximal DNA interactions in a population of fixed cells, the latter, based on DNA fluorescence in situ hybridization (FISH) on 3D-preserved nuclei, allows contemporary visualization of multiple loci at a single cell level (multicolor), examining their interactions and distribution within the nucleus (3D multicolor DNA FISH). The technique of 3D multicolor DNA FISH has a limitation of visualizing only a few predetermined loci, not permitting a comprehensive analysis of the nuclear architecture. However, given the robustness of its results, 3D multicolor DNA FISH in combination with 3D-microscopy and image reconstruction is a possible method to validate C-technology based results and to unambiguously study the position and organization of specific loci at a single cell level. Here, we propose a step by step method of 3D multicolor DNA FISH suitable for a wide range of human primary cells and discuss all the practical actions, crucial steps, notions of 3D imaging and data analysis needed to obtained a successful and informative 3D multicolor DNA FISH within different biological contexts.

Droplet-Transmitted Infection Risk Ranking Based on Close Proximity Interaction.

We propose an automatic method to identify people who are potentially-infected by droplet-transmitted diseases. This high-risk group of infection was previously identified by conducting large-scale visits/interviews, or manually screening among tons of recorded surveillance videos. Both are time-intensive and most likely to delay the control of communicable diseases like influenza. In this paper, we address this challenge by solving a multi-tasking problem from the captured surveillance videos. This multi-tasking framework aims to model the principle of Close Proximity Interaction and thus infer the infection risk of individuals. The complete workflow includes three essential sub-tasks: (1) person re-identification (REID), to identify the diagnosed patient and infected individuals across different cameras, (2) depth estimation, to provide a spatial knowledge of the captured environment, (3) pose estimation, to evaluate the distance between the diagnosed and potentially-infected subjects. Our method significantly reduces the time and labor costs. We demonstrate the advantages of high accuracy and efficiency of our method. Our method is expected to be effective in accelerating the process of identifying the potentially infected group and ultimately contribute to the well-being of public health.

Mapping the proximity interaction network of the Rho-family GTPases reveals signalling pathways and regulatory mechanisms.

Guanine nucleotide exchange factors (RhoGEFs) and GTPase-activating proteins (RhoGAPs) coordinate the activation state of the Rho family of GTPases for binding to effectors. Here, we exploited proximity-dependent biotinylation to systematically define the Rho family proximity interaction network from 28 baits to produce 9,939 high-confidence proximity interactions in two cell lines. Exploiting the nucleotide states of Rho GTPases, we revealed the landscape of interactions with RhoGEFs and RhoGAPs. We systematically defined effectors of Rho proteins to reveal candidates for classical and atypical Rho proteins. We used optogenetics to demonstrate that KIAA0355 (termed GARRE here) is a RAC1 interactor. A functional screen of RHOG candidate effectors identified PLEKHG3 as a promoter of Rac-mediated membrane ruffling downstream of RHOG. We identified that active RHOA binds the kinase SLK in Drosophila and mammalian cells to promote Ezrin-Radixin-Moesin phosphorylation. Our proximity interactions data pave the way for dissecting additional Rho signalling pathways, and the approaches described here are applicable to the Ras family.

The roles of factor Va and protein S in formation of the activated protein C/protein S/factor Va inactivation complex

BackgroundActivated protein C (APC)‐mediated inactivation of factor (F)Va is greatly enhanced by protein S. For inactivation to occur, a trimolecular complex among FVa, APC, and protein S must form on the phospholipid membrane. However, direct demonstration of complex formation has proven elusive. ObjectivesTo elucidate the nature of the phospholipid‐dependent interactions among APC, protein S, and FVa. MethodsWe evaluated binding of active site blocked APC to phospholipid‐coated magnetic beads in the presence and absence of protein S and/or FVa. The importance of protein S and FV residues were evaluated functionally. ResultsActivated protein C alone bound weakly to phospholipids. Protein S mildly enhanced APC binding to phospholipid surfaces, whereas FVa did not. However, FVa together with protein S enhanced APC binding (>14‐fold), demonstrating formation of an APC/protein S/FVa complex. C4b binding protein‐bound protein S failed to enhance APC binding, agreeing with its reduced APC cofactor function. Protein S variants (E36A and D95A) with reduced APC cofactor function exhibited essentially normal augmentation of APC binding to phospholipids, but diminished APC/protein S/FVa complex formation, suggesting involvement in interactions dependent upon FVa. Similarly, FVaNara (W1920R), an APC‐resistant FV variant, also did not efficiently incorporate into the trimolecular complex as efficiently as wild‐type FVa. FVa inactivation assays suggested that the mutation impairs its affinity for phospholipid membranes and with protein S within the complex. ConclusionsFVa plays a central role in the formation of its inactivation complex. Furthermore, membrane proximal interactions among FVa, APC, and protein S are essential for its cofactor function.

Global Interactome Mapping of Mitochondrial Intermembrane Space Proteases Identifies a Novel Function for HTRA2.

A number of unique proteases localize to specific sub-compartments of the mitochondria, but the functions of these enzymes are poorly defined. Here, in vivo proximity-dependent biotinylation (BioID) is used to map the interactomes of seven proteases localized to the mitochondrial intermembrane space (IMS). In total, 802 high confidence proximity interactions with 342 unique proteins are identified. While all seven proteases co-localized with the IMS markers OPA1 and CLPB, 230 of the interacting partners are unique to just one or two protease bait proteins, highlighting the ability of BioID to differentiate unique interactomes within the confined space of the IMS. Notably, high-temperature requirement peptidase 2 (HTRA2) interacts with eight of 13 components of the mitochondrial intermembrane space bridging (MIB) complex, a multiprotein assembly essential for the maintenance of mitochondrial cristae structure. Knockdown of HTRA2 disrupts cristae in HEK 293 and OCI-AML2 cells, and leads to increased intracellular levels of the MIB subunit IMMT. Using a cell-free assay it is demonstrated that HTRA2 can degrade recombinant IMMT but not two other core MIB complex subunits, SAMM50 and CHCHD3. The IMS protease interactome thus represents a rich dataset that can be mined to uncover novel IMS protease biology.

Repurposing Drugs by In Silico Methods to Target BCR Kinase Domain in Chronic Myeloid Leukemia.

Background:Targeted therapy in the form of highly selective tyrosine kinase inhibitors (TKIs) has transformed the treatment of chronic myeloid leukemia (CML). However, mutations in the kinase domain contribute to drug resistance against TKIs which compromises the treatment response. Our aim is to explore regions outside the BCR-ABL oncoprotein to identify potential therapeutic targets to curb drug resistance by targeting growth factor receptor-bound protein-2 (Grb-2) which binds to BCR-ABL at the phosphorylated tyrosine (Y177) thereby activating the Ras and PI3K/AKT signaling pathway. Methods:We have used in silico methods to repurpose drugs for identifying their potential to inhibit the binding of Grb-2 with Y177 by occupying the active binding site of the BCR domain. Results:Differentially expressed genes from GEO dataset were found to be associated with hematopoietic cell lineage, NK cell-mediated cytotoxicity, NF-κB and chemokine signaling, cytokine-cytokine receptor interaction, histidine metabolism and transcriptional misregulation in cancer. The fold recognition method of SPARKS-X tool was used to model the BCR domain (Z-score = 8.21). Connectivity Map generated a drug list based on the gene expression profile, which were docked with BCR. Schrodinger XP glide docking identified Diphosphopyridine nucleotide, Hesperidin, Butirosin, Ovoflavin, and Nor-dihydroguaiaretic acid to show strong interaction in close proximity to the active binding pocket containing Y177 of the target protein and was further validated using iGEMDOCK and Parallelized Open Babel and AutoDock suite Pipeline (POAP). Conclusion:Our study not only extends our current knowledge about repurposing drugs for newer indications but also provides a route towards combinatorial therapy with standard drugs used for CML treatment. However, the efficacy of these repurposed drugs needs to be further investigated using in vitro and in vivo studies.