Interaction Of Regulatory Proteins Research Articles

Impact of protein and small molecule interactions on kinase conformations.

Protein kinases act as central molecular switches in the control of cellular functions. Alterations in the regulation and function of protein kinases may provoke diseases including cancer. In this study we investigate the conformational states of such disease-associated kinases using the high sensitivity of the kinase conformation (KinCon) reporter system. We first track BRAF kinase activity conformational changes upon melanoma drug binding. Second, we also use the KinCon reporter technology to examine the impact of regulatory protein interactions on LKB1 kinase tumor suppressor functions. Third, we explore the conformational dynamics of RIP kinases in response to TNF pathway activation and small molecule interactions. Finally, we show that CDK4/6 interactions with regulatory proteins alter conformations which remain unaffected in the presence of clinically applied inhibitors. Apart from its predictive value, the KinCon technology helps to identify cellular factors that impact drug efficacies. The understanding of the structural dynamics of full-length protein kinases when interacting with small molecule inhibitors or regulatory proteins is crucial for designing more effective therapeutic strategies.

Impact of protein and small molecule interactions on kinase conformations

Protein kinases act as central molecular switches in the control of cellular functions. Alterations in the regulation and function of protein kinases may provoke diseases including cancer. In this study we investigate the conformational states of such disease-associated kinases using the high sensitivity of the kinase conformation (KinCon) reporter system. We first track BRAF kinase activity conformational changes upon melanoma drug binding. Second, we also use the KinCon reporter technology to examine the impact of regulatory protein interactions on LKB1 kinase tumor suppressor functions. Third, we explore the conformational dynamics of RIP kinases in response to TNF pathway activation and small molecule interactions. Finally, we show that CDK4/6 interactions with regulatory proteins alter conformations which remain unaffected in the presence of clinically applied inhibitors. Apart from its predictive value, the KinCon technology helps to identify cellular factors that impact drug efficacies. The understanding of the structural dynamics of full-length protein kinases when interacting with small molecule inhibitors or regulatory proteins is crucial for designing more effective therapeutic strategies.

DHX9 SUMOylation is required for the suppression of R-loop-associated genome instability

RNA helicase DHX9 is essential for genome stability by resolving aberrant R-loops. However, its regulatory mechanisms remain unclear. Here we show that SUMOylation at lysine 120 (K120) is crucial for DHX9 function. Preventing SUMOylation at K120 leads to R-loop dysregulation, increased DNA damage, and cell death. Cells expressing DHX9 K120R mutant which cannot be SUMOylated are more sensitive to genotoxic agents and this sensitivity is mitigated by RNase H overexpression. Unlike the mutant, wild-type DHX9 interacts with R-loop-associated proteins such as PARP1 and DDX21 via SUMO-interacting motifs. Fusion of SUMO2 to the DHX9 K120R mutant enhances its association with these proteins, reduces R-loop accumulation, and alleviates survival defects of DHX9 K120R. Our findings highlight the critical role of DHX9 SUMOylation in maintaining genome stability by regulating protein interactions necessary for R-loop balance.

Genome-Wide Identification of GRAS Transcription Factors and Their Functional Analysis in Salt Stress Response in Sugar Beet.

GAI-RGA-and-SCR (GRAS) transcription factors can regulate many biological processes such as plant growth and development and stress defense, but there are few related studies in sugar beet. Salt stress can seriously affect the yield and quality of sugar beet (Beta vulgaris). Therefore, this study used bioinformatics methods to identify GRAS transcription factors in sugar beet and analyzed their structural characteristics, evolutionary relationships, regulatory networks and salt stress response patterns. A total of 28 BvGRAS genes were identified in the whole genome of sugar beet, and the sequence composition was relatively conservative. According to the topology of the phylogenetic tree, BvGRAS can be divided into nine subfamilies: LISCL, SHR, PAT1, SCR, SCL3, LAS, SCL4/7, HAM and DELLA. Synteny analysis showed that there were two pairs of fragment replication genes in the BvGRAS gene, indicating that gene replication was not the main source of BvGRAS family members. Regulatory network analysis showed that BvGRAS could participate in the regulation of protein interaction, material transport, redox balance, ion homeostasis, osmotic substance accumulation and plant morphological structure to affect the tolerance of sugar beet to salt stress. Under salt stress, BvGRAS and its target genes showed an up-regulated expression trend. Among them, BvGRAS-15, BvGRAS-19, BvGRAS-20, BvGRAS-21, LOC104892636 and LOC104893770 may be the key genes for sugar beet's salt stress response. In this study, the structural characteristics and biological functions of BvGRAS transcription factors were analyzed, which provided data for the further study of the molecular mechanisms of salt stress and molecular breeding of sugar beet.

Advanced PamGene Coregulator Interactome Analysis of PPARgamma Reveals that Diet Influences Regulatory Protein Interactions and Signaling Mechanisms

Studies show a strong correlation with type 2 diabetes mellitus (T2DM) in obese patients developing congestive heart failure (CHF) with rosiglitazone treatment. Rosiglitazone, a thiazolidinedione, treats T2DM by improving insulin resistance. Its use has been halted due to a subset of patients developing CHF through unknown mechanisms. Rosiglitazone targets PPARγ, a nuclear receptor highly expressed in adipose tissue and, to a lesser extent, in cardiac tissue. An important mechanism of PPARγ regulation is through coregulators that can alter transcriptional activity through protein-protein interaction to drive PPARγ toward specific pathways. We hypothesized coregulator interaction with PPARγ may regulate its activity differently in adiposity, inducing CHF through adipose-derived peripheral signaling. To address this, we fed 8-week-old C57BL/6 mice a normal chow (NCD) or high-fat (HFD) diet for 16 weeks. Mice were then injected with rosiglitazone every 48 hours for 4 weeks. In NCD and HFD Rosi mice, we found significantly increased heart weights (p-value<0.05) and various weight changes in five adipose depots. To understand the roles of the PPARγ coregulator interactome in adiposity, we used our state-of-the-art PamGene PamStation Nuclear Hormone Receptor chip to measure the interaction of PPARγ with 155 coregulators in five adipose depots and the liver. In adipose depots increasing in weight due to Rosi treatment, such as retroperitoneal white adipose tissue (WAT) and mesenteric WAT, more coregulators associated with the PPARγ complex. Conversely, depots that did not change in weight with Rosi treatment, such as epididymal WAT and inguinal WAT, showed a reduction of coregulators leaving the PPARγ complex, indicating differential PPARγ regulation. Our data suggests that the coregulator interactome of PPARγ in adipose depots represents potential therapeutic targets, and understanding how PPARγ regulation is different in adiposity is crucial to understanding the negative side effects of rosiglitazone treatment. R01DK121797 (T.D.H.) R01DA058933 (T.D.H.). This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Cysteine post-translational modifications regulate protein interactions of caveolin-3.

Caveolae are small flask-shaped invaginations of the surface membrane which are proposed to recruit and co-localize signaling molecules. The distinctive caveolar shape is achieved by the oligomeric structural protein caveolin, of which three isoforms exist. Aside from the finding that caveolin-3 is specifically expressed in muscle, functional differences between the caveolin isoforms have not been rigorously investigated. Caveolin-3 is relatively cysteine-rich compared to caveolins 1 and 2, so we investigated its cysteine post-translational modifications. We find that caveolin-3 is palmitoylated at 6 cysteines and becomes glutathiolated following redox stress. We map the caveolin-3 palmitoylation sites to a cluster of cysteines in its C terminal membrane domain, and the glutathiolation site to an N terminal cysteine close to the region of caveolin-3 proposed to engage in protein interactions. Glutathiolation abolishes caveolin-3 interaction with heterotrimeric G protein alpha subunits. Our results indicate that a caveolin-3 oligomer contains up to 66 palmitates, compared to up to 33 for caveolin-1. The additional palmitoylation sites in caveolin-3 therefore provide a mechanistic basis by which caveolae in smooth and striated muscle can possess unique phospholipid and protein cargoes. These unique adaptations of the muscle-specific caveolin isoform have important implications for caveolar assembly and signaling.

DOP31 Gene correlation network analyses reveal transcript modules and pathogenic mechanisms associated with resistance and response to ustekinumab therapy in Ulcerative Colitis

Abstract Background Precision medicine in ulcerative colitis (UC) remain elusive. The heterogeneity in patients’ mucosal transcriptomic profiles suggests that stratification based on molecular mechanisms might be possible, which may link to treatment response. We interrogated a dataset of ustekinumab-treated patients treated to determine transcript modules (TMs) in active UC, investigate pathogenic pathways and consider which cells might be driving ustekinumab resistance. Methods Pre-treatment mucosal transcriptomes and outcome data were available for 358 ustekinumab-treated patients enrolled in the UNIFI programme. Modules of co-expressed genes were defined with weighted gene correlation network analysis (WGCNA) and their functional roles and regulatory interactions inferred with Fisher tests. Multivariate regression was used to test the ability of clinical and transcriptomic data to predict treatment resistance. Further insights into the cellular and molecular features of ustekinumab resistance were gauged from the analysis of single cell data (Single Cell Portal accession SCP259). Analyses were performed in R 4.2.3 (Vienna, Austria). Results WGCNA generated 23 transcript modules (TMs) whose correlation with mucosal healing ranged from -0.26 to 0.25. The three TMs most negatively correlated with response comprised genes enriched in neutrophil degranulation, extracellular matrix activity and endoplasmic reticulum function. The modules correlating highest with response were enriched in genes involved in mitochondrial function. The constituents of the ustekinumab resistance-related modules are regulated by a hierarchy of transcription factors downstream of NFKB1, AHR, JUN and RELA. They are also densely connected by regulatory protein-protein interactions (Figure 1). A multivariate model including TM1 enrichment score and clinical variables predicts resistance with area under the curve 0.76 (95% confidence interval: 0.69–0.82). Notably, TM1 included TREM1 and OSM, which were previously associated with anti-TNF resistance. Surmising that cell populations co-expressing these genes might be key to ustekinumab resistance too, we identified TREM1+ OSM+ inflammatory monocytes (IMs). These showed higher expression of genes such as IL1B, IL8 and CXCL2 compared to other IMs, and increased activity in pathogenic processes including interleukin (IL)10, IL4 and IL13 signalling and G-protein-coupled receptor signalling. Conclusion Gene co-expression analysis identified transcripts and molecular mechanisms associated with response and predictive of resistance to ustekinumab. TREM1+ OSM+ IMs may be key to driving resistance, suggesting an important role for innate immunity. These findings are important for developing precision medicine approaches in UC.

Chemokine binding to PSGL-1 is controlled by O-glycosylation and tyrosine sulfation

Protein glycosylation influences cellular recognition and regulates protein interactions, but how glycosylation functions alongside other common posttranslational modifications (PTMs), like tyrosine sulfation (sTyr), is unclear. We produced a library of 53 chemoenzymatically synthesized glycosulfopeptides representing N-terminal domains of human and murine P-selectin glycoprotein ligand-1 (PSGL-1), varying in sTyr and O-glycosylation (structure and site). Using these, we identified key roles of PSGL-1 O-glycosylation and sTyr in controlling interactions with specific chemokines. Results demonstrate that sTyr positively affects CCL19 and CCL21 binding to PSGL-1N terminus, whereas O-glycan branching and sialylation reduced binding. For murine PSGL-1, interference between PTMs is greater, attributed to proximity between the two PTMs. Using fluorescence polarization, we found sTyr is a positive determinant for some chemokines. We showed that synthetic sulfopeptides are potent in decreasing chemotaxis of human dendritic cells toward CCL19 and CCL21. Our results provide new research avenues into the interplay of PTMs regulating leukocyte/chemokine interactions.

A temporal difference in the stabilization of two mRNAs with a 3' iron-responsive element during iron deficiency.

The interactions of iron regulatory proteins (IRPs) with mRNAs containing an iron-responsive element (IRE) maintain cellular iron homeostasis and coordinate it with metabolism and possibly cellular behavior. The mRNA encoding transferrin receptor-1 (TFRC, TfR1), which is a major means of iron importation, has five IREs within its 3' UTR, and IRP interactions help maintain cytosolic iron through protection of the TfR1 mRNA from degradation. An IRE within the 3' UTR of a mRNA splice variant encoding human cell division cycle 14A (CDC14A) has the potential to coordinate the cellular iron status with cellular behavior through a similar IRP-mediated mechanism. However, the stability of the CDC14A splice variant was reported earlier to be unaffected by the cellular iron status, which suggested that the IRE is not functional. We labeled newly synthesized mRNA in HEK293 cells with 5-ethynyl uridine and found that the stability of the CDC14A variant is responsive to iron deprivation, but there are two major differences from the regulation of TfR1 mRNA stability. First, the decay of the CDC14A mRNA does not utilize the Roquin-mediated reaction that acts on the TfR1 mRNA indicating that there is flexibility in the degradative machinery antagonized by the IRE-IRP interactions. Second, the stabilization of the CDC14A mRNA is delayed relative to the TfR1 mRNA and does not occur until IRP binding activity has been induced. The result is consistent with a hierarchy of IRP interactions in which the maintenance of cellular iron through the stabilization of the TfR1 mRNA is initially prioritized.

Dynamics-Based Regulatory Switches of Type II Antitoxins: Insights into New Antimicrobial Discovery.

Type II toxin-antitoxin (TA) modules are prevalent in prokaryotes and are involved in cell maintenance and survival under harsh environmental conditions, including nutrient deficiency, antibiotic treatment, and human immune responses. Typically, the type II TA system consists of two protein components: a toxin that inhibits an essential cellular process and an antitoxin that neutralizes its toxicity. Antitoxins of type II TA modules typically contain the structured DNA-binding domain responsible for TA transcription repression and an intrinsically disordered region (IDR) at the C-terminus that directly binds to and neutralizes the toxin. Recently accumulated data have suggested that the antitoxin's IDRs exhibit variable degrees of preexisting helical conformations that stabilize upon binding to the corresponding toxin or operator DNA and function as a central hub in regulatory protein interaction networks of the type II TA system. However, the biological and pathogenic functions of the antitoxin's IDRs have not been well discussed compared with those of IDRs from the eukaryotic proteome. Here, we focus on the current state of knowledge about the versatile roles of IDRs of type II antitoxins in TA regulation and provide insights into the discovery of new antibiotic candidates that induce toxin activation/reactivation and cell death by modulating the regulatory dynamics or allostery of the antitoxin.

Local signaling enhances output specificity of bacterial c-di-GMP signaling networks.

For many years the surprising multiplicity, signal input diversity, and output specificity of c-di-GMP signaling proteins has intrigued researchers studying bacterial second messengers. How can several signaling pathways act in parallel to produce specific outputs despite relying on the same diffusible second messenger maintained at a certain global cellular concentration? Such high specificity and flexibility arise from combining modes of local and global c-di-GMP signaling in complex signaling networks. Local c-di-GMP signaling can be experimentally shown by three criteria being met: (i) highly specific knockout phenotypes for particular c-di-GMP-related enzymes, (ii) actual cellular c-di-GMP levels that remain unchanged by such mutations and/or below the Kd's of the relevant c-di-GMP-binding effectors, and (iii) direct interactions between the signaling proteins involved. Here, we discuss the rationale behind these criteria and present well-studied examples of local c-di-GMP signaling in Escherichia coli and Pseudomonas. Relatively simple systems just colocalize a local source and/or a local sink for c-di-GMP, i.e. a diguanylate cyclase (DGC) and/or a specific phosphodiesterase (PDE), respectively, with a c-di-GMP-binding effector/target system. More complex systems also make use of regulatory protein interactions, e.g. when a "trigger PDE" responds to locally provided c-di-GMP, and thereby serves as a c-di-GMP-sensing effector that directly controls a target's activity, or when a c-di-GMP-binding effector recruits and directly activates its own "private" DGC. Finally, we provide an outlook into how cells can combine local and global signaling modes of c-di-GMP and possibly integrate those into other signaling nucleotides networks.

Role of epigenetics and the high-throughput sensing techniques to detect stress adaptation mechanisms in crop plants: A mini review

Deciphering the epigenetic code, which will pave the road to understanding the link between genotypic and phenotypic variety, is one of the most fascinating topics of modern genetics. This may significantly contribute to our understanding of the complex mechanisms underlying plants\' epigenomic responses to environmental stressors in the context of climate change. As a result of epigenetic regulatory processes such DNA methylation, histone structural modification, and RNA-based regulatory mechanisms, it is hypothesised that chromatin will alter. The interactions of regulatory proteins, including various types of transcription factors, with DNA and chromatin would result in a variety of structural alterations that would impact how genes are expressed. High throughput sequencing techniques have recently been developed to better understand epigenomic alterations in the genome. The use of pharmacological and genetic methods to modify these networks should be made simpler by these strategies. The cytosine methylation of a cell\'s genomic regions or active cistrons, in particular, is an epigenetic change that these approaches are successful at identifying and studying. To speed up breeding programs for crop improvement, numerous investigations on the interactions between genotype, phenotype, and epigenotype utilising epiGWAS are being carried out. This review will briefly explore the role of epigenetic approaches and high throughput sensing techniques in order to better understand plant stress responses. The value of epigenomic methods and strategies in the nascent \"omic\" sciences is being emphasized

Using NMR Titration Experiments to Study E. coli FAS-II- and AcpP-Mediated Protein-Protein Interactions.

Acyl carrier proteins (ACPs) are central to many primary and secondary metabolic pathways. In E. coli fatty acid biosynthesis (FAB), the central ACP, AcpP, transports intermediates to a suite of partner proteins (PP) for iterative modification and elongation. The regulatory protein-protein interactions that occur between AcpP and the PP in FAB are poorly understood due to the dynamic and transient nature of these interactions. Solution-state NMR spectroscopy can reveal information at the atomic level through experiments such as the 2D heteronuclear single quantum coherence (HSQC). The following protocol describes NMR HSQC titration experiments that can elucidate biomolecular recognition events.

SEC14-GOLD protein PATELLIN2 binds IRON-REGULATED TRANSPORTER1 linking root iron uptake to vitamin E.

Organisms require micronutrients, and Arabidopsis (Arabidopsis thaliana) IRON-REGULATED TRANSPORTER1 (IRT1) is essential for iron (Fe2+) acquisition into root cells. Uptake of reactive Fe2+ exposes cells to the risk of membrane lipid peroxidation. Surprisingly little is known about how this is avoided. IRT1 activity is controlled by an intracellular variable region (IRT1vr) that acts as a regulatory protein interaction platform. Here, we describe that IRT1vr interacted with peripheral plasma membrane SEC14-Golgi dynamics (SEC14-GOLD) protein PATELLIN2 (PATL2). SEC14 proteins bind lipophilic substrates and transport or present them at the membrane. To date, no direct roles have been attributed to SEC14 proteins in Fe import. PATL2 affected root Fe acquisition responses, interacted with ROS response proteins in roots, and alleviated root lipid peroxidation. PATL2 had high affinity in vitro for the major lipophilic antioxidant vitamin E compound α-tocopherol. Molecular dynamics simulations provided insight into energetic constraints and the orientation and stability of the PATL2-ligand interaction in atomic detail. Hence, this work highlights a compelling mechanism connecting vitamin E with root metal ion transport at the plasma membrane with the participation of an IRT1-interacting and α-tocopherol-binding SEC14 protein.

A Nanobar-Supported Lipid Bilayer System for the Study of Membrane Curvature Sensing Proteins <em>in vitro</em>

Membrane curvature plays important rolesin various essential processes of cells, such as cell migration, cell division, and vesicle trafficking. It is not only passively generated by cellular activities, but also actively regulates protein interactions and is involved in many intracellular signaling. Thus, it is of great value to examine the role of membrane curvature in regulating the distribution and dynamics of proteins and lipids. Recently, many techniques have been developed to study the relationship between the curved membrane and protein in vitro. Compared to traditional techniques, the newly developed nanobar-supported lipid bilayer (SLB) offers both high-throughput and better accuracy in membrane curvature generation by forming a continuous lipid bilayer on patterned arrays of nanobars with a pre-defined membrane curvature and local flat control. Both the lipid fluidity and protein sensitivity to curved membranes can be quantitatively characterized using fluorescence microscopy imaging. Here, a detailed procedure on how to form a SLB on fabricated glass surfaces containing nanobar arraysand the characterization of curvature-sensitive proteins on such SLB are introduced. In addition, protocols for nanochip reusing and image processing are covered. Beyond the nanobar-SLB, this protocol is readily applicable to all types of nanostructured glass chips for curvature sensing studies.

Exploring the nucleotide molecular mechanism of compound kushen injection for lung adenocarcinoma based on network pharmacology and molecular docking.

Compound kushen injection is an effective traditional Chinese medicine for the treatment of lung cancer. However, its influence on the survival and prognosis of patients with lung adenocarcinoma patients was less studied; especially its pharmacological mechanism remains to be further elucidated. In the present study, we adopted a network pharmacology (NP)-based approach to screening effective compounds, screening and predicting target genes, analyzing biological functions and pathways, constructing a regulatory network and protein interaction network, and screening the key targets. Moreover, mass survival analysis and molecular docking were conducted. In the end, 35 key compounds and four possible central target genes were screened out, which could be used for the treatment of lung adenocarcinoma and affected the survival and prognosis of patients with lung adenocarcinoma. In addition, their key compounds had good docking affinity. Enrichment analysis showed that CKI might affect the treatment and prognosis of lung adenocarcinoma patients by regulating the PI3K-Akt signaling pathway, TNF signaling pathway, non-small cell lung cancer, Hepatitis C, etc. We discussed the pharmacological mechanisms and potential therapeutic targets of CKI in the treatment of lung adenocarcinoma, which verified the effect of CKI on the prognosis and survival of patients. The present study might promote the further clinical application of CKI and provide a theoretical basis for further experimental studies.

Plug-and-Display Photo-Switchable Systems on Plant Virus Nanoparticles.

Light can be used to regulate protein interactions with a high degree of spatial and temporal precision. Photo-switchable systems therefore allow the development of controllable protein complexes that can influence various cellular and molecular processes. Here, we describe a plant virus-based nanoparticle shuttle for the distribution of proteins that can be released when exposed to light. Potato virus X (PVX) is often used as a presentation system for heterologous proteins and epitopes, and has ideal properties for biomedical applications such as good tissue penetration and the ability to form hydrogels that present signaling molecules and promote cell adhesion. In this study, we describe three different systems attached to the surface of PVX particles: LOVTRAP, BphP1/QPAS1 and Dronpa145N. We demonstrated the functionality of all three photo-switchable protein complexes in vitro and the successful loading and unloading of PVX particles. The new systems provide the basis for promising applications in the biomedical and biomaterial sciences.

ALLOSTERIC REGULATION OF THE BLOOD CLOTTING CASCADE

Recognition of functional partners is a pivotal factor in the regulation of protein interactions. The areas of direct contact between complementary molecules that interact according to Koshland’s "key - lock" scheme deserve special attention. The relevance of the study of this kind of interactions is obvious. In the case of the simplest serine proteinases the increased affinity of the enzyme to a certain area of the target protein is ensured by the synchronous interaction of the binding and allosteric sub-sites with amino acid residues of the target protein, that are adequate by ligand specificity and placed in an optimal conformation. The purpose of this work is to clarify the compliance of the components of the blood clotting cascade with this rule. Comparison of the primary sequences of sites of activation cleavage, reactive centers of serpins and sites of proteolytic inactivation testifies in favor of this assumption.

Effect of Cisplatin on Renal Iron Homeostasis Components: Implication in Nephropathy.

Cisplatin is an important chemotherapeutic drug for the treatment of solid tumors but often causes nephropathy as part of the off-target toxicity. Iron accumulation and related damage were implicated in cisplatin-induced kidney injury. However, the role of cisplatin in the renal iron sensing mechanism and its target genes responsible for iron uptake, storage, and release have not been investigated. Cellular iron homeostasis is controlled by the interaction of iron regulatory proteins (IRP1 and IRP2) and iron-responsive elements (IREs) present in the untranslated regions of iron transport and storage components. Here, we report that cisplatin does not influence the expressions of IRP targets such as transferrin receptor-1 (TfR1), divalent metal transporter-1 (DMT1), and ferroportin in renal cells despite the increased heme oxygenase-1 (HO-1) level. Ferritin subunits (Ft-H and Ft-L) are elevated in different magnitudes due to the increased mRNA expression. Intriguingly, a higher expression of Ft-L mRNA is detected than that of Ft-H mRNA. The inability of cisplatin in altering the IRE–IRP interaction is confirmed by examining IRE-containing luciferase activity, RNA electrophoretic mobility shift assay, and activation of IRPs. The labile iron pool is depleted but reversed by silencing of either Ft-H or Ft-L, suggesting increased iron storage by ferritin. Silencing of Ft-H or Ft-L promotes cell death, suggesting that ferritin acts to protect the renal cells from cisplatin-mediated toxicity. A differential increase of transcripts and equivalent increase of proteins of Ft-H and Ft-L and unaltered TfR1 and DMT1 transcripts are found in the kidneys of cisplatin-treated rats along with iron accumulation. Our results reveal that cisplatin does not influence the IRE–IRP interaction despite alteration of the cellular iron pool in renal cells. This insensitivity of the IRE–IRP system may be implicated in the accumulation of iron to contribute to cisplatin-induced nephropathy.

Integrative Conformational Ensembles of Sic1 Using Different Initial Pools and Optimization Methods

Intrinsically disordered proteins play key roles in regulatory protein interactions, but their detailed structural characterization remains challenging. Here we calculate and compare conformational ensembles for the disordered protein Sic1 from yeast, starting from initial ensembles that were generated either by statistical sampling of the conformational landscape, or by molecular dynamics simulations. Two popular, yet contrasting optimization methods were used, ENSEMBLE and Bayesian Maximum Entropy, to achieve agreement with experimental data from nuclear magnetic resonance, small-angle X-ray scattering and single-molecule Förster resonance energy transfer. The comparative analysis of the optimized ensembles, including secondary structure propensity, inter-residue contact maps, and the distributions of hydrogen bond and pi interactions, revealed the importance of the physics-based generation of initial ensembles. The analysis also provides insights into designing new experiments that report on the least restrained features among the optimized ensembles. Overall, differences between ensembles optimized from different priors were greater than when using the same prior with different optimization methods. Generating increasingly accurate, reliable and experimentally validated ensembles for disordered proteins is an important step towards a mechanistic understanding of their biological function and involvement in various diseases.