FoldAffinity: Binding affinities from nDSF experiments

Differential scanning fluorimetry (DSF) using the inherent fluorescence of proteins (nDSF) is a popular technique to evaluate thermal protein stability in different conditions (e.g. buffer, pH). In many cases, ligand binding increases thermal stability of a protein and often this can be detected as a clear shift in nDSF experiments. Here, we evaluate binding affinity quantification based on thermal shifts. We present four protein systems with different binding affinity ligands, ranging from nM to high μM. Our study suggests that binding affinities determined by isothermal analysis are in better agreement with those from established biophysical techniques (ITC and MST) compared to apparent Kds obtained from melting temperatures. In addition, we describe a method to optionally fit the heat capacity change upon unfolding (Δ Cp) during the isothermal analysis. This publication includes the release of a web server for easy and accessible application of isothermal analysis to nDSF data.Fil: Niebling, Stephan. Centre for Structural Systems Biology; Alemania. European Molecular Biology Laboratory; AlemaniaFil: Burastero, Osvaldo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; Argentina. European Molecular Biology Laboratory; AlemaniaFil: Bürgi, Jérôme. European Molecular Biology Laboratory; AlemaniaFil: Günther, Christian. European Molecular Biology Laboratory; AlemaniaFil: Defelipe, Lucas Alfredo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. European Molecular Biology Laboratory; AlemaniaFil: Sander, Simon. Universitat Hamburg; AlemaniaFil: Gattkowski, Ellen. Universitat Hamburg; AlemaniaFil: Anjanappa, Raghavendra. Universitat Bremen. School of Engineering and Science Jacobs; AlemaniaFil: Wilmanns, Matthias. European Molecular Biology Laboratory; Alemania. Universitat Hamburg; AlemaniaFil: Springer, Sebastian. Universitat Bremen. School of Engineering and Science Jacobs; AlemaniaFil: Tidow, Henning. Universitat Hamburg; AlemaniaFil: García Alai, María. European Molecular Biology Laboratory; Alemania. Centre for Structural Systems Biology; Alemani

Immune Antibodies and Helminth Products Drive CXCR2-Dependent Macrophage-Myofibroblast Crosstalk to Promote Intestinal Repair

Helminth parasites can cause considerable damage when migrating through host tissues, thus making rapid tissue repair imperative to prevent bleeding and bacterial dissemination particularly during enteric infection. However, how protective type 2 responses targeted against these tissue-disruptive multicellular parasites might contribute to homeostatic wound healing in the intestine has remained unclear. Here, we observed that mice lacking antibodies (Aid-/-) or activating Fc receptors (Fcrg-/-) displayed impaired intestinal repair following infection with the murine helminth Heligmosomoides polygyrus bakeri (Hpb), whilst transfer of immune serum could partially restore chemokine production and rescue wound healing in Aid-/- mice. Impaired healing was associated with a reduced expression of CXCR2 ligands (CXCL2/3) by macrophages (MΦ) and myofibroblasts (MF) within intestinal lesions. Whilst antibodies and helminths together triggered CXCL2 production by MΦ in vitro via surface FcR engagement, chemokine secretion by intestinal MF was elicited by helminths directly via Fcrg-chain/dectin2 signaling. Blockade of CXCR2 during Hpb challenge infection reproduced the delayed wound repair observed in helminth infected Aid-/- and Fcrg-/- mice. Finally, conditioned media from human MΦ stimulated with infective larvae of the helminth Ascaris suum together with immune serum, promoted CXCR2-dependent scratch wound closure by human MF in vitro. Collectively our findings suggest that helminths and antibodies instruct a chemokine driven MΦ-MF crosstalk to promote intestinal repair, a capacity that may be harnessed in clinical settings of impaired wound healing

Unraveling the Physiological Role of Capillary Morphogenesis Gene 2 in Health and Disease

Capillary Morphogenesis Gene 2 (CMG2) is a 55kDa single-pass transmembrane protein best described as the main Anthrax Toxin Receptor. However, CMG2 physiological role remains elusive and understanding better its in vivo function was the main objective of my thesis. My first aim was to investigate the prevalence of intrinsically disordered domains in the human transmembrane proteome. Using prediction tools, I found that 50% of transmembrane proteins had at least one domain of minimum 30 amino-acids predicted as intrinsically disordered (IDD), these proteins being mainly involved in cell signaling and adhesion. The majority of the IDDs were localized in the cytoplasm, and the intrinsic disorder containing proteins were significantly more phosphorylated and interacted on average with more proteins than fully ordered proteins, corroborating their role in signaling. CMG2 loss-of-function mutations is the known cause of a rare inherited genetic disorder called Hyaline Fibromatosis Syndrome (HFS). HFS patients develop subcutaneous nodules, gingival hypertrophy, contracture of the large joints, and in the most severe cases diarrhea and premature death. In a second part of my thesis, I was involved in understanding the molecular defects underlying missense mutations localized in the ectodomain and a highly conserved cytoplasmic domain of CMG2. We found that CMG2 was able to bind the actin cytoskeleton through Talin and Vinculin when free of its extracellular ligand. Interestingly, the HFS mutation p.C218R, altered the cytoskeleton release and led to a CMG2 protein able to bind both the extracellular ligand and the actin cytoskeleton. Strikingly, we observed that all but one cytoplasmic missense mutation hindered actin binding, a defect potentially relevant to HFS pathogenesis. Furthermore, we showed that the Src-like kinase family are involved in the release of Talin upon ligand binding and that CMG2 binding to its extracellular ligand is critical for the correct orientation of the mitotic spindle of zebrafish epiblast cells, which allows cell division along the Animal/Vegetal axis. Through the analysis of cmg2 knock-out mice, along with the study of HFS patient samples, we aimed at better defining CMG2 function. We showed that type VI Collagen was strongly accumulating in the cmg2 KO mice uterus tissue leading to failure of parturition, an accumulation that was also observed in HFS patient nodules. In addition, we observed that CMG2 was able to interact and potentiate MT1-MMP, and that type VI Collagen is a bona fide ligand for CMG2, its binding leading to the phosphorylation of the receptor. With the scope to understand the HFS patient subcutaneous nodules pathogenesis, we investigated the gene expression profile of fibroblasts derived from non-affected and affected tissues by RNA sequencing. Fibroblasts derived from affected tissues appeared to differentially express genes involved in the TGFBeta pathway and cytoskeleton, such as alpha smooth muscle actin, a marker of myofibroblast activation. We observed the presence of myofibroblasts in the patient nodules, and showed that CMG2 was limiting their activation process, loss-of-function mutations in CMG2 leading to an exacerbated differentiation. As we observed CMG2 interaction with the TGFBeta receptor 2, we postulated that CMG2 influence the TGFBeta pathway, a process that is altered in HFS patient and potentially lead to the formation of nodules

Intrinsic Disorder in Transmembrane Proteins: Roles in Signaling and Topology Prediction

Intrinsically disordered regions (IDRs) are peculiar stretches of amino acids that lack stable conformations in solution. Intrinsic Disorder containing Proteins (IDP) are defined by the presence of at least one large IDR and have been linked to multiple cellular processes including cell signaling, DNA binding and cancer. Here we used computational analyses and publicly available databases to deepen insight into the prevalence and function of IDRs specifically in transmembrane proteins, which are somewhat neglected in most studies. We found that 50% of transmembrane proteins have at least one IDR of 30 amino acids or more. Interestingly, these domains preferentially localize to the cytoplasmic side especially of multi-pass transmembrane proteins, suggesting that disorder prediction could increase the confidence of topology prediction algorithms. This was supported by the successful prediction of the topology of the uncharacterized multi-pass transmembrane protein TMEM117, as confirmed experimentally. Pathway analysis indicated that IDPs are enriched in cell projection and axons and appear to play an important role in cell adhesion, signaling and ion binding. In addition, we found that IDP are enriched in phosphorylation sites, a crucial post translational modification in signal transduction, when compared to fully ordered proteins and to be implicated in more protein-protein interaction events. Accordingly, IDPs were highly enriched in short protein binding regions called Molecular Recognition Features (MoRFs). Altogether our analyses strongly support the notion that the transmembrane IDPs act as hubs in cellular signal events

Intrinsic Disorder in Transmembrane Proteins: Roles in Signaling and Topology Prediction

Intrinsically disordered regions (IDRs) are peculiar stretches of amino acids that lack stable conformations in solution. Intrinsic Disorder containing Proteins (IDP) are defined by the presence of at least one large IDR and have been linked to multiple cellular processes including cell signaling, DNA binding and cancer. Here we used computational analyses and publicly available databases to deepen insight into the prevalence and function of IDRs specifically in transmembrane proteins, which are somewhat neglected in most studies. We found that 50% of transmembrane proteins have at least one IDR of 30 amino acids or more. Interestingly, these domains preferentially localize to the cytoplasmic side especially of multi-pass transmembrane proteins, suggesting that disorder prediction could increase the confidence of topology prediction algorithms. This was supported by the successful prediction of the topology of the uncharacterized multi-pass transmembrane protein TMEM117, as confirmed experimentally. Pathway analysis indicated that IDPs are enriched in cell projection and axons and appear to play an important role in cell adhesion, signaling and ion binding. In addition, we found that IDP are enriched in phosphorylation sites, a crucial post translational modification in signal transduction, when compared to fully ordered proteins and to be implicated in more protein-protein interaction events. Accordingly, IDPs were highly enriched in short protein binding regions called Molecular Recognition Features (MoRFs). Altogether our analyses strongly support the notion that the transmembrane IDPs act as hubs in cellular signal events

Dataset of Access to Chiral Rigid Hemicyanine Fluorophores from Tröger Bases and alpha-Imino Carbenes

AbstractChiral hemicyanine fluorophores are afforded in three steps only from Tröger bases via α-imino carbene additions, an original aminal deprotection and Cu(II)-mediated oxidations. The stable benzodiazepinoindolium salts are readily isolated and present (chir)optical properties that can be fine-tuned by late-stage cross-coupling functionalization. The hemicyanine character of dyes was rationalized using first principles

Dataset of Chemical Science Article_[6]Helicene Atom Interchange

AbstractCalculations, HPLC, NMR, UV-Vis, ECD and X-ray files for the article entitled: Stereochemical significance of O to N atom interchanges within cationic helicenes: experimental and computational evidences of near racemization to remarkable enantiospecificit

Cellular localizations and functions of IDPs.

<p>(A) Cellular localizations of fully folded proteins and IDPs according to their UniProt annotations. The bar graph represent the percentage of fully folded proteins or IDPs associated with a particular GOTERM compared to the total number of proteins from our dataset associated with this GOTERM. The number within the bars show the number of proteins annotated with the GOTERM (B) Protein families enriched in fully folded proteins or IDPs. The enrichment is calculated with the number of proteins in the ordered or disordered dataset compared to the total amount of proteins known to be in this family. (C) Enrichment of GOTERM from the molecular function ontology for IDPs and fully folded proteins. The enrichment score was calculated by DAVID, an online tool for gene ontology. <b>(</b>D) Disorder prediction of Synaptotagmin 1 (UniProtID: P21579), a calcium binding protein involved in synaptic vesicles fusion. (E) Disorder prediction of UDP-glucuronosyltranferase 1–3 (UniProtID: P35503), an enzyme involved in the addition of glucoronic acid moieties to various compounds and important in detoxification. For (D and E) the blue dots represent the average disorder score using PONDR-FIT, IUPRED and DISOPRED2 prediction tools, and the errors bar the standard error. The blue lanes show the position of the transmembrane domains.</p

SwissPalm: Protein Palmitoylation database

Protein S-palmitoylation is a reversible post-translational modification that regulates many key biological processes, although the full extent and functions of protein S-palmitoylation remain largely unexplored. Recent developments of new chemical methods have allowed the establishment of palmitoyl-proteomes of a variety of cell lines and tissues from different species. As the amount of information generated by these high-throughput studies is increasing, the field requires centralization and comparison of this information. Here we present SwissPalm (http://swisspalm.epfl.ch), our open, comprehensive, manually curated resource to study protein S-palmitoylation. It currently encompasses more than 5000 S-palmitoylated protein hits from seven species, and contains more than 500 specific sites of S-palmitoylation. SwissPalm also provides curated information and filters that increase the confidence in true positive hits, and integrates predictions of S-palmitoylated cysteine scores, orthologs and isoform multiple alignments. Systems analysis of the palmitoyl-proteome screens indicate that 10% or more of the human proteome is susceptible to S-palmitoylation. Moreover, ontology and pathway analyses of the human palmitoyl-proteome reveal that key biological functions involve this reversible lipid modification. Comparative analysis finally shows a strong crosstalk between S-palmitoylation and other post-translational modifications. Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation. © 2015 Blanc M et al

Intrinsic disorder according to transmembrane protein classes and topology.

<p>(A) Organization of the different protein dataset depending on the transmembrane protein classes and the presence or not of IDRs. B) Percent of IDRs localized in the cytoplasm or the extracellular domain of single-pass and multi-pass proteins. (C) Prediction of MoRFs in the proteins from the fully folded protein (FOP) and IDP datasets. Mann-Whitney Significance test ***: p value < 0.0001. (D) Percentage of MoRFs localized either on the cytoplasmic or extracellular part of transmembrane proteins. (E) BMPR2 (UniProtID: Q13873) is a single-pass transmembrane protein with a long predicted IDR in the cytoplasmic side. The red boxes show the position of the MoRFs detected in BMPR2. (F) zDHHC8 (UniProtID: Q9ULC8) is a multi-pass transmembrane protein with a long predicted IDR in the cytoplasmic side. For (C) and (D), the blue dots represent the average disorder score using PONDR-FIT, IUPRED and DISOPRED2 prediction tools and the error bars the standard error. The blue lane shows the position of the transmembrane domain and the grey area the cytoplasmic C-terminal part of the protein.</p