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Jun 1848 - May 1849


The Question of Union. Comite de surete generale in Berlin. The Agreement Debates in Berlin. The Question of the Address. A New Partition of Poland.

The Shield of the Dynasty. Admission of Incompetence by Assemblies of Frankfurt and Berlin. The Berlin Debate on the Revolution. The Position of the Parties in Cologne. The Agreement Assembly of June The Agreement Assembly Session of June A New Policy in Posen.

The Downfall of the Camphausen Government. The Neue Berliner Zeitungen on the Chartists. Threat of the Gervinus Zeitung. The Democratic Character of the Uprising. Details about the 23rd of June. Image of Marx's article "The June Revolution". The Kolnische Zeitung on the June Revolution. Legal Proceedings against the Neue Rheinische Zeitung. The Berlin Agreement Debates. The Government of Action. The Agreement Debates of July 7. Herr Forstmann on the State Credit.

The Suppression of the Clubs in Stuttgart and Heidelberg. The Prussian Press Bill. The Faedreland on the Armistice with Denmark. The Civic Militia Bill. The Concordia of Turin. Armistice Negotiations with Denmark Broken Off.

The Dissolution of the Democratic Associations in Baden. The Agreement Debate about the Valdenaire Affair. The Kolnische Zeitung on the Compulsory Loan. Proudhon's Speech against Thiers. Debate about the Existing Redemption Legislation. The "Model State" of Belgium. The Danish Armistice and Hansemann. The German Citizenship and the Prussian Police. The Attempt to Expel Schapper.

The Kolnische Zeitung about Italy. The Zeitungs-Halle on the Rhine Province. The Conflict between Marx and Prussian Citizenship. The Fall of the Government of Action. The Crisis and the Counter-Revolution. The Faedreland on the Armistice. The Government of the Counter-Revolution. The Cologne Committee of Public Safety.

An Attempt to Arrest Moll. State of Siege in Cologne. The Latest News from the "Model State". Reply of the King of Prussia to the Delegation of the National. The Reforme on the June Insurrection.

English-French Mediation in Italy. The "Model Constitutional State". The Paris Reforme on the Situation in France. The Viennese Revolution and the Kolnische Zeitung. Our Bourgeoisie and Dr.

The Victory of the Counter-Revolution in Vienna. Image of Marx's article "The Crisis in Berlin". Decision of the Berlin National Assembly. Sitting of the Swiss Chambers. Cavaignac and the June Revolution. Confessions of a Noble Soul. A decree of Eichmann's. Tax Refusal and the Countryside. Elections to the Federal Court. State of Siege Everywhere. Position of the Left in the National Assembly. Result of the Elections to the National Council. Manteuffel and the Central Authority.

The German Central Authority and Switzerland. Drigalski-Legislator, Citizen and Communist. Debate in the National Council. Report of the Frankfurt Committee on Austrian Affairs. Personalities of the Federal Council. Sittings of the Federal Council and the Council of States. Joint Sitting of the Councils.

Organ of Manteuffel and Johann. The Revolutionary Movement in Italy. Sitting of the National Council. Berne Declared Federal Capital. Duel between Berg and Luvini. The Closing of the German Frontier.

The Federal Council and the Foreign Ambassadors. Herr Raumer Is Still Alive. Second Stage of the Counter-Revolution. The Coup d'Etat of the Counter-Revolution. Orange and magenta boxes depict interfaces residues while the orange ones contribute to interactions with the left partner and the magenta residues are thought to interact with the right partner in the oligomer. Green boxes indicate additional motifs as described in the text.

Instead, Apaf-1 utilizes two sets of WD40 repeats as receptor domain for sensing cytochrome c as specific trigger of apoptosis [20]. Apaf-1 1— is also the closest hit among structurally characterized homologues, and therefore was chosen for homology modelling to decipher the mechanistic and structural features defining organization and function of NLR family members.

A Apaf-1 structure and domain organization. ADP molecule bound to the active site is shown in sphere representation. Green fonts indicate human proteins, black fonts alternative organisms.

Circles and modified ovals over the clades indicate the type of domain present at the N-terminal region of the NACHT domain. Apaf-1 is used to root the tree. Variations thereof lie mainly within the effector domains, additional domains and within the length of the linker from the effector domain to the NACHT domain. As outlined above and despite the low sequence identity the structure of Apaf-1 can be used for homology modeling purposes to obtain insight into the mechanism of NLR function and furthermore to produce approximate models of NLR structures.

Since domain shuffling is a eukaryotic hallmark and has created a large complexity of functions in proteins, it hampers evolutionary analysis of full length proteins.

Taking this into account, we have chosen the NACHT domain to conduct a phylogenetic analysis, addressing the possible evolutionary history of NLR proteins. Similar results were obtained by including other NLR sequences of non-human origin, demonstrating a clear distribution in agreement with the effector domain content. Moreover, 9 out of 14 proteins NALP2, 4, 5, 7, 8, 9, 11, 12, 13 are located at chromosome 19 and clustered very closely together, which indicates a major expansion of this genomic region.

Thus, we further analyzed whether these proteins have corresponding orthologues in closely related organisms. For other organisms however, the expansion of this family originated from different members data not shown , suggesting that NLRs of non-human origin have been lost during evolution. Moreover, these observations point to the possibility that the development for human paralogues reflects a way to accommodate novel functions to match the complexity of innate immunity in highly developed organisms.

The outcome was then compared with FFAS [15] search results. Although, both residues, T and S, have been found in active ATPases, the detailed catalytic consequences of their preference in most NLR proteins remains undefined. The second acidic residue, usually glutamate, primes a water molecule for the hydrolysis of ATP [24]. Consequently, it is feasible to assume that NLRs use diverse mechanisms to prime the water molecule for ATP hydrolysis, where one might be the replacement of one conserved acidic amino acid by utilizing what we propose to term: Therefore, the here defined extended Walker B box represents a key element for the further investigation of distinct NLRs, their function and the involvement of ATP hydrolysis in their specific signaling pathways.

Within this sequence context, it has been suggested that arginine coordinates nucleotide hydrolysis and conformational changes between subunits [28]. This motif is usually characterized by a conserved arginine or lysine residue involved in nucleotide-binding and hydrolysis. We observed that this specific feature is generally missing in proteins belonging to the STAND class, or at least could not be functionally assigned based on their primary sequence.

However, by analyzing the structure of Apaf-1 in its closed form, we observed that a unique feature comes to light. Importantly, we observed that the conserved histidine is part of a highly conserved sequence patch among NLR family members Figure 1.

We observed that almost all NLRs harbour this conserved sequence with slight variations concerning the glutamate residue. Interestingly, the conserved proline interacts with the adenine moiety of the bound ATP molecule Figure 3.

As described, additional domains following the NACHT domain are the WH domain, also referred to as HETHS domain [19] containing the conserved histidine motif, and the SH domain, which consists of eight alpha helices in a superhelical arrangement of yet unknown function. Another feature is a highly conserved patch located in the WH domain of Apaf This interaction, which may lead to the stabilization of the dormant form seems to be conserved in the whole NLR family.

In NLR proteins there is in place of the methionine a highly conserved phenylalanine residue Figure 1 , Table 2. Also the glutamate residues are conserved to a certain degree or substituted by an aspartate residue within NLR proteins. These conserved motifs are most likely involved in intra- and intermolecular interactions required for stabilization of the closed form and formation of the active signaling platform.

Since our detailed sequence analyses revealed that most NLRs and Apaf-1 share the same domain architecture and many secondary structure features, the availability of structural and mechanistic data for Apaf-1 provides the opportunity to link conserved sequence features of NLRs to functional aspects of NLR signaling. Cytochrome c activated Apaf-1 has been shown to undergo an ATP-hydrolysis-dependent conformational rearrangement in order to form heptamers through an interaction of its NACHT domains.

A NLR oligomerization interface: Apaf-1 oligomer modeled on the basis of the NtrC1 heptamer crystal structure. For clarity only three NACHT domains are shown in ribbon representation with an ADP molecule depicted in sticks to highlight the nucleotide-binding site in each domain.

Side-chains of residues in the oligomerization interfaces are shown in sticks color-coded according to the alignment in Figure 1. Based on the fact that all structural features required for oligomerization are present Figure 4B , we hypothesize that NLRs are in principle capable of building signaling platforms like Apaf This suggests that NLRs also use the ring-like arrangement of effector domains to recognize and activate signaling partners.

Structural and mutational studies of the CARD domains of Apaf-1 and procaspase-9 have identified the essential motifs for procaspase-9 activation by Apaf-1 [34].

The interface of these two proteins has been shown to be mainly constituted by electrostatic interactions between an acidic and convex surface patch helices 1 and 4 within the CARD domain of Apaf-1 and by a basic and concave surface patch helices 2 and 3 within the CARD of procaspase Although the primary sequence conservation between CARD domains is generally low, we observed that the domains display a high degree of structural homology. These observations imply that the main principle of CARD-CARD interactions is based on the engagement of an acidic patch built of helices 1 and 4, with a basic patch composed of helices 2 and 3.

However, the surrounding residues within this interface most likely define the specificity for interactions between CARD domains thereby ensuring the selectivity for the right interaction partner. Following on this suggestion, one would expect that the residues in helices 2 and 3 of one PYD build an interface with the residues in helices 1 and 4 of a complementary PYD [37].

However, mutational studies showed that these residues, which are important in a certain CARD-CARD interaction, are dispensable in the homotypic interaction of other proteins e.

Hydrophobic residues of adjacent regions are also suggested to be important in this interaction. Nevertheless, it is not clear so far, if there is a limited repertoire of structurally conserved motifs that may mediate interactions among death domain superfamily members. Therefore, more structural studies and mutational analysis of complexes built of those domains are necessary to define the motifs and interacting residues involved. LRRs in general consist of 2—45 motifs of 20—30 amino acids in length and exhibit a typical curved horseshoe-like structure with a parallel beta sheet on the concave side and helical elements on the convex side [38].

Recently, some insight into the possible mechanism of ligand-receptor binding was provided by the two LRR-ligand complex structures of TLR1: In order to augment our understanding of the molecular mechanism of ligand recognition we generated a homology model of the NOD2 LRR domains based on the structure of the ribonuclease inhibitor aa1—, PDB id: Additionally, we utilized the Consurf Server for the identification of functional regions in NLRs by surface mapping of phylogenetic information.

The figure clearly shows an extensive patch of conserved residues spanning the surface hinting to a function of these residues in signal sensing or the activation mechanism. B Position of loss-of-function mutations shown in darkblue. Mutations found in CD patients are depicted in red. Core forming residues that do not contribute to the ligand-binding patch are highlighted in lightblue.

NOD2 model depicted as a cartoon color-coded according to domain structure: The truncation due to mutation LfsinsC is colored red. Our findings are in accordance with recently published work by Tanabe and colleagues, which showed loss of function mutations in the LRR domain to be located on the convex surface with additional residues on the concave region [41].

However, only those residues that are predicted to contribute to the convex surface are conserved in the corresponding regions of LRR proteins, whereas the residues on the concave surface are not Figure 6A and 6B.

On the other hand the loss-of-function mutations on the outer surface in the LRR domain do not form a continuous patch. They are scattered all over the molecule and are therefore not likely to form the ligand-binding site. Our homology model suggests a putative ligand-binding pocket situated in the concave surface and supports earlier observations, where the predicted loss-of function-mutations WL, VM, EK, CY, KE, SF as well as the Crohn's disease related mutation G have been mapped to the same area [41].

These amino acid residues do form a contiguous patch and therefore may point to the putative ligand-binding site Figure 6B. Supporting this, is the fact that the location of this particular surface patch corresponds to ligand-binding sites in other LRR proteins [42] — [44]. Taken together, these results point to a common putative binding pocket located at the concave surface of the LRR, which, however, differs from protein to protein. Whether the patches on the convex surface do contribute to ligand-binding or eventually contribute to locking the NLR proteins in the dormant form remains to be further investigated.

Several diseases were found to arise from aberrant NLR function [45] — [49]. P constitutes part of the nucleotide-binding interface where it interacts with the adenine moiety of ADP. PS disturbs the backbone conformation of the linker thus interferes with nucleotide binding and may alter the affinity and hydrolysis rate of the nucleotide-binding domain.

Hence, SNP5 impairs the fine-tuned conformational states of the active-inactive balance of the NOD2 receptor and has therefore most likely a direct impact on its signaling properties. In summary, our study clearly shows that the overall architecture and secondary structure features of most NLRs resemble those of Apaf Additionally, we identified one of the most intriguing features, which is the conserved histidine in the WH-domain, to be conserved among members of the NLR family.

NLRs displaying this feature most likely assemble similar to Apaf-1 and activate their targets by oligomerization. Whether their oligomerization mechanism and ATP hydrolysis capacity differ remains an open issue. Our analyses of the effector domains of NLRs as well as those of their adaptors and target caspases, or kinases reveal a common interface, which is composed of charged surface patches. The presence of acidic and basic surface patches theoretically renders all CARD and PYD domains compatible for interaction with each other.

Yet their distinct profile and that of surrounding residues found in the described interfaces ensure the specificity for each interaction. This selectivity allows a well-balanced fine-tuning of the elicited immune response. Finally, sequence comparison of LRRs in human NLRs does not reveal one particular region that serves as the general ligand-binding site. This suggests that individual NLRs evolved highly specialized modes to recognize specific ligands.

However, conserved residues found within this domain may contribute to the intramolecular interaction or backfolding of the LRR region in order to regulate NLR activation. Our results serve as a basis for further mutational and functional analyses required to more precisely define the role of LRRs in ligand recognition and NLR activation.

Secondary structure prediction was done using the predictprotein server http: Multiple alignments were created using muscle [23] and m-coffee [50] with default options in the aforementioned sequences and the Apaf-1 sequence. The alignment was manually adjusted according to secondary structure prediction. The alignments were used to run phylogenetic probabilistic analyses using the parallel implementation of MrBayes [51]. The sequence of Apaf-1 was used to root the tree in all cases.

A total number of generations were run in 4 independent chains. The model used to set the priors for amino acid data was an average of all the available models and a sample was obtained each 10 generations. Once convergence was reached, a total of a credible trees were sampled and clade credibility values probabilities calculated.

In order to check how the paralogues arrange in a bigger tree, homologous sequences were retrieved from Uniprot databases from close organisms. The new sequences 31 were re-aligned to the original multiple alignment using T-coffee.





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