Cytochrome analysis

Many key protein ET processes have become accessible to theoretical analysis recently because of high-resolution x-ray stmctural data. These proteins include the bacterial photosynthetic reaction centre [18], nitrogenase (responsible for nitrogen fixation), and cytochrome c oxidase (the tenninal ET protein in mammals) [19, 20]. Although much is understood about ET in these molecular machines, considerable debate persists about details of the molecular transfonnations. 

Liidemann et al., 1997] Liidemann, S. K., Carugo, O., and Wade, R. C. Substrate access to cytochrome P450cam A comparison of a thermal motion pathway analysis with moleculM dynamics simulation data. J. Mol. Model. 3 (1997) 369-374... 

Although not discussed in detail here, the normal mode analysis method has been used to calculate the electron transfer reorganization spectrum in / M-modified cytochrome c [65,66]. In this application the normal mode analysis fits comfortably into the theory of electron transfer. 

Valpuesta, J.M., Henderson, R., Frey, T.G. Electron cryo-microscopic analysis of crystalline cytochrome oxidase. /. Mol. Biol. 214 237-251, 1990. 

Figure 11.15 Cation-exchange mia O-LC analysis of a mixture of model proteins (a) the original sample consisting of myoglobin (M), cytochrome C (C) and lysozyme (L) (b) and (c) proteins adsorbed on to and then released from the polyaaylic acid coated fibre with exti ac-tion times of 5 and 240 s, respectively. Reprinted from Journal of Microcolumn Separations, 8, J.-L. Liao et al., Solid phase mia O exti action of biopolymers, exemplified with adsorption of basic proteins onto a fiber coated with polyaaylic acid, pp. 1-4, 1996, with permission from Jolm Wiley Sons, New York.

Cytochrome c is an enzyme found in the cells of all aerobic organisms. Elemental analysis of cytochrome c shows that it contains 0.43% iron. What is the minimum molecular weight of this enzyme ... 

Another new development of immediate clinical usefulness is the analysis of genetic variability in the cytochrome P450 enzyme system in patients, which... 

Table 5.9 Peptides detected during the LC-electrospray-MS (LC-ESMS) analysis of the endoproteinase Lys-C digest from native cytochrome c". Reprinted from Biochim. Biophys. Acta, 1412, Klarskov, K., Leys, D., Backers, K., Costa, H. S., Santos, H., Gnisez, Y. and Van Beenmen, J. J., Cytochrome c" from the obligate methylotroph Methylophilus methylotrophus, an unexpected homolog of sphaeroides heme protein from the phototroph Rhodobacter sphaeroides", 47-55, Copyright (1999), with permission from Elsevier Science...

Another important outcome of the structural analysis is the relative positioning of the metal sites and their distances in order to define plausible electron transfer pathways between electron donors and acceptors. A common pattern starts to emerge (the same applies to cytochrome oxidase (241, 242). Figure 11 gives a pictorial view of the electron transfer pathway ... 

Szklarz GD, Halpert JR. Use of homology modeling in conjunction with site-directed mutagenesis for analysis of structure-function relationships of mammalian cytochromes P450. Life Sci 1997 61 2507-20. 

Wang Q, Halpert JR. Combined three-dimensional qnantitative strnctnre-activity relationship analysis of cytochrome P450 2B6 snbstrates and protein homology modeling. Drug Metab Dispos 2002 30 86-95. 

A widely used 3-D QSAR method that makes use of PLS is comparative molecular field analysis (CoMFA), in which a probe atom is used to calculate the steric and electronic fields at numerous points in a 3D lattice within which the molecules have been aligned. Poso et al. [56] used the technique to model the binding of coumarins to cytochrome P450 2A5, with similar results to those obtained by Bravi and Wikel [55]. Shi et al. [57] used it to model the estrogen receptor binding of a large diverse set of compounds, and Cavalli et al. [58] used it to develop a pharmacophore for hERG potassium... 

The COMPACT (computer-optimized molecular parametric analysis of chemical toxicity) procedure, developed by Lewis and co-workers [92], uses a form of discriminant analysis based on two descriptors, namely, molecular planarity and electronic activation energy (the difference between the energies of the highest occupied and lowest unoccupied molecular orbitals), which predict the potential of a compound to act as a substrate for one of the cytochromes P450. Lewis et al. [93] found 64% correct predictions for 100 compounds tested by the NTP for mutagenicity. 

Analysis of reaction mixtures for 1-propanol and 2-propanol following incubation of NDPA with various rat liver fractions in the presence of an NADPH-generating system is shown in Table I ( ). Presence of microsomes leads to production of both alcohols, but there was no propanol formed with either the soluble enzyme fraction or with microsomes incubated with SKF-525A (an inhibitor of cytochrome P450-dependent oxidations). The combined yield of propanols from 280 ymoles of NDPA was 6.1 ymoles and 28.5 ymoles for the microsomal pellet and the 9000 g supernatant respectively. The difference in the ratio of 1- to 2-propanol in the two rat liver fractions may be due to differences in the chemical composition of the reaction mixtures (2) Subsequent experiments have shown that these ratios are quite reproducible. For comparison, Table I also shows formation of propanols following base catalyzed decomposition of N-propyl-N-nitrosourea. As expected (10,11), both propanol isomers were formed, the total yield in this case being almost quantitative. 

Ortiz de Montellano PR, JA Eruetel, JR Collins, DL Camper, GH Loew (1991) Theoretical and experimental analysis of the absolute stereochemistry of ci5-[l-methylstyrene epoxidation by cytochrome P-450,j . JAm Chem Soc 113 3195-3196. 

Louie TM, S Ni, L Xun, WW Mohn (1997) Purification, characterization and gene sequence analysis of a novel cytochrome c coinduced with reductive dechlorination activity in Desulfomonile tiedjei DCB-1. Arch Microbiol 168 520-527. 

Because LCEC had its initial impact in neurochemical analysis, it is not, surprising that many of the early enzyme-linked electrochemical methods are of neurologically important enzymes. Many of the enzymes involved in catecholamine metabolism have been determined by electrochemical means. Phenylalanine hydroxylase activity has been determined by el trochemicaUy monitoring the conversion of tetrahydro-biopterin to dihydrobiopterin Another monooxygenase, tyrosine hydroxylase, has been determined by detecting the DOPA produced by the enzymatic reaction Formation of DOPA has also been monitored electrochemically to determine the activity of L-aromatic amino acid decarboxylase Other enzymes involved in catecholamine metabolism which have been determined electrochemically include dopamine-p-hydroxylase phenylethanolamine-N-methyltransferase and catechol-O-methyltransferase . Electrochemical detection of DOPA has also been used to determine the activity of y-glutamyltranspeptidase The cytochrome P-450 enzyme system has been studied by observing the conversion of benzene to phenol and subsequently to hydroquinone and catechol... 

Once the resolution has been optimized as a function of gradient rate, one can continue to fine-tune the separation, raising flow rate and temperature. In a study of temperature and flowrate variation on the separation of the tryptic peptides from rabbit cytochrome c, column performance doubled while analysis time was reduced by almost half using this strategy.97 Commercially available software has been developed to aid in optimization. As a final note, in an industrial laboratory optimization is not completed until a separation has been shown to be rugged. It is a common experience to optimize a separation on one column, only to find that separation fails on a second column of identical type. Reproducibility and rigorous quality control in column manufacture remains a goal to be attained. 

Johansson, I., Oscarson, M., Yue, Q. Y. etal. (1994). Genetic analysis of the Chinese cytochrome P-4502D locus characterization of variant CYP2D6 gene present in subjects with diminished capacity for debrisoquine hydroxylation. Mol. Pharmacol. 46, 452-9. 

Goodacre, R. Karim, A. Kaderbhai, M. A. Kell, D. B. Rapid and quantitative analysis of recombinant protein expression using pyrolysis mass spectrometry and artificial neural networks Application to mammalian cytochrome b5 in Escherichia coli. J. Biotechnol. 1994,34,185-193. 

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