Metalloproteins

Cyclic peptides can be viewed as a step on the way from the modeling of unconstrained peptides to folded proteins. The copper(II) complex of a cyclic octapep-tide has been investigated by molecular mechanics and EPR spectroscopy and the structure was found to be in accord with those of closely related complexes 205]. Similar combined approaches are also applicable to metalloproteins. 

The opposite approach of keeping the bulk of the protein geometry fixed to that observed crystallographically while optimizing the geometry of the active site and its immediate surrounds has also been investigated. In a study of plastocyanin and amicyanin, the geometry about the copper(I) centers was well reproduced -391.  

An alternative approach to representing the metal center has been developed for zinc(II) centers and applied to the modeling of the interaction of natural substrates and inhibitors of the enzyme human carbonic anhydrase[105 392,3931. Structurally characterized four-, five- and six-coordinate small-molecule complexes of zinc(II) were analyzed to determine the distribution of bond lengths and angles about the zinc ion. A function was developed that was able to reproduce these structural features and was added to the program YETI[394), developed for modeling small molecule-metalloprotein interactions. 

The solution structures of a number of metalloproteins with paramagnetic metal centers were determined with molecular mechanics and dynamics in combination with NMR spectroscopy (see also Chapter 10)t332 335. Due to the complexity of the molecules, for metalloproteins a crystal structure of the compound or a derivative is often needed for the definition of the starting geometry. Molecular dynamics is then used to find low-energy conformers. The dynamics calculations 

Metalloenzymes pose a particular problem to both experimentalists and modelers. Crystal structures of metalloenzymes typically reveal only one state of the active site and the state obtained frequently depends on the crystallization conditions. In some cases, states probably not relevant to any aspect of the mechanism have been obtained, and in many cases it may not be possible to obtain states of interest, simply because they are too reactive. This is where molecular modeling can make a unique contribution and a recent study of urease provides a good example of what can be achieved119 1. A molecular mechanics study of urease as crystallized revealed that a water molecule was probably missing from the refined crystal structure. A conformational search of the active site geometry with the natural substrate, urea, bound led to the determination of a consensus binding model[I91]. Clearly, the urea complex cannot be crystallized because of the rate at which the urea is broken down to ammonia and, therefore, modeling approaches such as this represent a real contribution to the study of metalloenzymes. 

An alternative approach to representing the metal center has been developed for zinc(II) centers and applied to the modeling of the interaction of natural substrates and inhibitors of the enzyme human carbonic anhydrase1184-1861. Structurally charac- 

Detailed measurements have also been made on a cytochrome c peroxidase containing protohaemin or mesohaemin and obtained from baker s yeast 

The readiness with which haemeprotein samples can be obtained and the considerable data available on them from other types of investigation has resulted in a comparative neglect of other types of iron-bearing protein. However, several useful studies have been made, and the interesting properties of the haemeproteins are found to extend to other systems. 

The well-characterised metalloprotein ferrichrome A has been studied between 

The ferredoxin from the green alga Euglena has been isolated containing enriched Fe [28]. The two iron atoms appear to be identical, and in the oxidised Euglena ferredoxin give a quadrupole sphtting of 0-65 mm s at 

A ferredoxin with a molecular weight of 6000 and seven atoms of iron per molecule was extracted from Clostridium pasteurianum and oxidised samples show similar spectra [29], although with some evidence for at least two iron environments. An S = i configuration was proposed, but the confirmatory experiment of applying a magnetic field and looking for magnetic effects has not yet been carried out. 

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Spiro T G and Czernuszewicz R S 1995 Resonance Raman-spectroscopy of metalloproteins Biochemical Spectroscopy Methods Enzymol. vol 246, ed K Sauer (San Diego, CA Academic) pp 416-60... 

Tissue inhibitor of metalloproteins (TIMP, from human blood plasma), Mr -30,000. 

Computer simulations of electron transfer proteins often entail a variety of calculation techniques electronic structure calculations, molecular mechanics, and electrostatic calculations. In this section, general considerations for calculations of metalloproteins are outlined in subsequent sections, details for studying specific redox properties are given. Quantum chemistry electronic structure calculations of the redox site are important in the calculation of the energetics of the redox site and in obtaining parameters and are discussed in Sections III.A and III.B. Both molecular mechanics and electrostatic calculations of the protein are important in understanding the outer shell energetics and are discussed in Section III.C, with a focus on molecular mechanics. 

METALLOPROTEINS. Metalloproteins are either metal storage forms, as in the case of ferritin, or enzymes in which the metal atom participates in a catalyti-cally important manner. We encounter many examples throughout this book of the vital metabolic functions served by metalloenzymes. 

Metalloproteins contain metal atoms Ferritin Iron 35... 

HEMOPROTEINS. These proteins are actually a subclass of metalloproteins because their prosthetic group is heme, the name given to iron protoporphyrin IX (Figure 5.15). Because heme-containing proteins enjoy so many prominent biological functions, they are considered a class by themselves. 

Fritz G, Heizmann CW (2004) 3D-structures of the Ca2+-and Zn2+-binding SI00 proteins. In Messerschmidt A, Bode W, Cygler M, Handbook of metalloproteins. Wiley, Chichester, pp, 529—540... 

The investigation of coordinated water in paramagnetic metalloproteins through N.M.R. spectroscopy. I. Bertini, Comments Inorg. Chem., 1981,1, 227-243 (68). 

Redox reactions of sulphur-containing amino-acid residues in proteins and metalloproteins. 

Some of the critical enzymes in our cells are metalloproteins, large organic molecules made up of folded polymerized chains of amino acids that also include at least one metal atom. These metalloproteins are intensely studied by biochemists, because they control life and protect against disease. They have also been used to trace evolutionary paths. The d-block metals catalyze redox reactions, form components of membrane, muscle, skin, and bone, catalyze acid-base reactions, control the flow of energy and oxygen, and carry out nitrogen fixation. 

Overall practical features make the FucA and RhuA enzymes quite similar for synthetic applications. Both metalloproteins are quite robust under conditions of organic synthesis and show a very high stability in the presence of low Zn concentrations with half-lives in the range of months at room temperature. The... 

Sulfur-Containing Ligands in Metalloproteins and Enz mies (W. E. Newton)... 

Cohen lA (1980) Metal-Metal Interactions in the Metalloporphyrins, Metalloproteins and Metalloenzymes. 40 1-37... 

Maroney MJ, Davidson G, Allan CB, Figlar J (1998) The Structure and Function of Nickel Sites in Metalloproteins. 92 1-66... 

Therlen MJ, Chang J, Raphael AL, Bowler BE, Gray HB (1991) Long-Range Electron Transfer in Metalloproteins. 75 109-130... 

Weser U (1985) Redox Reactions of Sulphur-Containing Amino-Acid Residues in Proteins and Metalloproteins, an XPS Study. 61 145-160 Weser U (1973) Structural Aspects and Biochemical Function of Erythrocuprein. 17 1-65 Weser U, see Abolmaali B (1998) 91 91-190... 

The 2[4Fe-4S] and [3Fe-4S][4Fe-4S] ferredoxins are components of virtually all eubacteria and archaebacteria (3). Several comprehensive reviews dealing with these small metalloproteins have appeared (3, 8-12), but only those participating directly in the photosynthetic light reactions will be addressed here. 

Macrocyclic Complexes as Models for Nonporphine Metalloproteins Vickie McKee... 

TABLE 5 Ligand Preferences for Metals Commonly Found in Metalloproteins... 

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