Iron-sulfur protein | EPFL Graph Search

Iron–sulfur proteins are proteins characterized by the presence of iron–sulfur clusters containing sulfide-linked di-, tri-, and tetrairon centers in variable oxidation states. Iron–sulfur clusters are found in a variety of metalloproteins, such as the ferredoxins, as well as NADH dehydrogenase, hydrogenases, coenzyme Q – cytochrome c reductase, succinate – coenzyme Q reductase and nitrogenase. Iron–sulfur clusters are best known for their role in the oxidation-reduction reactions of electron transport in mitochondria and chloroplasts. Both Complex I and Complex II of oxidative phosphorylation have multiple Fe–S clusters. They have many other functions including catalysis as illustrated by aconitase, generation of radicals as illustrated by SAM-dependent enzymes, and as sulfur donors in the biosynthesis of lipoic acid and biotin. Additionally, some Fe–S proteins regulate gene expression. Fe–S proteins are vulnerable to attack by biogenic nitric oxide, forming dinitrosyl iron complexes

PDB-Explorer: a web-based interactive map of the protein data bank in shape space

Daniel Kostro, Luc Patiny, Jean-Louis Reymond, Michaël Giuseppe Zasso

Background: The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. Methods: A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. Results: The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. Conclusion: A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.cheminfo.org/pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB.

Biomed Central Ltd2015

Do synthetic Fe-zeolites mimic biological Fe-porphyrins in reactions with nitric oxide?

Bryan Bromley, Lioubov Kiwi

Iron containing ZSM-5 zeolites is extremely active in nitrous oxide decomposition. This reaction involves atomic oxygen species known as "alpha oxygen" on iron sites. Despite the multiple techniques devoted to its characterization, the active sites' structure remains nevertheless unknown. Herein, these centers are quantified via surface titration by nitrous oxide followed by temperature programmed desorption and characterized via nitric oxide probe molecule followed by infrared spectroscopy. In this latter case, two mono-nitrosyl species differing in the bonds' geometry are observed on the iron centers. Moreover, upon NO evacuation, the two corresponding IR bands suddenly transit to lower wavenumbers. A mirror trend is also reported in biology when NO interacts with iron porphyrins and explained in terms of linear to bent Fe-N-O modification. This structural change is reversible upon addition/evacuation of NO. In the present report, the same reversible nitrosyl transition is observed for Fe-ZSM-5. Based on the close analogies found, the active site's structure in Fe-ZSM-5 is built-up from the porphyrinatoiron(II) model. © 2010 Elsevier B.V. All rights reserved.

Elsevier2010

Stereoselective synthesis of alkenes via base-metal-catalyzed addition reactions to alkynes and activation of hydrogen peroxide and carbon dioxide by iron complexes

Fedor Zhurkin

Alkene functionality can be found in the majority of natural products, drugs, catalysts and organic materials. Therefore, methods of C-C double bond formation constitute a cornerstone of organic synthesis. Selective formation of either (Z)- or (E)-isomer is especially desirable. 1,2-Addition to alkynes unites a large arsenal of methods of C-C double bond formation, among which the addition of carbon-centered species is the most interesting, since it offers a possibility of construction of the carbon skeleton. The first part of the present dissertation is devoted to the development of methods of selective addition of carbon reagents to alkynes. Chapter 1 reviews the existing methods of addition of carbon-centered species, generated from organometallic reagents, organic halides or carbonyl compounds to C-C triple bond with the accent on their stereoselectivity. Carbometalative mechanisms lay in the background of the majority of the reactions in this chemistry. The Z/E selectivity of 1,2-addition to triple bond can be controlled via predominance of either syn- or anti-addition or via Z/E isomerization of the addition intermediates. In Chapter 2 a novel method of disubstituted alkene synthesis via reductive addition of alkyl halides to terminal arylalkynes is described. The remarkable feature of this method is highly selective formation of (Z)-alkenes (generally Z/E > 10:1). Minor modifications of the reducing agent allowed the extension of the substrate scope to the primary alkyl iodides. Mechanistic studies revealed that this reaction proceeds as a formal anti-carbozincation. The resulting organozinc species form disubstituted (Z)-alkenes upon aqueous work-up. On the other hand, it would be interesting to utilize these species in cross-coupling reactions to allow the selective synthesis of trisubstituted alkenes. In Chapter 3 a catalytic system for highly regioselective copper-catalyzed allylation of these reagents is described. In Chapter 4 the results on stereoselective intermolecular addition of aldehydes and ketones to alkynes in the presence of zinc and trimethylchlorosilane are summarized. This reaction gives 1-chloro-1,3-dienes as products. The activation of small molecules has become an increasingly attractive area of research over the last years. In Chapter 5 an outline is given of the literature examples of small-molecule activation, namely activation of carbon dioxide and hydrogen peroxide, by iron complexes. In Chapter 6 the studies on small-molecule activation by iron-sulfur cubane clusters are presented. Electrochemical reduction of carbon dioxide and hydrogenation of alkenes were studied. As an additional result, synthesis and characterization of an unprecedented organic iron(I) ate-complex is reported. Structural modification of a non-heme iron complex with hydrogen-bond-donating substituents is described in Chapter 7. The deep impact of these modifications on the structure and reactivity of the resulting complex is discussed.