Heme-based proteins

AIMD has been used extensively to elucidate structure/function relationships in myoglobin and cytochromes. 

Calculations on myoglobin mimics [34-39], provided a picture of the binding mode of O2 and ligands such as CO and NO. These studies have also shed light on the intricate interplay between structural and bonding properties of the complex and environment and temperature effects. 

Two cytochromes have been studied so far. In case of the electron-transfer protein cytochrome c, electronic structure calculations helped clarify the intriguing nature of the Fe-S bond at the active site [40] whereas for cytochrome P450, steps of the enzymatic reaction were investigated [41-44]. The P450 family of enzymes is involved in the metabolism of endogenous and xenobiotic compounds and this work can therefore be of potential use in toxicology research. 

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Myoglobin in many respects is the prototypical example of the larger family of heme containing proteins and enzymes that vary in function from the relatively simple process of reversible binding of an electron to the activation of dioxygen for substrate hydroxylation. The relationship between members of this family of proteins is not based simply on structural similarities but on similarities in chemical reactivity as well. As the structure of myoglobin is relatively simple compared to other heme proteins and as it was the first for which the three-dimensional... 

We have completed several structures each of NPl, NP2, and NP4 (31, 46 9, 110). These structures reveal the Rhodnius nitrophorins to have a fold dominated by an eight-stranded antiparallel beta-barrel, as shown in Fig. 15, and to rely on a remarkable ligand-induced conformational change for NO transport, described later. The structures confirm that the nitrophorins are completely unrelated to the globins, the only other heme-based gas transport proteins whose structures are known. Rather, their fold places them in the lipocalin family, for which several other examples are known (111-113). Our initial nitrophorin structure was of NPl and was determined using standard MIR and... 

As already mentioned above, the class of non-heme iron proteins is inhomogeneous and therefore often divided into subclasses. A distinction can be made based on the ligands that coordinate to the iron center and concomitantly on the types of potential iron cofactors. In most catalytically active non-heme iron proteins, the metal ions are coordinated via nitrogen and oxygen ligands. These types of proteins will be discussed in this chapter. 

Compared with the heme proteins discussed in Section 2.2, the non-heme iron proteins presented here have a much more flexible coordination geometry. Taken together with the differences in electronic properties - heme enzymes contain mostly low-spin iron whereas non-heme enzymes contain mostly a high-spin iron - this is responsible for the more diverse chemistry found for the non-heme iron proteins. The great versatility of these enzymes makes them a treasure trove for the development of iron-based catalysts. Inspired by their biological archetypes, numerous catalytic reactions await to be reproduced by iron catalysts in organic synthesis. 

Cytochrome c (cyt. c) has become a major protein for testing new approaches and techniques in protein science.1 This is partly due to the venerable position that cytochrome c holds in the field of biochemistry since it was isolated and characterized more than 70 years ago. Cyt. c was one of the first proteins to be sequenced,2 and to have its X-ray structure determined in 1967.3 Cyt. c also has the advantage of stability and a spectroscopically distinct heme group. More than 23,000 articles mentioning cyt. c were published between 1945-2002 (ISI Web of Science). Here, we describe an approach to tetraphenylporphyrin-based protein surface receptors and the characterization of their interactions with the principal target cyt. c. 

When the cell has adequate energy available, the citric acid cycle can also provide a source of building blocks for a host of important biomolecules, such as nucleotide bases, proteins, and heme groups. This use depletes the cycle of intermediates. When the cycle again needs to metabolize fuel, anaplerotic reactions replenish the cycle intermediates. 

An innovative immunochemo-proteomics method was developed that allowed the identification of an inhibitor of the heme-binding protein (83). This method is based on the coupling of a small molecule, bis-indolylmaleimide-III, a known inhibitor of protein kinase C-a, to the FLAG peptidic epitope. This leads to the isolation of binding proteins from a cell lysate via the reaction of the FLAG epitope with anti-FLAG antibody beads. 

Myriad metalloproteins bind iron-protoporphyrin IX, known as heme (Fig. 15). Heme protein properties are determined by a variety of factors within the inner coordination sphere and without. These include chemical modifications to the porphyrin macrocycle, different axial ligation, perturbations to conformation, and protein dynamics surrounding the cofactor. Because of the extensive proliferation of heme proteins, we will limit ourselves to a small subset. These will include the cytochromes c, myoglobins, heme oxygenases and peroxidases, and a heme-based chemical sensor. 

The chemical nature of the heme fragment-protein adduct remains to be elucidated. In principle, it could entail a Schiff-base between a protein NH2-group and the formyl group of a hydroxy-dipyrrolic fragment. Alternatively, it could involve attack hy a suitable nucleophilic protein moiety on the 2-formylated dipyrrole. The possibility of a protein adduct with the heme vinyl also exists, even though no vinyl-modified dipyrrolic species have been detected in model heme degradation systems. 

The importance of the porphyrin macrocycle to biology can not be overstated 1-3), Heme-based enzymes and proteins, which contain iron porphyrins in their active sites, are ubiquitous in biological systems. In mammals, key metabolic and catabolic pathways are mediated by these metallomacrocycles, including oxygen transport, storage and activation, catalysis, membrane transport, electron transfer, and substrate sensing (4). In... 

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